From huangyi1 at hkusua.hku.hk Wed Nov 1 03:25:10 2006 From: huangyi1 at hkusua.hku.hk (Huang Yi) Date: Wed, 1 Nov 2006 16:25:10 +0800 Subject: [Bioperl-l] bioperl1.5 and GD2.35 - solved In-Reply-To: <1A4207F8295607498283FE9E93B775B4023B5F3C@EX02.asurite.ad.asu.edu> Message-ID: <200611010825.kA18PGWu022850@hkusua.hku.hk> The problem was solved. I re-emerged gd-2.0.33 with png USE flag. Thanks again! Huang Yi -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Kevin Brown Sent: Tuesday, October 31, 2006 11:35 PM To: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] bioperl1.5 and GD2.35 Not really a Bioperl issue per se, but sounds like when you had Gentoo emerge GD it didn't include libpng and so didn't build the needed parts to create PNG type graphics. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Huang Yi > Sent: Monday, October 30, 2006 10:46 PM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] bioperl1.5 and GD2.35 > > Hi, > > > > I just installed bioperl 1.4 from CPAN to my Gentoo linux > computer. But the > installation was failed. I had to install by force. > > > > However, the GD module couldn't be installed for some unknown reasons. > > > > I therefore use "emerge" tool of Gentoo to get bioperl and GD > again. They > are fine. The version of bioperl became upgrade to1.5 and GD was 2.35. > > > > However, when I tested it by using the program in HOWTO wiki page > (http://www.bioperl.org/wiki/HOWTO:Graphics), it always told me: > > > > Can't locate object method "png" via package "GD::Image" at > /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Panel.pm line > 799, <> line 9. > > > > In my other computer, bioperl1.4 and GD2.34 work fine. I > therefore want to > remove the CPAN bioperl from the system and re-install it, > but it seems to > be impossible. > > > > Would you please give me some advices on how to let my GD and > bioperl work. > > > > Thanks! > > > > Huang Yi > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/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 nhansen at nhgri.nih.gov Wed Nov 1 08:43:32 2006 From: nhansen at nhgri.nih.gov (Nancy Hansen) Date: Wed, 1 Nov 2006 08:43:32 -0500 (EST) Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: References: Message-ID: On Tue, 31 Oct 2006, Brian Osborne wrote: > It looks like a good place to start would be the get_header() and > _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that > the author, at some point, wanted get_header to return meaningful > information but stepping through the test shows it returning a lot of UNDEF. > Now I don't know if this is due to the method or the source SCF file, but > you might be able to get these methods to work yourself. > > But to answer your questions, yes, it certainly sounds reasonable that these > values would be extracted by Bio::SeqIO::scf. Sounds great! So, if I make these changes, is there someone I should run them by before checking them into CVS? Is Chad Matsalla still involved in bioperl? I've never contributed to the project, so I'm not sure how things work... Thanks! --Nancy ************************************* Nancy F. Hansen, PhD nhansen at nhgri.nih.gov Bioinformatics Group NIH Intramural Sequencing Center (NISC) 5625 Fishers Lane Rockville, MD 20852 Phone: (301) 435-1560 Fax: (301) 435-6170 From arareko at campus.iztacala.unam.mx Wed Nov 1 09:30:34 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed, 01 Nov 2006 08:30:34 -0600 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: References: Message-ID: <4548AF8A.6090205@campus.iztacala.unam.mx> The usual way is to send your modifications as an 'enhancement' through the Bugzilla system (please add your patches as attachments after creating the report, not into the description field): http://bugzilla.open-bio.org/ Thanks for contributing! Regards, Mauricio. Nancy Hansen wrote: > On Tue, 31 Oct 2006, Brian Osborne wrote: > >> It looks like a good place to start would be the get_header() and >> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that >> the author, at some point, wanted get_header to return meaningful >> information but stepping through the test shows it returning a lot of UNDEF. >> Now I don't know if this is due to the method or the source SCF file, but >> you might be able to get these methods to work yourself. >> >> But to answer your questions, yes, it certainly sounds reasonable that these >> values would be extracted by Bio::SeqIO::scf. > > Sounds great! So, if I make these changes, is there someone I should run > them by before checking them into CVS? Is Chad Matsalla still involved in > bioperl? I've never contributed to the project, so I'm not sure how > things work... > > Thanks! > --Nancy > > ************************************* > Nancy F. Hansen, PhD nhansen at nhgri.nih.gov > Bioinformatics Group > NIH Intramural Sequencing Center (NISC) > 5625 Fishers Lane > Rockville, MD 20852 > Phone: (301) 435-1560 Fax: (301) 435-6170 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From cjfields at uiuc.edu Wed Nov 1 09:39:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 1 Nov 2006 08:39:38 -0600 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: Message-ID: <000c01c6fdc3$8ed54770$15327e82@pyrimidine> > On Tue, 31 Oct 2006, Brian Osborne wrote: > >> It looks like a good place to start would be the get_header() and >> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can >> see that the author, at some point, wanted get_header to return >> meaningful information but stepping through the test shows it >> returning a lot of UNDEF. Now I don't know if this is due to the >> method or the source SCF file, but you might be able to get these >> methods to work yourself. >> >> But to answer your questions, yes, it certainly sounds reasonable >> that these values would be extracted by Bio::SeqIO::scf. > > Sounds great! So, if I make these changes, is there someone > I should run them by before checking them into CVS? Is Chad > Matsalla still involved in bioperl? I've never contributed > to the project, so I'm not sure how things work... > > Thanks! > --Nancy You can check them into Bugzilla as a patch to a bug: http://bugzilla.open-bio.org/ There is a HOWTO for patch submission here: http://www.bioperl.org/wiki/HOWTO:SubmitPatch You could also send them to Brian or me. Bugzilla is probably your best bet as anyone with a developer account can check in the fix. You should also write up some tests for your code changes. You can use the test file mentioned above (t/scf.t) as a start. -chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Wed Nov 1 08:00:53 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 01 Nov 2006 09:00:53 -0400 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: Message-ID: Nancy, I suggest doing this through Bugzilla, http://bugzilla.open-bio.org. First add your proposal as a bug or as an enhancement, sounds like it could be either but I'd say it doesn't matter. Then contribute patches to the "bug" as you work, some one will apply them. Also add tests to t/scf.t, if you're working on scf.pm. Thank you in advance for your contributions. As for Chad, I have no idea but strictly speaking no one "owns" a module in Bioperl. Brian O. On 11/1/06 9:43 AM, "Nancy Hansen" wrote: > Sounds great! So, if I make these changes, is there someone I should run > them by before checking them into CVS? Is Chad Matsalla still involved in > bioperl? I've never contributed to the project, so I'm not sure how > things work... From keithplayer at hotmail.com Wed Nov 1 19:22:07 2006 From: keithplayer at hotmail.com (Keith Player) Date: Thu, 2 Nov 2006 00:22:07 +0000 (UTC) Subject: [Bioperl-l] Article Message-ID: Sorry I didn't attach the article link originally. You can view the full-text for free: http://www.genome.org/cgi/content/abstract/12/10/1599 When I was talking about the R-tree I was talking about the current implementation. I should point out that I didn't actually try the perl module directly but implemented the binning schema straight in mysql. I found that by using the SQL I mentioned previously the database performed better compared to using the binning schema, I assume because of less disk seeks. I tested on a dataset of around 30k records and another the same size as the paper. The binning outperformed the queries as described in the paper, but the SQL I mentioned in the first post outperformed the binning schema by around a factor of 3. The new binning schema might make all this moot, especially if it removes layers so that groups/features next to each other are saved on the same/adjacent pages. The only question then would be whether database optimization is effected by the binning. Also does needing to know the largest length of a group/feature make the SQL statement I created impractical? From limericksean at gmail.com Wed Nov 1 11:28:58 2006 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 1 Nov 2006 17:28:58 +0100 Subject: [Bioperl-l] Can't locate object method "new_instance" via package "Bio::DB::SeqFeature::Store::dbi::mysql" at /project/gbrowse/httpd_perllib_new/Bio/DB/SeqFeature/Store.pm line 336. Message-ID: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> Hi, I am currently in the process of trying testing Gbrowse with the (relatively new) Bio::DB::SeqFeature::Store adaptor method. A couple of teething problems, just wondering if anyone else had encountered the message above. Any insight appreciated. Also the package called (Bio::DB::SeqFeature::Store::dbi::mysql) had to be copied into the lowercase 'dbi' from its original DBI form - don't know if this was a previously reported bug. Thanks, Sean. From ybolo001 at student.ucr.edu Wed Nov 1 19:15:57 2006 From: ybolo001 at student.ucr.edu (Eugene Bolotin) Date: Wed, 1 Nov 2006 16:15:57 -0800 Subject: [Bioperl-l] Check sequence format, question Message-ID: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> Dear bioperl mailing list, I trying to get sequence from a file using Bio::SeqIO, before I do anything, I want to make sure that the file is in a correct Fasta sequence format. I want it to spit out an error message if it is in any other format. What is the easiest way to do it? Thanks, Eugene Bolotin Sladek Lab. From cjfields at uiuc.edu Wed Nov 1 23:28:11 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 1 Nov 2006 22:28:11 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> References: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> Message-ID: <24DED46C-4630-4E95-94D0-87810183F191@uiuc.edu> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: > Dear bioperl mailing list, > I trying to get sequence from a file using Bio::SeqIO, before I do > anything, > I want to make sure that the file is in a correct Fasta sequence > format. I > want it to spit out an error message if it is in any other format. > What is the easiest way to do it? > Thanks, > Eugene Bolotin > Sladek Lab. There is no formal FASTA definition that is universally accepted beyond having the first line start with '>' and an optional description, with the sequence in subsequent lines. http://www.bioperl.org/wiki/FASTA_sequence_format Bio::SeqIO isn't currently set up to validate sequence formats directly, but you could try preparsing the data using Bio::Tools::GuessSeqFormat. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Wed Nov 1 21:21:35 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 1 Nov 2006 21:21:35 -0500 Subject: [Bioperl-l] Can't locate object method "new_instance" via package "Bio::DB::SeqFeature::Store::dbi::mysql" at /project/gbrowse/httpd_perllib_new/Bio/DB/SeqFeature/Store.pm line 336. In-Reply-To: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> References: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> Message-ID: <6dce9a0b0611011821l45cd7f8enb2e77f286f7cf6f5@mail.gmail.com> Hi, DBI should be uppercased in the gbrowse config file: [GENERAL] description = C. elegans GFF3 Database db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn ws164_gff3 You shouldn't have to change anything to lowercase. Lincoln On 11/1/06, Sean O'Keeffe wrote: > > Hi, > I am currently in the process of trying testing Gbrowse with the > (relatively new) Bio::DB::SeqFeature::Store adaptor method. A couple > of teething problems, just wondering if anyone else had encountered > the message above. Any insight appreciated. > Also the package called (Bio::DB::SeqFeature::Store::dbi::mysql) had > to be copied into the lowercase 'dbi' from its original DBI form - > don't know if this was a previously reported bug. > > Thanks, > Sean. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From Bernhard.Schmalhofer at biomax.com Thu Nov 2 03:53:14 2006 From: Bernhard.Schmalhofer at biomax.com (Bernhard Schmalhofer) Date: Thu, 02 Nov 2006 09:53:14 +0100 Subject: [Bioperl-l] Is it possible to parse BLAST output using IO:String? In-Reply-To: <716af09c0610301244q1c6d4cd6y23e72371dda4fa4d@mail.gmail.com> References: <00e301c6fc5f$a36de9e0$e6028a0a@GOLHARMOBILE1> <716af09c0610301244q1c6d4cd6y23e72371dda4fa4d@mail.gmail.com> Message-ID: <4549B1FA.1020506@biomax.com> Bernd Web wrote: > Hi Ryan, > > I parse blastn output using IO::String w/o problems: > > my $stringfh = new IO::String($input); > my $in = new Bio::SearchIO(-format => 'blast', -fh => $stringfh); I do the same with implicitly using IO::String. Works like a charm at leaset with Perl 5.8.0. # get $blast_report from MySQL open my $blast_report_fh, '<', \$blast_report; my $in = Bio::SearchIO->new( -format => 'blast', -fh => $blast_report_fh ); Regards, Bernhard -- ************************************************** Dipl.-Physiker Bernhard Schmalhofer Senior Developer Biomax Informatics AG Lochhamer Str. 11 82152 Martinsried, Germany Tel: +49 89 895574-839 Fax: +49 89 895574-825 eMail: Bernhard.Schmalhofer at biomax.com Website: www.biomax.com ************************************************** From cjfields at uiuc.edu Thu Nov 2 10:11:01 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 09:11:01 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <85304914-322B-46BA-BED2-09722FE08D57@uiuc.edu> Brian, I think the validation issue is worthwhile but I can see logistical nightmares having every SeqIO parser validate sequence while parsing; GenBank and EMBL do this to some extent already but it isn't foolproof. Much of SeqIO (e.g. GenBank/EMBL/Swiss parsing) is already in dire need of an overhaul as is w/o adding validation. I wonder if it would be better if SeqIO has-a validator object instead of acting as a validator itself, i.e. SeqIO would focus on parsing and writing, the validator would focus on validation. It might be easier from the maintenance aspect. It's probably worthwhile exploring using Bio::Tools::GuessSeqFormat within SeqIO, or setting up a new system altogether. Validation using the sequence validator could then be enabled by having a validation option when instantiating SeqIO. We could even enable XML format validation using the DTD/Schema, which should be fairly straightforward. Of course, this all depends on someone writing it up... Chris On Nov 2, 2006, at 6:49 AM, Brian Osborne wrote: > Chris et al., > > As you know the question of whether SeqIO should or should not > validate or > check the given format is still an open one. In fact, some SeqIO > modules do > validate to some extent. See: > > http://bugzilla.open-bio.org/show_bug.cgi?id=1508 > > I can see that you've commented on this enhancement, I'm replying > just to > bring this to the attention of others. > > Brian O. > > > On 11/2/06 12:28 AM, "Chris Fields" wrote: > >> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: >> >>> Dear bioperl mailing list, >>> I trying to get sequence from a file using Bio::SeqIO, before I do >>> anything, >>> I want to make sure that the file is in a correct Fasta sequence >>> format. I >>> want it to spit out an error message if it is in any other format. >>> What is the easiest way to do it? >>> Thanks, >>> Eugene Bolotin >>> Sladek Lab. >> >> There is no formal FASTA definition that is universally accepted >> beyond having the first line start with '>' and an optional >> description, with the sequence in subsequent lines. >> >> http://www.bioperl.org/wiki/FASTA_sequence_format >> >> Bio::SeqIO isn't currently set up to validate sequence formats >> directly, but you could try preparsing the data using >> Bio::Tools::GuessSeqFormat. >> >> Chris >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Thu Nov 2 09:38:36 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 10:38:36 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <85304914-322B-46BA-BED2-09722FE08D57@uiuc.edu> Message-ID: Chris, Yes, and validation should always be optional. SeqIO is not always as fast as some want it to be and sometimes you're certain that your files don't need to be validated. Brian O. On 11/2/06 11:11 AM, "Chris Fields" wrote: > Brian, > > I think the validation issue is worthwhile but I can see logistical > nightmares having every SeqIO parser validate sequence while parsing; > GenBank and EMBL do this to some extent already but it isn't > foolproof. Much of SeqIO (e.g. GenBank/EMBL/Swiss parsing) is > already in dire need of an overhaul as is w/o adding validation. > > I wonder if it would be better if SeqIO has-a validator object > instead of acting as a validator itself, i.e. SeqIO would focus on > parsing and writing, the validator would focus on validation. It > might be easier from the maintenance aspect. It's probably > worthwhile exploring using Bio::Tools::GuessSeqFormat within SeqIO, > or setting up a new system altogether. Validation using the sequence > validator could then be enabled by having a validation option when > instantiating SeqIO. We could even enable XML format validation > using the DTD/Schema, which should be fairly straightforward. > > Of course, this all depends on someone writing it up... > > Chris > > On Nov 2, 2006, at 6:49 AM, Brian Osborne wrote: > >> Chris et al., >> >> As you know the question of whether SeqIO should or should not >> validate or >> check the given format is still an open one. In fact, some SeqIO >> modules do >> validate to some extent. See: >> >> http://bugzilla.open-bio.org/show_bug.cgi?id=1508 >> >> I can see that you've commented on this enhancement, I'm replying >> just to >> bring this to the attention of others. >> >> Brian O. >> >> >> On 11/2/06 12:28 AM, "Chris Fields" wrote: >> >>> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: >>> >>>> Dear bioperl mailing list, >>>> I trying to get sequence from a file using Bio::SeqIO, before I do >>>> anything, >>>> I want to make sure that the file is in a correct Fasta sequence >>>> format. I >>>> want it to spit out an error message if it is in any other format. >>>> What is the easiest way to do it? >>>> Thanks, >>>> Eugene Bolotin >>>> Sladek Lab. >>> >>> There is no formal FASTA definition that is universally accepted >>> beyond having the first line start with '>' and an optional >>> description, with the sequence in subsequent lines. >>> >>> http://www.bioperl.org/wiki/FASTA_sequence_format >>> >>> Bio::SeqIO isn't currently set up to validate sequence formats >>> directly, but you could try preparsing the data using >>> Bio::Tools::GuessSeqFormat. >>> >>> Chris >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > From bosborne11 at verizon.net Thu Nov 2 07:49:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 08:49:01 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <24DED46C-4630-4E95-94D0-87810183F191@uiuc.edu> Message-ID: Chris et al., As you know the question of whether SeqIO should or should not validate or check the given format is still an open one. In fact, some SeqIO modules do validate to some extent. See: http://bugzilla.open-bio.org/show_bug.cgi?id=1508 I can see that you've commented on this enhancement, I'm replying just to bring this to the attention of others. Brian O. On 11/2/06 12:28 AM, "Chris Fields" wrote: > On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: > >> Dear bioperl mailing list, >> I trying to get sequence from a file using Bio::SeqIO, before I do >> anything, >> I want to make sure that the file is in a correct Fasta sequence >> format. I >> want it to spit out an error message if it is in any other format. >> What is the easiest way to do it? >> Thanks, >> Eugene Bolotin >> Sladek Lab. > > There is no formal FASTA definition that is universally accepted > beyond having the first line start with '>' and an optional > description, with the sequence in subsequent lines. > > http://www.bioperl.org/wiki/FASTA_sequence_format > > Bio::SeqIO isn't currently set up to validate sequence formats > directly, but you could try preparsing the data using > Bio::Tools::GuessSeqFormat. > > Chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Thu Nov 2 13:07:45 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 12:07:45 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <93F383D1-6DDF-4238-954A-96CE1218C641@uiuc.edu> On Nov 2, 2006, at 8:38 AM, Brian Osborne wrote: > Chris, > > Yes, and validation should always be optional. SeqIO is not always > as fast > as some want it to be and sometimes you're certain that your files > don't > need to be validated. > > Brian O. Agreed. We could use the original Bugzilla bug (1508?) to track this and maybe gather ideas, but the wiki is probably a better place... Chris > On 11/2/06 11:11 AM, "Chris Fields" wrote: > >> ... Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Thu Nov 2 13:08:45 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 14:08:45 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <93F383D1-6DDF-4238-954A-96CE1218C641@uiuc.edu> Message-ID: Chris, Yes, in the Project priority list page. Speaking of this page, why is all of the text on the bottom half of this page crossed out? Many of these items have _not_ been done. Brian O. On 11/2/06 2:07 PM, "Chris Fields" wrote: > Agreed. We could use the original Bugzilla bug (1508?) to track this > and maybe gather ideas, but the wiki is probably a better place... From cjfields at uiuc.edu Thu Nov 2 14:22:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 13:22:48 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <0DA38665-F4CB-4000-974F-47915F0524A2@uiuc.edu> On Nov 2, 2006, at 12:08 PM, Brian Osborne wrote: > Chris, > > Yes, in the Project priority list page. > > Speaking of this page, why is all of the text on the bottom half of > this > page crossed out? Many of these items have _not_ been done. > > Brian O. You're right; they shouldn't be crossed out unless they are completed. If someone takes on a project then they attach their signature to it, not cross it off the list. I'll change that and add a disclaimer to the top of the page. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stewarta at nmrc.navy.mil Thu Nov 2 15:26:08 2006 From: stewarta at nmrc.navy.mil (Andrew Stewart) Date: Thu, 2 Nov 2006 15:26:08 -0500 Subject: [Bioperl-l] Bio::DB::GFF and feature order Message-ID: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> In attempting to determine some statistics on the distances between CDS features in my Bio::DB::GFF database, I ran a query on all CDS features as follows... my @CDS = $segment->features('CDS'); ...only to find that the features returned are not in order. Is there a way of returning the features in order or sorting them through some internal Bio::DB::GFF related method, aside from the more obvious path of sorting through the array itself (somehow)? -A -- Andrew Stewart Research Assistant, Genomics Team Navy Medical Research Center (NMRC) Biological Defense Research Directorate (BDRD) BDRD Annex 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 email: stewarta at nmrc.navy.mil phone: 301-231-6700 Ext 270 From lincoln.stein at gmail.com Thu Nov 2 15:41:06 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 2 Nov 2006 15:41:06 -0500 Subject: [Bioperl-l] [Gmod-gbrowse] Bio::DB::GFF and feature order In-Reply-To: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> References: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> Message-ID: <6dce9a0b0611021241i35f602f2q6ca59f23738d1013@mail.gmail.com> How do you want them sorted? To sort them by their start positions: my @CDS = sort {$a->start<=>$b->start} $segment->features('CDS'); Other people may want to sort features by end position, length, name, or who knows what. Lincoln On 11/2/06, Andrew Stewart wrote: > > In attempting to determine some statistics on the distances between CDS > features in my Bio::DB::GFF database, I ran a query on all CDS features as > follows... > my @CDS = $segment->features('CDS'); > > ...only to find that the features returned are not in order. Is there a > way of returning the features in order or sorting them through some internal > Bio::DB::GFF related method, aside from the more obvious path of sorting > through the array itself (somehow)? > > > -A > > -- > Andrew Stewart > Research Assistant, Genomics Team > Navy Medical Research Center (NMRC) > Biological Defense Research Directorate (BDRD) > BDRD Annex > 12300 Washington Avenue, 2nd Floor > Rockville, MD 20852 > > email: stewarta at nmrc.navy.mil > phone: 301-231-6700 Ext 270 > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From n.haigh at sheffield.ac.uk Thu Nov 2 17:12:28 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 02 Nov 2006 22:12:28 +0000 Subject: [Bioperl-l] $Bio::Root::Version:VERSION Message-ID: <454A6D4C.3020605@sheffield.ac.uk> When does $Bio::Root::Version::VERSION get incremented? immediately prior to a tag or straight after a tag so that CVS code is seen as more recent than an official release? For example, $VERSION is currently set to 1.52_01 but the code in CVS HEAD is passed 1.5.2 RC2 now so should is read 1.52_02 or be 1.52_03 for the upcoming 1.52 RC3? Cheers Nath From bix at sendu.me.uk Thu Nov 2 18:14:57 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 02 Nov 2006 23:14:57 +0000 Subject: [Bioperl-l] $Bio::Root::Version:VERSION In-Reply-To: <454A6D4C.3020605@sheffield.ac.uk> References: <454A6D4C.3020605@sheffield.ac.uk> Message-ID: <454A7BF1.1060705@sendu.me.uk> Nathan S. Haigh wrote: > When does $Bio::Root::Version::VERSION get incremented? immediately > prior to a tag or straight after a tag so that CVS code is seen as more > recent than an official release? Normally nothing happens. > For example, $VERSION is currently set to 1.52_01 but the code in CVS > HEAD is passed 1.5.2 RC2 now so should is read 1.52_02 or be 1.52_03 for > the upcoming 1.52 RC3? Once I've decided what to do based on the discussion we had, I'll update it. I'll currently leaning toward the 'clean break', pugs-style suggestion from Chris. If you've strong views in another direction, post in that thread. From bernd.web at gmail.com Fri Nov 3 07:57:03 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 3 Nov 2006 13:57:03 +0100 Subject: [Bioperl-l] Bio::DB::Query::GenBank Message-ID: <716af09c0611030457p678f4d30v935215ba3c4dd5dc@mail.gmail.com> Hi, In contrast to the doc of Bio::DB::Query::GenBank at http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Query/GenBank.html this following seems not the case: "If you provide an array reference of IDs in -ids, the query will be ignored and the list of IDs will be used when the query is passed to a Bio::DB::GenBank object's get_Stream_by_query() method" I used # $Id: GenBank.pm,v 1.19 2006/09/26 22:03:07 sendu Exp $ It looks like query always overrules the array(ref) given in -ids. bernd From staffa at niehs.nih.gov Fri Nov 3 11:29:19 2006 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Fri, 03 Nov 2006 12:29:19 -0400 Subject: [Bioperl-l] Bio::Tools::RestrictionEnzyme Message-ID: The module Bio::Tools::RestrictionEnzyme Uses the perl split function to generate the fragments of a digestion, Using the recognition pattern as the delimiter. It then glues onto the resulting strings that part of the pattern representing the sequence before and after the cut. This is fine for non-ambiguous patterns, but starts looking funny for patterns having ambiguities. Worse that in doing a double digest, one enzyme after another, the ambiguity code character can mask a true cut site. I was using BsaHI [GRCGYC] followed by HpaII [CCGG] Below is the example of the CCGG pattern being masked by a Y And the different results of the digestion. CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAA As opposed to the real thing: CGCCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAA Which when cut by HpaII [CCGG] really yields first A_B_frag : CGC Instead of : first A_B_frag = CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAAG ACTTGCTAGTGCTGTTGGGTCTCC TTGACTCTGAGACAATGATAACAATGTTGAAGGTGGTCTAGGCATTTGGGTGCTGTGGAGTTATAAAGAGGAAAAG AAAAGATAAAACAAAAAAAAATAG GAAACAAATGATTAAGCCACTACTAAGGGGTCTAGTCTAATGCCAACTGGGTAAATTCATGGGAACAATGTGTGCC AGTCTTTAGAAACACTGTTTCATA TTGCATATATTATGGCATGGTATTACATTGATTAATTTTACTTTAGAGATGAAGAAGCTGAGATTTGGGGTGAATA GCAATTATCCCAAAGTCTCTCAGA TAGCTGGAGGCAGCAGGGTCTGGGGTATTCACAGTCCCTACTCCATATTGTGTGGTCAGAACCAAATGAGACAGAT AAAGGGCAGACAAAAGAGAAAGTG GGGAGTATGATTTGAAAATGATGGTGTGACCCAGATTTCTGATGGAAATATCTAATGGCTGCAGACTGGATAGCTG TGACCATTTTAGTTACTGAATTCA GGAGATCTTATCTCAATGGAGGCATGTTGTCAACCAAAAGCCAGGATAAGCAAGGGTCAGTGTCTAGACATTGGAG TAAGGTTTGCCTGGATATTTCCAC AGGGAACCAAGTGTCATGGAGTCTTATTCATTGGGAGGTTATCTTTGTTACACACATGGACATATCATCAAGCCAG CAATTCAGCAAAACTGTCAACACA CAAATAGAGATGTATTGACAACGGGGAACCACAAGTCATGCTTATTCCAAGCTAAAGCCCTCATGTGGAACTTGTT TTGTATGGCATTTGTCTCATCTAC ACATTGATGGGAAGGGTAAAAGGAAGTCTTTGGTGGGATTACAGAAGTCAGTAAAAAAGCAAAAGGAAAGATTTAG AAAACAAAGAAAAAGAAAAGGGAG GAAAGGAAAAGAAAAAAGATTTCAGAGATCTCAACATCAATTCAGACCAAGGGTGCCTCTTATACTATGTCCAAGC CAGTAAGTGGGGTTGTTCTTGTTA ACTACAGCCATGTATAGAGGTGAACTTCAGGCTCCTGACTGATCCTCTGAGGTAGAAAGTAAACAGTACTCTTATG ACACACGCAGTTGTTCAGTGCTGA CATGAAAATGTCATTGCTTACAGCGCTAGGAGAC This subroutine yields, I believe, the true sequence, Although I don't know how efficient it is. I'm thinking it must be more efficient than having to turn each fragment from the first digestion into a BioPerl Sequence Object before applying the cut_seq method. sub cut_seq { my $number= 0; my @frags = (); my $bigline = shift @_; my $recognition_site = shift @_; my $cutsite = shift @_; my $pat = &expanded_string($recognition_site); while ($bigline){ #my $offset = index $bigline, $pat; if ($bigline =~/($pat)/){ my $first = substr $&,0,$cutsite; my $last = substr $&,$cutsite; my $frag = $`.$first; push @frags, $frag; $number++; #print "fragment # $number:\n$frag\n"; my $rest_of_bigline = $last.$'; $bigline = $rest_of_bigline;} else {push @frags, $bigline; #Last one $number++; #print "fragment # $number:\n$bigline\n"; $bigline = "";} } return @frags; } Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Information Technology Support Services Contract (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov ) National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From cjfields at uiuc.edu Fri Nov 3 13:28:53 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 3 Nov 2006 12:28:53 -0600 Subject: [Bioperl-l] Bio::Tools::RestrictionEnzyme In-Reply-To: References: Message-ID: <915FE028-7F12-4BCE-AD9D-7D8D7D74AD6F@uiuc.edu> Nick, Could you file this as a bug? Chris On Nov 3, 2006, at 10:29 AM, Staffa, Nick (NIH/NIEHS) wrote: > The module Bio::Tools::RestrictionEnzyme > Uses the perl split function to generate the fragments of a digestion, > Using the recognition pattern as the delimiter. It then glues onto > the > resulting strings that part of the pattern representing the > sequence before > and after the cut. This is fine for non-ambiguous patterns, but > starts > looking funny for patterns having ambiguities. > Worse that in doing a double digest, one enzyme after another, the > ambiguity > code character can mask a true cut site. > I was using BsaHI [GRCGYC] followed by HpaII [CCGG] > Below is the example of the CCGG pattern being masked by a Y > And the different results of the digestion. > > > CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAA > As opposed to the real thing: > CGCCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAA > > Which when cut by HpaII [CCGG] really yields > first A_B_frag : > CGC > > Instead of : > first A_B_frag = > > CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAAG > ACTTGCTAGTGCTGTTGGGTCTCC > TTGACTCTGAGACAATGATAACAATGTTGAAGGTGGTCTAGGCATTTGGGTGCTGTGGAGTTATAAAGAG > GAAAAG > AAAAGATAAAACAAAAAAAAATAG > GAAACAAATGATTAAGCCACTACTAAGGGGTCTAGTCTAATGCCAACTGGGTAAATTCATGGGAACAATG > TGTGCC > AGTCTTTAGAAACACTGTTTCATA > TTGCATATATTATGGCATGGTATTACATTGATTAATTTTACTTTAGAGATGAAGAAGCTGAGATTTGGGG > TGAATA > GCAATTATCCCAAAGTCTCTCAGA > TAGCTGGAGGCAGCAGGGTCTGGGGTATTCACAGTCCCTACTCCATATTGTGTGGTCAGAACCAAATGAG > ACAGAT > AAAGGGCAGACAAAAGAGAAAGTG > GGGAGTATGATTTGAAAATGATGGTGTGACCCAGATTTCTGATGGAAATATCTAATGGCTGCAGACTGGA > TAGCTG > TGACCATTTTAGTTACTGAATTCA > GGAGATCTTATCTCAATGGAGGCATGTTGTCAACCAAAAGCCAGGATAAGCAAGGGTCAGTGTCTAGACA > TTGGAG > TAAGGTTTGCCTGGATATTTCCAC > AGGGAACCAAGTGTCATGGAGTCTTATTCATTGGGAGGTTATCTTTGTTACACACATGGACATATCATCA > AGCCAG > CAATTCAGCAAAACTGTCAACACA > CAAATAGAGATGTATTGACAACGGGGAACCACAAGTCATGCTTATTCCAAGCTAAAGCCCTCATGTGGAA > CTTGTT > TTGTATGGCATTTGTCTCATCTAC > ACATTGATGGGAAGGGTAAAAGGAAGTCTTTGGTGGGATTACAGAAGTCAGTAAAAAAGCAAAAGGAAAG > ATTTAG > AAAACAAAGAAAAAGAAAAGGGAG > GAAAGGAAAAGAAAAAAGATTTCAGAGATCTCAACATCAATTCAGACCAAGGGTGCCTCTTATACTATGT > CCAAGC > CAGTAAGTGGGGTTGTTCTTGTTA > ACTACAGCCATGTATAGAGGTGAACTTCAGGCTCCTGACTGATCCTCTGAGGTAGAAAGTAAACAGTACT > CTTATG > ACACACGCAGTTGTTCAGTGCTGA > CATGAAAATGTCATTGCTTACAGCGCTAGGAGAC > > > This subroutine yields, I believe, the true sequence, > Although I don't know how efficient it is. > I'm thinking it must be more efficient than having to turn each > fragment > from the first digestion into a BioPerl Sequence Object before > applying the > cut_seq method. > > sub cut_seq { > my $number= 0; > my @frags = (); > my $bigline = shift @_; > my $recognition_site = shift @_; > my $cutsite = shift @_; > my $pat = &expanded_string($recognition_site); > while ($bigline){ > #my $offset = index $bigline, $pat; > if ($bigline =~/($pat)/){ > my $first = substr $&,0,$cutsite; > my $last = substr $&,$cutsite; > my $frag = $`.$first; > push @frags, $frag; > $number++; > #print "fragment # $number:\n$frag\n"; > my $rest_of_bigline = $last.$'; > $bigline = $rest_of_bigline;} > else {push @frags, $bigline; #Last one > $number++; > #print "fragment # $number:\n$bigline\n"; > $bigline = "";} > } > return @frags; > } > > > > > Nick Staffa > Telephone: 919-316-4569 (NIEHS: 6-4569) > Scientific Computing Support Group > NIEHS Information Technology Support Services Contract > (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov ) > National Institute of Environmental Health Sciences > National Institutes of Health > Research Triangle Park, North Carolina > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From johnson.biotech at gmail.com Fri Nov 3 11:47:56 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Fri, 3 Nov 2006 11:47:56 -0500 Subject: [Bioperl-l] BioSQL load_seqdatabase.pl -pipeline option Message-ID: Hello guys, I'm populating biosql database using "load_seqdatabase.pl" from genbank release files for primates. However, I only need sequences that belong to humans (taxon id: 9606). I assume that best way to filter the necessary sequences is to use '-pipeline' option of the script. The documentation seems a little vague to me on how to create my own processor to accomplish the task. Can anyone clarify the steps??? -- Best Regards, Seth Johnson Senior Bioinformatics Associate From er at xs4all.nl Fri Nov 3 14:59:47 2006 From: er at xs4all.nl (Erik) Date: Fri, 3 Nov 2006 20:59:47 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error Message-ID: <10596.156.83.1.241.1162583987.squirrel@webmail.xs4all.nl> Hi all, I noticed the parsing is borked with newest swisprot files: UniProt Knowledgebase Release 9 consists of: UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines in swissprot/trembl according to the new specification (see http://expasy.org/sprot/relnotes/sp_news.html). Basically, the change is as follows: ID EntryName DataClass; MoleculeType; SequenceLength. is changed to: ID EntryName DataClass; SequenceLength. The change I made was only in the regex capturing the entry name: method next_seq (Bio/SeqIO/swiss.pm) : =============== unless( m/ ^ ID \s+ # (\S+) \s+ # $1 entryname ([^\s;]+); \s+ # $2 DataClass [0-9]+[ ]AA \. # Sequencelength (capture?) $ /ox ) { $self->throw("swissprot stream with no ID. Not swissprot in my book"); } =============== I tested this (=entry parsable and SeqIO created) against several hundred Swissprot and Trembl entries. Of course, files with the older format are now broken - it may be better to leave old and new format, and try both (newest first). hth, Erik From er at xs4all.nl Fri Nov 3 15:56:47 2006 From: er at xs4all.nl (Erik) Date: Fri, 3 Nov 2006 21:56:47 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error - Message-ID: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> I should have mentioned two more changes needed in Bio/SeqIO/swiss.pm for the new Swissprot format: In Bio/SeqIO/swiss.pm, next_seq(): =============== $params{'-namespace'} = ($2 eq 'Reviewed' ) ? 'Swiss-Prot' : ($2 eq 'Unreviewed' ) ? 'TrEMBL' : # ($2 eq 'STANDARD' ) ? 'Swiss-Prot' : # ($2 eq 'PRELIMINARY') ? 'TrEMBL' : $2; =============== and in Bio/SeqIO/swiss.pm, write_seq(): =============== $div = ($ns eq 'Swiss-Prot') ? 'Reviewed' : ($ns eq 'TrEMBL') ? 'Unreviewed' : # ($ns eq 'Swiss-Prot') ? 'STANDARD' : # ($ns eq 'TrEMBL') ? 'PRELIMINARY' : $ns; =============== above, the old lines are shown as outcommented. again, hth, Erik From pllv_shrm at yahoo.com Fri Nov 3 16:14:14 2006 From: pllv_shrm at yahoo.com (pallavi sharma) Date: Fri, 3 Nov 2006 13:14:14 -0800 (PST) Subject: [Bioperl-l] need help Message-ID: <20061103211414.56111.qmail@web31712.mail.mud.yahoo.com> hii could ny one plz tell me how to convert bioperl module like Bio::SearchIO n Bio::alignIO module into perl lang --------------------------------- Check out the New Yahoo! Mail - Fire up a more powerful email and get things done faster. From hlapp at gmx.net Fri Nov 3 17:54:08 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 3 Nov 2006 17:54:08 -0500 Subject: [Bioperl-l] BioSQL load_seqdatabase.pl -pipeline option In-Reply-To: References: Message-ID: Close. It's not the --pipeline option you want to use for this purpose but the --seqfilter option. For example, to retain only sequence with taxon id 9606 you would say --seqfilter 'sub {my $s=shift->{"-species"}; return 1 unless $s; return 1 unless $s->ncbi_taxid; return 1 if $s->ncbi_taxid == 9606; return 0;}' Note that when formulating the conditions upon which to accept or reject the object you need to take into account that the closure may be called multiple times for one object, at various stages of completion of the properties hash. So, the above sequence of logic says, accept the object if there is no species attached (yet), or if the species doesn't have a taxon ID (yet; in Genbank format, the taxon ID is actually in the feature table, and hence will only be populated later, after parsing the organism lines), or if the taxon ID is 9606. Otherwise (i.e., there is a species object, it has a taxon ID defined, and the taxon ID is not 9606) reject the object. (Note that --seqfilter will read and parse a file if the argument refers to an existing and readable file. So if you are going to use this construct often, you may want to put into a file.) -hilmar On Nov 3, 2006, at 11:47 AM, Seth Johnson wrote: > Hello guys, > > I'm populating biosql database using "load_seqdatabase.pl" from > genbank release files for primates. However, I only need sequences > that belong to humans (taxon id: 9606). I assume that best way to > filter the necessary sequences is to use '-pipeline' option of the > script. The documentation seems a little vague to me on how to create > my own processor to accomplish the task. Can anyone clarify the > steps??? > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From akozik at atgc.org Fri Nov 3 17:29:49 2006 From: akozik at atgc.org (Alexander Kozik) Date: Fri, 03 Nov 2006 14:29:49 -0800 Subject: [Bioperl-l] SCF files Message-ID: <454BC2DD.5050405@atgc.org> Hi all, There is a contradiction in opinions (I have used google search) what type of data SCF files (sequencing chromatograms) carry. Could you help to clarify following topics: are these statements true or false: 1. SCF files can be generated by Phred program only. 2. new version of Phred can read SCF files produced by older version of Phred and re-do basecalling with new quality scores [new quality scores could be different because of the improvements/changes in a basecalling algorithm] 3. SCF files contain no less information as original AB1 files [in other words, no information lost during conversion of AB1 to SCF] Thanks, -Alex ======================================== Alexander Kozik Bioinformatics Specialist Genome and Biomedical Sciences Facility 451 East Health Sciences Drive University of California Davis, CA 95616-8816 Phone: (530) 754-9127 email: akozik at atgc.org web: http://www.atgc.org/ ======================================== From cjfields at uiuc.edu Sun Nov 5 16:56:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 5 Nov 2006 15:56:08 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error - In-Reply-To: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> References: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> Message-ID: <73A15B2C-A8FE-4F1B-B17E-B43A46B82140@uiuc.edu> We'll try to get these in. THe problem is we need to try and make this backwards compatible. I'll post this as a bug for now as a reminder. Chris On Nov 3, 2006, at 2:56 PM, Erik wrote: > > I should have mentioned two more changes needed > in Bio/SeqIO/swiss.pm for the new Swissprot > format: > > In Bio/SeqIO/swiss.pm, next_seq(): > =============== > $params{'-namespace'} = ($2 eq 'Reviewed' ) ? 'Swiss-Prot' : > ($2 eq 'Unreviewed' ) ? 'TrEMBL' : > # ($2 eq 'STANDARD' ) ? 'Swiss-Prot' : > # ($2 eq 'PRELIMINARY') ? 'TrEMBL' : > $2; > =============== > > > and in Bio/SeqIO/swiss.pm, write_seq(): > =============== > $div = ($ns eq 'Swiss-Prot') ? 'Reviewed' : > ($ns eq 'TrEMBL') ? 'Unreviewed' : > # ($ns eq 'Swiss-Prot') ? 'STANDARD' : > # ($ns eq 'TrEMBL') ? 'PRELIMINARY' : > $ns; > =============== > > above, the old lines are shown as outcommented. > > > again, hth, > > Erik > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From adsj at novozymes.com Mon Nov 6 08:03:21 2006 From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=) Date: Mon, 06 Nov 2006 14:03:21 +0100 Subject: [Bioperl-l] Subclassing Bio::Seq ? Extending Bio::Perl References: <934F95E71B6C9347A873C42AE3C196191299DFBF@NZT0004E.dknz.nzcorp.n et> <934F95E71B6C9347A873C42AE3C196190B84C5FC@NZT0004E.dknz.nzcorp.net> Message-ID: <87zmb4ohgm.fsf@topper.koldfront.dk> On Tue, 24 Oct 2006 14:57:02 -0400, Hilmar wrote: > On Oct 24, 2006, at 1:59 PM, JK ((Jesper Agerbo Krogh)) wrote: >>> The reason that this is a Bio::PrimarySeq and not a Bio::Seq or your >>> extension of the latter is that the Perl garbage collector can't deal >>> with circular references. >> Doesn't Scalar::Util::weaken solve that? > You're welcome to test and try. It should be a simple change in > Bio::Seq::add_SeqFeature(). You will see that it is this method and > not the feature object that makes sure the wrapped primarySeq gets > passed as sequence reference. Just change that to creating a new > reference to the sequence object and make it a weak reference before > passing it to the feature object. > (The feature object has no requirement (or knowledge) that the > referenced sequence object is a PrimarySeq.) I've tried implementing this approach - the only test that failed was FootPrinter.t, which I "solved" by not weakening if the object is a Bio::PrimarySeq. I am not sure how fragile this approach is; any comments (patch attached)? [...] > I'm not following you why this would make any difference (it would be > $seq->message_digest() compared to $seqCompute->message_digest > ($seq)), unless what you are saying is that you would like to cache > the result of the computation. You would have to create, or pass around, a $seqCompute object everywhere your $seq-object's digest was needed, which would be a bit of a pain? Best regards, Adam -- Adam Sj?gren adsj at novozymes.com -------------- next part -------------- A non-text attachment was scrubbed... Name: feature_seq_weaken.patch Type: text/x-patch Size: 3675 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061106/3dd65a9d/attachment.bin From n.haigh at sheffield.ac.uk Mon Nov 6 10:12:37 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 15:12:37 +0000 Subject: [Bioperl-l] return undef Message-ID: <454F50E5.3030702@sheffield.ac.uk> Is there any reason why a "return undef" can't simply be swapped over to just "return"? Cheers Nath From n.haigh at sheffield.ac.uk Mon Nov 6 11:19:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 16:19:08 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F5BED.6040406@sendu.me.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> Message-ID: <454F607C.5020808@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Is there any reason why a "return undef" can't simply be swapped over to >> just "return"? > > No, in fact if you see any 'return undef's, please change them to > 'return' since the former can lead to subtle bugs. We did do an audit > earlier to fix most of those; presumably there was some kind of issue > with the remainder (or they just weren't caught), so check that no > problems arise when you make the change. > Just been checking the bioperl-run modules and changed the ones I found. Running "make test" doesn't seem to show up any errors so I'll commit them shortly. On a similar note, is it safe to simply substitute "use vars" for "our" and correctly commenting the list of variables if qw() was previously used? e.g.: use vars qw($variable1 @array1 %hash1); # to: our ($variable1, @array1, %hash1); If so, there are 340+ "use vars" in the bioperl-run......any wise ideas on a generic script that can do an intelligent search and replace. Bearing in mind that these lists can span multiple lines? I set up the following page a couple of days ago to house some scripts that can be used to do audit checks of code: http://www.bioperl.org/wiki/Auditing If anyone has any scripts, Perl, shell or otherwise fell free to add them! :-) Cheers Nath -- > A: Yes. >> Q: Are you sure? >> >>> A: Because it reverses the logical flow of conversation. >>> >>>> Q: Why is top posting frowned upon? >>>> Get Thunderbird From bix at sendu.me.uk Mon Nov 6 10:59:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 15:59:41 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F50E5.3030702@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> Message-ID: <454F5BED.6040406@sendu.me.uk> Nathan S. Haigh wrote: > Is there any reason why a "return undef" can't simply be swapped over to > just "return"? No, in fact if you see any 'return undef's, please change them to 'return' since the former can lead to subtle bugs. We did do an audit earlier to fix most of those; presumably there was some kind of issue with the remainder (or they just weren't caught), so check that no problems arise when you make the change. From cjfields at uiuc.edu Mon Nov 6 11:35:52 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 10:35:52 -0600 Subject: [Bioperl-l] AlignIO::stockholm write_aln() Message-ID: I have added some experimental write_aln() support for Stockholm format to CVS along with some basic tests to AlignIO.t. I plan on cleaning it up a bit and adding more tests, along with possibly adding a builder option (similar to SeqIO::genbank) to have annotation parsing optional. Right now it is always on by default. It doesn't print meta data yet but does parse and store it; I'll probably add that in the next day or two. Be forewarned if testing this: I haven't tried clustal/msf/etc- >stockholm conversions yet so don't know if that works, but it should (it just won't print annotations). I'll add tests for that when I get time. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 6 11:55:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 16:55:55 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F607C.5020808@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> Message-ID: <454F691B.3090900@sendu.me.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: >> Nathan S. Haigh wrote: >>> Is there any reason why a "return undef" can't simply be swapped over to >>> just "return"? >> >> No, in fact if you see any 'return undef's, please change them to >> 'return' since the former can lead to subtle bugs. We did do an audit >> earlier to fix most of those; presumably there was some kind of issue >> with the remainder (or they just weren't caught), so check that no >> problems arise when you make the change. > > Just been checking the bioperl-run modules and changed the ones I found. > Running "make test" doesn't seem to show up any errors so I'll commit > them shortly. Thanks. > On a similar note, is it safe to simply substitute "use vars" for "our" > and correctly commenting the list of variables if qw() was previously used? Should be. But note that we didn't officially agree on having the Run package require Perl 5.6... Is there a particular person who maintains the Run package, or does that fall to the pumpkin of Core? > If so, there are 340+ "use vars" in the bioperl-run......any wise ideas > on a generic script that can do an intelligent search and replace. > Bearing in mind that these lists can span multiple lines? It'll need a little futzing, just be very careful it is working perfectly before applying it to everything. All of Core and the other packages need the same work done on them... > I set up the following page a couple of days ago to house some scripts > that can be used to do audit checks of code: > http://www.bioperl.org/wiki/Auditing > > If anyone has any scripts, Perl, shell or otherwise fell free to add > them! :-) I created a one-off for the conversion to 'use base', but its a bit of delirium-induced hack. I'll add it when I get the chance; its essentially a more complex version of what you want to do. It also ought to be applied to all the other Bioperl packages... (You should make mention of the existing audit scripts in CVS for bioperl-live in maintenance/) From cjfields at uiuc.edu Mon Nov 6 12:58:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 11:58:27 -0600 Subject: [Bioperl-l] return undef In-Reply-To: <454F691B.3090900@sendu.me.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> <454F691B.3090900@sendu.me.uk> Message-ID: <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> >> On a similar note, is it safe to simply substitute "use vars" for >> "our" >> and correctly commenting the list of variables if qw() was >> previously used? > > Should be. But note that we didn't officially agree on having the Run > package require Perl 5.6... Is there a particular person who maintains > the Run package, or does that fall to the pumpkin of Core? I believe Albert Vilella was taking care of bioperl-run, but I'm not absolutely sure. I think we can assume that, if core rel. 1.5.2 requires perl 5.6.1, anything that requires bioperl rel. 1.5.2 should likewise require perl 5.6.1 as well. Probably should make that explicitly stated somewhere. >> If so, there are 340+ "use vars" in the bioperl-run......any wise >> ideas >> on a generic script that can do an intelligent search and replace. >> Bearing in mind that these lists can span multiple lines? > > It'll need a little futzing, just be very careful it is working > perfectly before applying it to everything. All of Core and the other > packages need the same work done on them... I have gone through a few and manually switched 'use vars' over to 'our'. You can always try making the necessary changes globally but I think you'll see a lot of failed tests. >> I set up the following page a couple of days ago to house some >> scripts >> that can be used to do audit checks of code: >> http://www.bioperl.org/wiki/Auditing >> >> If anyone has any scripts, Perl, shell or otherwise fell free to add >> them! :-) > > I created a one-off for the conversion to 'use base', but its a bit of > delirium-induced hack. I'll add it when I get the chance; its > essentially a more complex version of what you want to do. It also > ought > to be applied to all the other Bioperl packages... > > (You should make mention of the existing audit scripts in CVS for > bioperl-live in maintenance/) Not sure how much more global code auditing should be done before the 1.5.2 final release, but if it passes tests then I don't have a problem. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 6 13:08:38 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 18:08:38 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> <454F691B.3090900@sendu.me.uk> <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> Message-ID: <454F7A26.9090800@sendu.me.uk> Chris Fields wrote: >>> I set up the following page a couple of days ago to house some scripts >>> that can be used to do audit checks of code: >>> http://www.bioperl.org/wiki/Auditing >>> >>> If anyone has any scripts, Perl, shell or otherwise fell free to add >>> them! :-) >> >> I created a one-off for the conversion to 'use base', but its a bit of >> delirium-induced hack. I'll add it when I get the chance; its >> essentially a more complex version of what you want to do. It also ought >> to be applied to all the other Bioperl packages... >> >> (You should make mention of the existing audit scripts in CVS for >> bioperl-live in maintenance/) > > Not sure how much more global code auditing should be done before the > 1.5.2 final release None; I won't add any to the branch (bug fixes and documentation only, for the most part). It is still valuable to do for the next release though! From n.haigh at sheffield.ac.uk Mon Nov 6 15:29:23 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 20:29:23 +0000 Subject: [Bioperl-l] StandAloneFasta::version Message-ID: <454F9B23.8010302@sheffield.ac.uk> Hi Sendu, I've written a version method for StandAloneFasta.pm. However, because of the way in which FASTA is versioned, it makes for difficult version comparisons i.e. they contain non-numeric characters e.g. 3.4t26. I have employed a private function that does a conversion of the non-numeric characters into their ascii value representation to build a float. e.g. the above version would result in: 3.411626 which can then be compared easily. At the moment, this is accessed via $factory->version like other modules as this will give access to a version number that is easily comparable. However, should there be a different function to return the unconverted version string e.g. 3.4t26? Or should there be a function that does a compare internally so it can be accessed something like: print "we have met the min version requirement\n" if $factory->at_least_version('3.4t26'); Ideas welcome! Nath From cjfields at uiuc.edu Mon Nov 6 16:21:10 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 15:21:10 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <454F9B23.8010302@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> Message-ID: <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> Nathan, Weren't the problems with the reported StandAloneFasta.pm test fails due to differences in the returned order of the Hits/HSPs in the FASTA reports from the different versions? The test results you posted on the wiki (where I commented on this) seem to indicate that: not ok 11 # Test 11 got: "0" (t/StandAloneFasta.t at line 75) # Expected: "994" # t/StandAloneFasta.t line 75 is: ok $hsp->num_identical, 994; not ok 12 # Test 12 got: "1977" (t/StandAloneFasta.t at line 76) # Expected: "994" # t/StandAloneFasta.t line 76 is: ok $hsp->length, 994; ok 13 not ok 14 # Test 14 got: "0" (t/StandAloneFasta.t at line 88) # Expected: "994" # t/StandAloneFasta.t line 88 is: ok $hsp->num_identical, 994; not ok 15 # Test 15 got: "1977" (t/StandAloneFasta.t at line 89) # Expected: "994" # t/StandAloneFasta.t line 89 is: ok $hsp->length, 994; It looks like a value is returned for the tests, so parsing isn't broken. They just aren't returned in the order specified, so the tests are faulty, not the parsing. The tests could be fixed by using id/score key/value pairs in a hash or something similar. We probably shouldn't limit to a specific version unless parsing is actually broken. Chris On Nov 6, 2006, at 2:29 PM, Nathan S. Haigh wrote: > Hi Sendu, > > I've written a version method for StandAloneFasta.pm. However, because > of the way in which FASTA is versioned, it makes for difficult version > comparisons i.e. they contain non-numeric characters e.g. 3.4t26. > > I have employed a private function that does a conversion of the > non-numeric characters into their ascii value representation to > build a > float. e.g. the above version would result in: 3.411626 which can then > be compared easily. At the moment, this is accessed via > $factory->version like other modules as this will give access to a > version number that is easily comparable. However, should there be a > different function to return the unconverted version string e.g. > 3.4t26? > Or should there be a function that does a compare internally so it can > be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26'); > > Ideas welcome! > Nath > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From torsten.seemann at infotech.monash.edu.au Mon Nov 6 15:41:24 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Tue, 07 Nov 2006 07:41:24 +1100 Subject: [Bioperl-l] return undef In-Reply-To: <454F607C.5020808@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> Message-ID: <454F9DF4.80702@infotech.monash.edu.au> > I set up the following page a couple of days ago to house some scripts > that can be used to do audit checks of code: > http://www.bioperl.org/wiki/Auditing Your 'grep' patterns should probably have "\s+" rather than " " between keywords as often coders have used multiple spaces or tabs. Your 'die/confess/...' patterns require a "(" after them. I'd say those functions are used without parentheses about half the time, eg. die "ech!"; Explicit "return undef" aren't too hard to find. It's the hidden ones where it's "my $value; ...lots of code...; return $value;" which are hard to identify. -- Torsten Seemann Victorian Bioinformatics Consortium, Monash University, Australia From n.appleby at uq.edu.au Mon Nov 6 21:11:06 2006 From: n.appleby at uq.edu.au (Nikki Appleby) Date: Tue, 7 Nov 2006 12:11:06 +1000 Subject: [Bioperl-l] go-perl error: ')' missing Message-ID: <005d01c70211$fbaf55a0$1b776682@IMBPC.AD> Thanks for being there when things go wrong. I have installed required modules as listed in Chris' instructions, then get stuck on this. C:\Perl\go-perl\go-perl-0.05>perl Makefile.PL The system cannot find the path specified. NOTICE: ** You do not have xsltproc ** This tool is not required for go-perl, but it is useful for for certain kinds of format conversion (eg converting to OWL format). You will also need this tool if you are installing go-db-perl You can safely ignore this notification message; Even if you do intend to use go-db-perl later, you can install xsltproc at a later date xsltproc is available as part of libxslt. See http://xmlsoft.org/XSLT/ for details Writing Makefile for GO C:\Perl\go-perl\go-perl-0.05>nmake Microsoft (R) Program Maintenance Utility Version 1.50 Copyright (c) Microsoft Corp 1988-94. All rights reserved. makefile(1706) : fatal error U1000: syntax error : ')' missing in macro invocati on Stop. Nikki Appleby. 07 334 62634 From n.haigh at sheffield.ac.uk Tue Nov 7 02:05:40 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 07 Nov 2006 07:05:40 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> Message-ID: <45503044.30000@sheffield.ac.uk> Chris Fields wrote: > Nathan, > > Weren't the problems with the reported StandAloneFasta.pm test fails > due to differences in the returned order of the Hits/HSPs in the FASTA > reports from the different versions? The test results you posted on > the wiki (where I commented on this) seem to indicate that: > > not ok 11 > # Test 11 got: "0" (t/StandAloneFasta.t at line 75) > # Expected: "994" > # t/StandAloneFasta.t line 75 is: ok $hsp->num_identical, 994; > not ok 12 > # Test 12 got: "1977" (t/StandAloneFasta.t at line 76) > # Expected: "994" > # t/StandAloneFasta.t line 76 is: ok $hsp->length, 994; > ok 13 > not ok 14 > # Test 14 got: "0" (t/StandAloneFasta.t at line 88) > # Expected: "994" > # t/StandAloneFasta.t line 88 is: ok $hsp->num_identical, 994; > not ok 15 > # Test 15 got: "1977" (t/StandAloneFasta.t at line 89) > # Expected: "994" > # t/StandAloneFasta.t line 89 is: ok $hsp->length, 994; > > It looks like a value is returned for the tests, so parsing isn't > broken. They just aren't returned in the order specified, so the > tests are faulty, not the parsing. The tests could be fixed by using > id/score key/value pairs in a hash or something similar. We probably > shouldn't limit to a specific version unless parsing is actually broken. > > Chris > Chris, I agree, I was going to update the tests later this morning :-P Any thoughts about version() or should I just leave it be for now? Cheers Nath From bix at sendu.me.uk Tue Nov 7 04:15:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 09:15:41 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45503044.30000@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> Message-ID: <45504EBD.2000708@sendu.me.uk> Nathan S. Haigh wrote: > I agree, I was going to update the tests later this morning :-P Any > thoughts about version() or should I just leave it be for now? If its no trouble, go ahead with a version() method. Its nice to have in any case. I'd suggest your latter option of 'there be a function that does a compare internally so it can be accessed something like: print "we have met the min version requirement\n" if $factory->at_least_version('3.4t26');' In fact, it ought to work with '34t26b3' as well (I guess the method would try what it was given, and on failure, try again with the last 2 characters removed, then try both cases again with a decimal added if there wasn't one). From n.haigh at sheffield.ac.uk Tue Nov 7 04:50:52 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 07 Nov 2006 09:50:52 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45504EBD.2000708@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> Message-ID: <455056FC.90608@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> I agree, I was going to update the tests later this morning :-P Any >> thoughts about version() or should I just leave it be for now? > > If its no trouble, go ahead with a version() method. Its nice to have > in any case. I'd suggest your latter option of 'there be a function > that does a compare internally so it can be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26');' > In fact, it ought to work with '34t26b3' as well (I guess the method > would try what it was given, and on failure, try again with the last 2 > characters removed, then try both cases again with a decimal added if > there wasn't one). I've contacted Bill Pearson to clarify his versioning scheme. Ideally, we could do as you say, compare variants of '34t26b3'. However, the software doesn't report the b3 part of the version string only 3.4t26 followed by a date. Therefore, I'm not sure it's possible to distinguish between 3.4t26b1 and 3.4t26b3 - unless we consider the date also returned by the software :-( . Bill said he is currently busy with a course at Cold Spring Harbor but will respond in full later. Therefore, until he's informed me of how he versions his releases, I'll hold off with the version() method for the time being. Nath From cjfields at uiuc.edu Tue Nov 7 10:58:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 09:58:48 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45504EBD.2000708@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> Message-ID: <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> On Nov 7, 2006, at 3:15 AM, Sendu Bala wrote: > Nathan S. Haigh wrote: >> I agree, I was going to update the tests later this morning :-P Any >> thoughts about version() or should I just leave it be for now? > > If its no trouble, go ahead with a version() method. Its nice to > have in > any case. I'd suggest your latter option of 'there be a function that > does a compare internally so it can be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26');' > In fact, it ought to work with '34t26b3' as well (I guess the method > would try what it was given, and on failure, try again with the last 2 > characters removed, then try both cases again with a decimal added if > there wasn't one). Is it possible to have the interface base class contain an abstract program_version() (or similar) method? One that could be implemented to just grab the current version of the program? I was thinking about something like this for the RNA-based wrappers I want to add but it seems to be something that most Run modules would benefit from. Just haven't had time to look into it with much detail. Almost wonder if it would be easier to have all bioperl-run modules have a Run-specific Root object for common methods, regardless of the other interfaces used. Maybe something inheriting Bio::Root::Root... chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Nov 7 11:54:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 10:54:48 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550AF3B.8000807@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> Message-ID: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: ... >> Is it possible to have the interface base class contain an >> abstract program_version() (or similar) method? One that could be >> implemented to just grab the current version of the program? I >> was thinking about something like this for the RNA-based wrappers >> I want to add but it seems to be something that most Run modules >> would benefit from. Just haven't had time to look into it with >> much detail. > > What's wrong with version() ? Didn't realize there was a version() already. >> Almost wonder if it would be easier to have all bioperl-run >> modules have a Run-specific Root object for common methods, >> regardless of the other interfaces used. Maybe something >> inheriting Bio::Root::Root... > > What's wrong with Bio::Tools::Run::WrapperBase ? I agree that WrapperBase fulfills most of this functionality. However, don't a few bioperl-run wrappers 'roll their own', i.e. not implement WrapperBase? Requiring all bioperl-run module inherit the same Run-specific base object would integrate them a bit more and distinguish them from the core modules (which would inherit Bio::Root::Root). Anyway, it's just a suggestion. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Tue Nov 7 10:54:06 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 07 Nov 2006 10:54:06 -0500 Subject: [Bioperl-l] Bio::SeqIO::gcg bug Message-ID: <4550AC1E.2070500@bms.com> Bio::SeqIO::gcg is checking the checksum against the GCG generated one. There is a problem with the way this is done: 1. Bio::SeqIO::gcg removes all characters, except [A-Za-z] (which by the way is always wrong). 2. GCG calculates the checksum on uppercase I assume Hilmar removed the $_ = uc($_); line for a very good reason, but the call to validate should be: _validate_checksum(uc($sequence),$chksum)) Also I believe the regexp for checking the alphabet should remove explicitly numbers and whitespaces. Removing everything else is not a good idea because gaps, end of translation are removed also and possible parsing errors might be suppressed incorrectly. Let me know if I am missing some other considerations here. If not I will commit these changes. Stefan From bix at sendu.me.uk Tue Nov 7 12:25:22 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 17:25:22 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> Message-ID: <4550C182.3000308@sendu.me.uk> Chris Fields wrote: > > On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: > >>> Almost wonder if it would be easier to have all bioperl-run modules >>> have a Run-specific Root object for common methods, regardless of the >>> other interfaces used. Maybe something inheriting Bio::Root::Root... >> >> What's wrong with Bio::Tools::Run::WrapperBase ? > > I agree that WrapperBase fulfills most of this functionality. However, > don't a few bioperl-run wrappers 'roll their own', i.e. not implement > WrapperBase? Requiring all bioperl-run module inherit the same > Run-specific base object would integrate them a bit more and distinguish > them from the core modules (which would inherit Bio::Root::Root). > Anyway, it's just a suggestion. Well, how would you 'require' them to use anything at all? There's not even anything 'requiring' that a core module inherit from Bio::Root::Root(I). We just (very strongly) advise that you inherit from there. So we can also advise that bioperl-run wrappers do not roll their own but use Bio::Tools::Run::WrapperBase. From cjfields at uiuc.edu Tue Nov 7 12:40:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 11:40:32 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C182.3000308@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> Message-ID: <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> > Well, how would you 'require' them to use anything at all? There's not > even anything 'requiring' that a core module inherit from > Bio::Root::Root(I). We just (very strongly) advise that you inherit > from > there. So we can also advise that bioperl-run wrappers do not roll > their > own but use Bio::Tools::Run::WrapperBase. Like I said, it's a suggestion. No need to get snippy. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Tue Nov 7 11:07:23 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 16:07:23 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> Message-ID: <4550AF3B.8000807@sendu.me.uk> Chris Fields wrote: > > On Nov 7, 2006, at 3:15 AM, Sendu Bala wrote: > >> Nathan S. Haigh wrote: >>> I agree, I was going to update the tests later this morning :-P Any >>> thoughts about version() or should I just leave it be for now? >> >> If its no trouble, go ahead with a version() method. Its nice to have in >> any case. I'd suggest your latter option of 'there be a function that >> does a compare internally so it can be accessed something like: >> print "we have met the min version requirement\n" if >> $factory->at_least_version('3.4t26');' >> In fact, it ought to work with '34t26b3' as well (I guess the method >> would try what it was given, and on failure, try again with the last 2 >> characters removed, then try both cases again with a decimal added if >> there wasn't one). > > Is it possible to have the interface base class contain an abstract > program_version() (or similar) method? One that could be implemented to > just grab the current version of the program? I was thinking about > something like this for the RNA-based wrappers I want to add but it > seems to be something that most Run modules would benefit from. Just > haven't had time to look into it with much detail. What's wrong with version() ? > Almost wonder if it would be easier to have all bioperl-run modules have > a Run-specific Root object for common methods, regardless of the other > interfaces used. Maybe something inheriting Bio::Root::Root... What's wrong with Bio::Tools::Run::WrapperBase ? From n.haigh at sheffield.ac.uk Tue Nov 7 12:48:56 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 07 Nov 2006 17:48:56 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> Message-ID: <4550C708.5060209@sheffield.ac.uk> Chris Fields wrote: > On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: > ... > > >>> Is it possible to have the interface base class contain an >>> abstract program_version() (or similar) method? One that could be >>> implemented to just grab the current version of the program? I >>> was thinking about something like this for the RNA-based wrappers >>> I want to add but it seems to be something that most Run modules >>> would benefit from. Just haven't had time to look into it with >>> much detail. >>> >> What's wrong with version() ? >> > > Didn't realize there was a version() already. > > >>> Almost wonder if it would be easier to have all bioperl-run >>> modules have a Run-specific Root object for common methods, >>> regardless of the other interfaces used. Maybe something >>> inheriting Bio::Root::Root... >>> >> What's wrong with Bio::Tools::Run::WrapperBase ? >> > > I agree that WrapperBase fulfills most of this functionality. > However, don't a few bioperl-run wrappers 'roll their own', i.e. not > implement WrapperBase? Requiring all bioperl-run module inherit the > same Run-specific base object would integrate them a bit more and > distinguish them from the core modules (which would inherit > Bio::Root::Root). Anyway, it's just a suggestion. > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > >From what i've seen of Bioperl-run there is not a whole lot of consistency between modules. I think it would be a good idea to have all run modules inherit WrapperBase - would this be a big change?? Nath From bix at sendu.me.uk Tue Nov 7 12:49:09 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 17:49:09 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> Message-ID: <4550C715.5090608@sendu.me.uk> Chris Fields wrote: >> Well, how would you 'require' them to use anything at all? There's not >> even anything 'requiring' that a core module inherit from >> Bio::Root::Root(I). We just (very strongly) advise that you inherit from >> there. So we can also advise that bioperl-run wrappers do not roll their >> own but use Bio::Tools::Run::WrapperBase. > > Like I said, it's a suggestion. No need to get snippy. You took that completely the wrong way. I am applying absolutely no value judgment on your suggestion. It may be an excellent one. I was simply explaining we have no programmatic way of requiring that modules use other modules - we rely on people following the advice/ status quo. Given that, are you still suggesting that it would be better to advise people to use Bio::Root::SomeNewRunThing, or is Bio::Tools::Run::WrapperBase satisfactory? From hlapp at gmx.net Tue Nov 7 12:55:12 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 7 Nov 2006 12:55:12 -0500 Subject: [Bioperl-l] Bio::SeqIO::gcg bug In-Reply-To: <4550AC1E.2070500@bms.com> References: <4550AC1E.2070500@bms.com> Message-ID: On Nov 7, 2006, at 10:54 AM, Stefan Kirov wrote: > I assume Hilmar removed the $_ = uc($_); line for a very good reason, > but the call to validate should be: > _validate_checksum(uc($sequence),$chksum)) I agree. The case of the sequence letters should remain untouched though for other purposes. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Tue Nov 7 12:55:22 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 11:55:22 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C708.5060209@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C708.5060209@sheffield.ac.uk> Message-ID: <8132EB4F-2FE0-4A46-A96D-E406CCB0F047@uiuc.edu> On Nov 7, 2006, at 11:48 AM, Nathan Haigh wrote: ... > From what i've seen of Bioperl-run there is not a whole lot of > consistency between modules. I think it would be a good idea to > have all > run modules inherit WrapperBase - would this be a big change?? > > Nath We really have no idea how many wrappers don't implement WrapperBase at the moment; until then we don't know how much work it would take. This might be a job for a maintenance script... Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From natalia.grabar at club-internet.fr Tue Nov 7 12:48:53 2006 From: natalia.grabar at club-internet.fr (natalia.grabar at club-internet.fr) Date: Tue, 7 Nov 2006 18:48:53 +0100 Subject: [Bioperl-l] perl conference in Paris Message-ID: hi all, are you fine? next 25 & 26 November there will be a Perl conference in Paris http://conferences.mongueurs.net/fpw2006/ I wonder if it would be possible to have a presentation (tutorial?) of the bioperl package during this conference. thanks have a nice day natalia From cjfields at uiuc.edu Tue Nov 7 14:49:47 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 13:49:47 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C715.5090608@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> <4550C715.5090608@sendu.me.uk> Message-ID: <4AC53CE6-20EC-4841-A28C-E083823F8487@uiuc.edu> On Nov 7, 2006, at 11:49 AM, Sendu Bala wrote: >> Like I said, it's a suggestion. No need to get snippy. > > You took that completely the wrong way. I am applying absolutely no > value judgment on your suggestion. It may be an excellent one. I > was simply explaining we have no programmatic way of requiring that > modules use other modules - we rely on people following the advice/ > status quo. There may not be a programmatic way of enforcing one to use WrapperBase or other base classes beyond using maintenance scripts. However, if we as a community agree on following a basic set of bioperl coding standards (Best Practices, using Bio::Root::Root/ RootI, POD, etc), then anyone should reasonably expect that their code may be changed to conform more with those standards, at least within reason. We recently enforced this with Bio::Root::Root/RootI, 'return undef', 'use base', and others, so I don't see the problem with doing so here. There will always be some controversial or grey areas (use of AUTOLOAD comes to mind), but in my opinion it is very reasonable to require that new modules use a particular base class or implement a specific interface if the new code is expected to interact properly with other BioPerl classes/objects. One could always use the mail list to express their opinions if they disagree or want some clarification or guidance. Sorry, Election Day in the States. Lots of snippiness around on this end (overdosed of negative ads)! > Given that, are you still suggesting that it would be better to > advise people to use Bio::Root::SomeNewRunThing, or is > Bio::Tools::Run::WrapperBase satisfactory? Either way will work, but.... I was thinking of something like this: Run-based |---WrapperBase Root class---| |---Non-WrapperBase (web apps and others) Bio::Root::Root works in this capacity already, but I was thinking of a base class unique to bioperl-run classes which could integrate similar methods from WrapperBase and non-WrapperBase'd modules. I suppose we could also have it as a simple interface; modules which implement it could be distinguished from core if needed. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Tue Nov 7 14:58:10 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 7 Nov 2006 11:58:10 -0800 Subject: [Bioperl-l] (no subject) Message-ID: Lincoln - I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql which call $sth->finish in the offset_boundary call and the fetch_sequence method as my code which does GFF3 -> CDS dumping was getting lots of " statement handle DBI::st=HASH(0x189bf8c) still Active at" Changes are here: http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/Bio/DB/ SeqFeature/Store/DBI/mysql.pm.diff?r1=1.25&r2=1.26 These changes should be migrated to the branch before the release if all is okay. Please let me know. -jason From jason at bioperl.org Tue Nov 7 13:27:27 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 7 Nov 2006 10:27:27 -0800 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C708.5060209@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C708.5060209@sheffield.ac.uk> Message-ID: <4A984083-23FA-42F6-8C73-901FD87DB5F6@bioperl.org> i think it is important - we just have not had a dedicated developer who enforced these requirements by auditing the code. I had tried to establish a standard through WrapperBase but some contributions ignored this and some modules had grown up before the wrapperbase was in place. I also think the ontology of applications is a bit screwed up so people were putting modules in directories willy-nilly. I think bioperl-run is even more cat-herding than the other aspects of the project because applications change and there are very many combinations of parameters and version of applications. There was a flurry of contributions and no good way to marshall them initially. So what to do - I guess make do with how it is but not rename anything at this point but try and standardize things - it will depend on your desire to really take this on. The PISE modules may need to be re-evaluated to insure they are still working - there was hope that some of them could be simplified through some automated class generation from the XML they are based on, but that was never developed. We will try and a have an open-bio linux server available as a platform where we can have a consistent testing environment but I am not sure if we want this to represent every possible version of apps or just the most recent. -jason On Nov 7, 2006, at 9:48 AM, Nathan Haigh wrote: > Chris Fields wrote: >> On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: >> ... >> >> >>>> Is it possible to have the interface base class contain an >>>> abstract program_version() (or similar) method? One that could be >>>> implemented to just grab the current version of the program? I >>>> was thinking about something like this for the RNA-based wrappers >>>> I want to add but it seems to be something that most Run modules >>>> would benefit from. Just haven't had time to look into it with >>>> much detail. >>>> >>> What's wrong with version() ? >>> >> >> Didn't realize there was a version() already. >> >> >>>> Almost wonder if it would be easier to have all bioperl-run >>>> modules have a Run-specific Root object for common methods, >>>> regardless of the other interfaces used. Maybe something >>>> inheriting Bio::Root::Root... >>>> >>> What's wrong with Bio::Tools::Run::WrapperBase ? >>> >> >> I agree that WrapperBase fulfills most of this functionality. >> However, don't a few bioperl-run wrappers 'roll their own', i.e. not >> implement WrapperBase? Requiring all bioperl-run module inherit the >> same Run-specific base object would integrate them a bit more and >> distinguish them from the core modules (which would inherit >> Bio::Root::Root). Anyway, it's just a suggestion. >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> From what i've seen of Bioperl-run there is not a whole lot of > consistency between modules. I think it would be a good idea to > have all > run modules inherit WrapperBase - would this be a big change?? > > Nath > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Wed Nov 8 05:24:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 08 Nov 2006 10:24:41 +0000 Subject: [Bioperl-l] (no subject) Message-ID: <4551B069.6060305@sendu.me.uk> [forwarded on behalf of Dave Howorth] Jason Stajich wrote: > Lincoln - > I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql > which call $sth->finish in the offset_boundary call and the > fetch_sequence method as my code which does GFF3 -> CDS dumping was > getting lots of " statement handle DBI::st=HASH(0x189bf8c) still > Active at" What version of DBD::mysql are you using? It sounds like this: http://rt.cpan.org/Public/Bug/Display.html?id=20464 Cheers, Dave From bix at sendu.me.uk Wed Nov 8 06:12:12 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 08 Nov 2006 11:12:12 +0000 Subject: [Bioperl-l] Bioperl versioning In-Reply-To: <6dce9a0b0610311224x79256b29sf102eb5c35865caf@mail.gmail.com> References: <453E309B.9090007@sendu.me.uk> <000001c6f78b$d1c65a30$15327e82@pyrimidine> <6dce9a0b0610311224x79256b29sf102eb5c35865caf@mail.gmail.com> Message-ID: <4551BB8C.5040606@sendu.me.uk> Lincoln Stein wrote: > Are you going to go ahead with 1.52_XX ? If so, I will code GBrowse to > look for 1.52 or higher. You should do the equivalent of use Bio::Root::Version 1.5.2; Eg. unless (eval{"require $Bio::Root::Version;" || ${Bio::Root::Version::VERSION'} < 1.005002) { #complain } Since most core modules get their version from Bio::Root::Version, you could also check the core module you're actually using in GBrowse, instead of asking Bio::Root::Version itself. So, if you do actually need to use Bio::Whatever in your module, the best thing to do is say: use Bio::Whatever 1.5.2; From jason at bioperl.org Wed Nov 8 10:56:55 2006 From: jason at bioperl.org (Jason Stajich) Date: Wed, 8 Nov 2006 07:56:55 -0800 Subject: [Bioperl-l] (no subject) In-Reply-To: <4551B069.6060305@sendu.me.uk> References: <4551B069.6060305@sendu.me.uk> Message-ID: <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> sounds like it. I am running 3.0006 The added sth->finish did take care of it for now since I assume a fair number of people are stuck with these vers? On Nov 8, 2006, at 2:24 AM, Sendu Bala wrote: > [forwarded on behalf of Dave Howorth] > > > Jason Stajich wrote: >> Lincoln - >> I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql >> which call $sth->finish in the offset_boundary call and the >> fetch_sequence method as my code which does GFF3 -> CDS dumping was >> getting lots of " statement handle DBI::st=HASH(0x189bf8c) still >> Active at" > > What version of DBD::mysql are you using? It sounds like this: > > http://rt.cpan.org/Public/Bug/Display.html?id=20464 > > Cheers, Dave > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California Dept of Plant and Microbial Biology 321 Koshland Hall #3102 Berkeley, CA 94720-3102 lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From dhoworth at mrc-lmb.cam.ac.uk Wed Nov 8 11:16:05 2006 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Wed, 08 Nov 2006 16:16:05 +0000 Subject: [Bioperl-l] (no subject) In-Reply-To: <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> References: <4551B069.6060305@sendu.me.uk> <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> Message-ID: <455202C5.9060609@mrc-lmb.cam.ac.uk> Jason Stajich wrote: > sounds like it. > > I am running 3.0006 > > The added sth->finish did take care of it for now since I assume a fair > number of people are stuck with these vers? Well, the current version on CPAN is fixed and the bug breaks lots of applications so upgrading DBD::mysql is a better cure. Or even downgrading to the one before it broke :) Cheers, Dave From bix at sendu.me.uk Thu Nov 9 05:28:34 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 10:28:34 +0000 Subject: [Bioperl-l] bptutorial.pl 0 In-Reply-To: <000601c6fc4a$c3e43450$15327e82@pyrimidine> References: <000601c6fc4a$c3e43450$15327e82@pyrimidine> Message-ID: <455302D2.1000901@sendu.me.uk> Chris Fields wrote: > What version of Bioperl are you running? > > As a warning, the bptutorial.pl script has been removed from CVS and will > not be included in future versions of Bioperl. It can be found on the > bioperl wiki instead: > > http://www.bioperl.org/wiki/Bptutorial It hasn't been removed, but should it be? AFAIK there was still a request from at least one person to keep it. But is it still out of date wrt the wiki version? From bix at sendu.me.uk Thu Nov 9 05:31:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 10:31:16 +0000 Subject: [Bioperl-l] bptutorial.pl 0 In-Reply-To: <455302D2.1000901@sendu.me.uk> References: <000601c6fc4a$c3e43450$15327e82@pyrimidine> <455302D2.1000901@sendu.me.uk> Message-ID: <45530374.1010001@sendu.me.uk> Sendu Bala wrote: > Chris Fields wrote: >> What version of Bioperl are you running? >> As a warning, the bptutorial.pl script has been removed from CVS and will >> not be included in future versions of Bioperl. It can be found on the >> bioperl wiki instead: >> >> http://www.bioperl.org/wiki/Bptutorial > > It hasn't been removed, but should it be? AFAIK there was still a > request from at least one person to keep it. But is it still out of date > wrt the wiki version? Scratch that, it was still in the 1.5.2 branch but I've removed it. From bix at sendu.me.uk Thu Nov 9 07:04:56 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 12:04:56 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 Message-ID: <45531968.6080607@sendu.me.uk> Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. See http://www.bioperl.org/wiki/Release_1.5.2 for instructions on getting and testing this RC. Developers: Once again I'm hopeful that this is the last RC. If all goes well expect final release in about a weeks time. Please check and update documentation. Users: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into. Thank you, Sendu. From avilella at gmail.com Thu Nov 9 07:15:20 2006 From: avilella at gmail.com (Albert Vilella) Date: Thu, 9 Nov 2006 12:15:20 +0000 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln Message-ID: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> Hi, I am musing on how to add trees to the AlignIO::Nexus objects. In PAML we have this "add_tree" method, and "get_rst_trees", which we could also apply to this case. I also would like to hear some feedback on how to write_aln nexus files that contain one or more trees in the object instance. Do we want this by default? Only if a "with_trees" parameter is set? Cheers, Albert. From n.haigh at sheffield.ac.uk Thu Nov 9 08:55:59 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Thu, 09 Nov 2006 13:55:59 +0000 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> Message-ID: <4553336F.2000000@sheffield.ac.uk> Albert Vilella wrote: > Hi, > > I am musing on how to add trees to the AlignIO::Nexus objects. > > In PAML we have this "add_tree" method, and "get_rst_trees", which we > could also apply to this case. > > I also would like to hear some feedback on how to write_aln nexus > files that contain one or more trees in the object instance. Do we > want this by default? Only if a "with_trees" parameter is set? > > Cheers, > > Albert. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > Hi Albert, I don't know if you are aware of this resource, so here it is: http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all I would suggest that if there are trees in the object instance, then write_aln should print them by default and then have a "no_trees" option. Nath From cjfields at uiuc.edu Thu Nov 9 09:13:09 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 08:13:09 -0600 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <4553336F.2000000@sheffield.ac.uk> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> <4553336F.2000000@sheffield.ac.uk> Message-ID: <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> On Nov 9, 2006, at 7:55 AM, Nathan Haigh wrote: > Albert Vilella wrote: >> Hi, >> >> I am musing on how to add trees to the AlignIO::Nexus objects. >> >> In PAML we have this "add_tree" method, and "get_rst_trees", which we >> could also apply to this case. >> >> I also would like to hear some feedback on how to write_aln nexus >> files that contain one or more trees in the object instance. Do we >> want this by default? Only if a "with_trees" parameter is set? >> >> Cheers, >> >> Albert. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > Hi Albert, > > I don't know if you are aware of this resource, so here it is: > http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all > > I would suggest that if there are trees in the object instance, then > write_aln should print them by default and then have a "no_trees" > option. > > Nath Another option is to store them in the SimpleAlign object as a queue of Tree objects. Stockholm format allows trees in the annotation section, so it makes sense that if some alignments contain this data then we should have a way of parsing and storing it, as long as we read/write support the particular tree format. Something like: my $aln = $alnin->next_aln(); # iterate... while (my $tree = $aln->next_tree()) { ... } # or SimpleAlign-like for my $tree ($aln->each_tree()) { ... } # all trees @trees = $aln->each_tree(); etc. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 9 10:28:45 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 09:28:45 -0600 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> <4553336F.2000000@sheffield.ac.uk> <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> Message-ID: <112C051C-0868-4933-A1CE-87E773B7FD05@uiuc.edu> On Nov 9, 2006, at 8:13 AM, Chris Fields wrote: > On Nov 9, 2006, at 7:55 AM, Nathan Haigh wrote: > >> Albert Vilella wrote: >>> Hi, >>> >>> I am musing on how to add trees to the AlignIO::Nexus objects. >>> >>> In PAML we have this "add_tree" method, and "get_rst_trees", >>> which we >>> could also apply to this case. >>> >>> I also would like to hear some feedback on how to write_aln nexus >>> files that contain one or more trees in the object instance. Do we >>> want this by default? Only if a "with_trees" parameter is set? >>> >>> Cheers, >>> >>> Albert. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> Hi Albert, >> >> I don't know if you are aware of this resource, so here it is: >> http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all >> >> I would suggest that if there are trees in the object instance, then >> write_aln should print them by default and then have a "no_trees" >> option. >> >> Nath > > Another option is to store them in the SimpleAlign object as a queue > of Tree objects. Stockholm format allows trees in the annotation > section, so it makes sense that if some alignments contain this data > then we should have a way of parsing and storing it, as long as we > read/write support the particular tree format. .... Forgot to mention the option of using a builder object, analogous to the one used for Bio::SeqIO::genbank (Bio::Seq::SeqBuilder); this would be similar to Nathan's suggestion but would tell the parser what data you want parsed (alignment annotation, tree data, sequences, accession/id, etc) based on 'slots' and particular conditions, and therefore determines what data is stored in SimpleAlign objects. I planned on setting one up for Bio::AlignIO::stockholm in the near future for optional annotation parsing, but tree parsing could be included as well. Were you thinking of something along those lines? Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bernd.web at gmail.com Thu Nov 9 18:07:48 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 10 Nov 2006 00:07:48 +0100 Subject: [Bioperl-l] Blast Writer Message-ID: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> Hi, I am using Bio::SearchIO and Bio::SearchIO::Writer::HTMLResultWriter and its filter, as my $writer = new Bio::SearchIO::Writer::HTMLResultWriter(); $writer->filter('hsp', \&hsp_filter); Can I change the contents of the HSP objects (apart from true/false filtering)? I would like to change some HSP values. Would it be possible to do so with HTMLResultWriter's filters? And if so, how to access the Hit/HSP objects in the filter? I'd be grateful for any suggestions. Best regards, Bernd From jason at bioperl.org Thu Nov 9 18:21:34 2006 From: jason at bioperl.org (Jason Stajich) Date: Thu, 9 Nov 2006 15:21:34 -0800 Subject: [Bioperl-l] Blast Writer In-Reply-To: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> References: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> Message-ID: <15C2FE1E-F0C8-43DD-96E7-FADA3421AA82@bioperl.org> You can always do this before you pass the Result object to the writer. The for loop will pass back the actual hit or hsp objects and so any updates should be stored. for my $hit ( $result->hits ) { for my $hsp ( $hit->hsps ) { # change the HSP } } -jason On Nov 9, 2006, at 3:07 PM, Bernd Web wrote: > Hi, > > I am using Bio::SearchIO and Bio::SearchIO::Writer::HTMLResultWriter > and its filter, as > my $writer = new Bio::SearchIO::Writer::HTMLResultWriter(); > $writer->filter('hsp', \&hsp_filter); > > Can I change the contents of the HSP objects (apart from true/ > false filtering)? > I would like to change some HSP values. Would it be possible to do so > with HTMLResultWriter's filters? And if so, how to access the Hit/HSP > objects in the filter? > > I'd be grateful for any suggestions. > > Best regards, > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California Dept of Plant and Microbial Biology 321 Koshland Hall #3102 Berkeley, CA 94720-3102 lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From James.Rose at UCHSC.edu Thu Nov 9 17:56:00 2006 From: James.Rose at UCHSC.edu (James.Rose at UCHSC.edu) Date: Thu, 9 Nov 2006 15:56:00 -0700 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI Message-ID: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Hi- apologies if this subject has been addressed before, but I can't seem to find a way to search prior threads short of downloading the entire archives. I'm trying to use Bioperl to do something I thought would be fairly simple: Ingredients: one file containing a list of GI numbers for various proteins 1) Read GI number from file. 2) run a remote tblastn search against the sequenced Spermophilus tridecemlineatus genome with the GI number as query. 3) save resultant BLAST file to disk for later parsing. As it stands, several hours of browsing and scripting has failed to turn up anything that might be useful in this regard. Any advice is very much appreciated. Thanks, James From ak at ebi.ac.uk Thu Nov 9 19:01:55 2006 From: ak at ebi.ac.uk (Andreas Kahari) Date: Fri, 10 Nov 2006 00:01:55 +0000 Subject: [Bioperl-l] Archive searching (was Re: Remote tblastn against a sequenced genome at NCBI) In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: <20061110000155.GA27524@ebi.ac.uk> On Thu, Nov 09, 2006 at 03:56:00PM -0700, James.Rose at UCHSC.edu wrote: > > > Hi- apologies if this subject has been addressed before, but I can't > seem to find a way to search prior threads short of downloading the > entire archives. [cut] See here: http://www.bioperl.org/wiki/Mailing_lists -- Andreas K?h?ri :: Ensembl Software Developer European Bioinformatics Institute (EMBL-EBI) -------------------------------------------- contentsofsignaturemightsettleduringtransfer From cjfields at uiuc.edu Thu Nov 9 19:46:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 18:46:35 -0600 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: <43D47332-B9A9-4D01-87FD-433D86B68853@uiuc.edu> > Hi- apologies if this subject has been addressed before, but I > can't seem to find a way to search prior threads short of > downloading the entire archives. I'm trying to use Bioperl to do > something I thought would be fairly simple: > > Ingredients: one file containing a list of GI numbers for various > proteins > > 1) Read GI number from file. > 2) run a remote tblastn search against the sequenced Spermophilus > tridecemlineatus genome with the GI number as query. > 3) save resultant BLAST file to disk for later parsing. > > As it stands, several hours of browsing and scripting has failed to > turn up anything that might be useful in this regard. > > Any advice is very much appreciated. > > Thanks, > > James NCBI has a little-known (but very useful) list of databases available for remote BLAST searches: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastdblist.html If you replace the database parameter with the exact string listed under the table, then it should work. 'Trace/ Spermophilus_tridecemlineatus_WGS' for the WGS sequences is probably what you want. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 9 19:49:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 18:49:24 -0600 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: On Nov 9, 2006, at 4:56 PM, wrote: > > > Hi- apologies if this subject has been addressed before, but I > can't seem to find a way to search prior threads short of > downloading the entire archives. I'm trying to use Bioperl to do > something I thought would be fairly simple: > > Ingredients: one file containing a list of GI numbers for various > proteins > > 1) Read GI number from file. > 2) run a remote tblastn search against the sequenced Spermophilus > tridecemlineatus genome with the GI number as query. > 3) save resultant BLAST file to disk for later parsing. > > As it stands, several hours of browsing and scripting has failed to > turn up anything that might be useful in this regard. > > Any advice is very much appreciated. > > Thanks, > > James Oops, sent you an old page. Here's the more up-to-date one: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/ remote_accessible_blastdblist.html Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sayali_salodkar at persistent.co.in Fri Nov 10 00:10:35 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Fri, 10 Nov 2006 10:40:35 +0530 Subject: [Bioperl-l] Bioperl parser for PolyPhred? Message-ID: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> Hi, I want to parse the output of polyphred http://droog.gs.washington.edu/PolyPhred.html. Is there a parser already available in Bioperl which would help me in doing the same. Thanks, Sayali DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From bix at sendu.me.uk Fri Nov 10 05:15:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 10:15:41 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) Message-ID: <4554514D.2020001@sendu.me.uk> Hi all, Since I'm seeing inadequacies with the current Makefile.PL scripts we have, I'm thinking of converting from ExtUtils::MakeMaker and the Makefile.PL scripts to Module::Build Build.PL scripts. The advantages this will bring would be creation and installation of documentation, sane handling of required and optional dependencies, and hopefully good META.yml output, for CPAN compatibility wrt version numbers. I'll be able to use Module::Build::Compat to automatically generate Makefile.PL scripts in 'passthrough' style (if an end-user tries to use Makefile.PL without having Module::Build installed, it will offer to install Module::Build for them) when it comes time to make distributions, but Makefile.PL would no longer be in CVS. One thing I'm not clear on with the current situation is what is supposed to happen when the user chooses to install scripts. Where are they supposed to get installed to, and where do end-users normally run them from and how? How does this compare to expectations from other perl module distributions that have installable scripts? Please comment and discuss, but I'd like to get this done for the 1.5.2 release so that the CPAN distribution will be happy. From Derek.Fairley at bll.n-i.nhs.uk Fri Nov 10 05:15:52 2006 From: Derek.Fairley at bll.n-i.nhs.uk (Fairley, Derek) Date: Fri, 10 Nov 2006 10:15:52 -0000 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: James, Try the nabble.com mirror of this forum for easy searching of prior threads: http://www.nabble.com/BioPerl-f13596.html Derek. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of James.Rose at UCHSC.edu Sent: 09 November 2006 22:56 To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI Hi- apologies if this subject has been addressed before, but I can't seem to find a way to search prior threads short of downloading the entire archives. I'm trying to use Bioperl to do something I thought would be fairly simple: Ingredients: one file containing a list of GI numbers for various proteins 1) Read GI number from file. 2) run a remote tblastn search against the sequenced Spermophilus tridecemlineatus genome with the GI number as query. 3) save resultant BLAST file to disk for later parsing. As it stands, several hours of browsing and scripting has failed to turn up anything that might be useful in this regard. Any advice is very much appreciated. Thanks, James _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Fri Nov 10 07:31:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 12:31:29 +0000 Subject: [Bioperl-l] Distribution files, versions Message-ID: <45547121.6040904@sendu.me.uk> Does anyone know what the following files are supposed to do and if they still used/needed? bioperl.lisp maintenance/symlink_scripts.pl maintenance/symlink_scripts.PLS doc/makedoc.PL scripts/install_bioperl_scripts.pl Most modules in the distribution take their version from Bio::Root::Version, but some do not. Is there some reason they must keep the version they currently have, or can they be made like the others? These are the modules that seem to define their own version (based on a quick grep): Bio/DB/NCBIHelper.pm Bio/DB/Expression/geo.pm Bio/DB/EUtilities/elink.pm Bio/SeqIO/tinyseq.pm Bio/Graphics/Glyph/cds.pm Bio/Graphics/Glyph/translation.pm Bio/Graphics/Glyph/so_transcript.pm Bio/Index/Blast.pm Bio/Index/Hmmer.pm Bio/Tools/WebBlat.pm Bio/Tools/HMM.pm Bio/Tools/dpAlign.pm From JK at novozymes.com Fri Nov 10 07:41:19 2006 From: JK at novozymes.com (JK (Jesper Agerbo Krogh)) Date: Fri, 10 Nov 2006 13:41:19 +0100 Subject: [Bioperl-l] Bio::SeqIO::fasta patch. Message-ID: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> Hi. Just a small patch for outputting stuff on the descriptionline i fasta format. Stuff like: DE test DE test2 DE test3 converted to fasta becomes: > testtest2test3 and not > test test2 test3 Index: fasta.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/fasta.pm,v retrieving revision 1.60 diff -r1.60 fasta.pm 203c203 < $desc =~ s/\n//g; --- > $desc =~ s/\n/ /g; Should probably be applied to the stable-branch . Jesper From arareko at campus.iztacala.unam.mx Fri Nov 10 10:14:18 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Fri, 10 Nov 2006 09:14:18 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: <4554974A.4010206@campus.iztacala.unam.mx> Sendu Bala wrote: > Does anyone know what the following files are supposed to do and if they > still used/needed? > > bioperl.lisp This a module template for Emacs users. > maintenance/symlink_scripts.pl > maintenance/symlink_scripts.PLS The 1st is created by Makefile.PL (basically its a rename of the 2nd) and is run during 'make install'. From the POD: "This script will create a symlink in the 'installscript' directory (as defined during install) to a script in that same directory. It was written to create a symlink with the name 'bp_pg_bulk_load_gff.pl' that targeted 'bp_bulk_load_gff.pl' but can be extended by adding files to the %symlink_scripts hash. Perl function 'symlink' is used to keep the script from crashing on systems that don't allow symbolic linking." > doc/makedoc.PL I have no idea :) > scripts/install_bioperl_scripts.pl This is also run automatically on 'make install'. Cheers, Mauricio. -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From aaron.j.mackey at gsk.com Fri Nov 10 08:59:55 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Fri, 10 Nov 2006 08:59:55 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> Message-ID: > bioperl.lisp This is a set of convenience macros for developers who use Emacs, but it's pretty out of date. Some may still use it, though. It's of no use being in the package distribution, however. > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must keep > the version they currently have, or can they be made like the others? if their current version is greater than the bioperl version, then they must keep it for backwards compatibility (as otherwise a "require" statement for a certain version of Bio::SeqIO::tinyseq won't work properly). -Aaron From dmessina at wustl.edu Fri Nov 10 09:55:44 2006 From: dmessina at wustl.edu (David Messina) Date: Fri, 10 Nov 2006 08:55:44 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: <256AAE6A-2ACC-4CFE-B66E-F94C536FA8C5@wustl.edu> > bioperl.lisp This is the emacs template for bioperl module writing. Should be kept I think. http://www.bioperl.org/wiki/Emacs_template > maintenance/symlink_scripts.pl > maintenance/symlink_scripts.PLS Don't know if they're still needed, but Makefile.PL still refers to them. > doc/makedoc.PL I think this does similar to what you propose below, namely redefining modules' version strings to be the same as Bio::Root::Version's. I don't see any reason to remove it, but I like your suggestion to have all the modules get their version from Bio::Root::Version. > scripts/install_bioperl_scripts.pl Does what it says. Don't know if it's still needed; I think Makefile.PL handles script installation. Re your other post about switching over to Build.PL, I think scripts go into /usr/local/bin by default, or wherever specified if PREFIX or the like is set when the user runs 'perl Makefile.PL'. That seems to fit with other CPAN distros' model, and is what I (as an end-user) would expect. Dave > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must > keep > the version they currently have, or can they be made like the others? > > These are the modules that seem to define their own version (based > on a > quick grep): > Bio/DB/NCBIHelper.pm > Bio/DB/Expression/geo.pm > Bio/DB/EUtilities/elink.pm > Bio/SeqIO/tinyseq.pm > Bio/Graphics/Glyph/cds.pm > Bio/Graphics/Glyph/translation.pm > Bio/Graphics/Glyph/so_transcript.pm > Bio/Index/Blast.pm > Bio/Index/Hmmer.pm > Bio/Tools/WebBlat.pm > Bio/Tools/HMM.pm > Bio/Tools/dpAlign.pm From cjfields at uiuc.edu Fri Nov 10 10:50:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 09:50:58 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > Hi all, > > Since I'm seeing inadequacies with the current Makefile.PL scripts we > have, I'm thinking of converting from ExtUtils::MakeMaker and the > Makefile.PL scripts to Module::Build Build.PL scripts. > > The advantages this will bring would be creation and installation of > documentation, sane handling of required and optional dependencies, > and > hopefully good META.yml output, for CPAN compatibility wrt version > numbers. > > I'll be able to use Module::Build::Compat to automatically generate > Makefile.PL scripts in 'passthrough' style (if an end-user tries to > use > Makefile.PL without having Module::Build installed, it will offer to > install Module::Build for them) when it comes time to make > distributions, but Makefile.PL would no longer be in CVS. > > > One thing I'm not clear on with the current situation is what is > supposed to happen when the user chooses to install scripts. Where are > they supposed to get installed to, and where do end-users normally run > them from and how? How does this compare to expectations from other > perl > module distributions that have installable scripts? > > > Please comment and discuss, but I'd like to get this done for the > 1.5.2 > release so that the CPAN distribution will be happy. I don't have a problem with this as long as it works for all systems. It sounds like a good long-term solution, esp. for CPAN developer releases. However, we've already had three RC's using the regular old Makefile.PL setup, which seems to work fine for now. It also sounds like we will need to update all relevant installation documentation (since we can't run 'perl Makefile.PL' w/o Makefile.PL, unless I'm missing something). Hence I'm a bit worried about adding something new like this after three RCs and just before a final release. I think it's something we should do, but I'm not sure we should have it for this release. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From dmessina at wustl.edu Fri Nov 10 10:40:21 2006 From: dmessina at wustl.edu (David Messina) Date: Fri, 10 Nov 2006 09:40:21 -0600 Subject: [Bioperl-l] Bioperl parser for PolyPhred? In-Reply-To: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> References: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> Message-ID: Sayali, I don't believe there is a BioPerl polyphred parser yet. This question came up on the list previously, however, and there was mention of a Perl script that appears to parse polyphred output: http://portal.open-bio.org/pipermail/bioperl-l/2003-December/014206.html Dave From bix at sendu.me.uk Fri Nov 10 10:59:54 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 15:59:54 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> Message-ID: <4554A1FA.6080003@sendu.me.uk> Chris Fields wrote: > On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > >> Hi all, >> >> Since I'm seeing inadequacies with the current Makefile.PL scripts we >> have, I'm thinking of converting from ExtUtils::MakeMaker and the >> Makefile.PL scripts to Module::Build Build.PL scripts. [snip] > I don't have a problem with this as long as it works for all systems. > It sounds like a good long-term solution, esp. for CPAN developer releases. > > However, we've already had three RC's using the regular old Makefile.PL > setup, which seems to work fine for now. It also sounds like we will > need to update all relevant installation documentation (since we can't > run 'perl Makefile.PL' w/o Makefile.PL, unless I'm missing something). > Hence I'm a bit worried about adding something new like this after three > RCs and just before a final release. > > I think it's something we should do, but I'm not sure we should have it > for this release. Now that I'm looking into it, it seems like quite a job, and yes, especially with all the documentation updates that need to be carefully looked at. Though to answer your question, Makefile.PL would be auto-generated by Build.PL immediately prior to a release and included in the distribution file for end users to use, but it wouldn't be in CVS. Such a Makefile.PL is essentially a front-end to the Build.PL for backwards-compatibility. For 1.5.2 I may just manually create a META.yml (the one generated via Makefile.PL isn't good enough) which only affects CPAN behaviour and nothing else we've been testing in the RCs. From bix at sendu.me.uk Fri Nov 10 11:03:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 16:03:04 +0000 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554974A.4010206@campus.iztacala.unam.mx> References: <45547121.6040904@sendu.me.uk> <4554974A.4010206@campus.iztacala.unam.mx> Message-ID: <4554A2B8.4010207@sendu.me.uk> Mauricio Herrera Cuadra wrote: > Sendu Bala wrote: >> Does anyone know what the following files are supposed to do and if >> they still used/needed? >> >> bioperl.lisp > > This a module template for Emacs users. I propose moving it to the wiki and removing it from CVS. >> maintenance/symlink_scripts.pl >> maintenance/symlink_scripts.PLS > The 1st is created by Makefile.PL (basically its a rename of the 2nd) > and is run during 'make install'. From the POD: > > "This script will create a symlink in the 'installscript' directory (as > defined during install) to a script in that same directory. It was > written to create a symlink with the name 'bp_pg_bulk_load_gff.pl' that > targeted 'bp_bulk_load_gff.pl' but can be extended by adding files to > the %symlink_scripts hash. > > Perl function 'symlink' is used to keep the script from crashing on > systems that don't allow symbolic linking." The question is, do we need this symlink? Is the bulk_load_gff stuff still relevant? Why was it needed in the first place? For me, it doesn't seem to do anything useful; it just creates a broken symlink in PREFIX/bin. >> scripts/install_bioperl_scripts.pl > This is also run automatically on 'make install'. Not any more it isn't. Makefile.PL has (some of, at least) this script's methods. Does anyone use it manually? I propose removing it from CVS. AFAICT, Makefile.PL only ever installs to scripts_temp? How would people normally expect to define the script installation directory? Maybe it used to install scripts to user-defined or typical places (eg. /usr/local/bin as David Messina suggests) but that got broken in a recent commit? Can anyone confirm if script installation works properly for them, and how they got it to work? From cjfields at uiuc.edu Fri Nov 10 11:11:17 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:11:17 -0600 Subject: [Bioperl-l] Bio::SeqIO::fasta patch. In-Reply-To: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> References: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> Message-ID: <7BBF2CEB-B012-4145-9818-6B69D10C7E8F@uiuc.edu> On Nov 10, 2006, at 6:41 AM, JK ((Jesper Agerbo Krogh)) wrote: > Hi. > > Just a small patch for outputting stuff on the descriptionline i > fasta format. > > Stuff like: > > DE test > DE test2 > DE test3 > > converted to fasta becomes: > >> testtest2test3 > > and not > >> test test2 test3 ... Actually, this should be fixed in the original input parser, not in fasta.pm. Was this from EMBL format? Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Fri Nov 10 11:16:24 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Fri, 10 Nov 2006 11:16:24 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> Message-ID: <4554A5D8.8000700@bms.com> I personally like the idea. Why not have both for this release to ensure smooth transition? Sendu, would having Makefile.PL (I mean the old one) along with the build script be a problem? I am not very familiar with both modules, but from the pdoc it seems it should not be too hard: Note that if you want to provide both a Makefile.PL and a Build.PL for your distribution, you probably want to add the following to "WriteMakefile" in your Makefile.PL so that MakeMaker doesn?t try to run your Build.PL as a nor? mal .PL file: PL_FILES => {}, Stefan Chris Fields wrote: > On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > > >> Hi all, >> >> Since I'm seeing inadequacies with the current Makefile.PL scripts we >> have, I'm thinking of converting from ExtUtils::MakeMaker and the >> Makefile.PL scripts to Module::Build Build.PL scripts. >> >> The advantages this will bring would be creation and installation of >> documentation, sane handling of required and optional dependencies, >> and >> hopefully good META.yml output, for CPAN compatibility wrt version >> numbers. >> >> I'll be able to use Module::Build::Compat to automatically generate >> Makefile.PL scripts in 'passthrough' style (if an end-user tries to >> use >> Makefile.PL without having Module::Build installed, it will offer to >> install Module::Build for them) when it comes time to make >> distributions, but Makefile.PL would no longer be in CVS. >> >> >> One thing I'm not clear on with the current situation is what is >> supposed to happen when the user chooses to install scripts. Where are >> they supposed to get installed to, and where do end-users normally run >> them from and how? How does this compare to expectations from other >> perl >> module distributions that have installable scripts? >> >> >> Please comment and discuss, but I'd like to get this done for the >> 1.5.2 >> release so that the CPAN distribution will be happy. >> > > I don't have a problem with this as long as it works for all > systems. It sounds like a good long-term solution, esp. for CPAN > developer releases. > > However, we've already had three RC's using the regular old > Makefile.PL setup, which seems to work fine for now. It also sounds > like we will need to update all relevant installation documentation > (since we can't run 'perl Makefile.PL' w/o Makefile.PL, unless I'm > missing something). Hence I'm a bit worried about adding something > new like this after three RCs and just before a final release. > > I think it's something we should do, but I'm not sure we should have > it for this release. > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at uiuc.edu Fri Nov 10 11:21:07 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:21:07 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: ... > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must > keep > the version they currently have, or can they be made like the others? > > These are the modules that seem to define their own version (based > on a > quick grep): > Bio/DB/NCBIHelper.pm > Bio/DB/Expression/geo.pm > Bio/DB/EUtilities/elink.pm > Bio/SeqIO/tinyseq.pm > Bio/Graphics/Glyph/cds.pm > Bio/Graphics/Glyph/translation.pm > Bio/Graphics/Glyph/so_transcript.pm > Bio/Index/Blast.pm > Bio/Index/Hmmer.pm > Bio/Tools/WebBlat.pm > Bio/Tools/HMM.pm > Bio/Tools/dpAlign.pm They probably shouldn't have their own unless there is a good reason (and I can't really think of one). The elink $VERSION is for the NCBI elink DTD, not the bioperl version, but that should be changed in elinks to something else beside $VERSION (my bad). The same reasoning may be relevant for the other modules; we'll just have to check them one-by-one. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Nov 10 11:29:42 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:29:42 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554A5D8.8000700@bms.com> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> Message-ID: On Nov 10, 2006, at 10:16 AM, Stefan Kirov wrote: > I personally like the idea. Why not have both for this release to > ensure smooth transition? Sendu, would having Makefile.PL (I mean > the old one) along with the build script be a problem? I am not > very familiar with both modules, but from the pdoc it seems it > should not be too hard: > > Note that if you want to provide both a Makefile.PL and a > Build.PL for your distribution, you probably want to add > the following to "WriteMakefile" in your Makefile.PL so > that MakeMaker doesn?t try to run your Build.PL as a nor > mal .PL file: > > PL_FILES => {}, > > > Stefan ... Sounds like a good compromise to me. Like I said, the only problem I had is introducing something drastically new after three RCs (and just prior to a final release; I think Sendu wanted to release the final 1.5.2 next week, just before Thanksgiving here.). There is no problem though if we have the old Makefile.PL to fall back to for this release. In fact, you could remove it from HEAD when needed; the file still exists on the 1.5.2 branch, right? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bernd.web at gmail.com Fri Nov 10 12:39:30 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 10 Nov 2006 18:39:30 +0100 Subject: [Bioperl-l] Bio::Graphics Message-ID: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> Hi, Lincoln made an excellent help on Graphics. Thanks for that!(http://www.bioperl.org/wiki/HOWTO:Graphics) I am just looking at the imagemap creation with my $map=$panel->create_web_map('mapname',\&linkrule,'bbb'); and would like to connect the PNG from a blast report to the blast results. I just realize that this likely has been done many times. Does someone have a pointer to code for creating an imagemap from a BLAST report and also write the blast results with links? Bernd From bosborne11 at verizon.net Fri Nov 10 13:10:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Fri, 10 Nov 2006 13:10:01 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554A2B8.4010207@sendu.me.uk> Message-ID: Sendu, No, no scripts installed either by bioperl-live or by 1.5.2-RC3 (Mac OS X, Perl 5.8.6). But yes, bioperl-live has certainly been capable of installing scripts in the past. Brian O. On 11/10/06 11:03 AM, "Sendu Bala" wrote: > Can anyone confirm if script installation works properly for them, and > how they got it to work? From hlapp at gmx.net Fri Nov 10 18:33:48 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:33:48 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: On Nov 10, 2006, at 7:31 AM, Sendu Bala wrote: > bioperl.lisp This is the macros file for emacs. Do not delete it from the repository ... -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Nov 10 18:37:32 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:37:32 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: References: Message-ID: <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: >> bioperl.lisp > > This is a set of convenience macros for developers who use Emacs, > but it's > pretty out of date. What is out of date in there? > Some may still use it, though. E.g., dinosaurs like me. > It's of no use being in the package distribution, however. I agree. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Nov 10 18:40:40 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:40:40 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554A2B8.4010207@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> <4554974A.4010206@campus.iztacala.unam.mx> <4554A2B8.4010207@sendu.me.uk> Message-ID: <2E617B21-BBFA-4865-AC50-6D6694B6CE2F@gmx.net> On Nov 10, 2006, at 11:03 AM, Sendu Bala wrote: >>> bioperl.lisp >> >> This a module template for Emacs users. > > I propose moving it to the wiki and removing it from CVS. This is not a good idea because the wiki is a bad platform for version controlling source code files, and this is a source code file. I don't have a problem with putting it up on the wiki, too. Better yet, link to the version in CVS. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Nov 10 19:35:06 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 19:35:06 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: Sounds like a good thing to do to me - I'd just be hesitant to do this for the 1.5.2 release. But I'm not the release master. -hilmar On Nov 10, 2006, at 5:15 AM, Sendu Bala wrote: > Hi all, > > Since I'm seeing inadequacies with the current Makefile.PL scripts we > have, I'm thinking of converting from ExtUtils::MakeMaker and the > Makefile.PL scripts to Module::Build Build.PL scripts. > > The advantages this will bring would be creation and installation of > documentation, sane handling of required and optional dependencies, > and > hopefully good META.yml output, for CPAN compatibility wrt version > numbers. > > I'll be able to use Module::Build::Compat to automatically generate > Makefile.PL scripts in 'passthrough' style (if an end-user tries to > use > Makefile.PL without having Module::Build installed, it will offer to > install Module::Build for them) when it comes time to make > distributions, but Makefile.PL would no longer be in CVS. > > > One thing I'm not clear on with the current situation is what is > supposed to happen when the user chooses to install scripts. Where are > they supposed to get installed to, and where do end-users normally run > them from and how? How does this compare to expectations from other > perl > module distributions that have installable scripts? > > > Please comment and discuss, but I'd like to get this done for the > 1.5.2 > release so that the CPAN distribution will be happy. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From kaboroev at sfu.ca Fri Nov 10 17:51:21 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Fri, 10 Nov 2006 14:51:21 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical Message-ID: <45550269.9050407@sfu.ca> Hi, I am attempting to add a few methods (ie. matching_bands_list) to the fpc map class but I am having a hard time inheriting the class properly. My first attempt was to inherit the "Bio::Map::Physical" class but the "next_map" package is not found. So I tried inheriting "Bio::MapIO" instead, and get a cannot find "matching_bands_list" via package "Bio::Map::Physical" The only way I can get it to work is with no inheritance and passing the map class variable to the function, but this isn't very elegant. Is there a correct way to inherit these classes that will allow me to execute this properly? keith From bernd.web at gmail.com Fri Nov 10 18:10:09 2006 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 11 Nov 2006 00:10:09 +0100 Subject: [Bioperl-l] POD HTML ResultWriter Message-ID: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> Hi, I just found the POD for HTMLResultWriter is truncated in Internet Explorer. http://doc.bioperl.org/bioperl-live/Bio/SearchIO/Writer/HTMLResultWriter.html. It stops with start_report. I think this is due to the tag (and , <BODY> tags in the text of start_report. In Firefox the page is rendered OK. Bernd From bix at sendu.me.uk Sat Nov 11 03:38:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 11 Nov 2006 08:38:27 +0000 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45550269.9050407@sfu.ca> References: <45550269.9050407@sfu.ca> Message-ID: <45558C03.8020903@sendu.me.uk> Keith Anthony Boroevich wrote: > Hi, > > I am attempting to add a few methods (ie. matching_bands_list) to the > fpc map class but I am having a hard time inheriting the class properly. > > My first attempt was to inherit the "Bio::Map::Physical" class but the > "next_map" package is not found. > So I tried inheriting "Bio::MapIO" instead, and get a cannot find > "matching_bands_list" via package "Bio::Map::Physical" > The only way I can get it to work is with no inheritance and passing the > map class variable to the function, but this isn't very elegant. Is > there a correct way to inherit these classes that will allow me to > execute this properly? It's hard to diagnose the problem without knowing exactly what you've tried. Please post some relevant code. Also, what version of Bioperl are you using? From bernd.web at gmail.com Sat Nov 11 08:53:55 2006 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 11 Nov 2006 14:53:55 +0100 Subject: [Bioperl-l] Bio::DB::Fasta index Message-ID: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Hi, A maybe strange question: is it possible to force Bio::DB::Fasta NOT to index the fasta file at any time (if there is already an index)? In the doc (http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Fasta.html), I read: " If one of the source fasta files is updated, the module reindexes just that one file. (You can also force reindexing manually)." Can I also switch off reindexing? (I realize that with Bio::Index::Fasta indexing can be separated). bernd From mkiwala at watson.wustl.edu Sat Nov 11 10:54:55 2006 From: mkiwala at watson.wustl.edu (mkiwala at watson.wustl.edu) Date: Sat, 11 Nov 2006 09:54:55 -0600 (CST) Subject: [Bioperl-l] Bio::DB::Fasta index In-Reply-To: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> References: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Message-ID: <58605.24.107.18.143.1163260495.squirrel@gscmail.wustl.edu> > A maybe strange question: is it possible to force Bio::DB::Fasta NOT > to index the fasta file at any time (if there is already an index)? I don't think so, but you could set the time stamp on the index file just before you run your script that uses the index. On a unix-like machine you would use the touch command. From cjfields at uiuc.edu Sat Nov 11 11:26:31 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 11 Nov 2006 10:26:31 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> References: <OF981FA506.80BA9953-ON85257222.004C99FF-85257222.004CE6C4@gsk.com> <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> Message-ID: <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> On Nov 10, 2006, at 5:37 PM, Hilmar Lapp wrote: > > On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: > >>> bioperl.lisp >> >> This is a set of convenience macros for developers who use Emacs, >> but it's >> pretty out of date. > > What is out of date in there? > >> Some may still use it, though. > > E.g., dinosaurs like me. > >> It's of no use being in the package distribution, however. > > I agree. > > -hilmar Maybe move it to it's own folder? It would be convenient if anyone else has helper macros (Komodo, vim, etc) or other developer stuff donated that we don't want included in the package distribution. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Sat Nov 11 11:31:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 11 Nov 2006 10:31:26 -0600 Subject: [Bioperl-l] POD HTML ResultWriter In-Reply-To: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> References: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> Message-ID: <27593A76-29AE-4295-A229-36A92F9F92F6@uiuc.edu> Bernd, Could you submit this as a bug? It likely has to do with PDOC. Include the IE version etc. Chris On Nov 10, 2006, at 5:10 PM, Bernd Web wrote: > Hi, > > I just found the POD for HTMLResultWriter is truncated in Internet > Explorer. > http://doc.bioperl.org/bioperl-live/Bio/SearchIO/Writer/ > HTMLResultWriter.html. > It stops with start_report. > I think this is due to the <HTML> tag (and <TITLE>, <BODY> tags in the > text of start_report. In Firefox the page is rendered OK. > > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Sat Nov 11 13:02:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 11 Nov 2006 13:02:18 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> References: <OF981FA506.80BA9953-ON85257222.004C99FF-85257222.004CE6C4@gsk.com> <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> Message-ID: <6E07DFB4-4D2A-4D66-9FAA-FEC20F6DE1B2@gmx.net> On Nov 11, 2006, at 11:26 AM, Chris Fields wrote: > > On Nov 10, 2006, at 5:37 PM, Hilmar Lapp wrote: > >> >> On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: >> >>>> bioperl.lisp >> >>> It's of no use being in the package distribution, however. >> >> I agree. >> >> -hilmar > > Maybe move it to it's own folder? It would be convenient if anyone > else has helper macros (Komodo, vim, etc) or other developer stuff > donated that we don't want included in the package distribution. Good idea, I agree. -hilmar > > chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From chhalling at verizon.net Sun Nov 12 13:11:54 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 12 Nov 2006 13:11:54 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC Message-ID: <455763EA.8080300@verizon.net> Quick summary: 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but not by Bio::Restriction::Enzyme. Should 'X' be removed from Bio::Tools::IUPAC or should it be added to Bio::Restriction::Enzyme? Detailed explanation: I tried to use the Bio::Restriction modules to perform a simple restriction analysis of some sequences I'm using at work, and I found the documentation and code confusing. So I'm volunteering to overhaul and redocument these modules. As part of this effort, I am also volunteering to fix the Bio::Restriction::IO::bairoch module. I have begun writing a test suite, RestrictionEnzyme.t, for the Bio::Restriction::Enzyme module. For one of the tests, I created a Bio::Restriction::Enzyme object with a recognition sequence that includes all of the IUPAC base symbols along with the caret ('^') symbol. A code excerpt is: use Bio::Tools::IUPAC; my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); ok $enzyme = Bio::Restriction::Enzyme->new( -name => 'IUPAC-IUB', -site => $site ); This test fails because Bio::Tools::IUPAC module includes 'X' as a valid base symbol, whereas Bio::Restriction::Enzyme does not. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 STACK: t/RestrictionEnzyme.t:184 ----------------------------------------------------------- The symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC need to be synchronized. Since 'X' is not recommended by "Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences" (see http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it stands for xanthine), I am in favor of removing it as a valid symbol. But I have a feeling that if 'X' is removed as a valid symbol from Bio::Tools::IUPAC, this will break a lot of existing code. So the simplest solution seems to be to add 'X' to the symbols recognized by Bio::Restriction::Enzyme. Does anyone have a recommendation? -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Sun Nov 12 17:21:06 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 12 Nov 2006 17:21:06 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> References: <455763EA.8080300@verizon.net> Message-ID: <45579E52.3010606@verizon.net> A followup: Bio::Tools::IUPAC::iupac_iub() also returns 'U' as a valid base. My idea of getting an authoritative set of base symbols from Bio::Tools::IUPAC does not work well. I will leave the valid bases in Bio::Restriction::Enzyme set to what is already used in the module ('ABCDGHKMNRSTVWY'). -- Conrad Conrad Halling wrote: > Quick summary: > > 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but not by > Bio::Restriction::Enzyme. Should 'X' be removed from Bio::Tools::IUPAC > or should it be added to Bio::Restriction::Enzyme? > > Detailed explanation: > > I tried to use the Bio::Restriction modules to perform a simple > restriction analysis of some sequences I'm using at work, and I found > the documentation and code confusing. So I'm volunteering to overhaul > and redocument these modules. As part of this effort, I am also > volunteering to fix the Bio::Restriction::IO::bairoch module. > > I have begun writing a test suite, RestrictionEnzyme.t, for the > Bio::Restriction::Enzyme module. For one of the tests, I created a > Bio::Restriction::Enzyme object with a recognition sequence that > includes all of the IUPAC base symbols along with the caret ('^') > symbol. A code excerpt is: > > use Bio::Tools::IUPAC; > my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); > my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); > ok $enzyme = > Bio::Restriction::Enzyme->new( > -name => 'IUPAC-IUB', > -site => $site ); > > This test fails because Bio::Tools::IUPAC module includes 'X' as a valid > base symbol, whereas Bio::Restriction::Enzyme does not. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 > STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 > STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 > STACK: t/RestrictionEnzyme.t:184 > ----------------------------------------------------------- > > The symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC > need to be synchronized. Since 'X' is not recommended by "Nomenclature > for Incompletely Specified Bases in Nucleic Acid Sequences" (see > http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it > stands for xanthine), I am in favor of removing it as a valid symbol. > > But I have a feeling that if 'X' is removed as a valid symbol from > Bio::Tools::IUPAC, this will break a lot of existing code. So the > simplest solution seems to be to add 'X' to the symbols recognized by > Bio::Restriction::Enzyme. > > Does anyone have a recommendation? > > -- Conrad Halling chhalling at verizon.net From dmessina at wustl.edu Sun Nov 12 17:30:59 2006 From: dmessina at wustl.edu (David Messina) Date: Sun, 12 Nov 2006 16:30:59 -0600 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> References: <455763EA.8080300@verizon.net> Message-ID: <C5C56BF0-8135-4CBE-BF30-B931E79B39C7@wustl.edu> > The symbols recognized by Bio::Restriction::Enzyme and > Bio::Tools::IUPAC > need to be synchronized. Since 'X' is not recommended by "Nomenclature > for Incompletely Specified Bases in Nucleic Acid Sequences" (see > http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it > stands for xanthine), I am in favor of removing it as a valid symbol. > > But I have a feeling that if 'X' is removed as a valid symbol from > Bio::Tools::IUPAC, this will break a lot of existing code. So the > simplest solution seems to be to add 'X' to the symbols recognized by > Bio::Restriction::Enzyme. How about adding a -strict option which would require valid IUPAC symbols (i.e. not 'X')? And the permissive, 'X'-okay behavior would be the default. Dave From cjfields at uiuc.edu Sun Nov 12 19:15:37 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 12 Nov 2006 18:15:37 -0600 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <45579E52.3010606@verizon.net> References: <455763EA.8080300@verizon.net> <45579E52.3010606@verizon.net> Message-ID: <59337785-5E63-4FD3-A490-FA9AC4715BBE@uiuc.edu> On Nov 12, 2006, at 4:21 PM, Conrad Halling wrote: > A followup: > > Bio::Tools::IUPAC::iupac_iub() also returns 'U' as a valid base. My > idea > of getting an authoritative set of base symbols from Bio::Tools::IUPAC > does not work well. > > I will leave the valid bases in Bio::Restriction::Enzyme set to > what is > already used in the module ('ABCDGHKMNRSTVWY'). > > -- Conrad Conrad, You could grab a hash of DNA/RNA codes from Bio::Tools::IUPAC using iupac_iub(), then modify that for internal use in Bio::Restriction modules by adding/deleting what you want. Or add a method to Bio::Tools::IUPAC that adds/deletes key-value pairs in the object to your specifications. If there are non-IUPAC symbols present in the module we should consider the reasons why they are there. Were they added as a quick fix, or for other reasons? Strictly speaking, I would say a module named Bio::Tools::IUPAC should not contain non-IUPAC symbols, and modifications should be made on a case-by-case basis (in objects), vs. universally (in classes). You could always remove any non- standard symbols and see what breaks. By the way, I think I can speak for many here by saying that we are happy you will take up the Bio::Restriction classes. They definitely need some work! Chris > Conrad Halling wrote: >> Quick summary: >> >> 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but >> not by >> Bio::Restriction::Enzyme. Should 'X' be removed from >> Bio::Tools::IUPAC >> or should it be added to Bio::Restriction::Enzyme? >> >> Detailed explanation: >> >> I tried to use the Bio::Restriction modules to perform a simple >> restriction analysis of some sequences I'm using at work, and I found >> the documentation and code confusing. So I'm volunteering to overhaul >> and redocument these modules. As part of this effort, I am also >> volunteering to fix the Bio::Restriction::IO::bairoch module. >> >> I have begun writing a test suite, RestrictionEnzyme.t, for the >> Bio::Restriction::Enzyme module. For one of the tests, I created a >> Bio::Restriction::Enzyme object with a recognition sequence that >> includes all of the IUPAC base symbols along with the caret ('^') >> symbol. A code excerpt is: >> >> use Bio::Tools::IUPAC; >> my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); >> my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); >> ok $enzyme = >> Bio::Restriction::Enzyme->new( >> -name => 'IUPAC-IUB', >> -site => $site ); >> >> This test fails because Bio::Tools::IUPAC module includes 'X' as a >> valid >> base symbol, whereas Bio::Restriction::Enzyme does not. >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 >> STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 >> STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 >> STACK: t/RestrictionEnzyme.t:184 >> ----------------------------------------------------------- >> >> The symbols recognized by Bio::Restriction::Enzyme and >> Bio::Tools::IUPAC >> need to be synchronized. Since 'X' is not recommended by >> "Nomenclature >> for Incompletely Specified Bases in Nucleic Acid Sequences" (see >> http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it >> stands for xanthine), I am in favor of removing it as a valid symbol. >> >> But I have a feeling that if 'X' is removed as a valid symbol from >> Bio::Tools::IUPAC, this will break a lot of existing code. So the >> simplest solution seems to be to add 'X' to the symbols recognized by >> Bio::Restriction::Enzyme. >> >> Does anyone have a recommendation? >> >> > > -- > Conrad Halling > chhalling at verizon.net > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Mon Nov 13 04:59:34 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 13 Nov 2006 09:59:34 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 Message-ID: <45584206.2040506@sheffield.ac.uk> I've done a test of the bioperl-run 1.5.2 RC3. I've posted results etc to the wiki. I have quite a lot of changes to commit regarding changing "return undef" to "return" and other issues about "bioperl best practices" - they are mainly only obvious changes. I also, moved some tests over to Test::More and added a few further tests for those modules. The test suite passes OK for me (other than the same issues for 1.5.2 RC3). Should It be OK to commit the to HEAD? or shall I wait till after the 1.5.2 release? Cheers Nath From avilella at gmail.com Mon Nov 13 08:25:44 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 13 Nov 2006 13:25:44 +0000 Subject: [Bioperl-l] new methods -- wiki or bugzilla? Message-ID: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Hi, Should the new methods/features be declared as ENH bugs in bugzilla or using the wiki? Cheers, Albert. From cjfields at uiuc.edu Mon Nov 13 10:10:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 09:10:27 -0600 Subject: [Bioperl-l] new methods -- wiki or bugzilla? In-Reply-To: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Message-ID: <013f01c70735$dbc09140$15327e82@pyrimidine> > Hi, > > Should the new methods/features be declared as ENH bugs in > bugzilla or using the wiki? > > Cheers, > > Albert. Historically we have used Bugzilla so we can keep track of them (the enhancement tag is also available there for that reason). You could use the wiki, but I personally think the wiki better serves as primarily a documentation site, both for current code and for the direction we plan on taking Bioperl. We could add a code requests page, though. We already have a Projects Priority page that details what we think are the top issues with Bioperl that need to be addressed; there have been a number of things added to that page that should be separated out into a code request page. However, I don't know how much will be implemented unless someone interested takes it up. Frankly, there are quite a number of requests in bugzilla that haven't been added b/c of lack of interest/time by the other developers. Either that, or we have a lack of knowledge about a certain format or program, as I had with the XMFA and ARP AlignIO parsers (see the POD for my comments; the parsing is pretty minimal). Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Mon Nov 13 10:17:03 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 09:17:03 -0600 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <45584206.2040506@sheffield.ac.uk> Message-ID: <014001c70736$c6e20c80$15327e82@pyrimidine> > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Nathan S. Haigh > Sent: Monday, November 13, 2006 4:00 AM > To: bioperl-l; sendu Bala > Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 > > I've done a test of the bioperl-run 1.5.2 RC3. I've posted > results etc to the wiki. > > I have quite a lot of changes to commit regarding changing > "return undef" to "return" and other issues about "bioperl > best practices" - they are mainly only obvious changes. I > also, moved some tests over to Test::More and added a few > further tests for those modules. The test suite passes OK for > me (other than the same issues for 1.5.2 RC3). > Should It be OK to commit the to HEAD? or shall I wait till after the > 1.5.2 release? > > Cheers > Nath I would say, if the tests pass, commit away. As an aside, I'm not sure how versioning works in the other bioperl distributions. We generally package them up at the same time but I don't remember them getting a specific version number upon release. For instance, bioperl-db was considered at version 0.1 for a long time, but I can't remember if it was officially assigned that. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 13 10:18:43 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 15:18:43 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <014001c70736$c6e20c80$15327e82@pyrimidine> References: <014001c70736$c6e20c80$15327e82@pyrimidine> Message-ID: <45588CD3.5020407@sendu.me.uk> Chris Fields wrote: > > As an aside, I'm not sure how versioning works in the other bioperl > distributions. We generally package them up at the same time but I don't > remember them getting a specific version number upon release. For instance, > bioperl-db was considered at version 0.1 for a long time, but I can't > remember if it was officially assigned that. I'm making their versions match that of core, which seems appropriate. From avilella at gmail.com Mon Nov 13 08:36:44 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 13 Nov 2006 13:36:44 +0000 Subject: [Bioperl-l] new methods -- wiki or bugzilla? In-Reply-To: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> References: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Message-ID: <358f4d650611130536sd99bc51u9df42f8bd71cb3a8@mail.gmail.com> and related to the previous question: can an email (presumably with a certain template format) be sent somewhere so that either one or the other system create a new feature ticket somewhere? I've been told that it can be done with wikis, but never seen it done. On 11/13/06, Albert Vilella <avilella at gmail.com> wrote: > Hi, > > Should the new methods/features be declared as ENH bugs in bugzilla or > using the wiki? > > Cheers, > > Albert. > From cjfields at uiuc.edu Mon Nov 13 11:51:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 10:51:24 -0600 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <45588CD3.5020407@sendu.me.uk> Message-ID: <000001c70743$f45b5ce0$15327e82@pyrimidine> > Chris Fields wrote: > > > > As an aside, I'm not sure how versioning works in the other bioperl > > distributions. We generally package them up at the same time but I > > don't remember them getting a specific version number upon > release. > > For instance, bioperl-db was considered at version 0.1 for a long > > time, but I can't remember if it was officially assigned that. > > I'm making their versions match that of core, which seems appropriate. Sounds good to me. We could at least state that run, db, and network 1.5.2 releases require bioperl rel. 1.5.2 (i.e. they are not guaranteed to work with older bioperl core versions), since that's what they were tested against. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 13 11:52:15 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 16:52:15 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <000001c70743$f45b5ce0$15327e82@pyrimidine> References: <000001c70743$f45b5ce0$15327e82@pyrimidine> Message-ID: <4558A2BF.7000405@sendu.me.uk> Chris Fields wrote: >> Chris Fields wrote: >>> As an aside, I'm not sure how versioning works in the other bioperl >>> distributions. We generally package them up at the same time but I >>> don't remember them getting a specific version number upon >> release. >>> For instance, bioperl-db was considered at version 0.1 for a long >>> time, but I can't remember if it was officially assigned that. >> I'm making their versions match that of core, which seems appropriate. > > Sounds good to me. We could at least state that run, db, and network 1.5.2 > releases require bioperl rel. 1.5.2 (i.e. they are not guaranteed to work > with older bioperl core versions), since that's what they were tested > against. Yes, they will (do already) require core 1.5.2 for Makefile.PL (Build.PL) to succeed. From alessandro.botton at unipd.it Mon Nov 13 13:10:36 2006 From: alessandro.botton at unipd.it (Alessandro Botton) Date: Mon, 13 Nov 2006 19:10:36 +0100 Subject: [Bioperl-l] Installation problems... Message-ID: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Sorry to disturb you... I tried to install BioPerl by means of cpan. I have previously installed Bundle::BioPerl and everything was ok, and then tried to force the Bioperl installation. Anyway, I attach the "make test" part taken from my shell during Bioperl installation and the result of the second test (tut1.pl, also in attachment) suggested to detect a good installation of Biopelr (the first one was ok). if you need further information please ask me. Thank you in advance for your precious help. Best wishes, A.Botton ??? ======================================= ALESSANDRO BOTTON, PhD student Department of Environmental Agronomy and Crop Science University of Padova AGRIPOLIS - V.le dell'Universit?, 16 35020 Legnaro (PD)-ITALY Fax ++39 049 8272850 Phone ++39 049 8272889 E-mail: alessandro.botton at unipd.it _______________________________________ Doctorate School of Crop Science www.daapv.unipd.it/spv _______________________________________ -------------- next part -------------- An HTML attachment was scrubbed... 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URL: http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0006.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: test_tut1.pl.txt Url: http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0003.txt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0007.html From bix at sendu.me.uk Mon Nov 13 14:16:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 19:16:58 +0000 Subject: [Bioperl-l] Installation problems... In-Reply-To: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> References: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Message-ID: <4558C4AA.6020004@sendu.me.uk> Alessandro Botton wrote: > Sorry to disturb you... > I tried to install BioPerl by means of cpan. I have previously installed > Bundle::BioPerl and everything was ok, and then tried to force the > Bioperl installation. Anyway, I attach the "make test" part taken from > my shell during Bioperl installation and the result of the second test > (tut1.pl, also in attachment) suggested to detect a good installation of > Biopelr (the first one was ok). if you need further information please > ask me. Unfortunately Bioperl 1.4 (the latest 'stable' edition in CPAN) is very old and yes, you're likely to get all sorts of failures. tut1.pl tries to do something that indeed no longer works in 1.4. We have a 'developer' release called 1.5.2 soon to be released which should in fact be suitable for use by everyone and everything should work. You can download a pre-release version and install it manually: http://bioperl.org/wiki/Release_1.5.2 Or wait a week or two and you'll be able to find the final release on CPAN. Hope that helps, Sendu. From n.haigh at sheffield.ac.uk Mon Nov 13 14:50:53 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 13 Nov 2006 19:50:53 +0000 Subject: [Bioperl-l] Installation problems... In-Reply-To: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> References: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Message-ID: <4558CC9D.2050507@sheffield.ac.uk> Alessandro Botton wrote: > Sorry to disturb you... > I tried to install BioPerl by means of cpan. I have previously > installed Bundle::BioPerl and everything was ok, and then tried to > force the Bioperl installation. Anyway, I attach the "make test" part > taken from my shell during Bioperl installation and the result of the > second test (tut1.pl, also in attachment) suggested to detect a good > installation of Biopelr (the first one was ok). if you need further > information please ask me. > Thank you in advance for your precious help. > Best wishes, > A.Botton > Hi Alessandro, The Bioperl 1.4 release is now somewhat out-of-date and you might be better to install the latest 1.5.x developer release. We are currently working towards a 1.5.2 release, which should be out within the next week or so. The latest version is 1.5.2 release candidate 3 - it should be installable via CPAN. I will refer you to what has been said about the 1.5.2 RC3 release: "Users: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into." At the moment CPAN doesn't see 1.5.x as a developer release (which should be fixed shortly). Therefore you should still be able to install it with: prompt> perl -MCPAN -e shell CPAN> install Bioperl Once the 1.5.2 RC3 distribution file is fixed, the above will not work. Let me know how you get on and if you get 1.5.2 RC3 installed. Cheers Nathan From jdw at ou.edu Mon Nov 13 18:50:15 2006 From: jdw at ou.edu (James D. White) Date: Mon, 13 Nov 2006 17:50:15 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> Message-ID: <455904B7.50504@ou.edu> "Erik" <er at xs4all.nl> wrote: >Hi all, > >I noticed the parsing is borked with newest swisprot files: > UniProt Knowledgebase Release 9 consists of: > UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 > UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 > > >I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines >in swissprot/trembl according to the new specification (see >http://expasy.org/sprot/relnotes/sp_news.html). > >Basically, the change is as follows: > ID EntryName DataClass; MoleculeType; SequenceLength. >is changed to: > ID EntryName DataClass; SequenceLength. > > > >The change I made was only in the regex capturing the entry name: >method next_seq (Bio/SeqIO/swiss.pm) : > >=============== > > unless( m/ > ^ > ID \s+ # > (\S+) \s+ # $1 entryname > ([^\s;]+); \s+ # $2 DataClass > [0-9]+[ ]AA \. # Sequencelength (capture?) > $ > /ox ) > { > $self->throw("swissprot stream with no ID. Not swissprot in my book"); > } > >=============== > > How about something like the following to recognize both old and new formats =============== unless( m/ ^ ID \s+ # (\S+) \s+ # $1 entryname ( (: [^\s;]+; \s+ )? ) # $2 DataClass (including ";\s+") [0-9]+[ ]AA \. # Sequencelength (capture?) $ /ox ) { $self->throw("swissprot stream with no ID. Not swissprot in my book"); } # Because $2 now contains a trailing ";\s+" in the new format, it needs to be fixed $DataClass = $2 || 'default DataClass'; # provide default for old file format $DataClass =~ s/;\s+$//; # remove trailing ";\s+" =============== The code trailing the unless block should be modified to use the appropriate variable names. This is provided only to show what post-match modification is needed. > >I tested this (=entry parsable and SeqIO created) against several >hundred Swissprot and Trembl entries. > >Of course, files with the older format are now broken - it may be better >to leave old and new format, and try both (newest first). > >hth, > >Erik > > > > > > From lincoln.stein at gmail.com Mon Nov 13 12:43:50 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 13 Nov 2006 12:43:50 -0500 Subject: [Bioperl-l] Bio::DB::Fasta index In-Reply-To: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> References: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Message-ID: <6dce9a0b0611130943n28600d66xb3fa37f7bb4a68b6@mail.gmail.com> You can always remove write permissions from the index file, in which case the attempted reindexing will fail quickly. Lincoln On 11/11/06, Bernd Web <bernd.web at gmail.com> wrote: > > Hi, > > A maybe strange question: is it possible to force Bio::DB::Fasta NOT > to index the fasta file at any time (if there is already an index)? In > the doc ( > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Fasta.html > ), > I read: " If one of the source fasta files is updated, the module > reindexes just that one file. (You can also force reindexing > manually)." > > Can I also switch off reindexing? (I realize that with > Bio::Index::Fasta indexing can be separated). > > bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Mon Nov 13 23:44:09 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 22:44:09 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <455904B7.50504@ou.edu> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> Message-ID: <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> On Nov 13, 2006, at 5:50 PM, James D. White wrote: > "Erik" <er at xs4all.nl> wrote: > >> Hi all, >> >> I noticed the parsing is borked with newest swisprot files: >> UniProt Knowledgebase Release 9 consists of: >> UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 >> UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 >> >> >> I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines >> in swissprot/trembl according to the new specification (see >> http://expasy.org/sprot/relnotes/sp_news.html). >> >> Basically, the change is as follows: >> ID EntryName DataClass; MoleculeType; SequenceLength. >> is changed to: >> ID EntryName DataClass; SequenceLength. >> >> >> >> The change I made was only in the regex capturing the entry name: >> method next_seq (Bio/SeqIO/swiss.pm) : >> >> =============== >> >> unless( m/ >> ^ >> ID \s+ # >> (\S+) \s+ # $1 entryname >> ([^\s;]+); \s+ # $2 DataClass >> [0-9]+[ ]AA \. # Sequencelength >> (capture?) >> $ >> /ox ) >> { >> $self->throw("swissprot stream with no ID. Not swissprot in my >> book"); >> } >> >> =============== >> >> > > How about something like the following to recognize both old and > new formats > > =============== > > unless( m/ > ^ > ID \s+ # > (\S+) \s+ # $1 entryname > ( (: [^\s;]+; \s+ )? ) # $2 DataClass > (including ";\s+") > [0-9]+[ ]AA \. # > Sequencelength (capture?) > $ > /ox ) > { > $self->throw("swissprot stream with no ID. Not swissprot in my > book"); > } > # Because $2 now contains a trailing ";\s+" in the new format, it > needs to be fixed > $DataClass = $2 || 'default DataClass'; # provide default > for old file format > $DataClass =~ s/;\s+$//; # remove trailing "; > \s+" > > =============== > > The code trailing the unless block should be modified to use the > appropriate > variable names. This is provided only to show what post-match > modification is > needed. > >> >> I tested this (=entry parsable and SeqIO created) against several >> hundred Swissprot and Trembl entries. >> >> Of course, files with the older format are now broken - it may be >> better >> to leave old and new format, and try both (newest first). >> >> hth, >> >> Erik This has been fixed to match old and new formats in CVS and passes all tests so far. You can try it out if you want. The regex is made to match up to (but not include) the ';', so there is no need to remove the extra space. ... unless( m{^ ID \s+ # (\S+) \s+ # $1 entryname ([^\s;]+); \s+ # $2 DataClass (?:PRT;)? \s+ # Molecule Type (optional) [0-9]+[ ]AA \. # Sequencelength (capture?) $ }ox ) { ... The molecule type was always PRT and was a carryover from EMBL format divisions. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From kaboroev at sfu.ca Tue Nov 14 00:55:46 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Mon, 13 Nov 2006 21:55:46 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45558C03.8020903@sendu.me.uk> References: <45550269.9050407@sfu.ca> <45558C03.8020903@sendu.me.uk> Message-ID: <45595A62.7090704@sfu.ca> Hi, I am using an up-to-date bioperl-live. The precise code is insignificant so I wrote some additional (shorter) code to attempt to explain my problem. What I want to do is the following. I want to add some functionality to the Bio::Map::Physical module so i created a module that inherits Physical module, Extended::FPC.pm. #----Test.pl-BEGIN---# use strict; use diagnostics; use Extended::FPC; my $mapio = new Extended::FPC(-format => "fpc",-file => $ARGV[0],-readcor => 1); my $map = $mapio->next_map(); $map->fpc_test(); exit 0; #---Test.pl-END------# #----Extended::FPC.pm-BEGIN---# package Extended::FPC; use strict; use base qw(Bio::Map::Physical Bio::MapIO); sub fpc_test { print STDERR "testing\n"; return 0; } 1; #----Extended::FPC.pm-END-----# The execution of test.pl results in a "Can't locate object method "next_map" via package "Extended::FPC"" error; Then I added the "Bio::MapIO" module to the "use base qw(Bio::Map::Physical Bio::MapIO);", because that is the module in which next_map is declared. When I again execute test.pl I now get the exception: Uncaught exception from user code: #-------- EXCEPTION ------- # ------------- EXCEPTION: Bio::Root::NotImplemented ------------- MSG: Abstract method "Bio::Factory::MapFactoryI::next_map" is not implemented by package Extended::FPC. This is not your fault - author of Extended::FPC should be blamed! STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.7/Bio/Root/Root.pm:359 STACK: Bio::Root::RootI::throw_not_implemented /usr/lib/perl5/site_perl/5.8.7/Bio/Root/RootI.pm:522 STACK: Bio::Factory::MapFactoryI::next_map /usr/lib/perl5/site_perl/5.8.7/Bio/Factory/MapFactoryI.pm:84 STACK: ./fpc.pl:12 ---------------------------------------------------------------- at /usr/lib/perl5/site_perl/5.8.7/Error.pm line 187 Error::throw('Bio::Root::NotImplemented', '-class', 'Bio::Root::NotImplemented', '-object', 'Extended::FPC=HASH(0x109ce10)', '-text', 'Abstract method "Bio::Factory::MapFactoryI::next_map" is not ...') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Root/Root.pm line 359 Bio::Root::Root::throw('Extended::FPC=HASH(0x109ce10)', '-text', 'Abstract method "Bio::Factory::MapFactoryI::next_map" is not ...', '-class', 'Bio::Root::NotImplemented') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Root/RootI.pm line 522 Bio::Root::RootI::throw_not_implemented('Extended::FPC=HASH(0x109ce10)') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Factory/MapFactoryI.pm line 84 Bio::Factory::MapFactoryI::next_map('Extended::FPC=HASH(0x109ce10)') called at ./fpc.pl line 12 #---- EXCEPTION END ----# This is where I am now and have no real idea of where to begin. I suppose the easiest way is to pass the $map variable to the function of interest and not to bother with inheriting any modules. Sendu Bala wrote: > Keith Anthony Boroevich wrote: > >> Hi, >> >> I am attempting to add a few methods (ie. matching_bands_list) to the >> fpc map class but I am having a hard time inheriting the class properly. >> >> My first attempt was to inherit the "Bio::Map::Physical" class but the >> "next_map" package is not found. >> So I tried inheriting "Bio::MapIO" instead, and get a cannot find >> "matching_bands_list" via package "Bio::Map::Physical" >> The only way I can get it to work is with no inheritance and passing the >> map class variable to the function, but this isn't very elegant. Is >> there a correct way to inherit these classes that will allow me to >> execute this properly? >> > > It's hard to diagnose the problem without knowing exactly what you've > tried. Please post some relevant code. Also, what version of Bioperl are > you using? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- ><)))?> -cGRASP- <?(((>< Keith Anthony Boroevich Simon Fraser University Tel: 604-268-7276 From bix at sendu.me.uk Tue Nov 14 03:49:52 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 14 Nov 2006 08:49:52 +0000 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45595A62.7090704@sfu.ca> References: <45550269.9050407@sfu.ca> <45558C03.8020903@sendu.me.uk> <45595A62.7090704@sfu.ca> Message-ID: <45598330.20400@sendu.me.uk> Keith Anthony Boroevich wrote: > Hi, > > I am using an up-to-date bioperl-live. The precise code is > insignificant so I wrote some additional (shorter) code to attempt to > explain my problem. What I want to do is the following. I want to add > some functionality to the Bio::Map::Physical module so i created a > module that inherits Physical module, Extended::FPC.pm. > > #----Test.pl-BEGIN---# > use strict; > use diagnostics; > use Extended::FPC; > my $mapio = new Extended::FPC(-format => "fpc",-file => > $ARGV[0],-readcor => 1); > my $map = $mapio->next_map(); > $map->fpc_test(); > exit 0; > #---Test.pl-END------# > > #----Extended::FPC.pm-BEGIN---# > package Extended::FPC; > use strict; > use base qw(Bio::Map::Physical Bio::MapIO); > > sub fpc_test { > print STDERR "testing\n"; > return 0; > } > > 1; > #----Extended::FPC.pm-END-----# > > The execution of test.pl results in a "Can't locate object method > "next_map" via package "Extended::FPC"" error; > Then I added the "Bio::MapIO" module to the "use base > qw(Bio::Map::Physical Bio::MapIO);", because that is the module in which > next_map is declared. Well I think alarm bells should have been ringing at that point. I think you're trying to inherit from the wrong module to do whatever it is you want to do. Bio::Map::Physical has no next_map() because it isn't a Map::IO module. It represents a /single/ map (only), and is the sort of object you might /receive/ as the result of calling next_map() on an actual Map::IO module. So perhaps you should take another look at the various Map modules and figure out the correct thing to inherit from, or you just need to correct your usage (only call next_map() on a Map::IO). From er at xs4all.nl Tue Nov 14 04:40:20 2006 From: er at xs4all.nl (Erik) Date: Tue, 14 Nov 2006 10:40:20 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> Message-ID: <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> Btw and FYI: I have run this regex through SwissProt and Trembl and a previous version of those two files (to be version-precise: swissprot 51 and 50; trembl 33 and 34). It matched all ID lines. Thanks :) Erik > ... > unless( m{^ > ID \s+ # > (\S+) \s+ # $1 entryname > ([^\s;]+); \s+ # $2 DataClass > (?:PRT;)? \s+ # Molecule Type (optional) > [0-9]+[ ]AA \. # Sequencelength (capture?) > $ > }ox ) { > ... > > The molecule type was always PRT and was a carryover from EMBL format > divisions. From cjfields at uiuc.edu Tue Nov 14 07:35:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 14 Nov 2006 06:35:24 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> Message-ID: <B5AD2308-6CC0-4250-ABFA-1E728196693F@uiuc.edu> On Nov 14, 2006, at 3:40 AM, Erik wrote: > Btw and FYI: > > I have run this regex through SwissProt and Trembl and a previous > version > of those two files (to be version-precise: swissprot 51 and 50; > trembl 33 > and 34). > > It matched all ID lines. > > Thanks :) > > Erik ... Thanks for letting us know. We like success stories! Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From gcarbajosa at cnio.es Tue Nov 14 05:39:41 2006 From: gcarbajosa at cnio.es (guillermo) Date: Tue, 14 Nov 2006 11:39:41 +0100 Subject: [Bioperl-l] Error while indexing whole genbank Message-ID: <80337800c106ece5f0c78ed0b098b8f8@cnio.es> Hello, I am trying to index the whole of genbank nucleotide (release number 156, October 15 2006), with the script (which uses Bio::Index::GenBank) that is attached at the end of this message the process crashes with this error message: sdbm store returned -1, errno 9, key "BF460808" at /usr/local/lib/perl5/site_perl/5.8.8/Bio/Index/Abstract.pm line 714, <GenBank> line 164732819. why could this be? Thanks, Guillermo #!/usr/local/bin/perl -w # Perl pragma to restrict unsafe constructs use strict; # Issue warnings about suspicious programming. use warnings; # Use the code module that contains BioPerl Services. use Bio::Index::GenBank; # Use to index GenBank file use Bio::SeqIO; # be prepare for command-line options/arguments use Getopt::Std; sub help { return<<"END_HELP"; Description: Make index from GenBank database Usage: createGenBankIndex.pl -d {index file} -g {GenBank database} -d path and file name of index database -g GenBank database path END_HELP } BEGIN { # Determines the options with values from program use vars qw/$opt_d $opt_g/; # these are switches taking an argument (a value) my $switches = 'dg'; # Get the switches getopt($switches); # If the user does not write nothing, skip to help unless (defined($opt_d) || defined($opt_g)){ print help; exit 0; } } ######################################################################## ####### # # DESCRIPTION: The next program creates an BioPerl index aside GenBank database. # # INPUT (BY CONSOLE): - (-d) Path where the Uniprot index is going to store. # - (-g) Path where GenBank database is located # # OUTPUT: - O => The program has finished sucessfully # - 1 => Some of database files has not founded # - 2 => There was an error while the process was running # # AUTHOR: Jos?? Manuel Rodr??guez Carrasco -jmrc at cnb.uam.es- (INB-CNB) ######################################################################## ####### # Check if the path of GenBank database is able to read unless (-f $opt_g && -r $opt_g) { # The GenBank database has not been found print "Error of createGenBankIndex program: The GenBank database has not been found\n"; # Return an error exit 1; } # Store the database paths my @DBList = ($opt_g); # Create new instance to index file. It is used the option my $indexSW = Bio::Index::GenBank->new ('-filename' => $opt_d, '-write_flag' => 1); # Make the index my $numFiles = $indexSW->make_index(@DBList); # Check how many databases have been indexed if ($numFiles == 1) { # There has been not exist error. print "\nThe creation of GenBank index has been executed successfully\n"; exit 0; } else { # There has been exist an process error print "\nThere was a problem while the creation of GenBank index was running\n"; exit 2; } **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From gcarbajosa at cnio.es Tue Nov 14 05:57:01 2006 From: gcarbajosa at cnio.es (guillermo) Date: Tue, 14 Nov 2006 11:57:01 +0100 Subject: [Bioperl-l] indexing with several processors Message-ID: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> Hello, While using the Bio::Index::GenBank module for indexing Genbank, is there any option to run the process with more than one processor. Thanks **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From lincoln.stein at gmail.com Tue Nov 14 11:08:55 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 14 Nov 2006 11:08:55 -0500 Subject: [Bioperl-l] Bio::Graphics In-Reply-To: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> References: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> Message-ID: <6dce9a0b0611140808md4edbe7ye2632714621da52d@mail.gmail.com> I don't think the dots have been connected on this. It should be straightforward following the example in the BioGraphics HOWTO. Lincoln On 11/10/06, Bernd Web <bernd.web at gmail.com> wrote: > > Hi, > > Lincoln made an excellent help on Graphics. Thanks for > that!(http://www.bioperl.org/wiki/HOWTO:Graphics) > I am just looking at the imagemap creation with > my $map=$panel->create_web_map('mapname',\&linkrule,'bbb'); > and would like to connect the PNG from a blast report to the blast > results. > > I just realize that this likely has been done many times. Does someone > have a pointer to code for creating an imagemap from a BLAST report > and also write the blast results with links? > > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bosborne11 at verizon.net Tue Nov 14 16:54:25 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 14 Nov 2006 16:54:25 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> Message-ID: <C17FA541.B55D%bosborne11@verizon.net> Conrad, The typical solution is to declare an alphabet, as in: my $seq = Bio::Seq->new(-seq => "xxxx", -alphabet => "dna") Then Bioperl will not check your sequence. This works since you'll know that the alphabet, in this case, has to be "dna". Brian O. On 11/12/06 1:11 PM, "Conrad Halling" <chhalling at verizon.net> wrote: > This test fails because Bio::Tools::IUPAC module includes 'X' as a valid > base symbol, whereas Bio::Restriction::Enzyme does not. From stewarta at nmrc.navy.mil Tue Nov 14 17:47:26 2006 From: stewarta at nmrc.navy.mil (Andrew Stewart) Date: Tue, 14 Nov 2006 17:47:26 -0500 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast Message-ID: <8AF15F1F-0C81-4506-97C4-D25A12804731@nmrc.navy.mil> Anyone have any opinions as to how easy/difficult it would be to incorporate mpiblast into Bio::Tools::Run::StandAloneBlast? It runs essentially the same way as blastall, and its output is nearly identical. -A -- Andrew Stewart Research Assistant, Genomics Team Navy Medical Research Center (NMRC) Biological Defense Research Directorate (BDRD) BDRD Annex 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 email: stewarta at nmrc.navy.mil phone: 301-231-6700 Ext 270 From bosborne11 at verizon.net Tue Nov 14 22:10:00 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 14 Nov 2006 22:10:00 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <45531968.6080607@sendu.me.uk> Message-ID: <C17FEF38.B565%bosborne11@verizon.net> Sendu, RC3 can't be released as it doesn't install its scripts and some of these scripts are critical (e.g. the bp_*load_gff.pl and bp_process*.pl scripts, used by GMOD and chado users). I believe I've fixed this though, the problem was in Makefile.PL, no surprise. BIO On 11/9/06 7:04 AM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Developers: > Once again I'm hopeful that this is the last RC. If all goes well > expect final release in about a weeks time. Please check and update > documentation. > > Users: > Even though 1.5.2 is a 'developer' release, we consider it the most > stable and capable version of Bioperl, and recommend that you use > it in all but the most critical production environments. Please > try it out and let us know of any problems or difficulties you run > into. > > > Thank you, > Sendu. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sayali_salodkar at persistent.co.in Wed Nov 15 09:15:52 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Wed, 15 Nov 2006 19:45:52 +0530 Subject: [Bioperl-l] Help needed urgently Message-ID: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> I wish to fetch consensus sequence and the names of the trace (chromat) files used in the assembly from the .ace file For this purpose, I am using Bio::Assembly::IO. But I am unable to find the appropriate methods which would enable me to fetch this information. Note: The BS line (base segment) in the .ace file indicates which read phrap has chosen to be the consensus at a particular position. For example: BS 1 515 K26-572c gives BS <padded start consensus position> <padded end consensus position> <read name> respectively. How do I retrieve this information contig wise? Kindly help. Regards, Sayali D Salodkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From cjfields at uiuc.edu Wed Nov 15 09:22:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 08:22:38 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <C17FEF38.B565%bosborne11@verizon.net> Message-ID: <000a01c708c1$80d37300$15327e82@pyrimidine> > Sendu, > > RC3 can't be released as it doesn't install its scripts and > some of these scripts are critical (e.g. the bp_*load_gff.pl > and bp_process*.pl scripts, used by GMOD and chado users). I > believe I've fixed this though, the problem was in > Makefile.PL, no surprise. > > BIO ... This is definitely something to think about with Sendu's proposed changeover to Module::Build, which would obviate having a Makefile.PL. The issue with broken script installation was raised previously, but there were few responses (probably b/c itr came up somewhat indirectly in relation to other files in CVS). Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 09:24:25 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 08:24:25 -0600 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast In-Reply-To: <8AF15F1F-0C81-4506-97C4-D25A12804731@nmrc.navy.mil> Message-ID: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> > Anyone have any opinions as to how easy/difficult it would be > to incorporate mpiblast into > Bio::Tools::Run::StandAloneBlast? It runs essentially the > same way as blastall, and its output is nearly identical. > > > -A > > -- > Andrew Stewart > Research Assistant, Genomics Team > Navy Medical Research Center (NMRC) > Biological Defense Research Directorate (BDRD) BDRD Annex > 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 > > email: stewarta at nmrc.navy.mil > phone: 301-231-6700 Ext 270 I think plans were to rewrite StandAloneBlast and RemoteBlast to make them more 'generic' (i.e. capable of running other BLAST-related programs), though I'm not sure at what stage everything is. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From sayali_salodkar at persistent.co.in Wed Nov 15 09:15:52 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Wed, 15 Nov 2006 19:45:52 +0530 Subject: [Bioperl-l] Help needed urgently Message-ID: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> I wish to fetch consensus sequence and the names of the trace (chromat) files used in the assembly from the .ace file For this purpose, I am using Bio::Assembly::IO. But I am unable to find the appropriate methods which would enable me to fetch this information. Note: The BS line (base segment) in the .ace file indicates which read phrap has chosen to be the consensus at a particular position. For example: BS 1 515 K26-572c gives BS <padded start consensus position> <padded end consensus position> <read name> respectively. How do I retrieve this information contig wise? Kindly help. Regards, Sayali D Salodkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From bix at sendu.me.uk Wed Nov 15 10:35:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 15:35:29 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: <455B33C1.1010800@sendu.me.uk> Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I propose removing it from CVS. Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL when a user does a normal install of Bioperl? Or can it safely be ignored, only run manually by people who want to install Deobfuscator? From nhansen at nhgri.nih.gov Wed Nov 15 10:52:05 2006 From: nhansen at nhgri.nih.gov (Nancy Hansen) Date: Wed, 15 Nov 2006 10:52:05 -0500 (EST) Subject: [Bioperl-l] Inheritance Bio::Map::Physical Message-ID: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Keith Anthony Boroevich wrote: > > I am using an up-to-date bioperl-live. The precise code is > insignificant so I wrote some additional (shorter) code to attempt to > explain my problem. What I want to do is the following. I want to add > some functionality to the Bio::Map::Physical module so i created a > module that inherits Physical module, Extended::FPC.pm. > > #----Test.pl-BEGIN---# > use strict; > use diagnostics; > use Extended::FPC; > my $mapio = new Extended::FPC(-format => "fpc",-file => > $ARGV[0],-readcor => 1); > my $map = $mapio->next_map(); > $map->fpc_test(); > exit 0; > #---Test.pl-END------# You're right that your Extended::FPC should inherit from Bio::Map::Physical, but you really don't want to use it to parse the fpc file (Bio::MapIO does that just fine, and gets all the data you need into the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical object using Bio::MapIO, then forcing it to be an Extended::FPC, which will allow it to use your method(s): my $mapio = Bio::MapIO->new(-format => 'fpc', -file => $ARGV[0], -readcor => 1); my $fpc_map = $mapio->next_map(); bless $fpc_map, Extended::FPC; my $ra_bands = $fpc_map->my_new_extended_method(); I've actually written my own method to return the band sizes as well, so it would probably make a good enhancement to Bio::Map::Physical, which already has a "matching_bands" method that returns the (scalar) number of bands that match at a given tolerance. If that method were "enhanced" to return an array of matching band sizes rather than the scalar number of bands, it would still return the number in scalar context, but give you the matching band info in list context. I'd be happy to submit a patch for this if others think it's backwardly-compatible enough. --Nancy ************************************* Nancy F. Hansen, PhD nhansen at nhgri.nih.gov Bioinformatics Group NIH Intramural Sequencing Center (NISC) 5625 Fishers Lane Rockville, MD 20852 Phone: (301) 435-1560 Fax: (301) 435-6170 From cjfields at uiuc.edu Wed Nov 15 11:24:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 10:24:57 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> Message-ID: <000001c708d2$97c9d610$15327e82@pyrimidine> > Does anyone know what purpose Bio/DB/Makefile.PL serves? If > none, I propose removing it from CVS. > > Dave: Do you need anything to happen with > doc/Deobfuscator/Makefile.PL when a user does a normal > install of Bioperl? Or can it safely be ignored, only run > manually by people who want to install Deobfuscator? The Bio/DB/Makefile.PL and MANIFEST could be GMOD- or Chado-related (they are both related to Bio::DB::GFF). I'm not sure though; I'm cc'ing this to Lincoln to see if they are still needed. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From arareko at campus.iztacala.unam.mx Wed Nov 15 11:23:45 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed, 15 Nov 2006 10:23:45 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> Message-ID: <455B3F11.6070102@campus.iztacala.unam.mx> I think Deobfuscator code should be manually installed only. Mauricio. Sendu Bala wrote: > Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I > propose removing it from CVS. > > Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL > when a user does a normal install of Bioperl? Or can it safely be > ignored, only run manually by people who want to install Deobfuscator? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From kaboroev at sfu.ca Wed Nov 15 12:14:14 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Wed, 15 Nov 2006 09:14:14 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> References: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Message-ID: <455B4AE6.509@sfu.ca> Thanks, this is exactly what I was looking for. I didn't know how to get Bio::MapIO to return "my" class and I was unaware that bless could be used in such a manner. Not to nit-pick, but just in case anyone else has such a problem, quotes are required around the class. bless $fpc_map "Extended::FPC"; Nancy Hansen wrote: > > > You're right that your Extended::FPC should inherit from > Bio::Map::Physical, but you really don't want to use it to parse the fpc > file (Bio::MapIO does that just fine, and gets all the data you need into > the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical > object using Bio::MapIO, then forcing it to be an Extended::FPC, which > will allow it to use your method(s): > > my $mapio = Bio::MapIO->new(-format => 'fpc', > -file => $ARGV[0], > -readcor => 1); > > my $fpc_map = $mapio->next_map(); > > bless $fpc_map, Extended::FPC; > my $ra_bands = $fpc_map->my_new_extended_method(); > -- ><)))?> -cGRASP- <?(((>< Keith Anthony Boroevich Simon Fraser University Tel: 604-268-7276 From pmiguel at purdue.edu Wed Nov 15 12:00:50 2006 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 15 Nov 2006 12:00:50 -0500 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <455B47C2.8020400@purdue.edu> Sayali wrote: > I wish to fetch consensus sequence and the names of the trace (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar > Hi Sayali, I don't think there is a pre-rolled bioperl method to do what you ask. (But it seems like one is under construction?) You can extract the contig sequences from a phrap .ace file with the following plain perl code: my $print_it = 0; while (<>){ $print_it = /^CO / ? 1 : /^$/ ? 0 : $print_it ; s/^CO />/; s/\*//g; #removes "pads"--optional print if $print_it; } To find the reads that went into each contig, you do *not* want the BS tagged records. My understanding is that BS is just what consed uses to populate its consensus line from the ace file. The simplest way is: egrep '^CO|AF' acefilename if you are on a unix system. Or with perl while (<>) { print if (/^CO|AF/); } -- Phillip Purdue Genomics Core Facility From cjfields at uiuc.edu Wed Nov 15 12:00:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:00:05 -0600 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> > I wish to fetch consensus sequence and the names of the trace > (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to > find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read > phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus > position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar It looks like the relevant part of the Bio::Assembly::IO::ace parser responsible for parsing this is commented out: # Loading base segments definitions (Base Segment field) # /^BS (\d+) (\d+) (\S+)/ && do { # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} {'segments'})) { # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . " " . $2; # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = $1 . " " . $2 } # }; I'm not sure why to be honest as I'm not very familiar with the Bio::Assembly. Have you tried removing the comments to see what happens? You could file a bug report noting this using Bugzilla: http://bugzilla.open-bio.org/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 12:00:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:00:05 -0600 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> > I wish to fetch consensus sequence and the names of the trace > (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to > find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read > phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus > position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar It looks like the relevant part of the Bio::Assembly::IO::ace parser responsible for parsing this is commented out: # Loading base segments definitions (Base Segment field) # /^BS (\d+) (\d+) (\S+)/ && do { # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} {'segments'})) { # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . " " . $2; # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = $1 . " " . $2 } # }; I'm not sure why to be honest as I'm not very familiar with the Bio::Assembly. Have you tried removing the comments to see what happens? You could file a bug report noting this using Bugzilla: http://bugzilla.open-bio.org/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 12:37:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:37:35 -0600 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> References: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Message-ID: <D7DFA98D-2107-4C4C-9BBA-8B029DD9CC41@uiuc.edu> On Nov 15, 2006, at 9:52 AM, Nancy Hansen wrote: > Keith Anthony Boroevich wrote: >> >> I am using an up-to-date bioperl-live. The precise code is >> insignificant so I wrote some additional (shorter) code to attempt to >> explain my problem. What I want to do is the following. I want >> to add >> some functionality to the Bio::Map::Physical module so i created a >> module that inherits Physical module, Extended::FPC.pm. >> >> #----Test.pl-BEGIN---# >> use strict; >> use diagnostics; >> use Extended::FPC; >> my $mapio = new Extended::FPC(-format => "fpc",-file => >> $ARGV[0],-readcor => 1); >> my $map = $mapio->next_map(); >> $map->fpc_test(); >> exit 0; >> #---Test.pl-END------# > > You're right that your Extended::FPC should inherit from > Bio::Map::Physical, but you really don't want to use it to parse > the fpc > file (Bio::MapIO does that just fine, and gets all the data you > need into > the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical > object using Bio::MapIO, then forcing it to be an Extended::FPC, which > will allow it to use your method(s): > > my $mapio = Bio::MapIO->new(-format => 'fpc', > -file => $ARGV[0], > -readcor => 1); > > my $fpc_map = $mapio->next_map(); > > bless $fpc_map, Extended::FPC; > my $ra_bands = $fpc_map->my_new_extended_method(); > > I've actually written my own method to return the band sizes as > well, so > it would probably make a good enhancement to Bio::Map::Physical, which > already has a "matching_bands" method that returns the (scalar) > number of > bands that match at a given tolerance. If that method were > "enhanced" to > return an array of matching band sizes rather than the scalar > number of > bands, it would still return the number in scalar context, but give > you > the matching band info in list context. I'd be happy to submit a > patch > for this if others think it's backwardly-compatible enough. > > --Nancy Keith, Nancy, Sendu Bala has taken over maintenance of the Bio::Map modules. I have cc'd him this in case he has missed it (he's in the middle of getting a bioperl developer release put together). In general we are more than happy to take new modules and patches for current ones. There is a HOWTO on submitting patches and new code: http://www.bioperl.org/wiki/HOWTO:SubmitPatch If you plan on submitting a patch, you should also consider adding some tests as well. I think the relevant tests for Bio::Map modules are in t/Map.t and t/MapIO.t. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 13:15:48 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 18:15:48 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> Message-ID: <455B5954.1080209@sendu.me.uk> Chris Fields wrote: > On Nov 10, 2006, at 10:16 AM, Stefan Kirov wrote: > >> I personally like the idea. Why not have both for this release to >> ensure smooth transition? Sendu, would having Makefile.PL (I mean >> the old one) along with the build script be a problem? [snip] > Sounds like a good compromise to me. Like I said, the only problem I > had is introducing something drastically new after three RCs (and > just prior to a final release; I think Sendu wanted to release the > final 1.5.2 next week, just before Thanksgiving here.). There is no > problem though if we have the old Makefile.PL to fall back to for > this release. In fact, you could remove it from HEAD when needed; > the file still exists on the 1.5.2 branch, right? I think the compromise isn't worth it. The old Makefile.PL is just too inadequate and I don't want to support it. Build.pl is simply far too superior and I really want all users to be using it. I've now made the changeover in HEAD for core only (so far). Can people please try it out, especially wrt to installation in default and user-specified locations? First, clean out your system of the old Makefile.PL stuff: perl Makefile.PL make clean rm Makefile.PL Makefile.old cvs update -d -P Now try out the new Build.PL: perl Build.PL ./Build test ./Build install Try out other things: http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm You'll notice you don't have a Makefile.PL anymore. Distributions will include one, and as a cvs user you can generate one by: ./Build manifest ./Build distmeta Now you can try out the things you used to be able to do: make test make install Please let me know how you get on, Sendu. From bosborne11 at verizon.net Wed Nov 15 13:33:06 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 13:33:06 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> Message-ID: <C180C792.B596%bosborne11@verizon.net> Sendu, I see: 175 ~/bioperl-live>perl Build.PL Checking prerequisites... ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Which is incorrect since there no "modules indicated above". Brian O. On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Please let me know how you get on, From gcarbajosa at cnio.es Wed Nov 15 12:43:10 2006 From: gcarbajosa at cnio.es (guillermo) Date: Wed, 15 Nov 2006 18:43:10 +0100 Subject: [Bioperl-l] Fwd: Error while indexing whole genbank Message-ID: <68874599fabff74a65fcc62568022288@cnio.es> Hello, I just indexed BCT without problems and now I am going to do it in parts, different indexes for each one, for PLN, PRI, ROD, etc. Anyways, I??l try to do it for the whole genbank and if it works I?ll let you know. Thanks for the support, Guille Inicio mensaje reenviado: > De: guillermo <gcarbajosa at cnio.es> > Fecha: 14 de noviembre de 2006 11:39:41 GMT+01:00 > Para: bioperl-l at bioperl.org > Asunto: Error while indexing whole genbank > > Hello, > > I am trying to index the whole of genbank nucleotide (release number > 156, October 15 2006), with the script (which uses > Bio::Index::GenBank) that is attached at the end of this message the > process crashes with this error message: > > sdbm store returned -1, errno 9, key "BF460808" at > /usr/local/lib/perl5/site_perl/5.8.8/Bio/Index/Abstract.pm line 714, > <GenBank> line 164732819. > > why could this be? > > Thanks, > Guillermo > > > #!/usr/local/bin/perl -w > > # Perl pragma to restrict unsafe constructs > use strict; > > # Issue warnings about suspicious programming. > use warnings; > > # Use the code module that contains BioPerl Services. > use Bio::Index::GenBank; # Use to index GenBank file > use Bio::SeqIO; > > # be prepare for command-line options/arguments > use Getopt::Std; > > sub help { > return<<"END_HELP"; > Description: Make index from GenBank database > Usage: > > createGenBankIndex.pl -d {index file} -g {GenBank database} > -d path and file name of index database > -g GenBank database path > > END_HELP > > } > > > BEGIN { > > # Determines the options with values from program > use vars qw/$opt_d $opt_g/; > > # these are switches taking an argument (a value) > my $switches = 'dg'; > > # Get the switches > getopt($switches); > > # If the user does not write nothing, skip to help > unless (defined($opt_d) || defined($opt_g)){ > print help; > exit 0; > } > > } > > ####################################################################### > ######## > # > # DESCRIPTION: The next program creates an BioPerl index aside GenBank > database. > # > # INPUT (BY CONSOLE): - (-d) Path where the Uniprot index is going to > store. > # - (-g) Path where GenBank database is located > # > # OUTPUT: - O => The program has finished sucessfully > # - 1 => Some of database files has not founded > # - 2 => There was an error while the process was running > # > # AUTHOR: Jos?? Manuel Rodr??guez Carrasco -jmrc at cnb.uam.es- (INB-CNB) > ####################################################################### > ######## > > > # Check if the path of GenBank database is able to read > unless (-f $opt_g && -r $opt_g) { > > # The GenBank database has not been found > print "Error of createGenBankIndex program: The GenBank database has > not been found\n"; > > # Return an error > exit 1; > } > > > # Store the database paths > my @DBList = ($opt_g); > > # Create new instance to index file. It is used the option > my $indexSW = Bio::Index::GenBank->new ('-filename' => $opt_d, > '-write_flag' => 1); > > # Make the index > my $numFiles = $indexSW->make_index(@DBList); > > # Check how many databases have been indexed > if ($numFiles == 1) { > > # There has been not exist error. > print "\nThe creation of GenBank index has been executed > successfully\n"; > exit 0; > > > } else { > > # There has been exist an process error > print "\nThere was a problem while the creation of GenBank index was > running\n"; > exit 2; > } > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3585 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061115/64a3cab3/attachment.bin From cain at cshl.edu Wed Nov 15 12:45:52 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 15 Nov 2006 12:45:52 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <000001c708d2$97c9d610$15327e82@pyrimidine> References: <000001c708d2$97c9d610$15327e82@pyrimidine> Message-ID: <1163612752.2599.2.camel@localhost.localdomain> I didn't even know those files were in the repository. I suspect they are leftovers from original Bio::DB::GFF development. Given that the last time they were touched was over five years ago, and neither GBrowse nor any other GMOD project use them (that I know of), I think they can be safely removed. Scott On Wed, 2006-11-15 at 10:24 -0600, Chris Fields wrote: > > Does anyone know what purpose Bio/DB/Makefile.PL serves? If > > none, I propose removing it from CVS. > > > > Dave: Do you need anything to happen with > > doc/Deobfuscator/Makefile.PL when a user does a normal > > install of Bioperl? Or can it safely be ignored, only run > > manually by people who want to install Deobfuscator? > > The Bio/DB/Makefile.PL and MANIFEST could be GMOD- or Chado-related (they > are both related to Bio::DB::GFF). I'm not sure though; I'm cc'ing this to > Lincoln to see if they are still needed. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061115/e5f0620c/attachment.bin From pabignone at gmail.com Wed Nov 15 09:51:43 2006 From: pabignone at gmail.com (Paola Bignone) Date: Wed, 15 Nov 2006 14:51:43 +0000 Subject: [Bioperl-l] reverse complement - and features Message-ID: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Hi all, do you know of an easy way to reverse complement the sequence of an embl entry and the features associated with that sequence. I'm looking at genomic syntenic regions, and in some organisms the gene is in the plus strand while in others is in the minus. Thanks in advance, PAB From cjfields at uiuc.edu Wed Nov 15 14:16:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:16:34 -0600 Subject: [Bioperl-l] Fwd: Error while indexing whole genbank In-Reply-To: <68874599fabff74a65fcc62568022288@cnio.es> References: <68874599fabff74a65fcc62568022288@cnio.es> Message-ID: <E99B3889-1800-4A69-9F40-FEED774FD653@uiuc.edu> On Nov 15, 2006, at 11:43 AM, guillermo wrote: > Hello, > > I just indexed BCT without problems and now I am going to do it in > parts, different indexes for each one, for PLN, PRI, ROD, etc. > Anyways, I??l try to do it for the whole genbank and if it works I > ?ll let you know. > > Thanks for the support, > Guille My guess is that the full genbank file was way too large, so breaking them up by division is probably the way to go. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 14:18:18 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:18:18 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> <455B5954.1080209@sendu.me.uk> Message-ID: <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> On Nov 15, 2006, at 12:15 PM, Sendu Bala wrote: > ... > I think the compromise isn't worth it. The old Makefile.PL is just too > inadequate and I don't want to support it. Build.pl is simply far too > superior and I really want all users to be using it. > > I've now made the changeover in HEAD for core only (so far). > > Can people please try it out, especially wrt to installation in > default > and user-specified locations? > > First, clean out your system of the old Makefile.PL stuff: > perl Makefile.PL > make clean > rm Makefile.PL Makefile.old > cvs update -d -P > > Now try out the new Build.PL: > perl Build.PL > ./Build test > ./Build install > > Try out other things: > http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm > > You'll notice you don't have a Makefile.PL anymore. Distributions will > include one, and as a cvs user you can generate one by: > ./Build manifest > ./Build distmeta > > Now you can try out the things you used to be able to do: > make test > make install > > > Please let me know how you get on, > Sendu. Will do. We'll need to change all docs in CVS/wiki to conform with the new install routine. You'll probably want to post another interim RC before a final release just to make sure any residual bugs are worked out, unless you are just doing this in CVS HEAD. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 14:22:08 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:22:08 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> <455B5954.1080209@sendu.me.uk> <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> Message-ID: <455B68E0.9090308@sendu.me.uk> Chris Fields wrote: > Will do. We'll need to change all docs in CVS/wiki to conform with the > new install routine. You'll probably want to post another interim RC > before a final release just to make sure any residual bugs are worked > out, unless you are just doing this in CVS HEAD. There needs to be another RC for 1.5.2 for the remaining run package problems, so what I'll do is wait a little while longer for Build.PL feedback and when all seems well it'll go into 1.5.2 branch and become part of RC4. From bix at sendu.me.uk Wed Nov 15 14:33:33 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:33:33 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <OFAAF39FAB.9EB9DA23-ON85257227.00675002-85257227.00676C9E@gsk.com> References: <OFAAF39FAB.9EB9DA23-ON85257227.00675002-85257227.00676C9E@gsk.com> Message-ID: <455B6B8D.30508@sendu.me.uk> Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: > What actual needs prompted the change from ExtUtils::MakeMaker to > Module::Build? For the old Makefile.PL: At the time I started, script installation was broken. Documentation installation hasn't worked in a very long time. Handling of true requirements and optional pre-requisites is completely inadequate. It can't generate a suitable META.yml, and leaves the package non-ideal for distribution on CPAN. It was also a nightmare keeping the Makefile.PL scripts in each cvs module (live, run, db, network) in sync with each other. Now they can have simple module-specific Build.PL scripts, with all the advanced functionality in a rarely-updated and unchanged-between-modules ModuleBuildBioperl.pm. > It seems that the switch was made without a complete understanding of > all the bits and bobs in the existing Makefile.PL I hope that's not the case; I tried to understand everything. Please let me know if I've missed something. (To tidy up a question I asked about the symlink script, I've resolved that and the symlink should also work given the proviso outlined in the POD for maintenance/symlink_script.pl) > For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered > by the main Makefile.PL) such that users can choose whether to test > the install vs. a live database or not. The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such functionality. Letting the user choose to do live database tests was a function of the main Makefile.PL, which I have carried over to the new Build.PL. (And made it better in the process.) > This is an example of encapsulation: the specializied testing/install > process for a module is kept with the module, and not in the > monolithic main script. From a maintenance point of view, it seems to me to be much easier if all install-related things are in one place rather than scattered where you might miss things. > For two, it seems that the ability to install bp_*.pl scripts was > "lost" in the transition. What makes you say that? It certainly shouldn't be. What should happen is you get asked what scripts you'd like to install (the same question as before), but again its done in a much nicer way. (The major difference, I suppose, is that scripts_temp is no longer generated; prior to "./Build install" you'll find the scripts in blib/script/) > For three, there's certainly a lot more that I can't remember right > now. Please try and remember. I spent a lot of time trying to make sure that Build.PL does everything Makefile.PL did, but much much better. Thank you, Sendu. From bix at sendu.me.uk Wed Nov 15 14:09:01 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:09:01 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180CA3A.B599%bosborne11@verizon.net> References: <C180CA3A.B599%bosborne11@verizon.net> Message-ID: <455B65CD.3020400@sendu.me.uk> Brian Osborne wrote: > Sendu, > > 177 ~/bioperl-live>./Build test > scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Can't copy('scripts/utilities/bp_sreformat.PLS', > 'blib/script/bp_sreformat.PLS'): Permission denied at > /Library/Perl/5.8.6/Module/Build/Base.pm line 3977. That's an odd one. Did you first start out with a clean bioperl-live (ie. one without a blib directory made by something else)? Is it consistent? If you run ./Build test again, does it keep happening? Does blib/script/bp_sreformat.PLS exist and what are its permissions? Did it manage to put anything at all in blib? Is ~/bioperl-live writable? From bix at sendu.me.uk Wed Nov 15 14:09:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:09:41 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <455B65F5.1030207@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > > Which is incorrect since there no "modules indicated above". Thanks, I'll look into it. Just to confirm, do you suppose that you have all pre-reqs installed? From cjfields at uiuc.edu Wed Nov 15 14:36:11 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:36:11 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <0FCFCA18-8FDC-4463-BF3B-1586145743CE@uiuc.edu> On Nov 15, 2006, at 12:33 PM, Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this > installation > > > Which is incorrect since there no "modules indicated above". > > > Brian O. > > > On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > >> Please let me know how you get on, Same here (Mac OS X). All tests pass, though (setting BIOPERLDEBUG=1): All tests successful, 6 subtests skipped. Files=236, Tests=12817, 398 wallclock secs (86.03 cusr + 14.12 csys = 100.15 CPU) I'll give WinXP a test to see how it fares. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Wed Nov 15 11:44:19 2006 From: jason at bioperl.org (Jason Stajich) Date: Wed, 15 Nov 2006 08:44:19 -0800 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> Message-ID: <1965DDC8-DC2E-4895-A6C9-BD7A15FACDF1@bioperl.org> On Nov 15, 2006, at 7:35 AM, Sendu Bala wrote: > Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I > propose removing it from CVS. this was from when Lincoln imported Bio::DB::GFF into Bioperl from a separate code base. I don't know that it serves any purpose but I would get an okay from Lincoln first. > > Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL > when a user does a normal install of Bioperl? Or can it safely be > ignored, only run manually by people who want to install Deobfuscator? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From bosborne11 at verizon.net Wed Nov 15 13:44:26 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 13:44:26 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> Message-ID: <C180CA3A.B599%bosborne11@verizon.net> Sendu, 177 ~/bioperl-live>./Build test scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Can't copy('scripts/utilities/bp_sreformat.PLS', 'blib/script/bp_sreformat.PLS'): Permission denied at /Library/Perl/5.8.6/Module/Build/Base.pm line 3977. Brian O. On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Please let me know how you get on, From bix at sendu.me.uk Wed Nov 15 15:20:26 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 20:20:26 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <455B768A.8060009@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > > Which is incorrect since there no "modules indicated above". Should be fixed now. From bix at sendu.me.uk Wed Nov 15 15:23:22 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 20:23:22 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C180E071.B5B0%bosborne11@verizon.net> References: <C180E071.B5B0%bosborne11@verizon.net> Message-ID: <455B773A.5080608@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I just looked at the most recent bioperl-db and bioperl-run, I don't see any > Build.pl there. Are you suggesting that the Bioperl core build should be > mediated by Build.pl yet all other packages are built by some Makefile.PL? No, once it seems like Build.PL is ok in core, I'll convert db, run and network over to it as well. From bosborne11 at verizon.net Wed Nov 15 14:24:12 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 14:24:12 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B65F5.1030207@sendu.me.uk> Message-ID: <C180D38C.B5A4%bosborne11@verizon.net> Sendu, According to my install of 1.5.2 RC3 I have all of the dependencies installed: *** Optional dependencies section *** All dependencies are installed So that line "ERRORS/WARNINGS FOUND IN PREREQUISITES.." shouldn't appear. Brian O. On 11/15/06 2:09 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Brian Osborne wrote: >> Sendu, >> >> I see: >> >> 175 ~/bioperl-live>perl Build.PL >> Checking prerequisites... >> >> ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the >> versions >> of the modules indicated above before proceeding with this installation >> >> >> Which is incorrect since there no "modules indicated above". > > Thanks, I'll look into it. Just to confirm, do you suppose that you have > all pre-reqs installed? From cjfields at uiuc.edu Wed Nov 15 15:52:23 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 14:52:23 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B68E0.9090308@sendu.me.uk> Message-ID: <001601c708f7$f441dd50$15327e82@pyrimidine> > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Sendu Bala > Sent: Wednesday, November 15, 2006 1:22 PM > To: bioperl-l > Subject: Re: [Bioperl-l] No more Makefile.PL (MakeMaker -> > Module::Build) > > Chris Fields wrote: > > Will do. We'll need to change all docs in CVS/wiki to conform with > > the new install routine. You'll probably want to post > another interim > > RC before a final release just to make sure any residual bugs are > > worked out, unless you are just doing this in CVS HEAD. > > There needs to be another RC for 1.5.2 for the remaining run > package problems, so what I'll do is wait a little while > longer for Build.PL feedback and when all seems well it'll go > into 1.5.2 branch and become part of RC4. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l All tests pass for WinXP. If anyone wants to install from CVS using WinXP we'll need to get them to install Module::Build, as it doesn't come standard with ActivePerl (although a PPM is available). I'm guessing make/nmake is still required, though not explicitly. One oddity I noticed is if you use: perl Build.PL Build On Mac it manifies the POD; on WinXP it manify's and HTMLifies the POD. No idea why there is a difference between the two. I would suggest that we make this optional, though; not everybody wants the HTML/man pages. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 16:10:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 21:10:27 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <001601c708f7$f441dd50$15327e82@pyrimidine> References: <001601c708f7$f441dd50$15327e82@pyrimidine> Message-ID: <455B8243.4080809@sendu.me.uk> Chris Fields wrote: > All tests pass for WinXP. If anyone wants to install from CVS using > WinXP we'll need to get them to install Module::Build, as it doesn't > come standard with ActivePerl (although a PPM is available). I'm > guessing make/nmake is still required, though not explicitly. I think one of the benefits of Module::Build is that it is more cross-platform, and doesn't rely on a make-like thing. If you tried to install without Module::Build on WinXP, did you get some kind of meaningful error message? > One oddity I noticed is if you use: > > perl Build.PL Build > > On Mac it manifies the POD; on WinXP it manify's and HTMLifies the > POD. Nothing to do with me. I guess WinXP people like HTML docs :) > I would suggest that we make this optional, though; not everybody > wants the HTML/man pages. I disagree with making it optional, default off. I've never been aware of having the option to not install man pages for things that had man pages to install. It just happens and I'm glad of it. Its telling that there doesn't seem to be command line arg to turn doc installation off in Module::Build. Its a new functionality I'd have to add, I think. Is there actually any significant value in not installing docs? From bosborne11 at verizon.net Wed Nov 15 15:19:13 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 15:19:13 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <C180E071.B5B0%bosborne11@verizon.net> Sendu, I just looked at the most recent bioperl-db and bioperl-run, I don't see any Build.pl there. Are you suggesting that the Bioperl core build should be mediated by Build.pl yet all other packages are built by some Makefile.PL? Brian O. On 11/15/06 2:33 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: >> What actual needs prompted the change from ExtUtils::MakeMaker to >> Module::Build? > > For the old Makefile.PL: > At the time I started, script installation was broken. Documentation > installation hasn't worked in a very long time. Handling of true > requirements and optional pre-requisites is completely inadequate. It > can't generate a suitable META.yml, and leaves the package non-ideal for > distribution on CPAN. > > It was also a nightmare keeping the Makefile.PL scripts in each cvs > module (live, run, db, network) in sync with each other. Now they can > have simple module-specific Build.PL scripts, with all the advanced > functionality in a rarely-updated and unchanged-between-modules > ModuleBuildBioperl.pm. > > >> It seems that the switch was made without a complete understanding of >> all the bits and bobs in the existing Makefile.PL > > I hope that's not the case; I tried to understand everything. Please let > me know if I've missed something. (To tidy up a question I asked about > the symlink script, I've resolved that and the symlink should also work > given the proviso outlined in the POD for maintenance/symlink_script.pl) > > >> For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered >> by the main Makefile.PL) such that users can choose whether to test >> the install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such > functionality. Letting the user choose to do live database tests was a > function of the main Makefile.PL, which I have carried over to the new > Build.PL. (And made it better in the process.) > > >> This is an example of encapsulation: the specializied testing/install >> process for a module is kept with the module, and not in the >> monolithic main script. > > From a maintenance point of view, it seems to me to be much easier if > all install-related things are in one place rather than scattered where > you might miss things. > > >> For two, it seems that the ability to install bp_*.pl scripts was >> "lost" in the transition. > > What makes you say that? It certainly shouldn't be. What should happen > is you get asked what scripts you'd like to install (the same question > as before), but again its done in a much nicer way. > > (The major difference, I suppose, is that scripts_temp is no longer > generated; prior to "./Build install" you'll find the scripts in > blib/script/) > > >> For three, there's certainly a lot more that I can't remember right >> now. > > Please try and remember. I spent a lot of time trying to make sure that > Build.PL does everything Makefile.PL did, but much much better. > > > Thank you, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From aaron.j.mackey at gsk.com Wed Nov 15 13:29:30 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Wed, 15 Nov 2006 13:29:30 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" Message-ID: <OFE989A597.3219BF40-ON85257227.0064E293-85257227.00659451@gsk.com> What actual needs prompted the change from ExtUtils::MakeMaker to Module::Build? It seems that the switch was made without a complete understanding of all the bits and bobs in the existing Makefile.PL For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered by the main Makefile.PL) such that users can choose whether to test the install vs. a live database or not. This is an example of encapsulation: the specializied testing/install process for a module is kept with the module, and not in the monolithic main script. For two, it seems that the ability to install bp_*.pl scripts was "lost" in the transition. For three, there's certainly a lot more that I can't remember right now. I know Module::Build is shiny and new and preferred for startup development projects, but that cruddy old Makefile.PL still works, and does a number of clever things that do have reasons for existence, even if the collective wit of the mailing list can't remember all of them right away. -Aaron -- Aaron J. Mackey, Ph.D. Principal Scientist Bioinformatics Discovery & Analysis, Upper Providence GlaxoSmithKline 1250 South Collegeville Road, UP1345 P.O. Box 5089 Collegeville, PA 19426-0989 phone: 610-917-5761/8-282-5761 fax: 610-917-7901 email: Aaron.J.Mackey at gsk.com From bix at sendu.me.uk Wed Nov 15 16:28:30 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 21:28:30 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C180E8B3.B5B6%bosborne11@verizon.net> References: <C180E8B3.B5B6%bosborne11@verizon.net> Message-ID: <455B867E.8010001@sendu.me.uk> Brian Osborne wrote: > Sendu, > > One problem here, as I see it, is the fact that this change has been > introduced just days before the intended release. My intent is to go to RC4 instead, which pushes release a week or two away. God knows I wanted to release over a month ago, but I'm a perfectionist. > http://www.bioperl.org/wiki/Release_1.5.2 > > You won't find any mention of changing the build there, nor of Build.pl, or > Module::Build. This page is a nice example of "best practice", where > everything about the release is lined up and laid out, and making a big > change at the last minute is not best practice. Now, has Bioperl always made > a big deal out of best practice? No, but that's what's been nice about this > particular release so far, an emphasis on doing things correctly. This is assuredly all valid. But I feel this is a case of a necessary last minute addition. Necessary because I don't feel the old Makefile.PL is up to the job. Its merely unfortunate that I only discovered this so late into the RC cycle. Evidently I and all the other testers don't test the installation side of things, only the test scripts in t/. > Also, I understand that you think that your approach is better but such a > central change can't be adopted without discussion and some semblance of > consensus. So far I'm not getting any sense that anyone is agreeing with the > change but I am sensing discomfort with the idea, or resignation. I asked for comments and discussions 5 days ago. The only responses were positive or neutral (with reservations regarding putting it into 1.5.2, but not for the idea itself). If you don't press on and make things happen after positive feedback, nothing will ever get done at all. So to clarify, is anyone actually uncomfortable or 'resigned' to the idea? Does anyone feel strongly in favour of keeping Makefile.PL? > I have no strong opinion one way or another, Makefile or Build, but I do not > want to see significant changes at the last minute and I do not want > significant changes coming unilaterally. I agree. But again, I'm even less happy with the idea of releasing something that I know is inadequate simply because I discovered that too late. From cjfields at uiuc.edu Wed Nov 15 17:33:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 16:33:26 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <001901c70906$1441aa50$15327e82@pyrimidine> > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: .... > > For one, the Bio::DB::GFF Makefile.PL is independent (yet > triggered by > > the main Makefile.PL) such that users can choose whether to > test the > > install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves > no such functionality. Letting the user choose to do live > database tests was a function of the main Makefile.PL, which > I have carried over to the new Build.PL. (And made it better > in the process.) Scott Cain also indicated the Bio/DB Makefile.PL and MANIFEST files were not used anymore. ... > > For three, there's certainly a lot more that I can't remember right > > now. > > Please try and remember. I spent a lot of time trying to make > sure that Build.PL does everything Makefile.PL did, but much > much better. > > > Thank you, > Sendu. We can always reinstate the Makefile.PL if things blow up; I don't think they will, but that's what CVS is good for. I haven't had any problems on WinXP or Mac OS X yet beyond the pre-req error message Brian pointed out (and scripts seem to install fine on both OS's). Personally, I would have liked to wait until after the 1.5.2 final release to avoid any confusion and documentation changes, but that's not my call. We do need to let Scott and Lincoln in on these changes (they only know about the removal of the Bio/DB Makefile.PL). I think various install scripts look for a Makefile.PL, so if it isn't there things will tank on their end. We also need to post this everywhere possible in very big neon-colored letters (with fireworks and so on), since most users are used to 'perl Makefile.PL; make; make install'. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From pabignone at gmail.com Wed Nov 15 09:51:43 2006 From: pabignone at gmail.com (Paola Bignone) Date: Wed, 15 Nov 2006 14:51:43 +0000 Subject: [Bioperl-l] reverse complement - and features Message-ID: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Hi all, do you know of an easy way to reverse complement the sequence of an embl entry and the features associated with that sequence. I'm looking at genomic syntenic regions, and in some organisms the gene is in the plus strand while in others is in the minus. Thanks in advance, PAB From bix at sendu.me.uk Wed Nov 15 18:08:00 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:08:00 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c70906$1441aa50$15327e82@pyrimidine> References: <001901c70906$1441aa50$15327e82@pyrimidine> Message-ID: <455B9DD0.5000409@sendu.me.uk> Chris Fields wrote: > > We do need to let Scott and Lincoln in on these changes (they only know > about the removal of the Bio/DB Makefile.PL). I think various install > scripts look for a Makefile.PL, so if it isn't there things will tank on > their end. We also need to post this everywhere possible in very big > neon-colored letters (with fireworks and so on), since most users are used > to 'perl Makefile.PL; make; make install'. It doesn't need to be neon because most users will still be able to do exactly that; Makefile.PL will be part of the distributions (having been generated by Build.PL). For most people, there's not going to be any significant difference with this change. It'll be more like a behind-the-scenes thing. From lincoln.stein at gmail.com Wed Nov 15 17:43:21 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 15 Nov 2006 17:43:21 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B867E.8010001@sendu.me.uk> References: <C180E8B3.B5B6%bosborne11@verizon.net> <455B867E.8010001@sendu.me.uk> Message-ID: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> > > This is assuredly all valid. But I feel this is a case of a necessary > last minute addition. Necessary because I don't feel the old Makefile.PL > is up to the job. Its merely unfortunate that I only discovered this so > late into the RC cycle. Evidently I and all the other testers don't test > the installation side of things, only the test scripts in t/ > I tested script installation last week and it was all fine as far as I could tell. Are there any details about how installation was failing? Lincoln > Also, I understand that you think that your approach is better but such a > > central change can't be adopted without discussion and some semblance of > > consensus. So far I'm not getting any sense that anyone is agreeing with > the > > change but I am sensing discomfort with the idea, or resignation. > > I asked for comments and discussions 5 days ago. The only responses were > positive or neutral (with reservations regarding putting it into 1.5.2, > but not for the idea itself). If you don't press on and make things > happen after positive feedback, nothing will ever get done at all. Sorry, but I didn't see the discussion. So to clarify, is anyone actually uncomfortable or 'resigned' to the > idea? Does anyone feel strongly in favour of keeping Makefile.PL? I'm sorry we have to push the release back. I was unaware that Makefile.PLwas broken -- my preference would have been to fix it rather than to rewrite things from scratch. Lincoln > I have no strong opinion one way or another, Makefile or Build, but I do > not > > want to see significant changes at the last minute and I do not want > > significant changes coming unilaterally. > > I agree. But again, I'm even less happy with the idea of releasing > something that I know is inadequate simply because I discovered that too > late. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Wed Nov 15 17:31:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 16:31:56 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B8243.4080809@sendu.me.uk> Message-ID: <001801c70905$dbdd7a40$15327e82@pyrimidine> > Chris Fields wrote: > > All tests pass for WinXP. If anyone wants to install from > CVS using > > WinXP we'll need to get them to install Module::Build, as > it doesn't > > come standard with ActivePerl (although a PPM is available). I'm > > guessing make/nmake is still required, though not explicitly. > > I think one of the benefits of Module::Build is that it is > more cross-platform, and doesn't rely on a make-like thing. > > If you tried to install without Module::Build on WinXP, did > you get some kind of meaningful error message? Yes: C:\Perl\src\bioperl\core>perl Build.PL Base class package "Module::Build" is empty. (Perhaps you need to 'use' the module which defines that package first.) at ModuleBuildBioperl.pm line 12 BEGIN failed--compilation aborted at ModuleBuildBioperl.pm line 12. Compilation failed in require at Build.PL line 16. BEGIN failed--compilation aborted at Build.PL line 16. Which clued me in immediately. > > One oddity I noticed is if you use: > > > > perl Build.PL Build > > > > On Mac it manifies the POD; on WinXP it manify's and HTMLifies the > > POD. > > Nothing to do with me. I guess WinXP people like HTML docs :) > > > > I would suggest that we make this optional, though; not everybody > > wants the HTML/man pages. > > I disagree with making it optional, default off. I've never > been aware of having the option to not install man pages for > things that had man pages to install. It just happens and I'm > glad of it. > > Its telling that there doesn't seem to be command line arg to > turn doc installation off in Module::Build. Its a new > functionality I'd have to add, I think. Is there actually any > significant value in not installing docs? HTML docs are made by PPM upon module installation, so there is no need for making HTML at least on WinXP (and the conversion almost triples the time for the Build step). However, oddly, using 'Build test' only manifies the docs on WinXP (using 'Build' does both man and HTML). I have a feeling we will run into this very rarely (the average WinXP user will install using PPM), so it's not an immediate problem. I would like to hear what Mauricio finds on FreeBSD and see how other OS's fare. I see that there is a PPMMaker module with Module::Build, so we'll have to look into that for WinXP PPMs.. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 18:19:47 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:19:47 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> References: <C180E8B3.B5B6%bosborne11@verizon.net> <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> Message-ID: <455BA093.8040603@sendu.me.uk> Lincoln Stein wrote: > Sendu Bala wrote: > This is assuredly all valid. But I feel this is a case of a necessary > last minute addition. Necessary because I don't feel the old Makefile.PL > is up to the job. Its merely unfortunate that I only discovered this so > late into the RC cycle. Evidently I and all the other testers don't test > the installation side of things, only the test scripts in t/ > > I tested script installation last week and it was all fine as far as I > could tell. Are there any details about how installation was failing? Maybe this aspect got broken since after you tested (I don't think so though, judging by the fix), but scripts only got put in scripts_temp and nowhere else. The major prompt for the change was needing a complete META.yml for CPAN... > So to clarify, is anyone actually uncomfortable or 'resigned' to the > idea? Does anyone feel strongly in favour of keeping Makefile.PL? > > I'm sorry we have to push the release back. I was unaware that > Makefile.PL was broken -- my preference would have been to fix it rather > than to rewrite things from scratch. ... I'd have had to do far more rewriting things from scratch to get a complete META.yml out of Makefile.PL. I didn't want to reinvent the wheel, and Module::Build has lots of other benefits as well. I'd already done major adjustments to Makefile.PL previously; the move to Build.PL can be seen as just one more major behind-the-scenes adjustment, since Makefile.PL will still exist in distributions (having been generated by Build.PL) and people can still install the same way they have done in the past. The only real change for most users is that they now need Module::Build installed. From bix at sendu.me.uk Wed Nov 15 18:57:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:57:14 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810D8A.B5D0%bosborne11@verizon.net> References: <C1810D8A.B5D0%bosborne11@verizon.net> Message-ID: <455BA95A.5040404@sendu.me.uk> Brian Osborne wrote: > Sendu, > > This is not right. I just removed all the build stuff, Makefile* and Build*, > and did an update. There's no Makefile.PL, it's not part of the > distribution, there is Build.PL. As I mentioned in the other thread, Makefile.PL isn't in CVS, but it will be generated and included in distributions (ie. in .tar.gz file that you download from the website or via CPAN). As a CVS user you can generate one for yourself by: perl Build.PL ./Build manifest ./Build distmeta You should now have Makefile.PL on which you can do the usual stuff: perl Makefile.PL make make test make install From bosborne11 at verizon.net Wed Nov 15 15:54:27 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 15:54:27 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <C180E8B3.B5B6%bosborne11@verizon.net> Sendu, One problem here, as I see it, is the fact that this change has been introduced just days before the intended release. Take a look at the page that's supposed to describe 1.5.2 and associated work: http://www.bioperl.org/wiki/Release_1.5.2 You won't find any mention of changing the build there, nor of Build.pl, or Module::Build. This page is a nice example of "best practice", where everything about the release is lined up and laid out, and making a big change at the last minute is not best practice. Now, has Bioperl always made a big deal out of best practice? No, but that's what's been nice about this particular release so far, an emphasis on doing things correctly. That, and having enough people to do the work! Also, I understand that you think that your approach is better but such a central change can't be adopted without discussion and some semblance of consensus. So far I'm not getting any sense that anyone is agreeing with the change but I am sensing discomfort with the idea, or resignation. I have no strong opinion one way or another, Makefile or Build, but I do not want to see significant changes at the last minute and I do not want significant changes coming unilaterally. Brian O. On 11/15/06 2:33 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: >> What actual needs prompted the change from ExtUtils::MakeMaker to >> Module::Build? > > For the old Makefile.PL: > At the time I started, script installation was broken. Documentation > installation hasn't worked in a very long time. Handling of true > requirements and optional pre-requisites is completely inadequate. It > can't generate a suitable META.yml, and leaves the package non-ideal for > distribution on CPAN. > > It was also a nightmare keeping the Makefile.PL scripts in each cvs > module (live, run, db, network) in sync with each other. Now they can > have simple module-specific Build.PL scripts, with all the advanced > functionality in a rarely-updated and unchanged-between-modules > ModuleBuildBioperl.pm. > > >> It seems that the switch was made without a complete understanding of >> all the bits and bobs in the existing Makefile.PL > > I hope that's not the case; I tried to understand everything. Please let > me know if I've missed something. (To tidy up a question I asked about > the symlink script, I've resolved that and the symlink should also work > given the proviso outlined in the POD for maintenance/symlink_script.pl) > > >> For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered >> by the main Makefile.PL) such that users can choose whether to test >> the install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such > functionality. Letting the user choose to do live database tests was a > function of the main Makefile.PL, which I have carried over to the new > Build.PL. (And made it better in the process.) > > >> This is an example of encapsulation: the specializied testing/install >> process for a module is kept with the module, and not in the >> monolithic main script. > > From a maintenance point of view, it seems to me to be much easier if > all install-related things are in one place rather than scattered where > you might miss things. > > >> For two, it seems that the ability to install bp_*.pl scripts was >> "lost" in the transition. > > What makes you say that? It certainly shouldn't be. What should happen > is you get asked what scripts you'd like to install (the same question > as before), but again its done in a much nicer way. > > (The major difference, I suppose, is that scripts_temp is no longer > generated; prior to "./Build install" you'll find the scripts in > blib/script/) > > >> For three, there's certainly a lot more that I can't remember right >> now. > > Please try and remember. I spent a lot of time trying to make sure that > Build.PL does everything Makefile.PL did, but much much better. > > > Thank you, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Wed Nov 15 18:59:19 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:59:19 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810E20.B5D2%bosborne11@verizon.net> References: <C1810E20.B5D2%bosborne11@verizon.net> Message-ID: <455BA9D7.6020906@sendu.me.uk> Brian Osborne wrote: > Lincoln, > > All I know was the scripts weren't being installed, I fixed this by adding > "use IO::File" to Makefile.PL. Sendu mentioned a problem with documentation, > I don't know what he meant by this. 'man' docs weren't being generated/installed apparently due to some kind of issue with command line length. That's been a long-standing issue. From cjfields at uiuc.edu Wed Nov 15 19:01:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 18:01:57 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810D8A.B5D0%bosborne11@verizon.net> Message-ID: <001d01c70912$723c8a60$15327e82@pyrimidine> Brian, I think he means the actual releases or the 1.5.2 branch, not CVS. Sendu, I am seeing a general consensus towards not using Module::Build just now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar and I also had stated previously that this should probably wait until after 1.5.2 (which you seemed to agree with). I think we are all for the idea of moving forward, but it's a lot to impose just prior to a release (not to mention Thanksgiving here!). I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we should stick with that for now (i.e. not change over to Module::Build on the 1.5.2 branch). The install script fix that Brian committed to Makefile.PL in CVS HEAD prior to removal could be merged to branch-1.5.2. We could leave the Module::Build stuff in CVS for the next release to work out the bugs. I'm not sure whether we can have both Build.PL and Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl Build.PL' just overwrite the old Makefile.PL anyway? chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign > -----Original Message----- > From: Brian Osborne [mailto:bosborne11 at verizon.net] > Sent: Wednesday, November 15, 2006 5:32 PM > To: Sendu Bala; Chris Fields > Cc: aaron.j.mackey at gsk.com; bioperl-l > Subject: Re: [Bioperl-l] "progress": useful changes vs. > "shiny new thingie" > > Sendu, > > This is not right. I just removed all the build stuff, > Makefile* and Build*, and did an update. There's no > Makefile.PL, it's not part of the distribution, there is Build.PL. > > Brian O. > > > On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > > > exactly that; Makefile.PL will be part of the distributions (having > > been generated by Build.PL). > > From bix at sendu.me.uk Wed Nov 15 19:27:31 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 00:27:31 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001d01c70912$723c8a60$15327e82@pyrimidine> References: <001d01c70912$723c8a60$15327e82@pyrimidine> Message-ID: <455BB073.9040205@sendu.me.uk> Chris Fields wrote: > Brian, > > I think he means the actual releases or the 1.5.2 branch, not CVS. > > Sendu, I am seeing a general consensus towards not using Module::Build just > now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar and I also > had stated previously that this should probably wait until after 1.5.2 > (which you seemed to agree with). I think we are all for the idea of moving > forward, but it's a lot to impose just prior to a release (not to mention > Thanksgiving here!). > > I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we > should stick with that for now (i.e. not change over to Module::Build on the > 1.5.2 branch). The install script fix that Brian committed to Makefile.PL > in CVS HEAD prior to removal could be merged to branch-1.5.2. Its certainly possible to stay with Makefile.PL on the 1.5.2 branch. I /think/ that if I took a META.yml generated from HEAD's Build.PL and added it to the branch that should solve the CPAN issue at least. I would just want clarification that the consensus really is to stay with Makefile.PL for 1.5.2. The primary argument seems to be to not have anything too new and untested in the branch, but Makefile.PL itself has lots of new additions. My Makefile.PL improvements and the change to Build.PL have all been in the name of making 1.5.2 install well. The move to Build.PL was just the most appropriate way to fix some bugs and make needed changes. > We could leave the Module::Build stuff in CVS for the next release to work > out the bugs. I'm not sure whether we can have both Build.PL and > Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl Build.PL' > just overwrite the old Makefile.PL anyway? It would, but why would we want both in CVS? I'd strongly advise the cessation of development on the old Makefile.PL, and if it isn't going to be added to anymore, nor used by anyone, why keep it in CVS? It's just going to cause confusion and problems with people coming across issues in the old Makefile.PL. Wasted development time if someone tries to fix something in Makefile.PL that was already solved in Build.PL. Bizarre behaviour if you were doing something with old Makefile.PL but then managed to overwrite it with Build.PL's Makefile.PL and suddenly you're working with a whole different script. In short, not the most optimal of situations. From bosborne11 at verizon.net Wed Nov 15 18:31:38 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 18:31:38 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B9DD0.5000409@sendu.me.uk> Message-ID: <C1810D8A.B5D0%bosborne11@verizon.net> Sendu, This is not right. I just removed all the build stuff, Makefile* and Build*, and did an update. There's no Makefile.PL, it's not part of the distribution, there is Build.PL. Brian O. On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > exactly that; Makefile.PL will be part of the distributions (having been > generated by Build.PL). From bosborne11 at verizon.net Wed Nov 15 18:34:08 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 18:34:08 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> Message-ID: <C1810E20.B5D2%bosborne11@verizon.net> Lincoln, All I know was the scripts weren't being installed, I fixed this by adding "use IO::File" to Makefile.PL. Sendu mentioned a problem with documentation, I don't know what he meant by this. Brian O. On 11/15/06 5:43 PM, "Lincoln Stein" <lincoln.stein at gmail.com> wrote: > I tested script installation last week and it was all fine as far as I could > tell. Are there any details about how installation was failing? From bosborne11 at verizon.net Wed Nov 15 20:43:32 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 20:43:32 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BA95A.5040404@sendu.me.uk> Message-ID: <C1812C74.B5E3%bosborne11@verizon.net> Sendu, If I'm understanding you correctly you're saying that someone checking out bioperl-live, HEAD, would not see a Makefile.PL if we chose to use Build.PL, yes? And there would be a Makefile.PL in the distributions, yes? Brian O. On 11/15/06 6:57 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Brian Osborne wrote: >> Sendu, >> >> This is not right. I just removed all the build stuff, Makefile* and Build*, >> and did an update. There's no Makefile.PL, it's not part of the >> distribution, there is Build.PL. > > As I mentioned in the other thread, Makefile.PL isn't in CVS, but it > will be generated and included in distributions (ie. in .tar.gz file > that you download from the website or via CPAN). > > As a CVS user you can generate one for yourself by: > perl Build.PL > ./Build manifest > ./Build distmeta > > You should now have Makefile.PL on which you can do the usual stuff: > perl Makefile.PL > make > make test > make install From stefan.kirov at bms.com Wed Nov 15 19:34:02 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Wed, 15 Nov 2006 19:34:02 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" Message-ID: <db32bddda3.ddda3db32b@bms.com> Maybe I will just reiterate myself. I think the idea is good, but timing is bad. Sendu, from purely socialogical point of view Makefile.PL should be there. I bet that significant percent of the users would do cvs checkout, type perl Makefile.PL and start cursing. Perhaps you would not do this, but many of us do not read most of the docs, unless nothing else works. As a result you would have confusion and frustration. Many people would google 'bioperl install' and come up with old docs and wonder why it does not work. In a perfect world it would work. Just my thoughts. Stefan ----- Original Message ----- From: Chris Fields <cjfields at uiuc.edu> Date: Wednesday, November 15, 2006 7:01 pm Subject: Re: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" > Brian, > > I think he means the actual releases or the 1.5.2 branch, not CVS. > > Sendu, I am seeing a general consensus towards not using > Module::Build just > now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar > and I also > had stated previously that this should probably wait until after 1.5.2 > (which you seemed to agree with). I think we are all for the idea > of moving > forward, but it's a lot to impose just prior to a release (not to > mentionThanksgiving here!). > > I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we > should stick with that for now (i.e. not change over to > Module::Build on the > 1.5.2 branch). The install script fix that Brian committed to > Makefile.PLin CVS HEAD prior to removal could be merged to branch- > 1.5.2. > > We could leave the Module::Build stuff in CVS for the next release > to work > out the bugs. I'm not sure whether we can have both Build.PL and > Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl > Build.PL'just overwrite the old Makefile.PL anyway? > > chris > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > -----Original Message----- > > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > Sent: Wednesday, November 15, 2006 5:32 PM > > To: Sendu Bala; Chris Fields > > Cc: aaron.j.mackey at gsk.com; bioperl-l > > Subject: Re: [Bioperl-l] "progress": useful changes vs. > > "shiny new thingie" > > > > Sendu, > > > > This is not right. I just removed all the build stuff, > > Makefile* and Build*, and did an update. There's no > > Makefile.PL, it's not part of the distribution, there is Build.PL. > > > > Brian O. > > > > > > On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > > > > > exactly that; Makefile.PL will be part of the distributions > (having > > > been generated by Build.PL). > > > > > > _______________________________________________ > 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 Nov 15 20:48:43 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 20:48:43 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> Message-ID: <C1812DAB.B5E5%bosborne11@verizon.net> Sendu, That's right. Brian O. On 11/15/06 7:27 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. From joannec at bii.a-star.edu.sg Wed Nov 15 21:11:31 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 02:11:31 +0000 (UTC) Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations Message-ID: <loom.20061116T030106-109@post.gmane.org> Hi, I am a new user to BioPerl and am encountering some problems while parsing location statements. I have read the link http://www.bioperl.org/wiki/FAQ#How_do_I_parse_the_CDS_join_or_complement_statements_in_GenBank_or_EMBL_files_to_get_the_sub-locations.3F and tried to implement this. However I am encountering some problems. Given a testcase: CDS join(752472..752685,752752..753298,753335..754039) CDS complement(637431..639525) CDS 741745..741781 This means that my file has join, complement and simple location statements. Using Bio::Location::SplitLocationI object to get the coordinates, my output is: CDS 752472..752685,752752..753298,753335..754039 CDS CDS The complement and simple location statements were not parsed properly. Am I using the right BioPerl module to parse? Kindly assist on the appropriate steps to retrieve all 3 different location types. Thanks! Joanne From cjfields at uiuc.edu Wed Nov 15 21:33:25 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 20:33:25 -0600 Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations In-Reply-To: <loom.20061116T030106-109@post.gmane.org> References: <loom.20061116T030106-109@post.gmane.org> Message-ID: <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> On Nov 15, 2006, at 8:11 PM, Joanne Chen wrote: > Hi, > I am a new user to BioPerl and am encountering some problems while > parsing > location statements. > > I have read the link > http://www.bioperl.org/wiki/ > FAQ#How_do_I_parse_the_CDS_join_or_complement_statements_in_GenBank_or > _EMBL_files_to_get_the_sub-locations.3F > and tried to implement this. > > However I am encountering some problems. > > Given a testcase: > > CDS join(752472..752685,752752..753298,753335..754039) > > > CDS complement(637431..639525) > > > CDS 741745..741781 > > > This means that my file has join, complement and simple location > statements. > > Using Bio::Location::SplitLocationI object to get the coordinates, > my output is: > > CDS 752472..752685,752752..753298,753335..754039 > > CDS > > CDS > > > The complement and simple location statements were not parsed > properly. Am I > using the right BioPerl module to parse? Kindly assist on the > appropriate steps > to retrieve all 3 different location types. Thanks! > > > Joanne > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l If you are using the loop as shown in the FAQ: foreach my $feature ($seqobj->top_SeqFeatures){ if ( $feature->location->isa('Bio::Location::SplitLocationI') and $feature->primary_tag eq 'CDS' ) { foreach my $location ( $feature->location->sub_Location ) { print $location->start , ".." , $location->end, "\n"; } } } it will skip over simple locations, so the last two are passed over. You probably should use: foreach my $feature ($seqobj->top_SeqFeatures){ if ( $feature->primary_tag eq 'CDS' ) { foreach my $location ( $feature->location->each_Location ) { print $location->start , ".." , $location->end, "\n"; } } } Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 21:44:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 20:44:05 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> Message-ID: <DEAB987E-4700-4677-979B-E5708F6905D3@uiuc.edu> On Nov 15, 2006, at 6:27 PM, Sendu Bala wrote: >> I think the old Makefile.PL is still in the 1.5.2 branch. So >> maybe we >> should stick with that for now (i.e. not change over to >> Module::Build on the >> 1.5.2 branch). The install script fix that Brian committed to >> Makefile.PL >> in CVS HEAD prior to removal could be merged to branch-1.5.2. > > Its certainly possible to stay with Makefile.PL on the 1.5.2 branch. I > /think/ that if I took a META.yml generated from HEAD's Build.PL and > added it to the branch that should solve the CPAN issue at least. > > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. The primary argument seems to be to not > have > anything too new and untested in the branch, but Makefile.PL itself > has > lots of new additions. My Makefile.PL improvements and the change to > Build.PL have all been in the name of making 1.5.2 install well. The > move to Build.PL was just the most appropriate way to fix some bugs > and > make needed changes. Right, but those changes were made w/o much discussion; what discussion there was seemed to end with the agreement this would wait until after rel. 1.5.2. I think that's the main point. That and the timing seems to be a little off for implementing this (after three RC's and just prior to a final release). Everyone seems to think that switching to Module::Build would be a good idea, but the move was made rather arbitrarily and (borrowing Brian's well-chosen word) unilaterally. And, although the Makefile.PL was a bit clunky, it works for now. >> We could leave the Module::Build stuff in CVS for the next release >> to work >> out the bugs. I'm not sure whether we can have both Build.PL and >> Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl >> Build.PL' >> just overwrite the old Makefile.PL anyway? > > It would, but why would we want both in CVS? I'd strongly advise the > cessation of development on the old Makefile.PL, and if it isn't going > to be added to anymore, nor used by anyone, why keep it in CVS? It's > just going to cause confusion and problems with people coming across > issues in the old Makefile.PL. Wasted development time if someone > tries > to fix something in Makefile.PL that was already solved in Build.PL. > Bizarre behaviour if you were doing something with old Makefile.PL but > then managed to overwrite it with Build.PL's Makefile.PL and suddenly > you're working with a whole different script. > > In short, not the most optimal of situations. Stefan has hit upon the problem very succinctly; there is no Makefile.PL in CVS, so anyone checking out bioperl-live will immediately run into problems. Hence, there has to be a Makefile.PL in CVS HEAD, be it the old one or a new one, at least for the time being. And it seems many still want the old Makefile.PL for now (which is why I suggested it). If you left the old Makefile.PL in you could always add a deprecation message indicating the switch. It will at least give everybody some time to get used to using Module::Build and the new system (and hopefully dissuade them from working on it). Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From joannec at bii.a-star.edu.sg Wed Nov 15 22:17:27 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 03:17:27 +0000 (UTC) Subject: [Bioperl-l] =?utf-8?q?Parsing_the_CDS_join_or_complement_statemen?= =?utf-8?q?ts_to=09get_the_sub-locations?= References: <loom.20061116T030106-109@post.gmane.org> <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> Message-ID: <loom.20061116T041551-540@post.gmane.org> Thanks a lot for your help. It works. =) However I have a small problem. Now I would also like to determine its strand-ie. negative strand for complement and positive for all others. Is there a function to determine and print its strand OR a function to determine if it is a complement, join or simple? Joanne. From pmiguel at purdue.edu Wed Nov 15 22:53:02 2006 From: pmiguel at purdue.edu (Phillip SanMiguel) Date: Wed, 15 Nov 2006 22:53:02 -0500 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> Message-ID: <455BE09E.4020408@purdue.edu> Chris Fields wrote: >> I wish to fetch consensus sequence and the names of the trace >> (chromat) >> files used in the assembly from the .ace file >> >> For this purpose, I am using Bio::Assembly::IO. But I am unable to >> find the >> appropriate methods which would enable me to fetch this information. >> >> >> >> [..base segment documentation elided...] >> >> >> How do I retrieve this information contig wise? >> >> Kindly help. >> >> Regards, >> >> Sayali D Salodkar >> > > It looks like the relevant part of the Bio::Assembly::IO::ace parser > responsible for parsing this is commented out: > > # Loading base segments definitions (Base Segment field) > # /^BS (\d+) (\d+) (\S+)/ && do { > # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} > {'segments'})) { > # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . > " " . $2; > # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = > $1 . " " . $2 } > # }; > > I'm not sure why to be honest as I'm not very familiar with the > Bio::Assembly. Have you tried removing the comments to see what > happens? > > Chris, I'm pretty sure that the Base Segment tag (BS) is not the one Sayali wants. At least that is my reading of Sayali's wanting to get the consensus sequence and the traces names used in the assembly. I write this because of an email sent me by David Gordon in 2001 included here without his permission: > Phrap writes BS lines which > indicate, for each consensus position, which read phrap uses at that > position to become the consensus. These BS ("base segments") are > manipulated by Consed when there are changes to the assembly, such as > joins, tears, removing reads, or changing the consensus. Which is basically what Sayali quoted from the documentation from phrap. But it is not consistent with "trace names used in the assembly". -- Phillip From hlapp at gmx.net Thu Nov 16 00:52:23 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Nov 2006 00:52:23 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> Message-ID: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. The primary argument seems to be to not > have > anything too new and untested in the branch, but Makefile.PL itself > has > lots of new additions. My Makefile.PL improvements and the change to > Build.PL have all been in the name of making 1.5.2 install well. The > move to Build.PL was just the most appropriate way to fix some bugs > and > make needed changes. My take on this, aside from having said before that the move to Module::Build is certainly a good one except with not-so-great timing, is that the distribution if at all possible should have a working Makefile.PL. If Build.PL can coexist that'd be great. That would give you the opportunity to have Makefile.PL print out a message right at the beginning that if the installation process messes up one should try Build.PL. This would spare you from fixing any problems in Makefile.PL that are fixed in the Build.PL approach. As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub that just prints out a message telling you to use Build.PL and does nothing else. If you check out bioperl-live from CVS you need to be prepared to having checked out the live edge of the code. Edges can be rough. The key thing is that the build process works. Finally let's not forget that this is still a developer release. That means that a) perfection isn't needed, rather shorter release cycles, and b) development implies change. So the main reason why I find the timing less than optimal is because it prolongs the time until the next release. Implementing changes like this do require a lot of energy. I very much appreciate that Sendu invested the time and energy to make it work, even though unfortunately at the last hour. Who knows who would have had the energy after the release. If Sendu hadn't put in the work now, the next release master may have been stuck with an even messier Makefile.PL system. Instead of Monday morning quarterbacking after no-one stopped him when he asked about it, we should all help him make the release - and the build change - successful now that he has done most if not all of the migration work already. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Thu Nov 16 02:47:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 07:47:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1812C74.B5E3%bosborne11@verizon.net> References: <C1812C74.B5E3%bosborne11@verizon.net> Message-ID: <455C1790.3080408@sendu.me.uk> Brian Osborne wrote: > Sendu, > > If I'm understanding you correctly you're saying that someone checking out > bioperl-live, HEAD, would not see a Makefile.PL if we chose to use Build.PL, > yes? And there would be a Makefile.PL in the distributions, yes? Yes, that is what I had meant. Though now following Hilmar's suggestion, I might create a stub in CVS for Makefile.PL that tells you to use Build.PL. I don't think it appropriate to have a working Makefile.PL in CVS though; not the old one for reasons outlined previously, and not one generated by Build.PL, because generated files don't need version control and only confuse matters when they become controlled. Ok, so the current plan is: # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml # CVS core gets a Makefile.PL stub telling you to use Build.PL # CVS db, run, network stay with Makefile.PL until after final release of 1.5.2, then move to Build.PL with Makefile.PL stub (because they don't have a 1.5.2 branch) Is everyone happy with that, or are there further suggestions for something better? From joannec at bii.a-star.edu.sg Thu Nov 16 02:55:22 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 07:55:22 +0000 (UTC) Subject: [Bioperl-l] =?utf-8?q?Parsing_the_CDS_join_or_complement_statemen?= =?utf-8?q?ts_to=09get_the_sub-locations?= References: <loom.20061116T030106-109@post.gmane.org> <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> <loom.20061116T041551-540@post.gmane.org> Message-ID: <loom.20061116T085446-347@post.gmane.org> Got the strand problem fixed. Thanks. =) From bix at sendu.me.uk Thu Nov 16 02:55:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 07:55:41 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C1790.3080408@sendu.me.uk> References: <C1812C74.B5E3%bosborne11@verizon.net> <455C1790.3080408@sendu.me.uk> Message-ID: <455C197D.6000107@sendu.me.uk> Sendu Bala wrote: > Brian Osborne wrote: >> Sendu, >> >> If I'm understanding you correctly you're saying that someone checking >> out >> bioperl-live, HEAD, would not see a Makefile.PL if we chose to use >> Build.PL, >> yes? And there would be a Makefile.PL in the distributions, yes? > > Yes, that is what I had meant. Though now following Hilmar's suggestion, > I might create a stub in CVS for Makefile.PL that tells you to use > Build.PL. I don't think it appropriate to have a working Makefile.PL in > CVS though; not the old one for reasons outlined previously, and not one > generated by Build.PL, because generated files don't need version > control and only confuse matters when they become controlled. > > Ok, so the current plan is: > # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml Also, # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who read the docs on the website/elsewhere (which will be updated to explain the new Build.PL system) don't get confused when that doesn't work, for wide testing, and to get people used to it for the next release. The old Makefile.PL will have 2 changes: Brians bug-fix and a little message pointing out that Build.PL is now the preferred installation system, but Makefile.PL still works. > # CVS core gets a Makefile.PL stub telling you to use Build.PL > # CVS db, run, network stay with Makefile.PL until after final release > of 1.5.2, then move to Build.PL with Makefile.PL stub (because they > don't have a 1.5.2 branch) > > Is everyone happy with that, or are there further suggestions for > something better? From rvosa at sfu.ca Thu Nov 16 02:19:43 2006 From: rvosa at sfu.ca (Rutger Vos) Date: Wed, 15 Nov 2006 23:19:43 -0800 Subject: [Bioperl-l] indexing with several processors In-Reply-To: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> References: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> Message-ID: <455C110F.4000600@sfu.ca> I notice nobody has responded yet. Without looking at the code I'm guessing here, but I would be very surprised if any part of bioperl is smart enough to be able to switch to some kind of mpi architecture, or any other clever way of parallelizing tasks on multi-processor architectures. If you can split the job up by hand and start scripts on the chunks, that might work. Good luck, Rutger guillermo wrote: > Hello, > > While using the Bio::Index::GenBank module for indexing Genbank, is > there any option to run the process with more than one processor. > > Thanks > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los > ficheros adjuntos, pueden contener informaci?n protegida para el uso > exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n > o cualquier otro tipo de transmisi?n por parte de otra persona que no > sea el destinatario. Si usted recibe por error este correo, se ruega > comunicarlo al remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any > attachments may contain confidential and privileged information for > the sole use of the designated recipient named above. Distribution, > reproduction or any other use of this transmission by any party other > than the intended recipient is prohibited. If you are not the intended > recipient please contact the sender and delete all copies. > > ------------------------------------------------------------------------ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > ------------------------------------------------------------------------ > > No virus found in this incoming message. > Checked by AVG Free Edition. > Version: 7.1.409 / Virus Database: 268.14.5/534 - Release Date: 11/14/2006 > -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Rutger A. Vos Postdoctoral research fellow University of British Columbia Personal site: http://www.sfu.ca/~rvosa CIPRES: http://www.phylo.org Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From n.haigh at sheffield.ac.uk Thu Nov 16 04:14:52 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 09:14:52 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> Message-ID: <455C2C0C.1080403@sheffield.ac.uk> Hilmar Lapp wrote: > On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > > >> I would just want clarification that the consensus really is to stay >> with Makefile.PL for 1.5.2. The primary argument seems to be to not >> have >> anything too new and untested in the branch, but Makefile.PL itself >> has >> lots of new additions. My Makefile.PL improvements and the change to >> Build.PL have all been in the name of making 1.5.2 install well. The >> move to Build.PL was just the most appropriate way to fix some bugs >> and >> make needed changes. >> > > My take on this, aside from having said before that the move to > Module::Build is certainly a good one except with not-so-great > timing, is that the distribution if at all possible should have a > working Makefile.PL. > I was in the process of writing a rather long e-mail to try to stem the tide of Sendu-bashing :-P But, this response serves as a better platform for my comments. I don't see the change to Build.PL as an issue - especially if we have another RC. I think it would be worse to introduce Build.PL in the "stable" 1.6 release than in the 1.5.x developer series. I think one good reason for using Build.PL when Sendu brought the issue up, is that it is more important as far as building a package for CPAN rather than an end user - and since Sendu is the release pumpkin he is the one with the strongest opinion for changing it now, rather than later - it would make his job much easier! I believe Sendu mentioned that a Makefile.PL would be included in the CPAN package but is not in CVS as it would be generated from Build.PL for backward compatibility - is that right Sendu? How does installing via CPAN affect this? Does it give higher priority to Build.PL over Makefile.PL and thus use Build.PL for the install? > If Build.PL can coexist that'd be great. That would give you the > opportunity to have Makefile.PL print out a message right at the > beginning that if the installation process messes up one should try > Build.PL. This would spare you from fixing any problems in > Makefile.PL that are fixed in the Build.PL approach. > Good idea, for anyone downloading the .tar.gz from CPAN if they issue "perl Makefile.PL" without knowing Build.PL was there it should hopefully work, but if not, issue a comment at the end to say try "perl Build.PL" if anything seemed to go wrong. > As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub > that just prints out a message telling you to use Build.PL and does > nothing else. If you check out bioperl-live from CVS you need to be > prepared to having checked out the live edge of the code. Edges can > be rough. The key thing is that the build process works. > I was going to suggest something like this with regard to a Makefile.PL in CVS. This would then be overwritten by the Makefile.PL produced from Build.PL by the release pumpkin when making the CPAN package. > Finally let's not forget that this is still a developer release. That > means that a) perfection isn't needed, rather shorter release cycles, > and b) development implies change. So the main reason why I find the > timing less than optimal is because it prolongs the time until the > next release. > If we go for short release cycles, and regular bug fix release, we will no longer have to say to users: "This is a known bug/issue in release x.y.z, it has been fixed in CVS HEAD so get it from there" we can roll out fixes in regular releases. This way CVS is then used solely by developers and those really wanting to live on the bleeding edge code. Therefore, it is important to get Build.PL in place to let the release cycle and CPAN packages built quickly, easily and without hassle - which I believe is the problem with Makefile.PL as it currently is. > Implementing changes like this do require a lot of energy. I very > much appreciate that Sendu invested the time and energy to make it > work, even though unfortunately at the last hour. Who knows who would > have had the energy after the release. If Sendu hadn't put in the > work now, the next release master may have been stuck with an even > messier Makefile.PL system. Instead of Monday morning quarterbacking > after no-one stopped him when he asked about it, we should all help > him make the release - and the build change - successful now that he > has done most if not all of the migration work already. > > -hilmar > Hear, hear - well done Sendu on all your hard work! Personally, I think the move to Build.PL is a good one - it may be a little late in this particular release, but I think that the problem is not that it is a late change, but that it wasn't picked up sooner. It fits well with the goal of making releases and big fix releases more regular, and if these are made available via CPAN, then the use of CVS is for developers and those wanting to live on the edge. Build.PL helps all this by making is easier and quicker to make CPAN packages. It also means we have a while before the "stable" 1.6 release to ensure it is working effectively - better than dropping it in on the 1.6 release isn't it? I think it's work the delay and an extra RC! Anyway, my 2 pence worth! Nath From n.haigh at sheffield.ac.uk Thu Nov 16 04:04:00 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 09:04:00 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> Message-ID: <455C2980.4000609@sheffield.ac.uk> Hilmar Lapp wrote: > On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > > >> I would just want clarification that the consensus really is to stay >> with Makefile.PL for 1.5.2. The primary argument seems to be to not >> have >> anything too new and untested in the branch, but Makefile.PL itself >> has >> lots of new additions. My Makefile.PL improvements and the change to >> Build.PL have all been in the name of making 1.5.2 install well. The >> move to Build.PL was just the most appropriate way to fix some bugs >> and >> make needed changes. >> > > My take on this, aside from having said before that the move to > Module::Build is certainly a good one except with not-so-great > timing, is that the distribution if at all possible should have a > working Makefile.PL. > I was in the process of writing a rather long e-mail to try to stem the tide of Sendu-bashing :-P But, this response serves as a better platform for my comments. I don't see the change to Build.PL as an issue - especially if we have another RC. I think it would be worse to introduce Build.PL in the "stable" 1.6 release than in the 1.5.x developer series. I think one good reason for using Build.PL when Sendu brought the issue up, is that it is more important as far as building a package for CPAN rather than an end user - and since Sendu is the release pumpkin he is the one with the strongest opinion for changing it now, rather than later - it would make his job much easier! I believe Sendu mentioned that a Makefile.PL would be included in the CPAN package but is not in CVS as it would be generated from Build.PL for backward compatibility - is that right Sendu? How does installing via CPAN affect this? Does it give higher priority to Build.PL over Makefile.PL and thus use Build.PL for the install? > If Build.PL can coexist that'd be great. That would give you the > opportunity to have Makefile.PL print out a message right at the > beginning that if the installation process messes up one should try > Build.PL. This would spare you from fixing any problems in > Makefile.PL that are fixed in the Build.PL approach. > Good idea, for anyone downloading the .tar.gz from CPAN if they issue "perl Makefile.PL" without knowing Build.PL was there it should hopefully work, but if not, issue a comment at the end to say try "perl Build.PL" if anything seemed to go wrong. > As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub > that just prints out a message telling you to use Build.PL and does > nothing else. If you check out bioperl-live from CVS you need to be > prepared to having checked out the live edge of the code. Edges can > be rough. The key thing is that the build process works. > I was going to suggest something like this with regard to a Makefile.PL in CVS. This would then be overwritten by the Makefile.PL produced from Build.PL by the release pumpkin when making the CPAN package. > Finally let's not forget that this is still a developer release. That > means that a) perfection isn't needed, rather shorter release cycles, > and b) development implies change. So the main reason why I find the > timing less than optimal is because it prolongs the time until the > next release. > If we go for short release cycles, and regular bug fix release, we will no longer have to say to users: "This is a known bug/issue in release x.y.z, it has been fixed in CVS HEAD so get it from there" we can roll out fixes in regular releases. This way CVS is then used solely by developers and those really wanting to live on the bleeding edge code. Therefore, it is important to get Build.PL in place to let the release cycle and CPAN packages built quickly, easily and without hassle - which I believe is the problem with Makefile.PL as it currently is. > Implementing changes like this do require a lot of energy. I very > much appreciate that Sendu invested the time and energy to make it > work, even though unfortunately at the last hour. Who knows who would > have had the energy after the release. If Sendu hadn't put in the > work now, the next release master may have been stuck with an even > messier Makefile.PL system. Instead of Monday morning quarterbacking > after no-one stopped him when he asked about it, we should all help > him make the release - and the build change - successful now that he > has done most if not all of the migration work already. > > -hilmar > Here, here - well done Sendu on all your hard work! Personally, I think the move to Build.PL is a good one - it may be a little late in this particular release, but I think that the problem is not that it is a late change, but that it wasn't picked up sooner. It fits well with the goal of making releases and big fix releases more regular, and if these are made available via CPAN, then the use of CVS is for developers and those wanting to live on the edge. Build.PL helps all this by making is easier and quicker to make CPAN packages. It also means we have a while before the "stable" 1.6 release to ensure it is working effectively - better than dropping it in on the 1.6 release isn't it? I think it's work the delay and an extra RC! Anyway, my 2 pence worth! Nath -- > A: Yes. >> Q: Are you sure? >> >>> A: Because it reverses the logical flow of conversation. >>> >>>> Q: Why is top posting frowned upon? >>>> Get Thunderbird <http://www.mozilla.org/products/thunderbird/> From bix at sendu.me.uk Thu Nov 16 04:26:45 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 09:26:45 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2C0C.1080403@sheffield.ac.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> <455C2C0C.1080403@sheffield.ac.uk> Message-ID: <455C2ED5.4060602@sendu.me.uk> Nathan S. Haigh wrote: > I believe Sendu mentioned that a Makefile.PL would be included in the > CPAN package but is not in CVS as it would be generated from > Build.PL for backward compatibility - is that right Sendu? Yes. > How does installing via CPAN affect this? Does it give higher > priority to Build.PL over Makefile.PL and thus use Build.PL for the > install? I don't know about priorities (but assume it would prefer Build.PL), but in any case, the generated Makefile.PL basically just calls Build.PL, so it makes no difference. > Build.PL helps all this by making is easier and quicker to make CPAN > packages. It also means we have a while before the "stable" 1.6 > release to ensure it is working effectively - better than dropping it > in on the 1.6 release isn't it? I think it's work the delay and an > extra RC! Yes, it surely needs to happen before 1.6. As suggested here and originally in the other thread, 1.5.2 can be the transition release with old Makefile.PL and Build.PL as well (set up to not overwrite Makefile.PL). From bix at sendu.me.uk Thu Nov 16 06:35:25 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 11:35:25 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <001801c70905$dbdd7a40$15327e82@pyrimidine> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> Message-ID: <455C4CFD.5080005@sendu.me.uk> Chris Fields wrote: > I see that there is a PPMMaker module with Module::Build, so we'll have to > look into that for WinXP PPMs.. Nathan, does: perl Build.PL ./Build ppmdist create anything useful? For me it generates a tar.gz containing blib, and a ppd file (the contents of which can be adjusted by supplying "an optional argument codebase which is used in the generated ppd file to specify the (usually relative) URL of the distribution. By default, this value is the distribution name without any path information", eg. ./Build ppmdist --codebase "MSWin32-x86-multi-thread/Bioperl....tar.gz"). Is this PPM4 format? What else needs to be done to it to make it suitable? I can easily extend the ppmdist action to do whatever you want, so let me know. From bix at sendu.me.uk Thu Nov 16 06:45:03 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 11:45:03 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <45531968.6080607@sendu.me.uk> References: <45531968.6080607@sendu.me.uk> Message-ID: <455C4F3F.1090901@sendu.me.uk> Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Developers: > Once again I'm hopeful that this is the last RC. If all goes well > expect final release in about a weeks time. Please check and update > documentation. Sadly all didn't go well. Some remaining bugs are present in the Run package which are now being worked on (there was also a WinXP core bug already fixed by Chris). Expect RC4 sometime this week, which will also include a transitional Build.PL as an alternative to installing with Makefile.PL. From bikash_lohia2000 at yahoo.com Thu Nov 16 07:30:04 2006 From: bikash_lohia2000 at yahoo.com (bikash lohia) Date: Thu, 16 Nov 2006 04:30:04 -0800 (PST) Subject: [Bioperl-l] i am new to group, require a help Message-ID: <20061116123004.87840.qmail@web54213.mail.yahoo.com> hello group, I am new to this group and want a help.i have list of accesion id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to manually search gene database of NCBI for converting this accession no. of cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i want to do it through perl programming where the program directly takes the list of id ( such as AK105331,Ak070197) from notepad file and searches in gene database of ncbi. to give results in accession id starting with OS****** .i want only the accession id of corresponding Ak***** id. for example - AK070197 of nucleotide databse = Os02g0669100 of gene database. i want to convert all this AK***** ids to OS***** ids through programming in perl/bioperl as manually not possible for long list. please help. i have no idea how can the code be. with thanks in advance from Bikash --------------------------------- Sponsored Link Degrees for working adults in as fast as 1 year. Bachelors, Masters, Associates. Top schools From n.haigh at sheffield.ac.uk Thu Nov 16 07:45:14 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 12:45:14 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C4CFD.5080005@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> Message-ID: <455C5D5A.5020205@sheffield.ac.uk> Sendu Bala wrote: > Chris Fields wrote: >> I see that there is a PPMMaker module with Module::Build, so we'll >> have to >> look into that for WinXP PPMs.. > > Nathan, does: > > perl Build.PL > ./Build ppmdist > > create anything useful? For me it generates a tar.gz containing blib, > and a ppd file (the contents of which can be adjusted by supplying "an > optional argument codebase which is used in the generated ppd file to > specify the (usually relative) URL of the distribution. By default, > this value is the distribution name without any path information", eg. > ./Build ppmdist --codebase "MSWin32-x86-multi-thread/Bioperl....tar.gz"). > > Is this PPM4 format? What else needs to be done to it to make it > suitable? I can easily extend the ppmdist action to do whatever you > want, so let me know. Sorry, but i've been busy this last week etc so haven't be able to test RC3 on WinXP yet - hopefully Chris' tests have been sufficient. Essentially a PPM dist comprises of the .tar.gz file you described (of the blib dir) and then the XML file (.ppd) which describes the package and it's dependencies. The syntax of the XML has changed for PPM4 (which required me to do these changes by hand on the ppd that was previously output by "make ppd". For PPM4 the XML in the ppd file can be copied over to packages.xml file in our PPM repository. the codebase URL can be relative/absolute and it's exact value depends on the relative position of the XML (whether in the .ppd or package.xml file) and the .tar.gz file. Thus, by default, they would have to reside in the same dir on our server. Without looking at the XML I couldn't say if it was PPM3 or PPM4 compatible. Could you e-mail me the ppd file and I'll take a look. Cheers Nath From cjfields at uiuc.edu Thu Nov 16 07:45:13 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 06:45:13 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C197D.6000107@sendu.me.uk> References: <C1812C74.B5E3%bosborne11@verizon.net> <455C1790.3080408@sendu.me.uk> <455C197D.6000107@sendu.me.uk> Message-ID: <F9D837E4-4614-4905-A171-9738ED1D01D8@uiuc.edu> On Nov 16, 2006, at 1:55 AM, Sendu Bala wrote: ... > Also, > # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who > read the docs on the website/elsewhere (which will be updated to > explain > the new Build.PL system) don't get confused when that doesn't work, > for wide testing, and to get people used to it for the next > release. The > old Makefile.PL will have 2 changes: Brians bug-fix and a little > message > pointing out that Build.PL is now the preferred installation > system, but > Makefile.PL still works. Sounds fine to me. The old Makefile.PL is in the branch along with the new system, we leave a stub in place for Makefile.PL in CVS HEAD, and everybody's happy (hopefully). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 08:08:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 07:08:57 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2980.4000609@sheffield.ac.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> <455C2980.4000609@sheffield.ac.uk> Message-ID: <4723715A-551A-4402-A98C-14B64EEDD80E@uiuc.edu> On Nov 16, 2006, at 3:04 AM, Nathan S. Haigh wrote: > ... >> If Build.PL can coexist that'd be great. That would give you the >> opportunity to have Makefile.PL print out a message right at the >> beginning that if the installation process messes up one should try >> Build.PL. This would spare you from fixing any problems in >> Makefile.PL that are fixed in the Build.PL approach. > > Good idea, for anyone downloading the .tar.gz from CPAN if they issue > "perl Makefile.PL" without knowing Build.PL was there it should > hopefully work, but if not, issue a comment at the end to say try > "perl > Build.PL" if anything seemed to go wrong. That's amazingly similar to the suggestion I made ;> Seriously, when we make any changes in Bioperl they should be made with the community in mind. If I were to download RC3 directly from the website, it uses the old Makefile.PL. Therefore I would expect the new RC and the final release to have a similar installation procedure. Same with CVS. And I'll note that the CVS docs and wiki still state that Makefile.PL is the one to use. If we can redirect them to the current way, all the better. But sudden dramatic changes, even in a developer release, are probably not the way to go. > If we go for short release cycles, and regular bug fix release, we > will > no longer have to say to users: > "This is a known bug/issue in release x.y.z, it has been fixed in CVS > HEAD so get it from there" > we can roll out fixes in regular releases. This way CVS is then used > solely by developers and those really wanting to live on the bleeding > edge code. Therefore, it is important to get Build.PL in place to let > the release cycle and CPAN packages built quickly, easily and without > hassle - which I believe is the problem with Makefile.PL as it > currently is. Shorter developer cycles are definitely better. Like Hilmar suggests, they don't have to be perfect (though relatively bug- free). If you look back through the old releases I don't think you'll find many with all tests passing on all OS's. I would like to get a 1.5.3 out by spring, then start towards cleaning up for a summer-fall rel. 1.6. Maybe that's wishful thinking. >> Implementing changes like this do require a lot of energy. I very >> much appreciate that Sendu invested the time and energy to make it >> work, even though unfortunately at the last hour. Who knows who would >> have had the energy after the release. If Sendu hadn't put in the >> work now, the next release master may have been stuck with an even >> messier Makefile.PL system. Instead of Monday morning quarterbacking >> after no-one stopped him when he asked about it, we should all help >> him make the release - and the build change - successful now that he >> has done most if not all of the migration work already. >> >> -hilmar >> > > Here, here - well done Sendu on all your hard work! > Personally, I think the move to Build.PL is a good one - it may be a > little late in this particular release, but I think that the > problem is > not that it is a late change, but that it wasn't picked up sooner. It > fits well with the goal of making releases and big fix releases more > regular, and if these are made available via CPAN, then the use of CVS > is for developers and those wanting to live on the edge. Build.PL > helps > all this by making is easier and quicker to make CPAN packages. It > also > means we have a while before the "stable" 1.6 release to ensure it is > working effectively - better than dropping it in on the 1.6 release > isn't it? I think it's work the delay and an extra RC! > > Anyway, my 2 pence worth! > Nath I don't think anyone is knocking Sendu for his effort here. I will remind everybody that this was discussed in a previous thread and a decision was made (and agreed to by Sendu) to wait until after this release to implement Build, hence the backlash. Brian summed it up quite well. We all support this; the timimg was just bad. That's all. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 08:21:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 13:21:27 +0000 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? Message-ID: <455C65D7.5060704@sendu.me.uk> Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if the intent was that it not be included in any distribution. I've had a very quick look at it and the docs seem a little out of date. More importantly, I couldn't get it to return any results. I can't find any tests for it in the t/ directory either. Is there any interest in developing this module to get it into a working and tested state, or should I exclude it from the up-coming release of Bioperl? If no one wants to maintain it, should it be deprecated? Thank you, Sendu. From roy at colibase.bham.ac.uk Thu Nov 16 08:18:55 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Thu, 16 Nov 2006 13:18:55 +0000 Subject: [Bioperl-l] reverse complement - and features In-Reply-To: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> References: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Message-ID: <455C653F.7010907@colibase.bham.ac.uk> > do you know of an easy way to reverse complement the sequence of an > embl entry and the features associated with that sequence. > I'm looking at genomic syntenic regions, and in some organisms the > gene is in the plus strand while in others is in the minus. Try the revcom_with_features method from Bio::SeqUtils: $revcom=Bio::SeqUtils->revcom_with_features($seq); (Apparently the documentation isn't correct for this. I have submitted a patch to Bugzilla.) Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From n.haigh at sheffield.ac.uk Thu Nov 16 08:37:33 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 13:37:33 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C6028.3060402@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455C6028.3060402@sendu.me.uk> Message-ID: <455C699D.1040407@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sorry, but i've been busy this last week etc so haven't be able to test >> RC3 on WinXP yet - hopefully Chris' tests have been sufficient. > > No problem, thanks for all your testing effort! > > >> Essentially a PPM dist comprises of the .tar.gz file you described (of >> the blib dir) and then the XML file (.ppd) which describes the package >> and it's dependencies. > > Is the .ppd ever included in the .tar.gz, or is it always separate? > > Nope - always separate. >> The syntax of the XML has changed for PPM4 (which >> required me to do these changes by hand on the ppd that was previously >> output by "make ppd". > > Is there a reference for the format anywhere? > Erm not really - that I know of. There is this thread which I use for reference: http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 > >> For PPM4 the XML in the ppd file can be copied >> over to packages.xml file in our PPM repository. the codebase URL can be >> relative/absolute and it's exact value depends on the relative position >> of the XML (whether in the .ppd or package.xml file) and the .tar.gz >> file. Thus, by default, they would have to reside in the same dir on our >> server. >> >> Without looking at the XML I couldn't say if it was PPM3 or PPM4 >> compatible. Could you e-mail me the ppd file and I'll take a look. > > It's pretty basic: > > <SOFTPKG NAME="bioperl" VERSION="1,005002003,0,0"> > <TITLE>bioperl > Bioinformatics Toolkit > Bioperl Team <bioperl-l at bioperl.org> > > > > > > If I made it output the sort of information in the current > http://bioperl.org/DIST/RC/package.xml, would that be fine? Did you > have any kind of automation for creating that package.xml, or do you > see a good potential way of automating it? This PPD doesn't contain any info about what modules it provides (ideally, it should have a provide tags for all modules in bioperl) or the dependencies via the require tag. I didn't have an automated way of making it. Previously, the output of "make ppd" used PREREQ_PM from makefile.pl to create PPM3 dependency tags for all modules in PREREQ_PM. I just modified the tags to REQUIRE and added '::' to the end of modules that didn't natively have one. This should all be detailed in the above in - here again for convenience: http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 There must be an automated way to generate the PPM4 compatible PPDs - I think there is a way to generate one from the CPAN distribution. I think this might be the way ActiveState does it? Nath From bix at sendu.me.uk Thu Nov 16 08:47:05 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 13:47:05 +0000 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> References: <455C65D7.5060704@sendu.me.uk> <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> Message-ID: <455C6BD9.6090100@sendu.me.uk> Allen Day wrote: > Hi Sendu, > > Several years ago I was asked by Jim Kent to stop maintaining it. He > was concerned it would overload the UCSC servers. It's not in the > distribution for the same reason. Thanks, I'll deprecate it then. From gcarbajosa at cnio.es Thu Nov 16 08:12:58 2006 From: gcarbajosa at cnio.es (guillermo) Date: Thu, 16 Nov 2006 14:12:58 +0100 Subject: [Bioperl-l] indexing whole genbank Message-ID: Hello, I wrote to this list before because I wasn?t able to index the whole of genebank. I?ve tried to do it spliting the work by creating small indexes and it has worked perfectly so that seems the way to do it. Thanks for your comments, Guillermo **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From cjfields at uiuc.edu Thu Nov 16 10:08:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:08:08 -0600 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <455C65D7.5060704@sendu.me.uk> Message-ID: <001501c70991$06b14fe0$15327e82@pyrimidine> > Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if > the intent was that it not be included in any distribution. > I've had a very quick look at it and the docs seem a little > out of date. More importantly, I couldn't get it to return > any results. > > I can't find any tests for it in the t/ directory either. Is > there any interest in developing this module to get it into a > working and tested state, or should I exclude it from the > up-coming release of Bioperl? > > If no one wants to maintain it, should it be deprecated? > > > Thank you, > Sendu. I would definitely exclude it if it doesn't work or have tests. Have you contacted the author (Allen Day)? I wonder if he has updated the code but hasn't committed it. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Thu Nov 16 10:17:23 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Nov 2006 10:17:23 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C197D.6000107@sendu.me.uk> References: <455C1790.3080408@sendu.me.uk> <455C197D.6000107@sendu.me.uk> Message-ID: <75FDB3A6-BFB6-4120-92B1-04D54D708E4C@gmx.net> Sounds great to me. -hilmar On Nov 16, 2006, at 2:55 AM, Sendu Bala wrote: >> Ok, so the current plan is: >> # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml > Also, > # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who > read the docs on the website/elsewhere (which will be updated to > explain > the new Build.PL system) don't get confused when that doesn't work, > for wide testing, and to get people used to it for the next > release. The > old Makefile.PL will have 2 changes: Brians bug-fix and a little > message > pointing out that Build.PL is now the preferred installation > system, but > Makefile.PL still works. > > >> # CVS core gets a Makefile.PL stub telling you to use Build.PL >> # CVS db, run, network stay with Makefile.PL until after final >> release >> of 1.5.2, then move to Build.PL with Makefile.PL stub (because they >> don't have a 1.5.2 branch) >> >> Is everyone happy with that, or are there further suggestions for >> something better? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Thu Nov 16 10:29:31 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:29:31 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C699D.1040407@sheffield.ac.uk> Message-ID: <001601c70994$02da28d0$15327e82@pyrimidine> ... > > > > Is there a reference for the format anywhere? > > > > Erm not really - that I know of. There is this thread which I use for > reference: > http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 Looks like kobes is using PPM::Make (he should; it's his distribution). We'll need to make sure that Module::Build uses that as well, since it seems there are some significant changes. ... > There must be an automated way to generate the PPM4 > compatible PPDs - I think there is a way to generate one from > the CPAN distribution. I think this might be the way > ActiveState does it? > > Nath I think ActiveState has it's own automated build process. For PPM3 they used the PPD section from the regular makefile (from Makefile.PL and ExtUtils::MakeMaker). Notably they still indicate using 'nmake ppd' when generating Makefile.PL, so maybe they use an updated or modified ExtUtils::MakeMaker? Or they add tags for the Makefile.PL: use ExtUtils::MakeMaker; # See lib/ExtUtils/MakeMaker.pm for details of how to influence # the contents of the Makefile that is written. WriteMakefile( 'NAME' => 'Term::Control', 'VERSION_FROM' => 'Control.pm', # finds $VERSION ($] ge '5.005') ? ( 'AUTHOR' => 'Johnny Doel (johnny at doel.org)', 'ABSTRACT' => 'Control the IO for terminals', # extra tags here? ) : (), ); The reason you may not see a certain distribution built into a PPM is b/c a particular dependency is not available for one reason or another, tests fail during the make process, etc. They will try to build specific ones upon request. Many of the ones in Kobes are generated by users who want up-to-date distros or ones not built automatically by ActiveState, though Randy Kobes himself sets up most of them. Significantly, he has already switched over to PPM4; maybe we should contact him about this? Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 10:31:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:31:08 -0600 Subject: [Bioperl-l] indexing whole genbank In-Reply-To: Message-ID: <001701c70994$3d332400$15327e82@pyrimidine> > Hello, > > I wrote to this list before because I wasn?t able to index > the whole of genebank. I?ve tried to do it spliting the work > by creating small indexes and it has worked perfectly so that > seems the way to do it. > > Thanks for your comments, > Guillermo Thanks for the update. I think that the problem was a full GenBank file is way too large for flatfile indexing (I think it's around 800 GB unpacked now). Nice to know doing it by divisions works. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 11:29:33 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 16:29:33 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <17756.36534.549232.263868@satchel.alerce.com> References: <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> <455BA093.8040603@sendu.me.uk> <17756.36534.549232.263868@satchel.alerce.com> Message-ID: <455C91ED.2030008@sendu.me.uk> George Hartzell wrote: > Sendu Bala writes: > > [...] > > The only real change for most users is that they now need Module::Build > > installed. > > Module::Build can be a real pain-in-the_%$* if you're used to > installing perl modules in a specialized place using something like > this: > > perl Makefile.PL PREFIX=~/perl-stuff > > Granted, MakeMaker's handling of that has been inconsistent across > platforms over the years, but on a single system at least it's > manageable. > > If/when bioperl swaps over to a Module::Build based system, PLEASE > make a big&loud reference to the "Installing in the same location as > ExtUtils::MakeMaker" section of the Module::Build::Cookbook so that > folks have a fighting chance of avoiding unpleasant surprises. Thanks, I've added a clarification to the INSTALL file. From hartzell at alerce.com Thu Nov 16 11:15:50 2006 From: hartzell at alerce.com (George Hartzell) Date: Thu, 16 Nov 2006 08:15:50 -0800 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BA093.8040603@sendu.me.uk> References: <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> <455BA093.8040603@sendu.me.uk> Message-ID: <17756.36534.549232.263868@satchel.alerce.com> Sendu Bala writes: > [...] > The only real change for most users is that they now need Module::Build > installed. Module::Build can be a real pain-in-the_%$* if you're used to installing perl modules in a specialized place using something like this: perl Makefile.PL PREFIX=~/perl-stuff Granted, MakeMaker's handling of that has been inconsistent across platforms over the years, but on a single system at least it's manageable. If/when bioperl swaps over to a Module::Build based system, PLEASE make a big&loud reference to the "Installing in the same location as ExtUtils::MakeMaker" section of the Module::Build::Cookbook so that folks have a fighting chance of avoiding unpleasant surprises. That section says, in part: With the introduction of "--prefix" in Module::Build 0.28 and "INSTALL_BASE" in ExtUtils::MakeMaker 6.31 its [sic] easy to get them both to install in the same locations. First, ensure you have at least version 0.28 of Module::Build installed and 6.31 of ExtUtils::MakeMaker. Prior versions have differeing installation behaviours. People may need to upgrade their installations [at least the ExtUtils::MakeMaker and Module::Build bits], but at least they'll see the train barreling down at them. g. From roy at colibase.bham.ac.uk Thu Nov 16 11:49:49 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Thu, 16 Nov 2006 16:49:49 +0000 Subject: [Bioperl-l] reverse complement - and features In-Reply-To: <40d6e6580611160828m5f7047e0gadec36f958a69990@mail.gmail.com> References: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> <455C653F.7010907@colibase.bham.ac.uk> <40d6e6580611160828m5f7047e0gadec36f958a69990@mail.gmail.com> Message-ID: <455C96AD.8030804@colibase.bham.ac.uk> > that method sounds promising, although the documentation seems to be > copy-and-paste from the trunc_with_features() method. Yes, I was a bit lazy with that. It has been fixed in CVS (thanks Chris) and will be included in the new 1.5.2 release. > I included in my script, although it doesn't complaint but no being > there, it doesn't do anything with the file. > I looked at the version of bioperl in the server where I'm running, > and it is 1.5.0 and the SeqUtils.pm does not include the > revcom_with_features(). > Do you know if I can install the SeqUtils.pm module in my directory, > and call it with use lib "/home/xxxx/xxxx/lib/perl"; ? Yes, that should work. You can download the most recent version from: http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioperl-live/Bio/SeqUtils.pm?rev=HEAD&content-type=text/plain You can put that file in the directory /home/xxxx/xxxx/lib/perl/Bio/ and it should then be recognised as the preferred Bio::SeqUtils module if you use lib as you say. Good luck with it. Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From cjfields at uiuc.edu Thu Nov 16 11:55:39 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 10:55:39 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2ED5.4060602@sendu.me.uk> Message-ID: <001901c709a0$0b6a6d50$15327e82@pyrimidine> > Nathan S. Haigh wrote: > > I believe Sendu mentioned that a Makefile.PL would be > included in the > > CPAN package but is not in CVS as it would be generated > from Build.PL > > for backward compatibility - is that right Sendu? > > Yes. > > > > How does installing via CPAN affect this? Does it give > higher priority > > to Build.PL over Makefile.PL and thus use Build.PL for the install? > > I don't know about priorities (but assume it would prefer > Build.PL), but in any case, the generated Makefile.PL > basically just calls Build.PL, so it makes no difference. > > > > Build.PL helps all this by making is easier and quicker to > make CPAN > > packages. It also means we have a while before the "stable" 1.6 > > release to ensure it is working effectively - better than > dropping it > > in on the 1.6 release isn't it? I think it's work the delay and an > > extra RC! > > Yes, it surely needs to happen before 1.6. As suggested here > and originally in the other thread, 1.5.2 can be the > transition release with old Makefile.PL and Build.PL as well > (set up to not overwrite Makefile.PL). So far, we have these modes of installation: 1) Direct installation using CPAN -> INSTALL 2) Regular distribution (either from the Bioperl website or CPAN) using 'make/nmake' ->INSTALL, INSTALL.WIN 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN 4) PPM (Windows-only) -> INSTALL.WIN Anything using make/nmake will need to be changed in docs. Do you want to switch everything over to using 'perl Build.PL'? Also, since the 'manifying' problem is now fixed we can remove the blurb about it from INSTALL and the wiki. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 11:59:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 16:59:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> References: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: <455C98F0.9050909@sendu.me.uk> Chris Fields wrote: > So far, we have these modes of installation: > > 1) Direct installation using CPAN -> INSTALL > 2) Regular distribution (either from the Bioperl website or CPAN) using > 'make/nmake' ->INSTALL, INSTALL.WIN > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > 4) PPM (Windows-only) -> INSTALL.WIN > > Anything using make/nmake will need to be changed in docs. Do you want to > switch everything over to using 'perl Build.PL'? > > Also, since the 'manifying' problem is now fixed we can remove the blurb > about it from INSTALL and the wiki. I've already updated docs in CVS. The emails are just very slow to get through to guts. Do an update and let me know if I missed anything. I'll add the changes to the wiki when I get a chance. From n.haigh at sheffield.ac.uk Thu Nov 16 12:44:28 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 17:44:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> References: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: <455CA37C.3070704@sheffield.ac.uk> --snip-- >> Yes, it surely needs to happen before 1.6. As suggested here >> and originally in the other thread, 1.5.2 can be the >> transition release with old Makefile.PL and Build.PL as well >> (set up to not overwrite Makefile.PL). >> > > So far, we have these modes of installation: > > 1) Direct installation using CPAN -> INSTALL > 2) Regular distribution (either from the Bioperl website or CPAN) using > 'make/nmake' ->INSTALL, INSTALL.WIN > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > Chris, Do you ever have a problem with nmake when doing an install from a regular distribution or CVS? I'm sure I used to get an nmake problem which wouldn't let you proceed further - might have been "nmake test" and it might be a while back now. Nath From cjfields at uiuc.edu Thu Nov 16 12:58:14 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 11:58:14 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455CA37C.3070704@sheffield.ac.uk> Message-ID: <000001c709a8$c9c1b760$15327e82@pyrimidine> > --snip-- > >> Yes, it surely needs to happen before 1.6. As suggested here and > >> originally in the other thread, 1.5.2 can be the > transition release > >> with old Makefile.PL and Build.PL as well (set up to not overwrite > >> Makefile.PL). > >> > > > > So far, we have these modes of installation: > > > > 1) Direct installation using CPAN -> INSTALL > > 2) Regular distribution (either from the Bioperl website or CPAN) > > using 'make/nmake' ->INSTALL, INSTALL.WIN > > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > > > > Chris, > > Do you ever have a problem with nmake when doing an install > from a regular distribution or CVS? I'm sure I used to get an > nmake problem which wouldn't let you proceed further - might > have been "nmake test" > and it might be a while back now. > > Nath I haven't had problems beyond the '-w' paranoia and 'Subroutine x redefined at' warnings, which is an ActivePerl issue. 'nmake test' works for me (that's what I have been using on all the RC's and using bioperl-live). I think 'Build test' also uses nmake, so if that works nmake should also work. I have used both an old version (1.5) and the recent VC++ nmake version (8.00.50727.42) w/o problems. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From pcantalupo at gmail.com Thu Nov 16 11:26:31 2006 From: pcantalupo at gmail.com (Paul Cantalupo) Date: Thu, 16 Nov 2006 11:26:31 -0500 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID Message-ID: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Hello, Is there a way with Bioperl (or some other tool - NCBI EUtils?) to convert a Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's that I need to convert to Mouse GeneIDs so that I can compare them to my Mouse microarray data. Thank you, Paul -- Paul Cantalupo Research Specialist/Systems Programmer 559 Crawford Hall Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Work: 412-624-4687 Fax: 412-624-4759 Ask me about Toastmasters: www.toastmasters.org Midday Club Treasurer From bosborne11 at verizon.net Thu Nov 16 13:09:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 16 Nov 2006 13:09:01 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: Chris, So a package like bioperl-ext, normally requiring a C compiler and make/nmake, now no longer needs make/nmake? I don't recall this coming up in our discussions... Brian O. On 11/16/06 11:55 AM, "Chris Fields" wrote: > Anything using make/nmake will need to be changed in docs. From bix at sendu.me.uk Thu Nov 16 13:14:12 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 18:14:12 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: References: Message-ID: <455CAA74.60500@sendu.me.uk> Brian Osborne wrote: > Chris, > > So a package like bioperl-ext, normally requiring a C compiler and > make/nmake, now no longer needs make/nmake? I don't recall this coming up in > our discussions... I'm sure you'd still need compiler tools to do compilation. I wasn't sure what to say about bioperl-ext in the docs, so I didn't change anything. bioperl-ext isn't my concern (see the thread where I was deciding which packages needed a unified release), so I'll not be trying to change it over to Build.PL From bix at sendu.me.uk Thu Nov 16 13:16:48 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 18:16:48 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: References: Message-ID: <455CAB10.1090703@sendu.me.uk> Brian Osborne wrote: > George, > > But the most recent versions of Module::Build do the installations > correctly? And it's as simple as specifying PREFIX or LIB? In Build.PL's case, it's --prefix or --lib, but yes. For both Module::Build and MakeMaker in recent versions, --install_base is recommended. From cjfields at uiuc.edu Thu Nov 16 13:41:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 12:41:56 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: Message-ID: <000101c709ae$e475bfb0$15327e82@pyrimidine> > Chris, > > So a package like bioperl-ext, normally requiring a C > compiler and make/nmake, now no longer needs make/nmake? I > don't recall this coming up in our discussions... > > Brian O. The makefile setup for bioperl-ext is much more complex than for the others, so I don't know how that would be handled using Module::Build. I tried it earlier on before the RCs on Mac OS X and it installed fine, but Inline complained when running other tests so I tossed it. I don't think it ever worked under Windows using nmake, unless you're using CygWin/GNU make. I believe the Build file must use make/nmake somehow, so there must be a way to compile C code included with the distribution. I just haven't had time to invesitgate yet. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Thu Nov 16 14:05:27 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 19:05:27 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <000101c709ae$e475bfb0$15327e82@pyrimidine> References: <000101c709ae$e475bfb0$15327e82@pyrimidine> Message-ID: <455CB677.6080608@sheffield.ac.uk> Chris Fields wrote: >> Chris, >> >> So a package like bioperl-ext, normally requiring a C >> compiler and make/nmake, now no longer needs make/nmake? I >> don't recall this coming up in our discussions... >> >> Brian O. >> > > The makefile setup for bioperl-ext is much more complex than for the others, > so I don't know how that would be handled using Module::Build. I tried it > earlier on before the RCs on Mac OS X and it installed fine, but Inline > complained when running other tests so I tossed it. I don't think it ever > worked under Windows using nmake, unless you're using CygWin/GNU make. > > I believe the Build file must use make/nmake somehow, so there must be a way > to compile C code included with the distribution. I just haven't had time > to invesitgate yet. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > I was under the impression that Module::Build is pure Perl and thus wouldn't use make/nmake. This page might help, look under "code" in this section: http://search.cpan.org/~kwilliams/Module-Build-0.2805/lib/Module/Build.pm#ACTIONS According to change logs they use ExtUtils::CBuilder to do all compiling of C code (since version 0.27_01) see: http://search.cpan.org/src/KWILLIAMS/Module-Build-0.27_03/Changes HTH Nathan From bosborne11 at verizon.net Thu Nov 16 13:05:15 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 16 Nov 2006 13:05:15 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <17756.36534.549232.263868@satchel.alerce.com> Message-ID: George, But the most recent versions of Module::Build do the installations correctly? And it's as simple as specifying PREFIX or LIB? Brian O. On 11/16/06 11:15 AM, "George Hartzell" wrote: > Module::Build can be a real pain-in-the_%$* if you're used to > installing perl modules in a specialized place using something like > this: > > perl Makefile.PL PREFIX=~/perl-stuff From er at xs4all.nl Thu Nov 16 16:01:12 2006 From: er at xs4all.nl (Erik) Date: Thu, 16 Nov 2006 22:01:12 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch Message-ID: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> Hi all, Using bioperl-live, I noticed a problem with the parsing in Bio/SeqIO/genbank.pm. It occurs in the DBSOURCE section, where the 'dblink' annotation gets its values. I got several values that had a double colon, like InterPro::IPR011000 etc. Not all 'dblink' values were affected. Here is a patch which seems to fix it / it works for me: ======= --- Bio/SeqIO/genbank.pm.orig 2006-11-16 18:33:30.060417520 +0100 +++ Bio/SeqIO/genbank.pm 2006-11-16 20:29:59.014934936 +0100 @@ -504,7 +504,7 @@ my $db; # this is because GenBank dropped the spaces!!! # I'm sure we're not going to get this right - if( $id =~ s/^(EchoBASE|IntAct|SWISS-2DPAGE|ECO2DBASE|ECOGENE|TIGRFAMs|TIGR|GO|InterPro|Pfam|PROSITE|SGD|GermOnline|HSSP|PhosSite)//i ) { + if( $id =~ s/^(EchoBASE|IntAct|SWISS-2DPAGE|ECO2DBASE|ECOGENE|TIGRFAMs|TIGR|GO|InterPro|Pfam|PROSITE|SGD|GermOnline|HSSP|PhosSite)://i ) { $db = $1; } $annotation->add_Annotation======= I also wrote a few tests for the problem, which also needed an extra file in t/data. I will attach the lot hth, Erik -------------- next part -------------- A non-text attachment was scrubbed... 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Name: genbank.pm.diff Type: application/octet-stream Size: 608 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061116/de8ee1cd/attachment-0002.obj From jason at bioperl.org Thu Nov 16 14:45:24 2006 From: jason at bioperl.org (Jason Stajich) Date: Thu, 16 Nov 2006 11:45:24 -0800 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> References: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Message-ID: have you tried ensembl's biomart? http://www.ensembl.org/Multi/martview you will want the ortholog table. -jason On Nov 16, 2006, at 8:26 AM, Paul Cantalupo wrote: > Hello, > > Is there a way with Bioperl (or some other tool - NCBI EUtils?) to > convert a > Human NCBI GeneID to a Mouse GeneID. I have a list of Human > GeneID's that I > need to convert to Mouse GeneIDs so that I can compare them to my > Mouse > microarray data. > > Thank you, > > Paul > > -- > Paul Cantalupo > Research Specialist/Systems Programmer > 559 Crawford Hall > Department of Biological Sciences > University of Pittsburgh > Pittsburgh, PA 15260 > Work: 412-624-4687 > Fax: 412-624-4759 > > Ask me about Toastmasters: www.toastmasters.org > Midday Club Treasurer > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From allenday at ucla.edu Thu Nov 16 08:43:35 2006 From: allenday at ucla.edu (Allen Day) Date: Thu, 16 Nov 2006 05:43:35 -0800 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <455C65D7.5060704@sendu.me.uk> References: <455C65D7.5060704@sendu.me.uk> Message-ID: <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> Hi Sendu, Several years ago I was asked by Jim Kent to stop maintaining it. He was concerned it would overload the UCSC servers. It's not in the distribution for the same reason. -Allen On 11/16/06, Sendu Bala wrote: > Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if the intent > was that it not be included in any distribution. I've had a very quick > look at it and the docs seem a little out of date. More importantly, I > couldn't get it to return any results. > > I can't find any tests for it in the t/ directory either. Is there any > interest in developing this module to get it into a working and tested > state, or should I exclude it from the up-coming release of Bioperl? > > If no one wants to maintain it, should it be deprecated? > > > Thank you, > Sendu. > From torsten.seemann at infotech.monash.edu.au Thu Nov 16 19:42:41 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 17 Nov 2006 11:42:41 +1100 Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch In-Reply-To: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> References: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> Message-ID: <455D0581.4010805@infotech.monash.edu.au> Erik, > Using bioperl-live, I noticed a problem with the parsing in > Bio/SeqIO/genbank.pm. > It occurs in the DBSOURCE section, where the 'dblink' annotation gets its > values. I got several values that had a double colon, like > InterPro::IPR011000 etc. Not all 'dblink' values were affected. > Here is a patch which seems to fix it / it works for me: Thank you very much for your contribution of bug fix and patch and new tests, you have been very thorough. However, these contributions are best done via the Bugzilla tracking system: http://bugzilla.open-bio.org/ For more information see: http://www.bioperl.org/wiki/Bugs -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From cjfields at uiuc.edu Thu Nov 16 08:47:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 07:47:26 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C5D5A.5020205@sheffield.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> Message-ID: On Nov 16, 2006, at 6:45 AM, Nathan S. Haigh wrote: > Sendu Bala wrote: >> Chris Fields wrote: >>> I see that there is a PPMMaker module with Module::Build, so we'll >>> have to >>> look into that for WinXP PPMs.. >> >> Nathan, does: >> >> perl Build.PL >> ./Build ppmdist >> >> create anything useful? For me it generates a tar.gz containing blib, >> and a ppd file (the contents of which can be adjusted by supplying >> "an >> optional argument codebase which is used in the generated ppd file to >> specify the (usually relative) URL of the distribution. By default, >> this value is the distribution name without any path information", >> eg. >> ./Build ppmdist --codebase "MSWin32-x86-multi-thread/ >> Bioperl....tar.gz"). >> >> Is this PPM4 format? What else needs to be done to it to make it >> suitable? I can easily extend the ppmdist action to do whatever you >> want, so let me know. > > Sorry, but i've been busy this last week etc so haven't be able to > test > RC3 on WinXP yet - hopefully Chris' tests have been sufficient. > > Essentially a PPM dist comprises of the .tar.gz file you described (of > the blib dir) and then the XML file (.ppd) which describes the package > and it's dependencies. The syntax of the XML has changed for PPM4 > (which > required me to do these changes by hand on the ppd that was previously > output by "make ppd". For PPM4 the XML in the ppd file can be copied > over to packages.xml file in our PPM repository. the codebase URL > can be > relative/absolute and it's exact value depends on the relative > position > of the XML (whether in the .ppd or package.xml file) and the .tar.gz > file. Thus, by default, they would have to reside in the same dir > on our > server. > > Without looking at the XML I couldn't say if it was PPM3 or PPM4 > compatible. Could you e-mail me the ppd file and I'll take a look. > > Cheers > Nath I'll also try making a PPM here. I noticed that Module::Build has a developer release; I may check with the developers about PPM compatibility. I hate to say it, but we might need to get a PPM3 rolled for this release if people ask for it. There has been some backlash about PPM4 so a lot of people are actually downgrading to an older ActivePerl installations for PPM3. We'll just make a barebones version if this pops up (and no Bundle). One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a developer release, but as the latest release (which implies it is stable): http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Not sure what's going on there, but I don't think that was intended, correct? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 21:51:49 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 20:51:49 -0600 Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations In-Reply-To: References: Message-ID: <277B1C9B-1719-47C5-9A34-9B4E179A78A0@uiuc.edu> On Nov 16, 2006, at 1:55 AM, Joanne Chen wrote: > Got the strand problem fixed. Thanks. =) No problem. Just as a heads up, we plan on making some changes to SplitLocations but nothing too dramatic (hopefully). chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From dmessina at wustl.edu Thu Nov 16 22:54:50 2006 From: dmessina at wustl.edu (David Messina) Date: Thu, 16 Nov 2006 21:54:50 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B3F11.6070102@campus.iztacala.unam.mx> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> <455B3F11.6070102@campus.iztacala.unam.mx> Message-ID: <450674EB-F9CA-4BBF-8EB9-D08423FD16FD@wustl.edu> Sorry, just seeing this now. > ignored, only run manually by people who want to install Deobfuscator? Thanks for asking. As Mauricio said, manual installation only is what I would suggest. Dave From torsten.seemann at infotech.monash.edu.au Thu Nov 16 19:19:42 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 17 Nov 2006 11:19:42 +1100 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast In-Reply-To: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> References: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> Message-ID: <455D001E.4000409@infotech.monash.edu.au> Andrew, >> Anyone have any opinions as to how easy/difficult it would be >> to incorporate mpiblast into >> Bio::Tools::Run::StandAloneBlast? It runs essentially the >> same way as blastall, and its output is nearly identical. > I think plans were to rewrite StandAloneBlast and RemoteBlast to make them > more 'generic' (i.e. capable of running other BLAST-related programs), > though I'm not sure at what stage everything is. Chris is correct is saying there were plans to rewrite the Blast modules - at the time myself, Roger Hall, Chris? and Jason were involved, but unfortunately Roger fell ill in Feb 2006 and had to have urgent heart surgery. (And my wife had a baby :-) Here's some of the early discussion: http://portal.open-bio.org/pipermail/bioperl-l/2006-February/020745.html ANYWAY, I think it might be possible to incorporate mpiblast easily, even without changing Bioperl if we are lucky, via the ->executable() setter method. If not, I added rpsblast support last year which is similar to blastall, so it'd probably be achievable. How does the the output of mpiblast differ to NCBI blastall ? What command line options does mpiblast take? -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From bix at sendu.me.uk Fri Nov 17 02:38:30 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 07:38:30 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> Message-ID: <455D66F6.4070804@sendu.me.uk> Chris Fields wrote: > One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a > developer release, but as the latest release (which implies it is stable): > > http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ > > Not sure what's going on there, but I don't think that was intended, > correct? It wasn't intended. I've deleted the file and if you refresh you should find that page doesn't exist anymore? From bix at sendu.me.uk Fri Nov 17 05:20:11 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 10:20:11 +0000 Subject: [Bioperl-l] Testing with Build.PL Message-ID: <455D8CDB.1070100@sendu.me.uk> Developers, For those not familiar with Module::Build and Build.PL I thought I'd point out some useful testing-related things. To run the whole test suite (the same thing that happens during an install process), say: perl Build.PL (answer 'n' to the script installation question to reduce the amount of output you see later on) ./Build test To run a single test script you can of course continue to do: perl -I. -w t/script.t However to see what would really happen during the full "./Build test" you can say: ./Build test --test_files t/script.t To do the same but see the full test output say: ./Build test --test_files t/script.t --verbose If anyone else has tips, please post them. Cheers, Sendu. From sanges at biogem.it Fri Nov 17 05:14:03 2006 From: sanges at biogem.it (Remo Sanges) Date: Fri, 17 Nov 2006 10:14:03 +0000 Subject: [Bioperl-l] Fellowships for Junior Scientists Message-ID: <455D8B6B.1050108@biogem.it> Apologies for the off topic post... AREA Science Park (http://www.area.trieste.it/opencms/opencms/area/en/) and CBM (http://www.cbm.fvg.it/?lang=en_US) are launching a mobility initiative aimed at attracting international scientists to work with the biomedical research community of Trieste. Research areas: * Biostatistics * Systems Biology * Algorithm Development The fellowships are funded by AREA Science Park and the CBM - Consortium for Molecular Biomedicine as part of an international mobility programme run by AREA Science Park and the CBM. The programme aims at attracting young scientists to the Friuli Venezia Giulia Region and adding them to the community of researchers operating in Trieste in the field of biomedicine. CBM and AREA Science Park are two research institutes recognised by the Ministry of Education, Universities and Research. Here there are laboratories integrating dry and wet lab research and developing a wide research program encompassing functional and comparative genomics, bioinformatics database, software development and algorithm development. The laboratories are already integrated in international collaborative projects tackling non-coding RNA genes, regulatory elements, and bioinformatics workflow management systems. For further information: http://www.cbm.fvg.it/?page=mobility&lang=en_US&id=2 Regards Remo Sanges From er at xs4all.nl Fri Nov 17 05:57:43 2006 From: er at xs4all.nl (Erik) Date: Fri, 17 Nov 2006 11:57:43 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch In-Reply-To: <455D0581.4010805@infotech.monash.edu.au> References: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> <455D0581.4010805@infotech.monash.edu.au> Message-ID: <16667.156.83.0.21.1163761063.squirrel@webmail.xs4all.nl> > However, these contributions are best done via the Bugzilla tracking > system: http://bugzilla.open-bio.org/ ok, I'll do that, but a little later today. Maybe just as well as I later thought of some, err.., imperfections in the tests anyway :) Erik From cjfields at uiuc.edu Fri Nov 17 08:43:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 07:43:38 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455D66F6.4070804@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> Message-ID: <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> On Nov 17, 2006, at 1:38 AM, Sendu Bala wrote: > Chris Fields wrote: >> One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a >> developer release, but as the latest release (which implies it is >> stable): >> >> http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ >> >> Not sure what's going on there, but I don't think that was intended, >> correct? > > It wasn't intended. I've deleted the file and if you refresh you > should > find that page doesn't exist anymore? The page is still there, but the distribution is gone (i.e. the 'Download' link is now dead). http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Fri Nov 17 08:51:03 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 13:51:03 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> Message-ID: <455DBE47.90501@sendu.me.uk> Chris Fields wrote: > > On Nov 17, 2006, at 1:38 AM, Sendu Bala wrote: > >> Chris Fields wrote: >>> One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a >>> developer release, but as the latest release (which implies it is >>> stable): >>> >>> http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ >>> >>> Not sure what's going on there, but I don't think that was intended, >>> correct? >> >> It wasn't intended. I've deleted the file and if you refresh you should >> find that page doesn't exist anymore? > > The page is still there, but the distribution is gone (i.e. the > 'Download' link is now dead). > > http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Hmm, I see just a big 'Not found' message for a non-existing page. I think the old page is still stuck in a cache somewhere for you. In any case, don't whatever you do look in the super-sekrit http://search.cpan.org/~sendu/ because I'm testing out CPAN stuff and getting it horribly wrong. Multiple times. I'll make a post when CPAN stuff is ready to test. From cuiw at ncbi.nlm.nih.gov Fri Nov 17 09:59:15 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Fri, 17 Nov 2006 09:59:15 -0500 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Message-ID: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> You can query HomoloGene DB using NCBI EUtils: ESearch like this: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=homologene& term=BRCA1[gene%20name]&retmode=text Once get HomoloGene id then Then Efetch: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=homologene&i d=5276 Just SOAP it to get the gi and acc via taxid. Good luck. Wenwu Cui -----Original Message----- From: Paul Cantalupo [mailto:pcantalupo at gmail.com] Sent: Thursday, November 16, 2006 11:27 AM To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID Hello, Is there a way with Bioperl (or some other tool - NCBI EUtils?) to convert a Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's that I need to convert to Mouse GeneIDs so that I can compare them to my Mouse microarray data. Thank you, Paul -- Paul Cantalupo Research Specialist/Systems Programmer 559 Crawford Hall Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Work: 412-624-4687 Fax: 412-624-4759 Ask me about Toastmasters: www.toastmasters.org Midday Club Treasurer _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Fri Nov 17 12:43:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 17:43:55 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455DF2BC.9010601@sheffield.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> Message-ID: <455DF4DB.5000808@sendu.me.uk> Nathan S. Haigh wrote: > Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked up as > a developer release? I didn't try that variation, but have decided to go with bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a developer release. I've outlined the numbering scheme here: http://www.bioperl.org/wiki/Making_a_BioPerl_release#Making_the_distribution_directory From cjfields at uiuc.edu Fri Nov 17 13:30:20 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 12:30:20 -0600 Subject: [Bioperl-l] CPAN Versioning, was [something else] In-Reply-To: <455DF4DB.5000808@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> Message-ID: <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> On Nov 17, 2006, at 11:43 AM, Sendu Bala wrote: > Nathan S. Haigh wrote: >> Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked >> up as >> a developer release? > > I didn't try that variation, but have decided to go with > bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a > developer > release. > > I've outlined the numbering scheme here: > http://www.bioperl.org/wiki/ > Making_a_BioPerl_release#Making_the_distribution_directory I noticed that Module::Build now has a developer release that uses this: Module-Build-0.2805_01.tar.gz So the '_###' seems to be key. If so I see a versioning dilemma that depends on what we want to call rel 1.5.2. If we used 'bioperl-1.5.2_004' for the RCs, then logically the final dev release would be 'bioperl-1.5.2', which would not be designated a dev release on CPAN (if the underscore rule holds up, that is). If we plan on having CPAN designate it a developer release (which I think is the consensus among the developers, since 1.6 would be the stable release), then the final 1.5.2 version would be something like 'bioperl-1.5_02' or 'bioperl-1.5_002'. RCs would be '1.5_02-RC#'. Or maybe even '1.5_02_##', which a few modules seem to use. However, even that is tricky; what do we call rel 1.6.1, a point release in the stable series? 'bioperl-1.6_2' would then be a developer release! Argghhh! Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Nov 17 13:51:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 12:51:27 -0600 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> References: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> Message-ID: <55142E31-33F7-442C-B358-E81FA57E9F9E@uiuc.edu> On Nov 17, 2006, at 8:59 AM, Cui, Wenwu ((NIH/NLM/NCBI)) [C] wrote: > You can query HomoloGene DB using NCBI EUtils: > > ESearch like this: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? > db=homologene& > term=BRCA1[gene%20name]&retmode=text > > Once get HomoloGene id then > Then Efetch: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? > db=homologene&i > d=5276 > > Just SOAP it to get the gi and acc via taxid. > > Good luck. > > Wenwu Cui > > > -----Original Message----- > From: Paul Cantalupo [mailto:pcantalupo at gmail.com] > Sent: Thursday, November 16, 2006 11:27 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID > > Hello, > > Is there a way with Bioperl (or some other tool - NCBI EUtils?) to > convert a > Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's > that I > need to convert to Mouse GeneIDs so that I can compare them to my > Mouse > microarray data. > > Thank you, > > Paul > ... You could also use esearch(homologene, using history)->elink (homologene_gene, using history)->esummary(elink 'cookie'). I have set up a (very) experimental BioPerl interface to NCBI eutils (Bio::DB::EUtilities). If you update from CVS (this won't be in the 1.5.2 release), you could do something like this: ------------------------------------------------------ use Bio::DB::EUtilities; my $term = 'BRCA1[gene name]'; # grab BRCA1 homologene UID my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => $term, -usehistory => 'y'); $esearch->get_response; my @h_genes = $esearch->get_ids; # what Gene UIDs are linked to the Homologene UID? my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', -db => 'gene', -cookie => $esearch->next_cookie, -cmd => 'neighbor_history'); $elink->get_response; # what taxids go with which GeneID? my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', -cookie => $elink->next_cookie); $esum->get_response; while (my $docsum = $esum->next_docsum) { print $docsum->esummary_id,"\n"; print "\t\tTaxID: ",$docsum->get_Content_by_name('TaxID'),"\n"; print "\t\tOrganism: ",$docsum->get_Content_by_name ('Orgname'),"\n"; } ------------------------------------------------------ A future bioperl SOAP interface for eutils is also not out of the question either, just haven't had time to play around with it. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Fri Nov 17 14:35:11 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 19:35:11 +0000 Subject: [Bioperl-l] CPAN Versioning, was [something else] In-Reply-To: <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> Message-ID: <455E0EEF.4080806@sendu.me.uk> Chris Fields wrote: > > On Nov 17, 2006, at 11:43 AM, Sendu Bala wrote: > >> Nathan S. Haigh wrote: >>> Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked up as >>> a developer release? >> >> I didn't try that variation, but have decided to go with >> bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a developer >> release. >> >> I've outlined the numbering scheme here: >> http://www.bioperl.org/wiki/Making_a_BioPerl_release#Making_the_distribution_directory >> > > I noticed that Module::Build now has a developer release that uses this: > > Module-Build-0.2805_01.tar.gz > > So the '_###' seems to be key. If so I see a versioning dilemma that > depends on what we want to call rel 1.5.2. [snip] See the page I linked above. It shows what the filenames will be for RCs , releases and point releases for developer and non-developer releases. From gwu at molbio.mgh.harvard.edu Sat Nov 18 01:39:46 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 01:39:46 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455E0EEF.4080806@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> Message-ID: <455EAAB2.4010004@molbio.mgh.harvard.edu> Hi everyone, I saw some problems when installing BioPerl 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could not solve all the dependency issues with one shot of 'install Bundle::BioPerl'. Some packages such as GD-2.35 just could not be installed. And it turned out that CPAN refused to install BioPerl with some test return value 255. Then I went to /root/.cpan/build to configure, test, rebuild those problematic packages. After several more runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl successfully. Below attached is the output of CPAN, which stills complains three packages have issues: Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel. I think the first two are typos somewhere in the Bundle::BioPerl. And the third module is not on the server and could be found on the CPAN site. So my question is : Is this the right way to install BioPerl? It took me two days to figure it out but still not 100% sure all packages are installed properly. Any feedback is appreciated. Gang ================================================= cpan> install Bundle::BioPerl Ace is up to date. Bio::ASN1::EntrezGene is up to date. Class::AutoClass is up to date. Clone is up to date. Convert::Binary::C is up to date. Running install for module Data::Stag::writer The module Data::Stag::writer isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i Data::Stag::writer'. DBD::mysql is up to date. GD::SVG is up to date. GD is up to date. Graph::Directed is up to date. HTML::Parser is up to date. Running install for module HTTP::Request::Common- The module HTTP::Request::Common- isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i HTTP::Request::Common-'. LWP::UserAgent is up to date. Set::Scalar is up to date. SOAP::Lite is up to date. Running install for module Spreadhseet::ParseExcel The module Spreadhseet::ParseExcel isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i Spreadhseet::ParseExcel'. Storable is up to date. SVG is up to date. SVG::Graph is up to date. Text::Shellwords is up to date. XML::DOM::XPath is up to date. XML::Parser::PerlSAX is up to date. XML::SAX is up to date. XML::SAX::Base is up to date. XML::SAX::Writer is up to date. XML::Simple is up to date. XML::Twig is up to date. XML::Writer is up to date. Bundle summary: The following items in bundle Bundle::BioPerl had installation problems: Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel ==================================================== From bix at sendu.me.uk Sat Nov 18 03:04:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 18 Nov 2006 08:04:14 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <455EBE7E.4060105@sendu.me.uk> gang wu wrote: > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. What problems did you run into specifically with GD? > And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. Do you remember what the other problematic packages were, and what you had to do to get them working? > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. All three are typos. We'll get those fixed. > So my question is : Is this the right way to install BioPerl? At the present moment, yes. For 1.5.2 I'll probably be recommending not using Bundle::BioPerl once I fix some other things. > It took me two days to figure it out but still not 100% sure all packages are > installed properly. I'm sorry for the troubles you ran into. We'll try and do better for the final release of 1.5.2. From gwu at molbio.mgh.harvard.edu Sat Nov 18 03:07:47 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:07:47 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <455EBF53.4010701@molbio.mgh.harvard.edu> It turned out that most of the modules of BioPerl were not installed at all. And none of the scripts were installed. I had to download and install bioperl-1.5.2-RC3.tar.gz again. A similar problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually copied all stuff under Bio folder to the corresponding Perl library folder. Is it Ok to do it in this way? Gang gang wu wrote: > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. > > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. > > So my question is : Is this the right way to install BioPerl? It took me > two days to figure it out but still not 100% sure all packages are > installed properly. > > Any feedback is appreciated. > > Gang > > ================================================= > cpan> install Bundle::BioPerl > Ace is up to date. > Bio::ASN1::EntrezGene is up to date. > Class::AutoClass is up to date. > Clone is up to date. > Convert::Binary::C is up to date. > Running install for module Data::Stag::writer > > The module Data::Stag::writer isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Data::Stag::writer'. > DBD::mysql is up to date. > GD::SVG is up to date. > GD is up to date. > Graph::Directed is up to date. > HTML::Parser is up to date. > Running install for module HTTP::Request::Common- > > The module HTTP::Request::Common- isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i HTTP::Request::Common-'. > LWP::UserAgent is up to date. > Set::Scalar is up to date. > SOAP::Lite is up to date. > Running install for module Spreadhseet::ParseExcel > > The module Spreadhseet::ParseExcel isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Spreadhseet::ParseExcel'. > Storable is up to date. > SVG is up to date. > SVG::Graph is up to date. > Text::Shellwords is up to date. > XML::DOM::XPath is up to date. > XML::Parser::PerlSAX is up to date. > XML::SAX is up to date. > XML::SAX::Base is up to date. > XML::SAX::Writer is up to date. > XML::Simple is up to date. > XML::Twig is up to date. > XML::Writer is up to date. > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > ==================================================== > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From N.Haigh at sheffield.ac.uk Sat Nov 18 03:22:00 2006 From: N.Haigh at sheffield.ac.uk (Nathan Haigh) Date: Sat, 18 Nov 2006 08:22:00 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Hi Gang, At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - we are in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things wrong with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such that it may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 and CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as dependencies will fail to install. I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - these will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install process much easier to the users. Thanks Nathan Quoting gang wu : > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. > > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. > > So my question is : Is this the right way to install BioPerl? It took me > two days to figure it out but still not 100% sure all packages are > installed properly. > > Any feedback is appreciated. > > Gang > > ================================================= > cpan> install Bundle::BioPerl > Ace is up to date. > Bio::ASN1::EntrezGene is up to date. > Class::AutoClass is up to date. > Clone is up to date. > Convert::Binary::C is up to date. > Running install for module Data::Stag::writer > > The module Data::Stag::writer isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Data::Stag::writer'. > DBD::mysql is up to date. > GD::SVG is up to date. > GD is up to date. > Graph::Directed is up to date. > HTML::Parser is up to date. > Running install for module HTTP::Request::Common- > > The module HTTP::Request::Common- isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i HTTP::Request::Common-'. > LWP::UserAgent is up to date. > Set::Scalar is up to date. > SOAP::Lite is up to date. > Running install for module Spreadhseet::ParseExcel > > The module Spreadhseet::ParseExcel isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Spreadhseet::ParseExcel'. > Storable is up to date. > SVG is up to date. > SVG::Graph is up to date. > Text::Shellwords is up to date. > XML::DOM::XPath is up to date. > XML::Parser::PerlSAX is up to date. > XML::SAX is up to date. > XML::SAX::Base is up to date. > XML::SAX::Writer is up to date. > XML::Simple is up to date. > XML::Twig is up to date. > XML::Writer is up to date. > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > ==================================================== > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From gwu at molbio.mgh.harvard.edu Sat Nov 18 03:30:30 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:30:30 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EBE7E.4060105@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> Message-ID: <455EC4A6.4040103@molbio.mgh.harvard.edu> Sendu Bala wrote: > gang wu wrote: >> Hi everyone, >> >> I saw some problems when installing BioPerl >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could >> not solve all the dependency issues with one shot of 'install >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >> installed. > > What problems did you run into specifically with GD? If I enable JPEG, GIFS and XPM, none of the test could pass. Since I usually use only PNG for output, I can live without them. I am not sure if it's system related problem. All of them work fine with my 32 bit Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with newer libgd runnig Redhat AS4 AMD/EM64T does not work. > >> And it turned out that CPAN refused to install BioPerl with >> some test return value 255. Then I went to /root/.cpan/build to >> configure, test, rebuild those problematic packages. After several more >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >> successfully. > > Do you remember what the other problematic packages were, and what you > had to do to get them working? > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I guess it should be XML::DOM::XPath.pm. I could not recall what other packages had issues, but basically it's special package configuration issue. >> Below attached is the output of CPAN, which stills complains three >> packages have issues: Data::Stag::writer HTTP::Request::Common- >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in >> the Bundle::BioPerl. And the third module is not on the server and could >> be found on the CPAN site. > > All three are typos. We'll get those fixed. > > >> So my question is : Is this the right way to install BioPerl? > > At the present moment, yes. For 1.5.2 I'll probably be recommending > not using Bundle::BioPerl once I fix some other things. > See my another message for other issues. > >> It took me two days to figure it out but still not 100% sure all >> packages are >> installed properly. > > I'm sorry for the troubles you ran into. We'll try and do better for > the final release of 1.5.2. Actually your hard work is benifiting the whole community and we all owe you a Thank You. From gwu at molbio.mgh.harvard.edu Sat Nov 18 03:44:45 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:44:45 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Message-ID: <455EC7FD.5010707@molbio.mgh.harvard.edu> Hi Nathan, Thanks for your message. I saw the C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you use 'install Bundle::BioPerl', which will definitely frustrate a bunch of users. Can this release be held for a while before most of the bugs are cleared? Thanks again. Gang Gang Nathan Haigh wrote: > Hi Gang, > > At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - we are > in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things wrong > with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). > > I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such that it > may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 and > CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as > dependencies will fail to install. > > I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - these > will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. > > If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install process > much easier to the users. > > Thanks > Nathan > > > Quoting gang wu : > > >> Hi everyone, >> >> I saw some problems when installing BioPerl >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could >> not solve all the dependency issues with one shot of 'install >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >> installed. And it turned out that CPAN refused to install BioPerl with >> some test return value 255. Then I went to /root/.cpan/build to >> configure, test, rebuild those problematic packages. After several more >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >> successfully. >> >> Below attached is the output of CPAN, which stills complains three >> packages have issues: Data::Stag::writer HTTP::Request::Common- >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in >> the Bundle::BioPerl. And the third module is not on the server and could >> be found on the CPAN site. >> >> So my question is : Is this the right way to install BioPerl? It took me >> two days to figure it out but still not 100% sure all packages are >> installed properly. >> >> Any feedback is appreciated. >> >> Gang >> >> ================================================= >> cpan> install Bundle::BioPerl >> Ace is up to date. >> Bio::ASN1::EntrezGene is up to date. >> Class::AutoClass is up to date. >> Clone is up to date. >> Convert::Binary::C is up to date. >> Running install for module Data::Stag::writer >> >> The module Data::Stag::writer isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i Data::Stag::writer'. >> DBD::mysql is up to date. >> GD::SVG is up to date. >> GD is up to date. >> Graph::Directed is up to date. >> HTML::Parser is up to date. >> Running install for module HTTP::Request::Common- >> >> The module HTTP::Request::Common- isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i HTTP::Request::Common-'. >> LWP::UserAgent is up to date. >> Set::Scalar is up to date. >> SOAP::Lite is up to date. >> Running install for module Spreadhseet::ParseExcel >> >> The module Spreadhseet::ParseExcel isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i Spreadhseet::ParseExcel'. >> Storable is up to date. >> SVG is up to date. >> SVG::Graph is up to date. >> Text::Shellwords is up to date. >> XML::DOM::XPath is up to date. >> XML::Parser::PerlSAX is up to date. >> XML::SAX is up to date. >> XML::SAX::Base is up to date. >> XML::SAX::Writer is up to date. >> XML::Simple is up to date. >> XML::Twig is up to date. >> XML::Writer is up to date. >> Bundle summary: The following items in bundle Bundle::BioPerl had >> installation problems: >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >> ==================================================== >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 gwu at molbio.mgh.harvard.edu Sat Nov 18 03:57:49 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:57:49 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <455EC4A6.4040103@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> Message-ID: <455ECB0D.5090606@molbio.mgh.harvard.edu> Hi everyone, I used to use MySQL to host the BioSQL schema and load Genbank into it with the 'load_seqdatabase.pl' without problem(except extremely slow. It took about 12 hours to load Arabidopsis thaliana). I just loaded the BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database without problem. When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with MySQL while always saw an error with Oracle: Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. , where the code is $sth->bind_param(); Any idea what the problem is? Gang From N.Haigh at sheffield.ac.uk Sat Nov 18 04:56:57 2006 From: N.Haigh at sheffield.ac.uk (Nathan Haigh) Date: Sat, 18 Nov 2006 09:56:57 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EC7FD.5010707@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> Message-ID: <1163843817.455ed8e970075@webmail.shef.ac.uk> Hi Chris, Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it contains some errors. I think Sendu *may* have some further instructions regarding this package a bit closer to the 1.5.2 release. Cheers Nathan Quoting gang wu : > Hi Nathan, > > Thanks for your message. I saw the > C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you > use 'install Bundle::BioPerl', which will definitely frustrate a bunch > of users. Can this release be held for a while before most of the bugs > are cleared? > > Thanks again. > Gang > > > Gang > > Nathan Haigh wrote: > > Hi Gang, > > > > At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - > we are > > in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things > wrong > > with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). > > > > I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such > that it > > may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 > and > > CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as > > dependencies will fail to install. > > > > I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - > these > > will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. > > > > If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install > process > > much easier to the users. > > > > Thanks > > Nathan > > > > > > Quoting gang wu : > > > > > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > >> > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in > >> the Bundle::BioPerl. And the third module is not on the server and could > >> be found on the CPAN site. > >> > >> So my question is : Is this the right way to install BioPerl? It took me > >> two days to figure it out but still not 100% sure all packages are > >> installed properly. > >> > >> Any feedback is appreciated. > >> > >> Gang > >> > >> ================================================= > >> cpan> install Bundle::BioPerl > >> Ace is up to date. > >> Bio::ASN1::EntrezGene is up to date. > >> Class::AutoClass is up to date. > >> Clone is up to date. > >> Convert::Binary::C is up to date. > >> Running install for module Data::Stag::writer > >> > >> The module Data::Stag::writer isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i Data::Stag::writer'. > >> DBD::mysql is up to date. > >> GD::SVG is up to date. > >> GD is up to date. > >> Graph::Directed is up to date. > >> HTML::Parser is up to date. > >> Running install for module HTTP::Request::Common- > >> > >> The module HTTP::Request::Common- isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i HTTP::Request::Common-'. > >> LWP::UserAgent is up to date. > >> Set::Scalar is up to date. > >> SOAP::Lite is up to date. > >> Running install for module Spreadhseet::ParseExcel > >> > >> The module Spreadhseet::ParseExcel isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i Spreadhseet::ParseExcel'. > >> Storable is up to date. > >> SVG is up to date. > >> SVG::Graph is up to date. > >> Text::Shellwords is up to date. > >> XML::DOM::XPath is up to date. > >> XML::Parser::PerlSAX is up to date. > >> XML::SAX is up to date. > >> XML::SAX::Base is up to date. > >> XML::SAX::Writer is up to date. > >> XML::Simple is up to date. > >> XML::Twig is up to date. > >> XML::Writer is up to date. > >> Bundle summary: The following items in bundle Bundle::BioPerl had > >> installation problems: > >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > >> ==================================================== > >> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/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 uiuc.edu Sat Nov 18 09:35:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 18 Nov 2006 08:35:38 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163843817.455ed8e970075@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> Message-ID: It probably doesn't need to be pulled, just updated to fix errors, spelling, etc. The problems reported with GD are common and normally are due to libgd issues or C code compilation problems during the test run (the DEPENDENCIES doc and wiki page indicate this). DBI/ DBD::mysql is another one that sometimes requires finessing (I remember it giving problems on CygWin and Mac OS X). Chris D. probably just needs a list of issues that need fixing. You also have to realize we're heading into Thanksgiving so some people may be incommunicado for the time being. Spelling is the main problem. Beyond that there really isn't anything we can do about those requirements beside not requiring them (i.e. removing them then explaining that particular components won't work), but then it wouldn't be a proper Bundle package. It's a catch-22. If there isn't a place in the install docs yet some of these issues could use a bit more detail or explanation, or at least redirect to some proper installation instructions based on the platform. I think, now that this is on CPAN, you'll likely see many more questions popping up. Chris (F.) On Nov 18, 2006, at 3:56 AM, Nathan Haigh wrote: > Hi Chris, > > Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it > contains some errors. I think Sendu *may* have some further > instructions regarding > this package a bit closer to the 1.5.2 release. > > Cheers > Nathan > > > > Quoting gang wu : > >> Hi Nathan, >> >> Thanks for your message. I saw the >> C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you >> use 'install Bundle::BioPerl', which will definitely frustrate a >> bunch >> of users. Can this release be held for a while before most of the >> bugs >> are cleared? >> >> Thanks again. >> Gang >> >> >> Gang >> >> Nathan Haigh wrote: >>> Hi Gang, >>> >>> At the moment we are having a few teathing problems with CPAN >>> packages. I notice that you are trying to install the 1.5.2 >>> release candidate 3 - >> we are >>> in the final stages of getting out the official 1.5.2 developer >>> release (hopefully in the next couple of weeks). There are indeed >>> a few things >> wrong >>> with the latest Bundle::BioPerl package but we thought we'd hold >>> off updating it until the 1.5.2 release (or shortly before). >>> >>> I think that the problem with CPAN installing dependencies is >>> that it has no way to correctly ordering the installation of >>> dependencies, such >> that it >>> may be neccessary to run the install several time in order to get >>> everything installed. For example, if prerequisite 2 depends on >>> prerequisite 1 >> and >>> CPAN installs prerequisite 2 first, then it's test suite will >>> probably fail and thus the installation of the package siting >>> both these as >>> dependencies will fail to install. >>> >>> I believe you are correct in the way you are installing bioperl, >>> but we still have a few issues to sort out with regards to the >>> CPAN packages - >> these >>> will definately be sorted out by the time of the 1.5.2 release in >>> a matter of weeks. >>> >>> If anyone is aware of a way to force CPAN to install modules in a >>> specific order, please let Sendu know - we may be able to make >>> the install >> process >>> much easier to the users. >>> >>> Thanks >>> Nathan >>> >>> >>> Quoting gang wu : >>> >>> >>>> Hi everyone, >>>> >>>> I saw some problems when installing BioPerl >>>> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>>> CPAN could >>>> not solve all the dependency issues with one shot of 'install >>>> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>>> installed. And it turned out that CPAN refused to install >>>> BioPerl with >>>> some test return value 255. Then I went to /root/.cpan/build to >>>> configure, test, rebuild those problematic packages. After >>>> several more >>>> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>>> successfully. >>>> >>>> Below attached is the output of CPAN, which stills complains three >>>> packages have issues: Data::Stag::writer HTTP::Request::Common- >>>> Spreadhseet::ParseExcel. I think the first two are typos >>>> somewhere in >>>> the Bundle::BioPerl. And the third module is not on the server >>>> and could >>>> be found on the CPAN site. >>>> >>>> So my question is : Is this the right way to install BioPerl? It >>>> took me >>>> two days to figure it out but still not 100% sure all packages are >>>> installed properly. >>>> >>>> Any feedback is appreciated. >>>> >>>> Gang >>>> >>>> ================================================= >>>> cpan> install Bundle::BioPerl >>>> Ace is up to date. >>>> Bio::ASN1::EntrezGene is up to date. >>>> Class::AutoClass is up to date. >>>> Clone is up to date. >>>> Convert::Binary::C is up to date. >>>> Running install for module Data::Stag::writer >>>> >>>> The module Data::Stag::writer isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i Data::Stag::writer'. >>>> DBD::mysql is up to date. >>>> GD::SVG is up to date. >>>> GD is up to date. >>>> Graph::Directed is up to date. >>>> HTML::Parser is up to date. >>>> Running install for module HTTP::Request::Common- >>>> >>>> The module HTTP::Request::Common- isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i HTTP::Request::Common-'. >>>> LWP::UserAgent is up to date. >>>> Set::Scalar is up to date. >>>> SOAP::Lite is up to date. >>>> Running install for module Spreadhseet::ParseExcel >>>> >>>> The module Spreadhseet::ParseExcel isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i Spreadhseet::ParseExcel'. >>>> Storable is up to date. >>>> SVG is up to date. >>>> SVG::Graph is up to date. >>>> Text::Shellwords is up to date. >>>> XML::DOM::XPath is up to date. >>>> XML::Parser::PerlSAX is up to date. >>>> XML::SAX is up to date. >>>> XML::SAX::Base is up to date. >>>> XML::SAX::Writer is up to date. >>>> XML::Simple is up to date. >>>> XML::Twig is up to date. >>>> XML::Writer is up to date. >>>> Bundle summary: The following items in bundle Bundle::BioPerl had >>>> installation problems: >>>> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >>>> ==================================================== >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Sat Nov 18 12:13:10 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sat, 18 Nov 2006 12:13:10 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EC4A6.4040103@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> Message-ID: <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> What version of libgd do you have installed? With recent versions of libgd (more recent than two years old) you will not be given the chance to select whether to compile JPEG, GIF and XPM support, since these options are selected automatically by running libgd-config. Lincoln On 11/18/06, gang wu wrote: > > > Sendu Bala wrote: > > gang wu wrote: > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN > could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. > > > > What problems did you run into specifically with GD? > If I enable JPEG, GIFS and XPM, none of the test could pass. Since I > usually use only PNG for output, I can live without them. I am not sure > if it's system related problem. All of them work fine with my 32 bit > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with newer > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > >> And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > > > > Do you remember what the other problematic packages were, and what you > > had to do to get them working? > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > guess it should be XML::DOM::XPath.pm. I could not recall what other > packages had issues, but basically it's special package configuration > issue. > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in > >> the Bundle::BioPerl. And the third module is not on the server and > could > >> be found on the CPAN site. > > > > All three are typos. We'll get those fixed. > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > At the present moment, yes. For 1.5.2 I'll probably be recommending > > not using Bundle::BioPerl once I fix some other things. > > > See my another message for other issues. > > > >> It took me two days to figure it out but still not 100% sure all > >> packages are > >> installed properly. > > > > I'm sorry for the troubles you ran into. We'll try and do better for > > the final release of 1.5.2. > Actually your hard work is benifiting the whole community and we all owe > you a Thank You. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From dag at sonsorol.org Sat Nov 18 12:47:07 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Sat, 18 Nov 2006 12:47:07 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> Message-ID: <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> Hi folks, On November 17th, Victor de Jager filed a bug report with CPAN (thanks Victor!) covering the following issues with the 2.1.6 bundle: > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > > This should be Spreadsheet::ParseExcel of course. > Data::Stag::writer does not exist in CPAN, should be > Data::Stag::Writer > > Hope it helps, meanwhile I got around using the CVS version. > Best regards I immediately fixed the errors and uploaded version 2.1.7 on the same day, by now it has probably propagated through the CPAN mirror system but you can find it directly here: http://search.cpan.org/~craffi/ Please let me know directly (email: dag at sonsorol.org) if there are *other* things that need to be added or updated. Sorry for the problems with 2.1.6 -- the contents of that Bundle were given to me by someone else on Oct 17th :) and I think I was sitting on a plane at the time and did not have time to do a local CPAN test with it. My apologies. Regards, Chris On Nov 18, 2006, at 9:35 AM, Chris Fields wrote: > It probably doesn't need to be pulled, just updated to fix errors, > spelling, etc. The problems reported with GD are common and > normally are due to libgd issues or C code compilation problems > during the test run (the DEPENDENCIES doc and wiki page indicate > this). DBI/DBD::mysql is another one that sometimes requires > finessing (I remember it giving problems on CygWin and Mac OS X). > Chris D. probably just needs a list of issues that need fixing. > You also have to realize we're heading into Thanksgiving so some > people may be incommunicado for the time being. > > Spelling is the main problem. Beyond that there really isn't > anything we can do about those requirements beside not requiring > them (i.e. removing them then explaining that particular components > won't work), but then it wouldn't be a proper Bundle package. It's > a catch-22. If there isn't a place in the install docs yet some of > these issues could use a bit more detail or explanation, or at > least redirect to some proper installation instructions based on > the platform. > > I think, now that this is on CPAN, you'll likely see many more > questions popping up. > > Chris (F.) > > On Nov 18, 2006, at 3:56 AM, Nathan Haigh wrote: > >> Hi Chris, >> >> Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it >> contains some errors. I think Sendu *may* have some further >> instructions regarding >> this package a bit closer to the 1.5.2 release. >> >> Cheers >> Nathan >> >> >> >> Quoting gang wu : >> >>> Hi Nathan, >>> >>> Thanks for your message. I saw the >>> C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if >>> you >>> use 'install Bundle::BioPerl', which will definitely frustrate a >>> bunch >>> of users. Can this release be held for a while before most of the >>> bugs >>> are cleared? >>> >>> Thanks again. >>> Gang >>> >>> >>> Gang >>> >>> Nathan Haigh wrote: >>>> Hi Gang, >>>> >>>> At the moment we are having a few teathing problems with CPAN >>>> packages. I notice that you are trying to install the 1.5.2 >>>> release candidate 3 - >>> we are >>>> in the final stages of getting out the official 1.5.2 developer >>>> release (hopefully in the next couple of weeks). There are >>>> indeed a few things >>> wrong >>>> with the latest Bundle::BioPerl package but we thought we'd hold >>>> off updating it until the 1.5.2 release (or shortly before). >>>> >>>> I think that the problem with CPAN installing dependencies is >>>> that it has no way to correctly ordering the installation of >>>> dependencies, such >>> that it >>>> may be neccessary to run the install several time in order to >>>> get everything installed. For example, if prerequisite 2 depends >>>> on prerequisite 1 >>> and >>>> CPAN installs prerequisite 2 first, then it's test suite will >>>> probably fail and thus the installation of the package siting >>>> both these as >>>> dependencies will fail to install. >>>> >>>> I believe you are correct in the way you are installing bioperl, >>>> but we still have a few issues to sort out with regards to the >>>> CPAN packages - >>> these >>>> will definately be sorted out by the time of the 1.5.2 release >>>> in a matter of weeks. >>>> >>>> If anyone is aware of a way to force CPAN to install modules in >>>> a specific order, please let Sendu know - we may be able to make >>>> the install >>> process >>>> much easier to the users. >>>> >>>> Thanks >>>> Nathan >>>> >>>> >>>> Quoting gang wu : >>>> >>>> >>>>> Hi everyone, >>>>> >>>>> I saw some problems when installing BioPerl >>>>> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>>>> CPAN could >>>>> not solve all the dependency issues with one shot of 'install >>>>> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>>>> installed. And it turned out that CPAN refused to install >>>>> BioPerl with >>>>> some test return value 255. Then I went to /root/.cpan/build to >>>>> configure, test, rebuild those problematic packages. After >>>>> several more >>>>> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>>>> successfully. >>>>> >>>>> Below attached is the output of CPAN, which stills complains three >>>>> packages have issues: Data::Stag::writer HTTP::Request::Common- >>>>> Spreadhseet::ParseExcel. I think the first two are typos >>>>> somewhere in >>>>> the Bundle::BioPerl. And the third module is not on the server >>>>> and could >>>>> be found on the CPAN site. >>>>> >>>>> So my question is : Is this the right way to install BioPerl? >>>>> It took me >>>>> two days to figure it out but still not 100% sure all packages are >>>>> installed properly. >>>>> >>>>> Any feedback is appreciated. >>>>> >>>>> Gang >>>>> >>>>> ================================================= >>>>> cpan> install Bundle::BioPerl >>>>> Ace is up to date. >>>>> Bio::ASN1::EntrezGene is up to date. >>>>> Class::AutoClass is up to date. >>>>> Clone is up to date. >>>>> Convert::Binary::C is up to date. >>>>> Running install for module Data::Stag::writer >>>>> >>>>> The module Data::Stag::writer isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i Data::Stag::writer'. >>>>> DBD::mysql is up to date. >>>>> GD::SVG is up to date. >>>>> GD is up to date. >>>>> Graph::Directed is up to date. >>>>> HTML::Parser is up to date. >>>>> Running install for module HTTP::Request::Common- >>>>> >>>>> The module HTTP::Request::Common- isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i HTTP::Request::Common-'. >>>>> LWP::UserAgent is up to date. >>>>> Set::Scalar is up to date. >>>>> SOAP::Lite is up to date. >>>>> Running install for module Spreadhseet::ParseExcel >>>>> >>>>> The module Spreadhseet::ParseExcel isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i Spreadhseet::ParseExcel'. >>>>> Storable is up to date. >>>>> SVG is up to date. >>>>> SVG::Graph is up to date. >>>>> Text::Shellwords is up to date. >>>>> XML::DOM::XPath is up to date. >>>>> XML::Parser::PerlSAX is up to date. >>>>> XML::SAX is up to date. >>>>> XML::SAX::Base is up to date. >>>>> XML::SAX::Writer is up to date. >>>>> XML::Simple is up to date. >>>>> XML::Twig is up to date. >>>>> XML::Writer is up to date. >>>>> Bundle summary: The following items in bundle Bundle::BioPerl had >>>>> installation problems: >>>>> Data::Stag::writer HTTP::Request::Common- >>>>> Spreadhseet::ParseExcel >>>>> ==================================================== >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/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 > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > From n.haigh at sheffield.ac.uk Sat Nov 18 13:32:17 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Sat, 18 Nov 2006 18:32:17 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> Message-ID: <455F51B1.6000301@sheffield.ac.uk> Chris Dagdigian wrote: > > Hi folks, > > On November 17th, Victor de Jager filed a bug report with CPAN (thanks > Victor!) covering the following issues with the 2.1.6 bundle: > >> Bundle summary: The following items in bundle Bundle::BioPerl had >> installation problems: >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >> >> This should be Spreadsheet::ParseExcel of course. >> Data::Stag::writer does not exist in CPAN, should be Data::Stag::Writer >> >> Hope it helps, meanwhile I got around using the CVS version. >> Best regards > > I immediately fixed the errors and uploaded version 2.1.7 on the same > day, by now it has probably propagated through the CPAN mirror system > but you can find it directly here: > > http://search.cpan.org/~craffi/ > > Please let me know directly (email: dag at sonsorol.org) if there are > *other* things that need to be added or updated. > > Sorry for the problems with 2.1.6 -- the contents of that Bundle were > given to me by someone else on Oct 17th :) and I think I was sitting > on a plane at the time and did not have time to do a local CPAN test > with it. My apologies. > > Regards, > Chris > > That was me - my bad! :-[ Nath From hlapp at gmx.net Sat Nov 18 22:08:00 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 18 Nov 2006 22:08:00 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <455ECB0D.5090606@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> Message-ID: <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> This is very odd. I would mean that preparing the statement failed, i.e., that the generated SQL was not accepted by the server (or the Oracle client library). Which test does this happen with? Could you run the test alone in which it happens with TEST_VERBOSE turned on? E.g., $ make test_03simpleseq TEST_VERBOSE=1 if it's the simpleseq test that's causing the failure. Capture the output in a file and send it to me. -hilmar On Nov 18, 2006, at 3:57 AM, gang wu wrote: > Hi everyone, > > I used to use MySQL to host the BioSQL schema and load Genbank into it > with the 'load_seqdatabase.pl' without problem(except extremely > slow. It > took about 12 hours to load Arabidopsis thaliana). I just loaded the > BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database > without > problem. > > When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with > MySQL while always saw an error with Oracle: > Can't call method "bind_param" on an undefined value at > /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm > line 939. > > , where the code is $sth->bind_param(); > > Any idea what the problem is? > > Gang > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From gwu at molbio.mgh.harvard.edu Sat Nov 18 22:09:08 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 22:09:08 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> Message-ID: <455FCAD4.7050709@molbio.mgh.harvard.edu> Lincoln, Thanks for your message. I have gd-2.0.28-4.4E.1 and gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. Attached is the output. Gang ================================================== [root at elegans GD-2.35]# perl Makefile.PL NOTICE: This module requires libgd 2.0.28 or higher. If you are using Math::Trig 1.01 or lower, it has a bug that causes a "prerequisite not found" warning to be issued. You may safely ignore this warning. Type perl Makefile.PL -h for command-line option summary Where is libgd installed? [/usr/lib] Please choose the features that match how libgd was built: Build JPEG support? [y] Build PNG support? [y] Build FreeType support? [y] Build GIF support? [y] Build support for animated GIFs? [y] Build XPM support? [y] If you experience compile problems, please check the @INC, @LIBPATH and @LIBS arrays defined in Makefile.PL and manually adjust, if necessary. Checking if your kit is complete... Looks good Writing Makefile for GD [root at elegans GD-2.35]# make cp GD/Polyline.pm blib/lib/GD/Polyline.pm cp qd.pl blib/lib/qd.pl cp GD/Image.pm blib/lib/GD/Image.pm cp GD.pm blib/lib/GD.pm AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) cp GD/Simple.pm blib/lib/GD/Simple.pm cp GD/Polygon.pm blib/lib/GD/Polygon.pm /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc && mv GD.xsc GD.c gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c GD.xs: In function `XS_GD__Image_STORABLE_thaw': GD.xs:923: warning: cast from pointer to integer of different size GD.xs: In function `XS_GD__Image_gifanimbegin': GD.xs:990: warning: cast to pointer from integer of different size GD.xs: In function `XS_GD__Image_gifanimadd': GD.xs:1015: warning: cast to pointer from integer of different size GD.xs: In function `XS_GD__Image_gifanimend': GD.xs:1034: warning: cast to pointer from integer of different size Running Mkbootstrap for GD () chmod 644 GD.bs rm -f blib/arch/auto/GD/GD.so gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11 /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11 /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when searching for -lXpm /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when searching for -lXpm /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc chmod 755 blib/arch/auto/GD/GD.so cp GD.bs blib/arch/auto/GD/GD.bs chmod 644 blib/arch/auto/GD/GD.bs cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bdf2gdfont.pl Manifying blib/man1/bdf2gdfont.pl.1 Manifying blib/man3/GD::Polyline.3pm Manifying blib/man3/GD::Image.3pm Manifying blib/man3/GD::Simple.3pm Manifying blib/man3/GD.3pm Manifying blib/man3/GD::Polygon.3pm [root at elegans GD-2.35]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. at t/GD.t line 14 Compilation failed in require at t/GD.t line 14. BEGIN failed--compilation aborted at t/GD.t line 14. t/GD..........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-12 Failed 12/12 tests, 0.00% okay t/Polyline....Can't load '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 Compilation failed in require at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. BEGIN failed--compilation aborted at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. Compilation failed in require at t/Polyline.t line 10. BEGIN failed--compilation aborted at t/Polyline.t line 10. t/Polyline....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED test 1 Failed 1/1 tests, 0.00% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/GD.t 255 65280 12 23 191.67% 1-12 t/Polyline.t 255 65280 1 2 200.00% 1 Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. make: *** [test_dynamic] Error 255 [root at elegans GD-2.35]# =========================================================== Lincoln Stein wrote: > What version of libgd do you have installed? With recent versions of > libgd (more recent than two years old) you will not be given the > chance to select whether to compile JPEG, GIF and XPM support, since > these options are selected automatically by running libgd-config. > > Lincoln > > On 11/18/06, *gang wu* > wrote: > > > Sendu Bala wrote: > > gang wu wrote: > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously > CPAN could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. > > > > What problems did you run into specifically with GD? > If I enable JPEG, GIFS and XPM, none of the test could pass. Since I > usually use only PNG for output, I can live without them. I am not > sure > if it's system related problem. All of them work fine with my 32 bit > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with > newer > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > >> And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After > several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > > > > Do you remember what the other problematic packages were, and > what you > > had to do to get them working? > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > guess it should be XML::DOM::XPath.pm. I could not recall what other > packages had issues, but basically it's special package > configuration issue. > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos > somewhere in > >> the Bundle::BioPerl. And the third module is not on the server > and could > >> be found on the CPAN site. > > > > All three are typos. We'll get those fixed. > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > At the present moment, yes. For 1.5.2 I'll probably be recommending > > not using Bundle::BioPerl once I fix some other things. > > > See my another message for other issues. > > > >> It took me two days to figure it out but still not 100% sure all > >> packages are > >> installed properly. > > > > I'm sorry for the troubles you ran into. We'll try and do better for > > the final release of 1.5.2. > Actually your hard work is benifiting the whole community and we > all owe > you a Thank You. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu From bix at sendu.me.uk Sun Nov 19 10:51:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 19 Nov 2006 15:51:55 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EBF53.4010701@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> Message-ID: <45607D9B.4010703@sendu.me.uk> gang wu wrote: > It turned out that most of the modules of BioPerl were not installed at > all. And none of the scripts were installed. I had to download and > install bioperl-1.5.2-RC3.tar.gz > again. A similar > problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually > copied all stuff under Bio folder to the corresponding Perl library > folder. Is it Ok to do it in this way? It will work, but is hardly good enough from our point of view (you shouldn't have to do that). Can you tell me exactly what you mean by 'were not installed'? What did you do to try and install? How did you determine that installation had failed? With CPAN, if you were still getting errors during testing, what were those remaining errors, and did you do a forced install to ignore the errors? If a forced install didn't actually install anything, what message did CPAN give you about that, if any? With the manual download, after doing "perl Makefile.PL", what is your output of "make install"? Thank you, Sendu. From lincoln.stein at gmail.com Sun Nov 19 10:54:11 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sun, 19 Nov 2006 10:54:11 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455FCAD4.7050709@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> <455FCAD4.7050709@molbio.mgh.harvard.edu> Message-ID: <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> That's very odd. gd.0.28 should install gdlib-config, and the existence of this executable should inhibit the interactive questions. Could you see if there's a gdlib-config executable installed on your system? Lincoln On 11/18/06, gang wu wrote: > > Lincoln, > Thanks for your message. I have gd-2.0.28-4.4E.1 and > gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. > Attached is the output. > > Gang > > ================================================== > [root at elegans GD-2.35]# perl Makefile.PL > NOTICE: This module requires libgd 2.0.28 or higher. > > If you are using Math::Trig 1.01 or lower, it has a bug that > causes a "prerequisite not found" warning to be issued. You may > safely ignore this warning. > > Type perl Makefile.PL -h for command-line option summary > > > Where is libgd installed? [/usr/lib] > > Please choose the features that match how libgd was built: > Build JPEG support? [y] > Build PNG support? [y] > Build FreeType support? [y] > Build GIF support? [y] > Build support for animated GIFs? [y] > Build XPM support? [y] > > If you experience compile problems, please check the @INC, @LIBPATH and > @LIBS > arrays defined in Makefile.PL and manually adjust, if necessary. > > Checking if your kit is complete... > Looks good > Writing Makefile for GD > [root at elegans GD-2.35]# make > cp GD/Polyline.pm blib/lib/GD/Polyline.pm > cp qd.pl blib/lib/qd.pl > cp GD/Image.pm blib/lib/GD/Image.pm > cp GD.pm blib/lib/GD.pm > AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) > cp GD/Simple.pm blib/lib/GD/Simple.pm > cp GD/Polygon.pm blib/lib/GD/Polygon.pm > /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap > /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc > && mv GD.xsc GD.c > gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE > -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g > -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC > "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG > -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c > GD.xs: In function `XS_GD__Image_STORABLE_thaw': > GD.xs:923: warning: cast from pointer to integer of different size > GD.xs: In function `XS_GD__Image_gifanimbegin': > GD.xs:990: warning: cast to pointer from integer of different size > GD.xs: In function `XS_GD__Image_gifanimadd': > GD.xs:1015: warning: cast to pointer from integer of different size > GD.xs: In function `XS_GD__Image_gifanimend': > GD.xs:1034: warning: cast to pointer from integer of different size > Running Mkbootstrap for GD () > chmod 644 GD.bs > rm -f blib/arch/auto/GD/GD.so > gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 > -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 > -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm > /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz > /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz > /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm > /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when > searching for -lX11 > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when > searching for -lX11 > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when > searching for -lXpm > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when > searching for -lXpm > /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc > /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc > chmod 755 blib/arch/auto/GD/GD.so > cp GD.bs blib/arch/auto/GD/GD.bs > chmod 644 blib/arch/auto/GD/GD.bs > cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" > blib/script/bdf2gdfont.pl > Manifying blib/man1/bdf2gdfont.pl.1 > Manifying blib/man3/GD::Polyline.3pm > Manifying blib/man3/GD::Image.3pm > Manifying blib/man3/GD::Simple.3pm > Manifying blib/man3/GD.3pm > Manifying blib/man3/GD::Polygon.3pm > [root at elegans GD-2.35]# make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: > ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at > /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. > at t/GD.t line 14 > Compilation failed in require at t/GD.t line 14. > BEGIN failed--compilation aborted at t/GD.t line 14. > t/GD..........dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-12 > Failed 12/12 tests, 0.00% okay > t/Polyline....Can't load > '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: > /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: > gdImageGifAnimAddPtr at > /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. > at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 > Compilation failed in require at > /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. > BEGIN failed--compilation aborted at > /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. > Compilation failed in require at t/Polyline.t line 10. > BEGIN failed--compilation aborted at t/Polyline.t line 10. > t/Polyline....dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED test 1 > Failed 1/1 tests, 0.00% okay > Failed Test Stat Wstat Total Fail Failed List of Failed > > ------------------------------------------------------------------------------- > t/GD.t 255 65280 12 23 191.67% 1-12 > t/Polyline.t 255 65280 1 2 200.00% 1 > Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. > make: *** [test_dynamic] Error 255 > [root at elegans GD-2.35]# > =========================================================== > > Lincoln Stein wrote: > > What version of libgd do you have installed? With recent versions of > > libgd (more recent than two years old) you will not be given the > > chance to select whether to compile JPEG, GIF and XPM support, since > > these options are selected automatically by running libgd-config. > > > > Lincoln > > > > On 11/18/06, *gang wu* > > wrote: > > > > > > Sendu Bala wrote: > > > gang wu wrote: > > >> Hi everyone, > > >> > > >> I saw some problems when installing BioPerl > > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously > > CPAN could > > >> not solve all the dependency issues with one shot of 'install > > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > > >> installed. > > > > > > What problems did you run into specifically with GD? > > If I enable JPEG, GIFS and XPM, none of the test could pass. Since > I > > usually use only PNG for output, I can live without them. I am not > > sure > > if it's system related problem. All of them work fine with my 32 bit > > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with > > newer > > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > > > >> And it turned out that CPAN refused to install BioPerl with > > >> some test return value 255. Then I went to /root/.cpan/build to > > >> configure, test, rebuild those problematic packages. After > > several more > > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > > >> successfully. > > > > > > Do you remember what the other problematic packages were, and > > what you > > > had to do to get them working? > > > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > > guess it should be XML::DOM::XPath.pm. I could not recall what other > > packages had issues, but basically it's special package > > configuration issue. > > >> Below attached is the output of CPAN, which stills complains > three > > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > > >> Spreadhseet::ParseExcel. I think the first two are typos > > somewhere in > > >> the Bundle::BioPerl. And the third module is not on the server > > and could > > >> be found on the CPAN site. > > > > > > All three are typos. We'll get those fixed. > > > > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > > > At the present moment, yes. For 1.5.2 I'll probably be > recommending > > > not using Bundle::BioPerl once I fix some other things. > > > > > See my another message for other issues. > > > > > >> It took me two days to figure it out but still not 100% sure all > > >> packages are > > >> installed properly. > > > > > > I'm sorry for the troubles you ran into. We'll try and do better > for > > > the final release of 1.5.2. > > Actually your hard work is benifiting the whole community and we > > all owe > > you a Thank You. > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From lincoln.stein at gmail.com Sun Nov 19 12:22:25 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sun, 19 Nov 2006 12:22:25 -0500 Subject: [Bioperl-l] [Gmod-gbrowse] aggregators issue? In-Reply-To: <455CE3CE.4060305@mail.med.upenn.edu> References: <455CE3CE.4060305@mail.med.upenn.edu> Message-ID: <6dce9a0b0611190922h7eb79928y46104c17266eccce@mail.gmail.com> Hi, What you want to do is what the heterogeneous_segments glyph does. The redgreen_box glyph originally only operated on the top level feature and not with aggregated features. However, since what you want to do is reasonable I've added a new color_subparts option, so that you will get the right effect with this modified stanza: [Linkage2] feature = qtl color_subparts = 1 glyph = redgreen_box key = Linkage2 You'll need to update bioperl to get this fix. The xyplot issue that you reported was a real bug in bioperl. This has now been fixed in both the release candidate and HEAD CVS repositories. Lincoln On 11/16/06, mmorley wrote: > > Hello All, > > Not sure where the problem lies but I'm trying to display results from a > Linkage analysis (many really).. > Perhaps my logic on the data structure is wrong but I have a peak > (locus,QTL,etc) that exceeds some defined significance that I have > predefined. > Within each peak there are markers (SNPs in this case) each with a level > of significance(score). Instead of displaying each SNP value as say in > XY plot... I have a score for the SNP to SNP interval.. The idea being > is I'd like to display the data using the redgreen_box glyph. > > To make it easier I created a little small test set which can be placed > on the Volvox tutorial ctgA > > Here is the gff data: > ---------------------------------------- > ctgA test peak 0 40000 . . . peak 3 ; Note > "EIF4G2" > ctgA test signal 0 1 0.4 . . peak 3 ; > ctgA test signal 2 25000 0.7 . . peak 3 ; > ctgA test signal 25000 35000 0.6 . . peak 3 ; > ctgA test signal 35000 40000 0.5 . . peak 3 ; > ctgA test peak 0 40000 . . . peak 10 ; Note "LRAP" > ctgA test signal 0 1 0.3 . . peak 10 ; > ctgA test signal 2 25000 0.4 . . peak 10 ; > ctgA test signal 25000 35000 0.7 . . peak 10 ; > ctgA test signal 35000 40000 0.5 . . peak 10 ; > --------------------------------------------------- > > here is my aggregator: > -------------------------------------- > qtl{signal/peak} > ----------------------------------------- > and my track: > --------------------------------------------- > [Linkage2] > feature = qtl > glyph = redgreen_box > key = Linkage2 > ------------------------------------------- > > right now very basic... the problem is well nothing is displayed using > that track... I do however get the label for each printed.. but no > graphic. If I change the feature to "signal" I do get data plotted but > each signal is on a different line,which is expected but not what I want. > > Also as a side note if I decide to plot the data as an xy_plot using the > following track stanza: > [Linkage] > feature = qtl > glyph = xyplot > graph_type = line > height = 50 > min_score = 0 > max_score = 1 > scale = right > key = Linkage > > I get both peaks plotted but within the same plot... However a second > plot is created it is just empty. > > Hopefully I'm convening this well... and if not hopefully fairly easy to > test... > > > -Mike > > > -- > Michael Morley > Bioinformatics Specialist > University of Pennsylvania > Department of Pediatrics > 3516 Civic Center Blvd., > 510B Abramson Pediatric Research Center, > Philadelphia, PA 19104-4318. > Phone: (215) 590-7673 > FAX: (215) 590-3709 > > > > > > > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From pmiguel at purdue.edu Sun Nov 19 19:58:42 2006 From: pmiguel at purdue.edu (Phillip SanMiguel) Date: Sun, 19 Nov 2006 19:58:42 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <45607D9B.4010703@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> Message-ID: <4560FDC2.4000309@purdue.edu> Sendu Bala wrote: > gang wu wrote: > >> It turned out that most of the modules of BioPerl were not installed at >> all. And none of the scripts were installed. I had to download and >> install bioperl-1.5.2-RC3.tar.gz >> again. A similar >> problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually >> copied all stuff under Bio folder to the corresponding Perl library >> folder. Is it Ok to do it in this way? >> > > It will work, but is hardly good enough from our point of view (you > shouldn't have to do that). > > Can you tell me exactly what you mean by 'were not installed'? What did > you do to try and install? How did you determine that installation had > failed? > > [...] My guess is that he thought that bioperl bundle installed the dependencies *and* bioperl itself. That was my presumption the first time I saw it on CPAN. -- Phillip From bikash_lohia2000 at yahoo.com Mon Nov 20 07:45:38 2006 From: bikash_lohia2000 at yahoo.com (bikash lohia) Date: Mon, 20 Nov 2006 04:45:38 -0800 (PST) Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi Message-ID: <20061120124538.40740.qmail@web54205.mail.yahoo.com> hello group, I am new to this group and want a help.i have list of accesion id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to manually search gene database of NCBI for converting this accession no. of cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i want to do it through perl programming where the program directly takes the list of id ( such as AK105331,Ak070197) from notepad file and searches in gene database of ncbi. to give results in accession id starting with OS****** .i want only the accession id of corresponding Ak***** id. for example - AK070197 of nucleotide databse = Os02g0669100 of gene database. i want to convert all this AK***** ids to OS***** ids through programming in perl/bioperl as manually not possible for long list. please help. i have no idea how can the code be. with thanks in advance from Bikash --------------------------------- Everyone is raving about the all-new Yahoo! Mail beta. From sdavis2 at mail.nih.gov Mon Nov 20 08:31:48 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 08:31:48 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi In-Reply-To: <20061120124538.40740.qmail@web54205.mail.yahoo.com> References: <20061120124538.40740.qmail@web54205.mail.yahoo.com> Message-ID: <200611200831.49098.sdavis2@mail.nih.gov> On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean From sdavis2 at mail.nih.gov Mon Nov 20 08:31:48 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 08:31:48 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi In-Reply-To: <20061120124538.40740.qmail@web54205.mail.yahoo.com> References: <20061120124538.40740.qmail@web54205.mail.yahoo.com> Message-ID: <200611200831.49098.sdavis2@mail.nih.gov> On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean From avilella at gmail.com Mon Nov 20 09:53:08 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 20 Nov 2006 14:53:08 +0000 Subject: [Bioperl-l] mmap perl Message-ID: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> Hi all, A bit of an off-topic: Has anyone ever investigated with libcache-mmap-perl or libcache-fastmmap-perl? Cheers, Albert. From cuiw at ncbi.nlm.nih.gov Mon Nov 20 10:45:13 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 10:45:13 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812330@NIHCESMLBX8.nih.gov> This script only works for 1 ACC to 1 Gene ID. perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 10:45:13 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 10:45:13 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812330@NIHCESMLBX8.nih.gov> This script only works for 1 ACC to 1 Gene ID. perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 11:03:44 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 11:03:44 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812332@NIHCESMLBX8.nih.gov> Correction: perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id")' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 11:03:44 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 11:03:44 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812332@NIHCESMLBX8.nih.gov> Correction: perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id")' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From gwu at molbio.mgh.harvard.edu Mon Nov 20 10:57:48 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 10:57:48 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> Message-ID: <4561D07C.4060800@molbio.mgh.harvard.edu> Hi Hilmar, Thanks for your message. Below are several tests for Oracle and MySQL. MySQL actually also has two tests with failed items which may be related to data in BioSQL database. Could it be my Oracle installation/configuration has some issues? Thanks. Gang Output of 'make test' for Oracle ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....ok 14/19Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. t/01dbadaptor.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-19 Failed 5/19 tests, 73.68% okay t/02species.......ok 5/65Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. t/02species.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-65 Failed 60/65 tests, 7.69% okay t/03simpleseq.....ok 5/59Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/03simpleseq.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-59 Failed 54/59 tests, 8.47% okay t/04swiss.........ok 5/52Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 78. t/04swiss.........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-52 Failed 47/52 tests, 9.62% okay t/05seqfeature....ok 3/48Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/05seqfeature....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 4-48 Failed 45/48 tests, 6.25% okay t/06comment.......ok 2/11Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/06comment.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-11 Failed 9/11 tests, 18.18% okay t/07dblink........ok 2/18Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/07dblink........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/08genbank.......ok 2/18Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/08genbank.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/09fuzzy2........ok 2/21Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 64. t/09fuzzy2........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-21 Failed 19/21 tests, 9.52% okay t/10ensembl.......ok 2/15Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1420. t/10ensembl.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-15 Failed 13/15 tests, 13.33% okay t/11locuslink.....ok 4/110Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/11locuslink.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-110 Failed 106/110 tests, 3.64% okay t/12ontology......ok 4/738Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 98. t/12ontology......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-738 Failed 734/738 tests, 0.54% okay t/13remove........ok 1/59Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. t/13remove........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-59 Failed 58/59 tests, 1.69% okay t/14query.........ok t/15cluster.......ok 5/160Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/15cluster.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-160 Failed 155/160 tests, 3.12% okay t/16obda..........ok 2/12Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/16obda..........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-12 Failed 10/12 tests, 16.67% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 t/02species.t 255 65280 65 120 184.62% 6-65 t/03simpleseq.t 255 65280 59 108 183.05% 6-59 t/04swiss.t 255 65280 52 94 180.77% 6-52 t/05seqfeature.t 255 65280 48 90 187.50% 4-48 t/06comment.t 255 65280 11 18 163.64% 3-11 t/07dblink.t 255 65280 18 32 177.78% 3-18 t/08genbank.t 255 65280 18 32 177.78% 3-18 t/09fuzzy2.t 255 65280 21 38 180.95% 3-21 t/10ensembl.t 255 65280 15 26 173.33% 3-15 t/11locuslink.t 255 65280 110 212 192.73% 5-110 t/12ontology.t 255 65280 738 1468 198.92% 5-738 t/13remove.t 255 65280 59 116 196.61% 2-59 t/15cluster.t 255 65280 160 310 193.75% 6-160 t/16obda.t 255 65280 12 20 166.67% 3-12 Failed 15/16 test scripts, 6.25% okay. 1347/1423 subtests failed, 5.34% okay. make: *** [test_dynamic] Error 255 ======================================================= Output of 'make test TEST_VERBOSE=1' for Oracle ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....1..19 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-19 Failed 5/19 tests, 73.68% okay t/02species.......1..65 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-65 Failed 60/65 tests, 7.69% okay t/03simpleseq.....1..59 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-59 Failed 54/59 tests, 8.47% okay t/04swiss.........1..52 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 78. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-52 Failed 47/52 tests, 9.62% okay t/05seqfeature....1..48 ok 1 ok 2 ok 3 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 4-48 Failed 45/48 tests, 6.25% okay t/06comment.......1..11 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-11 Failed 9/11 tests, 18.18% okay t/07dblink........1..18 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/08genbank.......1..18 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/09fuzzy2........1..21 todo 17; ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 64. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-21 Failed 19/21 tests, 9.52% okay t/10ensembl.......1..15 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1420. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-15 Failed 13/15 tests, 13.33% okay t/11locuslink.....1..110 ok 1 ok 2 ok 3 ok 4 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-110 Failed 106/110 tests, 3.64% okay t/12ontology......1..738 ok 1 ok 2 ok 3 ok 4 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 98. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-738 Failed 734/738 tests, 0.54% okay t/13remove........1..59 ok 1 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-59 Failed 58/59 tests, 1.69% okay t/14query.........1..18 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok t/15cluster.......1..160 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-160 Failed 155/160 tests, 3.12% okay t/16obda..........1..12 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-12 Failed 10/12 tests, 16.67% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 t/02species.t 255 65280 65 120 184.62% 6-65 t/03simpleseq.t 255 65280 59 108 183.05% 6-59 t/04swiss.t 255 65280 52 94 180.77% 6-52 t/05seqfeature.t 255 65280 48 90 187.50% 4-48 t/06comment.t 255 65280 11 18 163.64% 3-11 t/07dblink.t 255 65280 18 32 177.78% 3-18 t/08genbank.t 255 65280 18 32 177.78% 3-18 t/09fuzzy2.t 255 65280 21 38 180.95% 3-21 t/10ensembl.t 255 65280 15 26 173.33% 3-15 t/11locuslink.t 255 65280 110 212 192.73% 5-110 t/12ontology.t 255 65280 738 1468 198.92% 5-738 t/13remove.t 255 65280 59 116 196.61% 2-59 t/15cluster.t 255 65280 160 310 193.75% 6-160 t/16obda.t 255 65280 12 20 166.67% 3-12 Failed 15/16 test scripts, 6.25% okay. 1347/1423 subtests failed, 5.34% okay. make: *** [test_dynamic] Error 255 ======================================================= Output of 'make test' for MySQL =================================================== [root at elegans bioperl-db-1.5.2-RC3]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....ok t/02species.......FAILED tests 11, 14-40, 49-119 Failed 99/65 tests, -52.31% okay t/03simpleseq.....ok t/04swiss.........ok t/05seqfeature....ok t/06comment.......ok t/07dblink........ok t/08genbank.......ok t/09fuzzy2........ok t/10ensembl.......ok t/11locuslink.....ok t/12ontology......ok t/13remove........ok t/14query.........ok t/15cluster.......ok 155/160 -------------------- WARNING --------------------- MSG: failed to store one or more child objects for an instance of class Bio::Cluster::UniGene (PK=168) --------------------------------------------------- t/15cluster.......ok t/16obda..........ok Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/02species.t 65 136 209.23% 11 14-40 49-119 Failed 1/16 test scripts, 93.75% okay. 28/1423 subtests failed, 98.03% okay. make: *** [test_dynamic] Error 255 ====================================================== Output of 'make test_02species TEST_VERBOSE=1' for MySQL ====================================================== [root at elegans bioperl-db-1.5.2-RC3]# make test_02species TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests @ARGV;' t/02species.t t/02species....1..65 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 not ok 11 # Test 11 got: '29' (t/02species.t at line 45) # Expected: '11' ok 12 ok 13 not ok 14 # Test 14 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 49 fail #3) # Expected: 'Hominidae' not ok 15 # Test 15 got: 'Hominidae' (t/02species.t at line 49 fail #4) # Expected: 'Catarrhini' not ok 16 # Test 16 got: 'Hominoidea' (t/02species.t at line 49 fail #5) # Expected: 'Primates' not ok 17 # Test 17 got: 'Catarrhini' (t/02species.t at line 49 fail #6) # Expected: 'Eutheria' not ok 18 # Test 18 got: 'Simiiformes' (t/02species.t at line 49 fail #7) # Expected: 'Mammalia' not ok 19 # Test 19 got: 'Haplorrhini' (t/02species.t at line 49 fail #8) # Expected: 'Vertebrata' not ok 20 # Test 20 got: 'Primates' (t/02species.t at line 49 fail #9) # Expected: 'Chordata' not ok 21 # Test 21 got: 'Euarchontoglires' (t/02species.t at line 49 fail #10) # Expected: 'Metazoa' not ok 22 # Test 22 got: 'Eutheria' (t/02species.t at line 49 fail #11) # Expected: 'Eukaryota' not ok 23 # Failed test 23 in t/02species.t at line 49 fail #12 not ok 24 # Failed test 24 in t/02species.t at line 49 fail #13 not ok 25 # Failed test 25 in t/02species.t at line 49 fail #14 not ok 26 # Failed test 26 in t/02species.t at line 49 fail #15 not ok 27 # Failed test 27 in t/02species.t at line 49 fail #16 not ok 28 # Failed test 28 in t/02species.t at line 49 fail #17 not ok 29 # Failed test 29 in t/02species.t at line 49 fail #18 not ok 30 # Failed test 30 in t/02species.t at line 49 fail #19 not ok 31 # Failed test 31 in t/02species.t at line 49 fail #20 not ok 32 # Failed test 32 in t/02species.t at line 49 fail #21 not ok 33 # Failed test 33 in t/02species.t at line 49 fail #22 not ok 34 # Failed test 34 in t/02species.t at line 49 fail #23 not ok 35 # Failed test 35 in t/02species.t at line 49 fail #24 not ok 36 # Failed test 36 in t/02species.t at line 49 fail #25 not ok 37 # Failed test 37 in t/02species.t at line 49 fail #26 not ok 38 # Failed test 38 in t/02species.t at line 49 fail #27 not ok 39 # Failed test 39 in t/02species.t at line 49 fail #28 not ok 40 # Failed test 40 in t/02species.t at line 49 fail #29 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 not ok 49 # Test 49 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 63 fail #3) # Expected: 'Hominidae' not ok 50 # Test 50 got: 'Hominidae' (t/02species.t at line 63 fail #4) # Expected: 'Catarrhini' not ok 51 # Test 51 got: 'Hominoidea' (t/02species.t at line 63 fail #5) # Expected: 'Primates' not ok 52 # Test 52 got: 'Catarrhini' (t/02species.t at line 63 fail #6) # Expected: 'Eutheria' not ok 53 # Test 53 got: 'Simiiformes' (t/02species.t at line 63 fail #7) # Expected: 'Mammalia' not ok 54 # Test 54 got: 'Haplorrhini' (t/02species.t at line 63 fail #8) # Expected: 'Vertebrata' not ok 55 # Test 55 got: 'Primates' (t/02species.t at line 63 fail #9) # Expected: 'Chordata' not ok 56 # Test 56 got: 'Euarchontoglires' (t/02species.t at line 63 fail #10) # Expected: 'Metazoa' not ok 57 # Test 57 got: 'Eutheria' (t/02species.t at line 63 fail #11) # Expected: 'Eukaryota' not ok 58 # Failed test 58 in t/02species.t at line 63 fail #12 not ok 59 # Failed test 59 in t/02species.t at line 63 fail #13 not ok 60 # Failed test 60 in t/02species.t at line 63 fail #14 not ok 61 # Failed test 61 in t/02species.t at line 63 fail #15 not ok 62 # Failed test 62 in t/02species.t at line 63 fail #16 not ok 63 # Failed test 63 in t/02species.t at line 63 fail #17 not ok 64 # Failed test 64 in t/02species.t at line 63 fail #18 not ok 65 # Failed test 65 in t/02species.t at line 63 fail #19 not ok 66 # Failed test 66 in t/02species.t at line 63 fail #20 not ok 67 # Failed test 67 in t/02species.t at line 63 fail #21 not ok 68 # Failed test 68 in t/02species.t at line 63 fail #22 not ok 69 # Failed test 69 in t/02species.t at line 63 fail #23 not ok 70 # Failed test 70 in t/02species.t at line 63 fail #24 not ok 71 # Failed test 71 in t/02species.t at line 63 fail #25 not ok 72 # Failed test 72 in t/02species.t at line 63 fail #26 not ok 73 # Failed test 73 in t/02species.t at line 63 fail #27 not ok 74 # Failed test 74 in t/02species.t at line 63 fail #28 not ok 75 # Failed test 75 in t/02species.t at line 63 fail #29 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 not ok 90 # Test 90 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 91 fail #3) # Expected: 'Hominidae' not ok 91 # Test 91 got: 'Hominidae' (t/02species.t at line 91 fail #4) # Expected: 'Catarrhini' not ok 92 # Test 92 got: 'Hominoidea' (t/02species.t at line 91 fail #5) # Expected: 'Primates' not ok 93 # Test 93 got: 'Catarrhini' (t/02species.t at line 91 fail #6) # Expected: 'Eutheria' not ok 94 # Test 94 got: 'Simiiformes' (t/02species.t at line 91 fail #7) # Expected: 'Mammalia' not ok 95 # Test 95 got: 'Haplorrhini' (t/02species.t at line 91 fail #8) # Expected: 'Vertebrata' not ok 96 # Test 96 got: 'Primates' (t/02species.t at line 91 fail #9) # Expected: 'Chordata' not ok 97 # Test 97 got: 'Euarchontoglires' (t/02species.t at line 91 fail #10) # Expected: 'Metazoa' not ok 98 # Test 98 got: 'Eutheria' (t/02species.t at line 91 fail #11) # Expected: 'Eukaryota' not ok 99 # Failed test 99 in t/02species.t at line 91 fail #12 not ok 100 # Failed test 100 in t/02species.t at line 91 fail #13 not ok 101 # Failed test 101 in t/02species.t at line 91 fail #14 not ok 102 # Failed test 102 in t/02species.t at line 91 fail #15 not ok 103 # Failed test 103 in t/02species.t at line 91 fail #16 not ok 104 # Failed test 104 in t/02species.t at line 91 fail #17 not ok 105 # Failed test 105 in t/02species.t at line 91 fail #18 not ok 106 # Failed test 106 in t/02species.t at line 91 fail #19 not ok 107 # Failed test 107 in t/02species.t at line 91 fail #20 not ok 108 # Failed test 108 in t/02species.t at line 91 fail #21 not ok 109 # Failed test 109 in t/02species.t at line 91 fail #22 not ok 110 # Failed test 110 in t/02species.t at line 91 fail #23 not ok 111 # Failed test 111 in t/02species.t at line 91 fail #24 not ok 112 # Failed test 112 in t/02species.t at line 91 fail #25 not ok 113 # Failed test 113 in t/02species.t at line 91 fail #26 not ok 114 # Failed test 114 in t/02species.t at line 91 fail #27 not ok 115 # Failed test 115 in t/02species.t at line 91 fail #28 not ok 116 # Failed test 116 in t/02species.t at line 91 fail #29 ok 117 ok 118 ok 119 FAILED tests 11, 14-40, 49-119 Failed 99/65 tests, -52.31% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/02species.t 65 136 209.23% 11 14-40 49-119 Failed 1/1 test scripts, 0.00% okay. 28/65 subtests failed, 56.92% okay. make: *** [test_02species] Error 255 ======================================================= Output of 'make test_15cluster TEST_VERBOSE=1' for MySQL ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test_15cluster TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests @ARGV;' t/15cluster.t t/15cluster....1..160 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 -------------------- WARNING --------------------- MSG: failed to store one or more child objects for an instance of class Bio::Cluster::UniGene (PK=201) --------------------------------------------------- ok 156 ok 157 ok 158 ok 159 ok 160 ok All tests successful. Files=1, Tests=160, 18 wallclock secs ( 4.39 cusr + 0.37 csys = 4.76 CPU) ======================================================= Hilmar Lapp wrote: > This is very odd. I would mean that preparing the statement failed, > i.e., that the generated SQL was not accepted by the server (or the > Oracle client library). > > Which test does this happen with? > > Could you run the test alone in which it happens with TEST_VERBOSE > turned on? E.g., > > $ make test_03simpleseq TEST_VERBOSE=1 > > if it's the simpleseq test that's causing the failure. Capture the > output in a file and send it to me. > > -hilmar > > On Nov 18, 2006, at 3:57 AM, gang wu wrote: > >> Hi everyone, >> >> I used to use MySQL to host the BioSQL schema and load Genbank into it >> with the 'load_seqdatabase.pl' without problem(except extremely slow. It >> took about 12 hours to load Arabidopsis thaliana). I just loaded the >> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database without >> problem. >> >> When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with >> MySQL while always saw an error with Oracle: >> Can't call method "bind_param" on an undefined value at >> /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm >> >> line 939. >> >> , where the code is $sth->bind_param(); >> >> Any idea what the problem is? >> >> Gang >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > --=========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > > From dmessina at wustl.edu Mon Nov 20 11:31:55 2006 From: dmessina at wustl.edu (David Messina) Date: Mon, 20 Nov 2006 10:31:55 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4560FDC2.4000309@purdue.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> Message-ID: On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: > [...] > My guess is that he thought that bioperl bundle installed the > dependencies *and* bioperl itself. That was my presumption the first > time I saw it on CPAN. Me too, actually. Perhaps there could be a big, bold warning displayed when using CPAN to install Bundle::BioPerl, saying something like "you will still need to install BioPerl separately by doing ..." ? Likewise, I think the INSTALL document that comes with the BioPerl distribution (and on the wiki) implies the difference between BioPerl and Bundle::BioPerl but doesn't say so explicitly. I'd be happy to add this to INSTALL if there are no objections... Dave From sdavis2 at mail.nih.gov Mon Nov 20 12:23:33 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 12:23:33 -0500 Subject: [Bioperl-l] mmap perl In-Reply-To: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> References: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> Message-ID: <200611201223.33703.sdavis2@mail.nih.gov> On Monday 20 November 2006 09:53, Albert Vilella wrote: > Hi all, > > A bit of an off-topic: > > Has anyone ever investigated with libcache-mmap-perl or > libcache-fastmmap-perl? Hi, Albert. You will probably need to be more specific here. Yes, there are perl implementations of MANY caching schemes. Sean From cjfields at uiuc.edu Mon Nov 20 12:36:41 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 11:36:41 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: Message-ID: <000301c70cca$70f8d030$15327e82@pyrimidine> > On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: > > [...] > > My guess is that he thought that bioperl bundle installed the > > dependencies *and* bioperl itself. That was my presumption > the first > > time I saw it on CPAN. > > Me too, actually. > > Perhaps there could be a big, bold warning displayed when > using CPAN to install Bundle::BioPerl, saying something like > "you will still need to install BioPerl separately by doing ..." ? > > Likewise, I think the INSTALL document that comes with the > BioPerl distribution (and on the wiki) implies the difference > between BioPerl and Bundle::BioPerl but doesn't say so explicitly. > > I'd be happy to add this to INSTALL if there are no objections... > > Dave Dave, Go ahead. We need to also make the change on the wiki in the relevant pages. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 20 12:46:02 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 20 Nov 2006 17:46:02 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> Message-ID: <4561E9DA.3020002@sendu.me.uk> David Messina wrote: > On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: >> [...] >> My guess is that he thought that bioperl bundle installed the >> dependencies *and* bioperl itself. That was my presumption the first >> time I saw it on CPAN. > > Me too, actually. > > Perhaps there could be a big, bold warning displayed when using CPAN > to install Bundle::BioPerl, saying something like "you will still > need to install BioPerl separately by doing ..." ? > > Likewise, I think the INSTALL document that comes with the BioPerl > distribution (and on the wiki) implies the difference between BioPerl > and Bundle::BioPerl but doesn't say so explicitly. The description for Bundle::BioPerl (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) says: "NOTE: This Bundle does not install BioPerl" > I'd be happy to add this to INSTALL if there are no objections... I'll be changing the INSTALL docs to say not to use Bundle::BioPerl when installing with CPAN (you don't need it). Bundle::BioPerl is only for convenience when installing manually from archives or CVS. From cjfields at uiuc.edu Mon Nov 20 12:52:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 11:52:12 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4561D07C.4060800@molbio.mgh.harvard.edu> Message-ID: <000701c70ccc$9b9c9360$15327e82@pyrimidine> > Hi Hilmar, > > Thanks for your message. Below are several tests for Oracle > and MySQL. > MySQL actually also has two tests with failed items which may > be related to data in BioSQL database. > > Could it be my Oracle installation/configuration has some issues? > > Thanks. > > Gang ... You stated in a previous post that you had preloaded taxonomy; the various species test fails may be from that. Hilmar pointed out in a previous thread that tests require a BioSQL database without NCBI taxonomy loaded (i.e. just the schema). The INSTALL doc should now state that. As for the rest, could it be the DBharness.biosql.conf file setup, which assumes MySQL by default? If you switch to Oracle you have to indicate the proper DBD driver in the conf file: ... # DBD driver to use - mandatory 'driver' => 'oracle', ... Chris > Hilmar Lapp wrote: > > This is very odd. I would mean that preparing the statement failed, > > i.e., that the generated SQL was not accepted by the server (or the > > Oracle client library). > > > > Which test does this happen with? > > > > Could you run the test alone in which it happens with TEST_VERBOSE > > turned on? E.g., > > > > $ make test_03simpleseq TEST_VERBOSE=1 > > > > if it's the simpleseq test that's causing the failure. Capture the > > output in a file and send it to me. > > > > -hilmar > > > > On Nov 18, 2006, at 3:57 AM, gang wu wrote: > > > >> Hi everyone, > >> > >> I used to use MySQL to host the BioSQL schema and load > Genbank into it > >> with the 'load_seqdatabase.pl' without problem(except > extremely slow. It > >> took about 12 hours to load Arabidopsis thaliana). I just > loaded the > >> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy > database without > >> problem. > >> > >> When I 'make test' with bioperl-db-1.5.2.R3, all tests can > pass with > >> MySQL while always saw an error with Oracle: > >> Can't call method "bind_param" on an undefined value at > >> > /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ BasePersistenceAdaptor.pm > >> > >> line 939. > >> > >> , where the code is $sth->bind_param(); > >> > >> Any idea what the problem is? > >> > >> Gang > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > --=========================================================== > > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > > =========================================================== > > > > > > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From dmessina at wustl.edu Mon Nov 20 13:34:27 2006 From: dmessina at wustl.edu (David Messina) Date: Mon, 20 Nov 2006 12:34:27 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4561E9DA.3020002@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> <4561E9DA.3020002@sendu.me.uk> Message-ID: <911B53D4-1E95-4B52-A604-DA3C776EB71A@wustl.edu> On Nov 20, 2006, at 11:46 AM, Sendu Bala wrote: > The description for Bundle::BioPerl > (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) > > says: > "NOTE: This Bundle does not install BioPerl" Right, but if you are in the CPAN shell, you won't see that: cpan[2]> b Bundle::BioPerl CPAN_USERID CRAFFI (Chris Dagdigian ) CPAN_VERSION 2.001008 CPAN_FILE C/CR/CRAFFI/Bundle-BioPerl-2.1.8.tar.gz UPLOAD_DATE 2006-11-18 MANPAGE Bundle::BioPerl - A bundle to install external CPAN modules used by BioPerl 1.5.2 CONTAINS Ace Bio::ASN1::EntrezGene Class::AutoClass Clone Convert::Binary::C Data::Stag::Writer DBD::mysql GD::SVG GD Graph::Directed HTML::Parser HTTP::Request::Common LWP::UserAgent Set::Scalar SOAP::Lite Spreadsheet::ParseExcel Storable SVG SVG::Graph Text::Shellwords XML::DOM::XPath XML::Parser::PerlSAX XML::SAX XML::SAX::Base XML::SAX::Writer XML::Simple XML::Twig XML::Writer INST_FILE /Users/davemessina/.cpan/Bundle/BioPerl.pm INST_VERSION 2.1.8 Nor if you type: cpan[6]> readme Bundle::BioPerl Not to make too much of this (some will miss it no matter how many warnings there are), but I am suggesting that it could be a little more noticeable, that's all. > I'll be changing the INSTALL docs to say not to use Bundle::BioPerl > when installing with CPAN (you don't need it). Bundle::BioPerl is > only for convenience when installing manually from archives or CVS. Ah, okay, great, Sendu. I didn't know that. ;) I'll leave it to you, then. Dave From gwu at molbio.mgh.harvard.edu Mon Nov 20 13:31:34 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:31:34 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <45607D9B.4010703@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> Message-ID: <4561F486.9050601@molbio.mgh.harvard.edu> Hi Sendu, I think the package was not installed at all. The only thing I saw in the Bio folder is ANS1 which was another package(I mistakenly thought it's the only package installed by Bundle-BioPerl 2.1.16). I did not force install with CPAN. So is it possible that the three typos forbid bioperl be installed? Thanks. Gang Sendu Bala wrote: > gang wu wrote: >> It turned out that most of the modules of BioPerl were not installed >> at all. And none of the scripts were installed. I had to download and >> install bioperl-1.5.2-RC3.tar.gz >> again. A similar >> problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually >> copied all stuff under Bio folder to the corresponding Perl library >> folder. Is it Ok to do it in this way? > > It will work, but is hardly good enough from our point of view (you > shouldn't have to do that). > > Can you tell me exactly what you mean by 'were not installed'? What > did you do to try and install? How did you determine that installation > had failed? > > With CPAN, if you were still getting errors during testing, what were > those remaining errors, and did you do a forced install to ignore the > errors? If a forced install didn't actually install anything, what > message did CPAN give you about that, if any? > > With the manual download, after doing "perl Makefile.PL", what is your > output of "make install"? > > > Thank you, > Sendu. From gwu at molbio.mgh.harvard.edu Mon Nov 20 13:39:55 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:39:55 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> <455FCAD4.7050709@molbio.mgh.harvard.edu> <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> Message-ID: <4561F67B.7070401@molbio.mgh.harvard.edu> No gdlib-config was found on my system. The rpm is the newest version from Redhat AS 4 channel for AMD/EM64T. Do you think I need to update the package myself? Thanks Gang Lincoln Stein wrote: > That's very odd. gd.0.28 should install gdlib-config, and the existence of > this executable should inhibit the interactive questions. Could you see if > there's a gdlib-config executable installed on your system? > > Lincoln > > On 11/18/06, gang wu wrote: > >> Lincoln, >> Thanks for your message. I have gd-2.0.28-4.4E.1 and >> gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. >> Attached is the output. >> >> Gang >> >> ================================================== >> [root at elegans GD-2.35]# perl Makefile.PL >> NOTICE: This module requires libgd 2.0.28 or higher. >> >> If you are using Math::Trig 1.01 or lower, it has a bug that >> causes a "prerequisite not found" warning to be issued. You may >> safely ignore this warning. >> >> Type perl Makefile.PL -h for command-line option summary >> >> >> Where is libgd installed? [/usr/lib] >> >> Please choose the features that match how libgd was built: >> Build JPEG support? [y] >> Build PNG support? [y] >> Build FreeType support? [y] >> Build GIF support? [y] >> Build support for animated GIFs? [y] >> Build XPM support? [y] >> >> If you experience compile problems, please check the @INC, @LIBPATH and >> @LIBS >> arrays defined in Makefile.PL and manually adjust, if necessary. >> >> Checking if your kit is complete... >> Looks good >> Writing Makefile for GD >> [root at elegans GD-2.35]# make >> cp GD/Polyline.pm blib/lib/GD/Polyline.pm >> cp qd.pl blib/lib/qd.pl >> cp GD/Image.pm blib/lib/GD/Image.pm >> cp GD.pm blib/lib/GD.pm >> AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) >> cp GD/Simple.pm blib/lib/GD/Simple.pm >> cp GD/Polygon.pm blib/lib/GD/Polygon.pm >> /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap >> /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc >> && mv GD.xsc GD.c >> gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE >> -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include >> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g >> -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC >> "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG >> -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c >> GD.xs: In function `XS_GD__Image_STORABLE_thaw': >> GD.xs:923: warning: cast from pointer to integer of different size >> GD.xs: In function `XS_GD__Image_gifanimbegin': >> GD.xs:990: warning: cast to pointer from integer of different size >> GD.xs: In function `XS_GD__Image_gifanimadd': >> GD.xs:1015: warning: cast to pointer from integer of different size >> GD.xs: In function `XS_GD__Image_gifanimend': >> GD.xs:1034: warning: cast to pointer from integer of different size >> Running Mkbootstrap for GD () >> chmod 644 GD.bs >> rm -f blib/arch/auto/GD/GD.so >> gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 >> -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 >> -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm >> /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz >> /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz >> /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm >> /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when >> searching for -lX11 >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when >> searching for -lX11 >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when >> searching for -lXpm >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when >> searching for -lXpm >> /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc >> /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc >> chmod 755 blib/arch/auto/GD/GD.so >> cp GD.bs blib/arch/auto/GD/GD.bs >> chmod 644 blib/arch/auto/GD/GD.bs >> cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" >> blib/script/bdf2gdfont.pl >> Manifying blib/man1/bdf2gdfont.pl.1 >> Manifying blib/man3/GD::Polyline.3pm >> Manifying blib/man3/GD::Image.3pm >> Manifying blib/man3/GD::Simple.3pm >> Manifying blib/man3/GD.3pm >> Manifying blib/man3/GD::Polygon.3pm >> [root at elegans GD-2.35]# make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: >> ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at >> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. >> at t/GD.t line 14 >> Compilation failed in require at t/GD.t line 14. >> BEGIN failed--compilation aborted at t/GD.t line 14. >> t/GD..........dubious >> >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-12 >> Failed 12/12 tests, 0.00% okay >> t/Polyline....Can't load >> '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: >> /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: >> gdImageGifAnimAddPtr at >> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. >> at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 >> Compilation failed in require at >> /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. >> BEGIN failed--compilation aborted at >> /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. >> Compilation failed in require at t/Polyline.t line 10. >> BEGIN failed--compilation aborted at t/Polyline.t line 10. >> t/Polyline....dubious >> >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED test 1 >> Failed 1/1 tests, 0.00% okay >> Failed Test Stat Wstat Total Fail Failed List of Failed >> >> ------------------------------------------------------------------------------- >> t/GD.t 255 65280 12 23 191.67% 1-12 >> t/Polyline.t 255 65280 1 2 200.00% 1 >> Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. >> make: *** [test_dynamic] Error 255 >> [root at elegans GD-2.35]# >> =========================================================== >> >> Lincoln Stein wrote: >> >>> What version of libgd do you have installed? With recent versions of >>> libgd (more recent than two years old) you will not be given the >>> chance to select whether to compile JPEG, GIF and XPM support, since >>> these options are selected automatically by running libgd-config. >>> >>> Lincoln >>> >>> On 11/18/06, *gang wu* >> > wrote: >>> >>> >>> Sendu Bala wrote: >>> > gang wu wrote: >>> >> Hi everyone, >>> >> >>> >> I saw some problems when installing BioPerl >>> >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>> CPAN could >>> >> not solve all the dependency issues with one shot of 'install >>> >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>> >> installed. >>> > >>> > What problems did you run into specifically with GD? >>> If I enable JPEG, GIFS and XPM, none of the test could pass. Since >>> >> I >> >>> usually use only PNG for output, I can live without them. I am not >>> sure >>> if it's system related problem. All of them work fine with my 32 bit >>> Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with >>> newer >>> libgd runnig Redhat AS4 AMD/EM64T does not work. >>> > >>> >> And it turned out that CPAN refused to install BioPerl with >>> >> some test return value 255. Then I went to /root/.cpan/build to >>> >> configure, test, rebuild those problematic packages. After >>> several more >>> >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>> >> successfully. >>> > >>> > Do you remember what the other problematic packages were, and >>> what you >>> > had to do to get them working? >>> > >>> XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I >>> guess it should be XML::DOM::XPath.pm. I could not recall what other >>> packages had issues, but basically it's special package >>> configuration issue. >>> >> Below attached is the output of CPAN, which stills complains >>> >> three >> >>> >> packages have issues: Data::Stag::writer HTTP::Request::Common- >>> >> Spreadhseet::ParseExcel. I think the first two are typos >>> somewhere in >>> >> the Bundle::BioPerl. And the third module is not on the server >>> and could >>> >> be found on the CPAN site. >>> > >>> > All three are typos. We'll get those fixed. >>> > >>> > >>> >> So my question is : Is this the right way to install BioPerl? >>> > >>> > At the present moment, yes. For 1.5.2 I'll probably be >>> >> recommending >> >>> > not using Bundle::BioPerl once I fix some other things. >>> > >>> See my another message for other issues. >>> > >>> >> It took me two days to figure it out but still not 100% sure all >>> >> packages are >>> >> installed properly. >>> > >>> > I'm sorry for the troubles you ran into. We'll try and do better >>> >> for >> >>> > the final release of 1.5.2. >>> Actually your hard work is benifiting the whole community and we >>> all owe >>> you a Thank You. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 >>> (516) 367-8380 (voice) >>> (516) 367-8389 (fax) >>> FOR URGENT MESSAGES & SCHEDULING, >>> PLEASE CONTACT MY ASSISTANT, >>> SANDRA MICHELSEN, AT michelse at cshl.edu >>> >> > > > From gwu at molbio.mgh.harvard.edu Mon Nov 20 13:54:46 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:54:46 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4561E9DA.3020002@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> <4561E9DA.3020002@sendu.me.uk> Message-ID: <4561F9F6.5020700@molbio.mgh.harvard.edu> Sendu Bala wrote: > David Messina wrote: > >> On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: >> >>> [...] >>> My guess is that he thought that bioperl bundle installed the >>> dependencies *and* bioperl itself. That was my presumption the first >>> time I saw it on CPAN. >>> >> Me too, actually. >> >> Perhaps there could be a big, bold warning displayed when using CPAN >> to install Bundle::BioPerl, saying something like "you will still >> need to install BioPerl separately by doing ..." ? >> >> Likewise, I think the INSTALL document that comes with the BioPerl >> distribution (and on the wiki) implies the difference between BioPerl >> and Bundle::BioPerl but doesn't say so explicitly. >> > > The description for Bundle::BioPerl > (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) > > says: > "NOTE: This Bundle does not install BioPerl" > > > >> I'd be happy to add this to INSTALL if there are no objections... >> > > I'll be changing the INSTALL docs to say not to use Bundle::BioPerl when > installing with CPAN (you don't need it). Bundle::BioPerl is only for > convenience when installing manually from archives or CVS. > This can save a lot of time and confusion. But why can't BioPerl be installed with Bundle::BioPerl when using CPAN? It sounds convenient. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From gwu at molbio.mgh.harvard.edu Mon Nov 20 14:40:56 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 14:40:56 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000701c70ccc$9b9c9360$15327e82@pyrimidine> References: <000701c70ccc$9b9c9360$15327e82@pyrimidine> Message-ID: <456204C8.8000404@molbio.mgh.harvard.edu> Chris Fields wrote: >> Hi Hilmar, >> >> Thanks for your message. Below are several tests for Oracle >> and MySQL. >> MySQL actually also has two tests with failed items which may >> be related to data in BioSQL database. >> >> Could it be my Oracle installation/configuration has some issues? >> >> Thanks. >> >> Gang >> > > ... > > You stated in a previous post that you had preloaded taxonomy; the various > species test fails may be from that. Hilmar pointed out in a previous > thread that tests require a BioSQL database without NCBI taxonomy loaded > (i.e. just the schema). The INSTALL doc should now state that. > You are right, all tests can pass for MySQL after unloading NCBI Taxonomy data. But output for Oracle tests were not affected. Thanks. > As for the rest, could it be the DBharness.biosql.conf file setup, which > assumes MySQL by default? If you switch to Oracle you have to indicate the > proper DBD driver in the conf file: > > ... > > # DBD driver to use - mandatory > 'driver' => 'oracle', > > ... > > I did change the configuration, or it can not pass the DBI connection tests. Below is part of my parameters: 'driver' => 'Oracle', 'host' => 'elegans', 'user' => 'biosqldb_sgowner', 'port' => '1521', 'password' => 'pass', 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], 'dbname' => 'oracle_sid', 'database' => 'biosql', > Chris > > > >> Hilmar Lapp wrote: >> >>> This is very odd. I would mean that preparing the statement failed, >>> i.e., that the generated SQL was not accepted by the server (or the >>> Oracle client library). >>> >>> Which test does this happen with? >>> >>> Could you run the test alone in which it happens with TEST_VERBOSE >>> turned on? E.g., >>> >>> $ make test_03simpleseq TEST_VERBOSE=1 >>> >>> if it's the simpleseq test that's causing the failure. Capture the >>> output in a file and send it to me. >>> >>> -hilmar >>> >>> On Nov 18, 2006, at 3:57 AM, gang wu wrote: >>> >>> >>>> Hi everyone, >>>> >>>> I used to use MySQL to host the BioSQL schema and load >>>> >> Genbank into it >> >>>> with the 'load_seqdatabase.pl' without problem(except >>>> >> extremely slow. It >> >>>> took about 12 hours to load Arabidopsis thaliana). I just >>>> >> loaded the >> >>>> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy >>>> >> database without >> >>>> problem. >>>> >>>> When I 'make test' with bioperl-db-1.5.2.R3, all tests can >>>> >> pass with >> >>>> MySQL while always saw an error with Oracle: >>>> Can't call method "bind_param" on an undefined value at >>>> >>>> >> /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ >> > BasePersistenceAdaptor.pm > >>>> line 939. >>>> >>>> , where the code is $sth->bind_param(); >>>> >>>> Any idea what the problem is? >>>> >>>> Gang >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> --=========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >>> >>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > From cjfields at uiuc.edu Mon Nov 20 15:19:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 14:19:56 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <456204C8.8000404@molbio.mgh.harvard.edu> Message-ID: <000301c70ce1$3ee70190$15327e82@pyrimidine> ... > You are right, all tests can pass for MySQL after unloading > NCBI Taxonomy data. But output for Oracle tests were not > affected. Thanks. Yes, the oracle tests were by far the worst, which suggests something in the driver/configuration. > > As for the rest, could it be the DBharness.biosql.conf file setup, > > which assumes MySQL by default? If you switch to Oracle > you have to > > indicate the proper DBD driver in the conf file: > > > > ... > > > > # DBD driver to use - mandatory > > 'driver' => 'oracle', > > > > ... > > > > > I did change the configuration, or it can not pass the DBI > connection tests. Below is part of my parameters: > 'driver' => 'Oracle', > 'host' => 'elegans', > 'user' => 'biosqldb_sgowner', > 'port' => '1521', > 'password' => 'pass', > 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], > 'dbname' => 'oracle_sid', > 'database' => 'biosql', Try changing the driver to all lower case (i.e. from 'Oracle' to 'oracle'). Also, the schema_sql is still set to the mysql schema (not oracle). That shouldn't make a difference, but you never know. Hopefully that isn't your real password! Chris From gwu at molbio.mgh.harvard.edu Mon Nov 20 15:34:07 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 15:34:07 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000301c70ce1$3ee70190$15327e82@pyrimidine> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> Message-ID: <4562113F.6040306@molbio.mgh.harvard.edu> Chris Fields wrote: > ... > >> You are right, all tests can pass for MySQL after unloading >> NCBI Taxonomy data. But output for Oracle tests were not >> affected. Thanks. >> > > Yes, the oracle tests were by far the worst, which suggests something in the > driver/configuration. > > >>> As for the rest, could it be the DBharness.biosql.conf file setup, >>> which assumes MySQL by default? If you switch to Oracle >>> >> you have to >> >>> indicate the proper DBD driver in the conf file: >>> >>> ... >>> >>> # DBD driver to use - mandatory >>> 'driver' => 'oracle', >>> >>> ... >>> >>> >>> >> I did change the configuration, or it can not pass the DBI >> connection tests. Below is part of my parameters: >> 'driver' => 'Oracle', >> 'host' => 'elegans', >> 'user' => 'biosqldb_sgowner', >> 'port' => '1521', >> 'password' => 'pass', >> 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], >> 'dbname' => 'oracle_sid', >> 'database' => 'biosql', >> > > Try changing the driver to all lower case (i.e. from 'Oracle' to 'oracle'). > Also, the schema_sql is still set to the mysql schema (not oracle). That > shouldn't make a difference, but you never know. > Can not change 'Oracle' to 'oracle', the DBD driver name is DBD::Oracle. It's an odd naming inconsistence. MySQL DBD driver name is DBD::mysql. How about PostgreSQL DBD driver naming? > Hopefully that isn't your real password! > > Chris > > From ryanx07 at hotmail.com Mon Nov 20 15:42:47 2006 From: ryanx07 at hotmail.com (L Xu) Date: Mon, 20 Nov 2006 15:42:47 -0500 Subject: [Bioperl-l] Error message for installation Message-ID: I got an error message when I installed Bioperl through ActivePerl following the online instruction about window installation: ERROR: Installing File-Spec-0.82 would downgrade File::Spec from version 3.12 to 0.82 and File::Spec::Functions from version 1.3 to 1.1 and File::Spec::Mac from version 1.4 to 1.2 and File::Spec::OS2 from version 1.2 to 1.1 and File::Spec::Unix from version 1.5 to 1.2 and File::Spec::VMS from version 1.4 to 1.1 and File::Spec::Win32 from version 1.6 to 1.2 It looks like the Bioperl 1.4 using some old version files compared to ActivePerl. I wonder if these old version files can cause some problems and how to fix them. Thanks and happy thanksgiving. L _________________________________________________________________ Get FREE company branded e-mail accounts and business Web site from Microsoft Office Live http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ From hlapp at gmx.net Mon Nov 20 16:28:29 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:28:29 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4561F0F4.3060106@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> Message-ID: <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> It looks like you are using the MySQL schema under Oracle. There are different DDL scripts for each supported RDBMS. The ones for Oracle are in the sql/biosql-ora subdirectory. Note the INSTALL document in that directory. -hilmar On Nov 20, 2006, at 1:16 PM, gang wu wrote: > Hi Hilmar, > > Below is the output. Thanks. > > Gang > ========================================================== > [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 > [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor > TEST_VERBOSE=1 > PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ > perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e > 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests > @ARGV;' t/01dbadaptor.t > t/01dbadaptor....1..19 > ok 1 > ok 2 > ok 3 > ok 4 > ok 5 > ok 6 > ok 7 > ok 8 > ok 9 > ok 10 > ok 11 > attempting to load adaptor class for BioNamespace > ok 12 > attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor > instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor > ok 13 > ok 14 > attempting to load driver for adaptor class > Bio::DB::BioSQL::BioNamespaceAdaptor > attempting to load driver for adaptor class > Bio::DB::BioSQL::BasePersistenceAdaptor > Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as > driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor > preparing UK select statement: SELECT biodatabase.oid, > biodatabase.name, biodatabase.authority FROM biodatabase WHERE name > = ? > DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": > invalid identifier (DBD ERROR: error possibly near <*> indicator at > char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = :p1') [for > Statement "SELECT biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ > Bio/DB/BioSQL/BaseDriver.pm line 1800. > BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) > Can't call method "bind_param" on an undefined value at blib/lib/ > Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. > dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-19 > Failed 5/19 tests, 73.68% okay > Failed Test Stat Wstat Total Fail Failed List of Failed > ---------------------------------------------------------------------- > --------- > t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 > Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% > okay. > make: *** [test_01dbadaptor] Error 2 > ========================================================= > > > Hilmar Lapp wrote: >> Hi Gang, >> >> what I wanted to get at was the error message from the driver when >> it fails to generate the prepared statement, but this is not in >> the output. >> >> I believe you need set the HARNESS_VERBOSE environment variable to >> 1 before testing to get what I need: >> >> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >> csh/tcsh >> $ make test_01dbadaptor TEST_VERBOSE=1 >> >> This will lead to _a lot_ of debugging output. Do not run this for >> the entire test suite. >> >> The errors for mysql I believe are related to the fact that have >> loaded the NCBI taxonomy before testing? Run the tests on a fresh >> (completely empty) instance of BioSQL. >> >> Let me know what you get for the Oracle test above. >> >> -hilmar >> >> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >> >>> Hi Hilmar, >>> >>> Thanks for your message. Below are several tests for Oracle and >>> MySQL. MySQL actually also has two tests with failed items which >>> may be related to data in BioSQL database. >>> >>> Could it be my Oracle installation/configuration has some issues? >>> >>> Thanks. >>> >>> Gang >> >> --=========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> >> -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Nov 20 16:33:50 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:33:50 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000301c70ce1$3ee70190$15327e82@pyrimidine> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> Message-ID: <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> On Nov 20, 2006, at 3:19 PM, Chris Fields wrote: > Try changing the driver to all lower case (i.e. from 'Oracle' to > 'oracle'). This can in fact be harmful. The driver-specific code is loaded from files or directories named after the driver. On case-sensitive file systems, changing the case will render those files inaccessible. > Also, the schema_sql is still set to the mysql schema (not > oracle). That > shouldn't make a difference, but you never know. It doesn't make a difference if the schema instance exists already (and I wouldn't recommend anything else). -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Nov 20 16:34:30 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:34:30 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4562113F.6040306@molbio.mgh.harvard.edu> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> <4562113F.6040306@molbio.mgh.harvard.edu> Message-ID: <24789A58-9A86-4B83-9CBB-CE2597B1DA60@gmx.net> On Nov 20, 2006, at 3:34 PM, gang wu wrote: > How about PostgreSQL DBD driver naming? DBD::Pg -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From Kevin.M.Brown at asu.edu Mon Nov 20 16:44:22 2006 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Mon, 20 Nov 2006 14:44:22 -0700 Subject: [Bioperl-l] Budle::BioPerl dependency issues Message-ID: <1A4207F8295607498283FE9E93B775B4024C58D3@EX02.asurite.ad.asu.edu> Redhat tends to have two different packages. GD and GD-devel. The first is for runtime applications to use, the other is needed to be able to build code against GD. They do this for almost all the libraries (e.g. glibc & glibc-devel, x11 and x11-devel, etc...). > No gdlib-config was found on my system. The rpm is the newest version > from Redhat AS 4 channel for AMD/EM64T. Do you think I need to update > the package myself? Thanks From n.haigh at sheffield.ac.uk Mon Nov 20 17:45:24 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 20 Nov 2006 22:45:24 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <45623004.1010807@sheffield.ac.uk> Could you answer the following questions, so that we know your setup and are better able to respond: 1) Can you confirm what version of ActivePerl you are running. 2) Can you confirm what PPM repositories you have enabled. 3) Can you confirm what version of Bioperl you tried to install. This issue has cropped up before, but I can't remember off hand exactly what the problem was, or how it was solved. I think it might be a problem with using the new PPM4 GUI to install bioperl 1.4 from the old style PPD. I'll await your response before making further comments. Thanks Nath L Xu wrote: > I got an error message when I installed Bioperl through ActivePerl following > the online instruction about window installation: > > ERROR: Installing File-Spec-0.82 would downgrade File::Spec from version > 3.12 to 0.82 and File::Spec::Functions from version 1.3 to 1.1 and > File::Spec::Mac from version 1.4 to 1.2 and File::Spec::OS2 from version 1.2 > to 1.1 and File::Spec::Unix from version 1.5 to 1.2 and File::Spec::VMS from > version 1.4 to 1.1 and File::Spec::Win32 from version 1.6 to 1.2 > > It looks like the Bioperl 1.4 using some old version files compared to > ActivePerl. I wonder if these old version files can cause some problems and > how to fix them. > > Thanks and happy thanksgiving. > > > L > > _________________________________________________________________ > Get FREE company branded e-mail accounts and business Web site from > Microsoft Office Live > http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From n.haigh at sheffield.ac.uk Mon Nov 20 17:49:51 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 20 Nov 2006 22:49:51 +0000 Subject: [Bioperl-l] Bioperl 1.4 on Windows Message-ID: <4562310F.8080403@sheffield.ac.uk> There have been at least a coupl eof posts recently about users having problems installing bioperl 1.4 using the PPM GUI shipped with ActivePerl 5.8.8.819. I think this is because the Bioperl 1.4 ppd is built for PPM3 and not PPM4. Would it make sense to update the Bioperl 1.4 PPD since it is the official "stable" release? Nath From cjfields at uiuc.edu Mon Nov 20 18:07:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 17:07:12 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> Message-ID: On Nov 20, 2006, at 3:33 PM, Hilmar Lapp wrote: > > On Nov 20, 2006, at 3:19 PM, Chris Fields wrote: > >> Try changing the driver to all lower case (i.e. from 'Oracle' to >> 'oracle'). > > This can in fact be harmful. The driver-specific code is loaded > from files or directories named after the driver. On case-sensitive > file systems, changing the case will render those files inaccessible. Yeah, just noticed that the driver is DBD::Oracle. I thought it might be lowercase, like DBD::mysql. >> Also, the schema_sql is still set to the mysql schema (not >> oracle). That >> shouldn't make a difference, but you never know. > > It doesn't make a difference if the schema instance exists already > (and I wouldn't recommend anything else). > > -hilmar The conf file indicates that as well. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Mon Nov 20 18:33:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 17:33:48 -0600 Subject: [Bioperl-l] Bioperl 1.4 on Windows In-Reply-To: <4562310F.8080403@sheffield.ac.uk> References: <4562310F.8080403@sheffield.ac.uk> Message-ID: On Nov 20, 2006, at 4:49 PM, Nathan S. Haigh wrote: > There have been at least a coupl eof posts recently about users having > problems installing bioperl 1.4 using the PPM GUI shipped with > ActivePerl 5.8.8.819. I think this is because the Bioperl 1.4 ppd is > built for PPM3 and not PPM4. Would it make sense to update the Bioperl > 1.4 PPD since it is the official "stable" release? > > Nath We could change the PPD to remove any versioning requirements. It's possible that PPM4 treats them as explicit version requirements, so instead of installing rel. X or greater, it only tries to install rel. X, which then has version requirements of it's own that PPM4 misreads. Not sure if this is a common problem with PPM4 but it's definitely bad. The best course of action for Windows users will be to update to 1.5.2 when the final version is released. The vast majority will be using it for parsing BLAST reports and retrieving sequences, both of which have undergone major revisions since 1.4 (in fact, I don't think BLAST report parsing will work if they run a BLAST version before 2.2.13). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jcv128 at psu.edu Mon Nov 20 19:52:47 2006 From: jcv128 at psu.edu (Juan Cristobal Vera) Date: Mon, 20 Nov 2006 19:52:47 -0500 Subject: [Bioperl-l] GO terms not present in Swiss annotation object Message-ID: <1164070364l.1106082l.0l@psu.edu> Hi, I'm writing a simple application to extract various fields from swissprot objects and I can't access the GO terms found in "dblink" part of the swiss format flat files. I'm not a professional programmer and I can't figure out why this is occuring. All the other "dblink" keys are being generated as far as I can tell (e.g. embl, pfam, etc). The GO terms are just skipped over and it's driving me crazy. Not sure if this is a bug or a deliberate strategy I'm unfamiliar with. I apologize if this is not the correct forum to ask for this sort of help and would ask to be directed to the proper one. Juan Cristobal Vera Graduate Student Department of Biology Penn State University 208 Mueller Laboratory University Park, PA 16802 (814)863-2957 From cjfields at uiuc.edu Tue Nov 21 01:19:59 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 00:19:59 -0600 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164070364l.1106082l.0l@psu.edu> References: <1164070364l.1106082l.0l@psu.edu> Message-ID: Juan, The DBLink objects should be generated. You'll need to give us a bit more information to go on, though. We need an example sequence, your local version of Bioperl, maybe a test script, etc. This is the right forum for this, yes, if you are using BioPerl. Chris On Nov 20, 2006, at 6:52 PM, Juan Cristobal Vera wrote: > > > Hi, > I'm writing a simple application to extract various fields from > swissprot objects and I can't access the GO terms found in > "dblink" part of the swiss format flat files. I'm not a > professional programmer and I can't figure out why this is > occuring. All the other "dblink" keys are being > generated as far as I can tell (e.g. embl, pfam, etc). The GO > terms are just skipped over and it's driving me crazy. Not sure if > this is a bug or a deliberate strategy I'm unfamiliar with. I > apologize if this is not the correct forum to ask for this sort of > help and would ask to be directed to the proper one. > > > > Juan Cristobal Vera > > Graduate Student > > Department of Biology > > Penn State University > > 208 Mueller Laboratory > > University Park, PA 16802 > > (814)863-2957 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From gwu at molbio.mgh.harvard.edu Tue Nov 21 03:11:03 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 03:11:03 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> Message-ID: <4562B497.6080805@molbio.mgh.harvard.edu> Can you show me where it indicates I am actually using the MySQL schema. I am pretty sure that I used the sql script files from sql/biosql-ora(Has anyone actually tried to install MySQL schema on Oracle?). I can reinstall the schema if you think that's the way to solve the problem. Thanks very much. Gang Hilmar Lapp wrote: > It looks like you are using the MySQL schema under Oracle. There are > different DDL scripts for each supported RDBMS. The ones for Oracle > are in the sql/biosql-ora subdirectory. Note the INSTALL document in > that directory. > > -hilmar > > > On Nov 20, 2006, at 1:16 PM, gang wu wrote: > > >> Hi Hilmar, >> >> Below is the output. Thanks. >> >> Gang >> ========================================================== >> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >> TEST_VERBOSE=1 >> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >> @ARGV;' t/01dbadaptor.t >> t/01dbadaptor....1..19 >> ok 1 >> ok 2 >> ok 3 >> ok 4 >> ok 5 >> ok 6 >> ok 7 >> ok 8 >> ok 9 >> ok 10 >> ok 11 >> attempting to load adaptor class for BioNamespace >> ok 12 >> attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor >> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >> ok 13 >> ok 14 >> attempting to load driver for adaptor class >> Bio::DB::BioSQL::BioNamespaceAdaptor >> attempting to load driver for adaptor class >> Bio::DB::BioSQL::BasePersistenceAdaptor >> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >> preparing UK select statement: SELECT biodatabase.oid, >> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >> = ? >> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >> invalid identifier (DBD ERROR: error possibly near <*> indicator at >> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >> Statement "SELECT biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >> Bio/DB/BioSQL/BaseDriver.pm line 1800. >> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >> Can't call method "bind_param" on an undefined value at blib/lib/ >> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >> dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 15-19 >> Failed 5/19 tests, 73.68% okay >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ---------------------------------------------------------------------- >> --------- >> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >> okay. >> make: *** [test_01dbadaptor] Error 2 >> ========================================================= >> >> >> Hilmar Lapp wrote: >> >>> Hi Gang, >>> >>> what I wanted to get at was the error message from the driver when >>> it fails to generate the prepared statement, but this is not in >>> the output. >>> >>> I believe you need set the HARNESS_VERBOSE environment variable to >>> 1 before testing to get what I need: >>> >>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>> csh/tcsh >>> $ make test_01dbadaptor TEST_VERBOSE=1 >>> >>> This will lead to _a lot_ of debugging output. Do not run this for >>> the entire test suite. >>> >>> The errors for mysql I believe are related to the fact that have >>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>> (completely empty) instance of BioSQL. >>> >>> Let me know what you get for the Oracle test above. >>> >>> -hilmar >>> >>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>> >>> >>>> Hi Hilmar, >>>> >>>> Thanks for your message. Below are several tests for Oracle and >>>> MySQL. MySQL actually also has two tests with failed items which >>>> may be related to data in BioSQL database. >>>> >>>> Could it be my Oracle installation/configuration has some issues? >>>> >>>> Thanks. >>>> >>>> Gang >>>> >>> --=========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >>> >>> >>> > > From n.haigh at sheffield.ac.uk Tue Nov 21 03:47:40 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 21 Nov 2006 08:47:40 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <4562BD2C.4000906@sheffield.ac.uk> L Xu wrote: > Thank you for the prompt response. Here is the information you needed: > (1)ActivePerl version 5.8.8.819 and PPM version 4.00 > (2)http://ppm4.activestate.com/MsWin32-x86/5.8/819/package.xml > http://bioperl.org/DIST/RC > http://bioperl.org/DIST > http://theoryx5.uwinnipeg.ca/ppms > http://www.Bribes.org/perl/ppm > (3)bioperl-1.4 > > Once again, thank you very much. > > L When you do a search for Bioperl, do you also get listing for Bioperl 1.5.2 RC2. If you do, try to install that and let us know how you get on. If you don't see a 1.5.2 RC2 let me know and I'll try to find out what the problem is. The PPM package is a little behind since there is an RC4 - I'll try to get the RC4 packaged today if I have time. We are hoping that RC4 is the last release candidate before the official 1.5.2 release, so if you do install the RC2 remember to upgrade the package in a week or two. Cheers Nath From er at xs4all.nl Tue Nov 21 07:16:53 2006 From: er at xs4all.nl (Erik) Date: Tue, 21 Nov 2006 13:16:53 +0100 (CET) Subject: [Bioperl-l] double-colon bug Message-ID: <6661.156.83.1.251.1164111413.squirrel@webmail.xs4all.nl> Hi all, Could one of the committers apply the fix as proposed for bug 2146 ? It's a small change: added a ':' to the regex at line 507. I did add a 'show the bug' snippet, albeit somewhat belatedly. It passes all 135 genbank tests with that change. Also, it fixes my application :) Thanks, Erik http://bugzilla.open-bio.org/show_bug.cgi?id=2146 From cjfields at uiuc.edu Tue Nov 21 08:21:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 07:21:35 -0600 Subject: [Bioperl-l] Error message for installation In-Reply-To: <4562BD2C.4000906@sheffield.ac.uk> References: <4562BD2C.4000906@sheffield.ac.uk> Message-ID: <67BD6F52-A994-4FC7-8E4F-375F21D1E1F9@uiuc.edu> All of the RCs are in their own directory; http://www.bioperl.org/DIST/RC I couldn't install 1.5.2 myself unless I set the repository to that directory. I think that's fine as long as we set the final release to the regular installation directory (http://www.bioperl.org/DIST) and use package.xml to point to the other required packages in the RC directory. Chris On Nov 21, 2006, at 2:47 AM, Nathan S. Haigh wrote: > L Xu wrote: >> Thank you for the prompt response. Here is the information you >> needed: >> (1)ActivePerl version 5.8.8.819 and PPM version 4.00 >> (2)http://ppm4.activestate.com/MsWin32-x86/5.8/819/package.xml >> http://bioperl.org/DIST/RC >> http://bioperl.org/DIST >> http://theoryx5.uwinnipeg.ca/ppms >> http://www.Bribes.org/perl/ppm >> (3)bioperl-1.4 >> >> Once again, thank you very much. >> >> L > > When you do a search for Bioperl, do you also get listing for Bioperl > 1.5.2 RC2. If you do, try to install that and let us know how you get > on. If you don't see a 1.5.2 RC2 let me know and I'll try to find out > what the problem is. > > The PPM package is a little behind since there is an RC4 - I'll try to > get the RC4 packaged today if I have time. We are hoping that RC4 > is the > last release candidate before the official 1.5.2 release, so if you do > install the RC2 remember to upgrade the package in a week or two. > > Cheers > Nath > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Tue Nov 21 09:56:29 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 21 Nov 2006 14:56:29 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <4563139D.2040108@sheffield.ac.uk> L Xu wrote: > I tried to install 1,5,2RC2, but got the following error message: > ################### > ...... > Generating HTML for Heap-0.71 ... DONE > Generating HTML for Error-0.17008 ... DONE > Generating HTML for XML-RegExp-0.03 ... DONE > Installing to site area ... failed > > ERROR: File conflict; package Bioperl-1.4 already provide > C:/Perl/html/bin/bp_aacomp.html > ########################## > Should I first uninstall Bioperl-1.4, if so how to do it? Thanks. > > > L > I'll have a look at this a bit later this afternoon. If you are using the PPM4 GUI, you should be able to right click an installed package and click remove (or something to that effect) and you will then have to apply the changes (like when you install a package). Once it's uninstalled, try installing 1.5.2 RC2 and let me know how you go. Cheers Nath From akarger at CGR.Harvard.edu Tue Nov 21 10:21:18 2006 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 21 Nov 2006 10:21:18 -0500 Subject: [Bioperl-l] Translating alternate start codons Message-ID: I think this is more a Bio question than a Bioperl question. I did this: ######### #!/usr/local/bin/perl use strict; use warnings; use Bio::Seq; use Bio::Tools::CodonTable; my $seqobj = Bio::PrimarySeq->new ( -seq => 'ATATGATAA', -id => 'GeneFragment-12', -accession_number => 'X78121', -alphabet => 'dna', ); $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; print "ATA $is a valid start codon\n"; print "Table 4: ", $seqobj->translate("-codontable_id" => 4)->seq,"\n"; print "Table 1: ", $seqobj->translate("-codontable_id" => 1)->seq,"\n"; ########### I got this: ATA is a valid start codon Table 4: IW* Table 1: I** But EMBL tells me that EMBLCDS:AAT64955 starts with an M: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[EMBLCDS:'A AT64955']+-qnum+1+-enum+3 So, does Bioperl purposely not translate start codons to M, while EMBL does? Am I supposed to just change the I to M explicitly in my code? I didn't see an obvious option to translate() to do it. Thanks, - Amir Karger Research Computing Life Sciences Division Harvard University 617-496-0626 From bix at sendu.me.uk Tue Nov 21 10:21:34 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 15:21:34 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Message-ID: <4563197E.7010909@sendu.me.uk> Nathan Haigh wrote: > > If anyone is aware of a way to force CPAN to install modules in a > specific order, please let Sendu know - we may be able to make the > install process much easier to the users. As regards the Bundle, you just have to specify the modules in the desired order. The question is, what order of installation, if any, results in no first-time failures? From akarger at CGR.Harvard.edu Tue Nov 21 11:16:01 2006 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 21 Nov 2006 11:16:01 -0500 Subject: [Bioperl-l] Translating alternate start codons Message-ID: > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > Amir, > > The best documentation for translate() is in the online > Bioperl Tutorial, > have you checked that? > > Brian O. Thanks for the quick response. The tutorial is quite informative. It seems to me that the POD needs to document -complete more thoroughly, though: Or if you expect a complete coding sequence (CDS) translation, with inititator at the beginning and terminator at the end: $protein_seq_obj = $cds_seq_obj->translate(-complete => 1); This doesn't really explain what it does. I guess -complete was chosen as a compromise between having too many options and having lots of functionality. In my case, I want to keep the *, and I don't want warnings about terminators in the middle, because I've got a bunch of pseudogenes. So I'll just translate the M myself. I'm sure you've had many "the documentation is spread out in too many places" discussions before, and I know keeping docs up to date is Hard. Oh well. -Amir > > > On 11/21/06 10:21 AM, "Amir Karger" wrote: > > > I think this is more a Bio question than a Bioperl question. > > > > I did this: > > > > ######### > > #!/usr/local/bin/perl > > > > use strict; > > use warnings; > > > > use Bio::Seq; > > use Bio::Tools::CodonTable; > > > > my $seqobj = Bio::PrimarySeq->new ( > > -seq => 'ATATGATAA', > > -id => 'GeneFragment-12', > > -accession_number => 'X78121', > > -alphabet => 'dna', > > ); > > > > $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); > > my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; > > print "ATA $is a valid start codon\n"; > > print "Table 4: ", $seqobj->translate("-codontable_id" => > 4)->seq,"\n"; > > print "Table 1: ", $seqobj->translate("-codontable_id" => > 1)->seq,"\n"; > > ########### > > > > I got this: > > ATA is a valid start codon > > Table 4: IW* > > Table 1: I** > > > > But EMBL tells me that EMBLCDS:AAT64955 starts with an M: > > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ > EMBLCDS:'A > > AT64955']+-qnum+1+-enum+3 > > > > So, does Bioperl purposely not translate start codons to M, > while EMBL > > does? Am I supposed to just change the I to M explicitly in > my code? I > > didn't see an obvious option to translate() to do it. > > > > Thanks, > > > > - Amir Karger > > Research Computing > > Life Sciences Division > > Harvard University > > 617-496-0626 > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From gwu at molbio.mgh.harvard.edu Tue Nov 21 12:00:55 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 12:00:55 -0500 Subject: [Bioperl-l] Two BioPerl-1.5.2-RC3 installation issues Message-ID: <456330C7.1020801@molbio.mgh.harvard.edu> When installing bioperl-1.5.2RC3, I chose to run the BioDBGFF tests with MySQL database. Below is the warning message. =============================================== Checking if your kit is complete... Warning: the following files are missing in your kit: t/BioDBSeqFeature_mysql.t Please inform the author. Writing Makefile for Bio =============================================== Another thins is the installation of Bio-ASN1-EntrezGene-1.09, the 'make test' requires bioperl be preinstalled(Bio::Index::...) while bioperl requires it be preinstalled. Is this a circle reference issue? Gang Gang From bix at sendu.me.uk Tue Nov 21 12:31:37 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:31:37 +0000 Subject: [Bioperl-l] Two BioPerl-1.5.2-RC3 installation issues In-Reply-To: <456330C7.1020801@molbio.mgh.harvard.edu> References: <456330C7.1020801@molbio.mgh.harvard.edu> Message-ID: <456337F9.6090001@sendu.me.uk> gang wu wrote: > When installing bioperl-1.5.2RC3, I chose to run the BioDBGFF tests with > MySQL database. Below is the warning message. > =============================================== > Checking if your kit is complete... > Warning: the following files are missing in your kit: > t/BioDBSeqFeature_mysql.t > Please inform the author. > Writing Makefile for Bio > =============================================== That should get resolved in RC4. > Another thins is the installation of Bio-ASN1-EntrezGene-1.09, the 'make > test' requires bioperl be preinstalled(Bio::Index::...) while bioperl > requires it be preinstalled. Is this a circle reference issue? Yes it is. You'll have to force install one of them. Again, it should get resolved in RC4 (Bio::ASN1::EntrezGene won't be a requirement). Thank you for your feedback, Sendu. From bix at sendu.me.uk Tue Nov 21 12:41:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:41:04 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read Message-ID: <45633A30.7060009@sendu.me.uk> With the new Build.PL, when it does its check to see if optional external modules are installed or not, for each module that isn't installed I can print out details of what Bioperl modules need it and why and then ask if you'd like to install that module before proceeding. This is obviously very useful for people doing one-off installations from CPAN, giving them informed choices and letting them avoid any problems with particular external modules (vs. having all or nothing by installing Bundle::BioPerl). But for developers, if you choose not to install a module, you'll keep getting asked if you want to install it every time you run Build.PL. So the question is, would this be too annoying? How often do you run Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I run it all the time because I'm developing the thing and trying to sort out installation issues, but would it bother anyone else? Cheers, Sendu. From bix at sendu.me.uk Tue Nov 21 12:45:46 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:45:46 +0000 Subject: [Bioperl-l] Changing default reply-to on this list Message-ID: <45633B4A.6060804@sendu.me.uk> Hi, I'd like to propose changing the default reply-to for posts on this list from the current 'reply to the poster' to 'reply to the mailing list'. That way people can just hit 'reply' instead of 'reply to all' in order to get a reply back to the list. If people then changed the current habit of 'reply to all' to just 'reply' it would avoid people being replied to getting multiple copies of the reply - one direct, a second from the mailing list. Cheers, Sendu. From stefan.kirov at bms.com Tue Nov 21 13:08:02 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 13:08:02 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: <45634082.6040001@bms.com> Sendu, This is not a problem - see prerequisites_policy ask/follow options for CPAN config. Hope this helps. Stefan Sendu Bala wrote: > With the new Build.PL, when it does its check to see if optional > external modules are installed or not, for each module that isn't > installed I can print out details of what Bioperl modules need it and > why and then ask if you'd like to install that module before proceeding. > > This is obviously very useful for people doing one-off installations > from CPAN, giving them informed choices and letting them avoid any > problems with particular external modules (vs. having all or nothing by > installing Bundle::BioPerl). > > But for developers, if you choose not to install a module, you'll keep > getting asked if you want to install it every time you run Build.PL. > > So the question is, would this be too annoying? How often do you run > Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I > run it all the time because I'm developing the thing and trying to sort > out installation issues, but would it bother anyone else? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bix at sendu.me.uk Tue Nov 21 13:17:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 18:17:10 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45634082.6040001@bms.com> References: <45633A30.7060009@sendu.me.uk> <45634082.6040001@bms.com> Message-ID: <456342A6.4060000@sendu.me.uk> Stefan Kirov wrote: > Sendu, > This is not a problem - see > prerequisites_policy ask/follow > options for CPAN config. That does not apply to the situation I describe. The follow policy applies to required modules when installing with CPAN. I am talking about installing modules that are /not/ required when using CPAN and even when /not/ using CPAN to do an installation. From n.haigh at sheffield.ac.uk Tue Nov 21 13:20:15 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 21 Nov 2006 18:20:15 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <4563435F.5010400@sheffield.ac.uk> Sendu Bala wrote: > Hi, > > I'd like to propose changing the default reply-to for posts on this list > from the current 'reply to the poster' to 'reply to the mailing list'. > That way people can just hit 'reply' instead of 'reply to all' in order > to get a reply back to the list. > > If people then changed the current habit of 'reply to all' to just > 'reply' it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > I don't seem to get multiple copies! However, the first reason (to just hit replay) is reason enough to change the default behaviour! :-) Nath From stefan.kirov at bms.com Tue Nov 21 13:24:39 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 13:24:39 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <456342A6.4060000@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> <45634082.6040001@bms.com> <456342A6.4060000@sendu.me.uk> Message-ID: <45634467.5010300@bms.com> Sendu Bala wrote: > Stefan Kirov wrote: >> Sendu, >> This is not a problem - see >> prerequisites_policy ask/follow >> options for CPAN config. > > That does not apply to the situation I describe. The follow policy > applies to required modules when installing with CPAN. I am talking > about installing modules that are /not/ required when using CPAN and > even when /not/ using CPAN to do an installation. > Sorry, I did not get that.... I personally do not run make often and would guess this to be case for most people as well. Stefan From stefan.kirov at bms.com Tue Nov 21 12:20:34 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 12:20:34 -0500 Subject: [Bioperl-l] Performance of Bio::Species Message-ID: <45633562.2030107@bms.com> New Bio::Species implementation seems to degrade significantly performance. It seems this happens when the Bio::Tree::Tree is constructed. See the stats bellow (based on simple Bio::Species object construction, script and test sequence file attached): 10000 iterrations new implementation: Constructor: 115 wallclock secs (113.50 usr + 0.67 sys = 114.17 CPU) Accessor: 0 wallclock secs ( 0.17 usr + 0.00 sys = 0.17 CPU) old implementation (bioperl-1.4 Constructor: 1 wallclock secs ( 0.84 usr + 0.10 sys = 0.94 CPU) Accessor: 0 wallclock secs ( 0.13 usr + 0.01 sys = 0.14 CPU) You can see that when reading a genbank file you would double the time necessary to construct the Bio::Seq object (100 iterations): old implementation (bioperl-1.4 Constructor: 0 wallclock secs ( 0.01 usr + 0.00 sys = 0.01 CPU) Accessor: 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU) Constructor(seqio)/reading seq: 3 wallclock secs ( 2.51 usr + 0.31 sys = 2.83 CPU) new implementation: Constructor: 2 wallclock secs ( 1.14 usr + 0.01 sys = 1.15 CPU) Accessor: 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU) Constructor(seqio)/reading seq: 5 wallclock secs ( 5.10 usr + 0.20 sys = 5.30 CPU) This may not pose a problem to people who read few sequences or files with no lineage data, but it could be a significant headache otherwise. I saw from CVS that Sendu knows there are memory leaks (I find cycles). If the classification is supplied incorrectly (includes a reference to an array in the classification array) things get really messy (~17 GB of RAM for a Bio::Species object), though weird enough the cycle is not indefinite. If I have more time I will try to debug this further and submit a formal bug report/patch, but I am not sure if I will anytime soon. I am sure there are people who understand Bio::Taxon/Bio::Tree::Tree better than me and might have better idea how to fix this. Stefan /// use Bio::Species; use Benchmark; use Bio::SeqIO; my @classification=qw( sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota ); my $species; my $t1 = new Benchmark; for my $i (1..100) { $species = Bio::Species->new(-classification => [@classification]); } my $t2 = new Benchmark; for my $i (1..100) { my $bin = $species->binomial; } my $t3 = new Benchmark; print "Constructor: ", timestr(timediff($t2, $t1)),"\n"; print "Accessor: ", timestr(timediff($t3, $t2)),"\n"; my $f=shift; my $t4= new Benchmark; for my $i (1..100) { my $sio=new Bio::SeqIO(-file=>$f,-format=>'genbank'); my $seq=$sio->next_seq; } my $t5= new Benchmark; print "Constructor(seqio)/reading seq: ", timestr(timediff($t5, $t4)),"\n"; -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: NM_000161.genbank Url: http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061121/5d9e857e/attachment.pl From dmessina at wustl.edu Tue Nov 21 14:06:38 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:06:38 -0600 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> > it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. This behavior can be changed by going to http://lists.open-bio.org/mailman/listinfo/bioperl-l entering your subscribed email address in the last field on the page, clicking the "unsubscribe or edit options" button to the right of that field. On the next page, enter your password in the password field and click "Log in". On the options page that you see next, the last option, called "Avoid duplicate copies of messages?", should be set to "Yes" if you don't want multiple copies. Dave From dmessina at wustl.edu Tue Nov 21 14:11:06 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:11:06 -0600 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> Would it be possible to set it up such that when the user is asked whether to install an unrequired module, the possible answers are "yes", "no", "skip all"? The latter being to skip all subsequent questions about unrequired modules. Dave From bix at sendu.me.uk Tue Nov 21 14:30:52 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:30:52 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> References: <45633A30.7060009@sendu.me.uk> <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> Message-ID: <456353EC.9030304@sendu.me.uk> David Messina wrote: > Would it be possible to set it up such that when the user is asked > whether to install an unrequired module, the possible answers are "yes", > "no", "skip all"? The latter being to skip all subsequent questions > about unrequired modules. Yes, thanks, that's a good idea. I currently (in my private copy) have the default as 'no', but if changed as above, should the default be to 'skip all'? Or, perhaps have an initial question 'do you want to be asked to install optional modules you don't have' would be better? From hlapp at gmx.net Tue Nov 21 14:33:11 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:33:11 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4562B497.6080805@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> Message-ID: The Oracle error is ORA-00904: "BIODATABASE"."OID": invalid identifier and if you look at the accompanying statement, it's the UK select statement: SELECT <*>biodatabase.oid, biodatabase.name, biodatabase.authority FROM biodatabase WHERE name = :p1 The column OID must exist in the Biodatabase table (which actually is a synonym to the SG_BIODATABASE table), if it is the Oracle schema. This actually prompts another suggestion, sorry for not asking that first: did you actually install the BioSQL-API on top of the schema by running the script BS-create-Biosql-API.sql? (It seems that the statement it chokes on is also the first statement being prepared, so this may well be the reason) -hilmar On Nov 21, 2006, at 3:11 AM, gang wu wrote: > Can you show me where it indicates I am actually using the MySQL > schema. > I am pretty sure that I used the sql script files from > sql/biosql-ora(Has anyone actually tried to install MySQL schema on > Oracle?). I can reinstall the schema if you think that's the way to > solve the problem. Thanks very much. > > Gang > > Hilmar Lapp wrote: >> It looks like you are using the MySQL schema under Oracle. There are >> different DDL scripts for each supported RDBMS. The ones for Oracle >> are in the sql/biosql-ora subdirectory. Note the INSTALL document in >> that directory. >> >> -hilmar >> >> >> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >> >> >>> Hi Hilmar, >>> >>> Below is the output. Thanks. >>> >>> Gang >>> ========================================================== >>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>> TEST_VERBOSE=1 >>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>> @ARGV;' t/01dbadaptor.t >>> t/01dbadaptor....1..19 >>> ok 1 >>> ok 2 >>> ok 3 >>> ok 4 >>> ok 5 >>> ok 6 >>> ok 7 >>> ok 8 >>> ok 9 >>> ok 10 >>> ok 11 >>> attempting to load adaptor class for BioNamespace >>> ok 12 >>> attempting to load module >>> Bio::DB::BioSQL::BioNamespaceAdaptor >>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>> ok 13 >>> ok 14 >>> attempting to load driver for adaptor class >>> Bio::DB::BioSQL::BioNamespaceAdaptor >>> attempting to load driver for adaptor class >>> Bio::DB::BioSQL::BasePersistenceAdaptor >>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>> preparing UK select statement: SELECT biodatabase.oid, >>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >>> = ? >>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>> invalid identifier (DBD ERROR: error possibly near <*> indicator at >>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>> Statement "SELECT biodatabase.oid, biodatabase.name, >>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >>> Can't call method "bind_param" on an undefined value at blib/lib/ >>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>> dubious >>> Test returned status 255 (wstat 65280, 0xff00) >>> DIED. FAILED tests 15-19 >>> Failed 5/19 tests, 73.68% okay >>> Failed Test Stat Wstat Total Fail Failed List of Failed >>> -------------------------------------------------------------------- >>> -- >>> --------- >>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>> okay. >>> make: *** [test_01dbadaptor] Error 2 >>> ========================================================= >>> >>> >>> Hilmar Lapp wrote: >>> >>>> Hi Gang, >>>> >>>> what I wanted to get at was the error message from the driver when >>>> it fails to generate the prepared statement, but this is not in >>>> the output. >>>> >>>> I believe you need set the HARNESS_VERBOSE environment variable to >>>> 1 before testing to get what I need: >>>> >>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>> csh/tcsh >>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>> >>>> This will lead to _a lot_ of debugging output. Do not run this for >>>> the entire test suite. >>>> >>>> The errors for mysql I believe are related to the fact that have >>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>> (completely empty) instance of BioSQL. >>>> >>>> Let me know what you get for the Oracle test above. >>>> >>>> -hilmar >>>> >>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>> >>>> >>>>> Hi Hilmar, >>>>> >>>>> Thanks for your message. Below are several tests for Oracle and >>>>> MySQL. MySQL actually also has two tests with failed items which >>>>> may be related to data in BioSQL database. >>>>> >>>>> Could it be my Oracle installation/configuration has some issues? >>>>> >>>>> Thanks. >>>>> >>>>> Gang >>>>> >>>> --=========================================================== >>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>> =========================================================== >>>> >>>> >>>> >>>> >>>> >>>> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From dmessina at wustl.edu Tue Nov 21 14:36:10 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:36:10 -0600 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <456353EC.9030304@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> <456353EC.9030304@sendu.me.uk> Message-ID: <5DF4D1D9-754F-443F-ADDE-4127C579BF82@wustl.edu> On Nov 21, 2006, at 1:30 PM, Sendu Bala wrote: > Yes, thanks, that's a good idea. I currently (in my private copy) > have the default as 'no', but if changed as above, should the > default be to 'skip all'? Yeah, that makes sense to me. > Or, perhaps have an initial question 'do you want to be asked to > install optional modules you don't have' would be better? I think that would work fine, too -- whichever is easiest for you... Dave From bix at sendu.me.uk Tue Nov 21 14:37:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:37:14 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45633562.2030107@bms.com> References: <45633562.2030107@bms.com> Message-ID: <4563556A.1050101@sendu.me.uk> Stefan Kirov wrote: > New Bio::Species implementation seems to degrade significantly > performance. It seems this happens when the Bio::Tree::Tree is constructed. > See the stats bellow (based on simple Bio::Species object construction, > script and test sequence file attached): [snip] Thanks. If you come up with anything, please file that bug report. I certainly regard this as an important thing that must be fixed, though I don't know if I should hold up release of 1.5.2 for it. Now that you've reported on it I'm leaning toward yes, since the new Bio::Species implementation is one of the major new features of 1.5.2 and it ought to work well. Anyway, for the memory leak I have some ideas I haven't tried yet; I don't know if my efforts will solve the speed issue though. If anyone can spare the time to look at the problem, please do. Cheers, Sendu. From hlapp at gmx.net Tue Nov 21 14:46:45 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:46:45 -0500 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <93D5ABA0-290A-4087-8999-4FFBA6CFD918@gmx.net> I don't think that's a good idea. First, it is really hard to reply to someone off-list that way. Second, it is especially annoying given that reply-to-poster is generally considered best-practice and so therefore almost all lists reply off-list if you just hit reply. In fact I had this set to reply-to-list on one of our (NESCent's) own listserves to help the less computer-savvy but it was so annoying that I set it back to reply-to-sender within days. Compared to that, hitting the delete key on the duplicate takes about 0.2 seconds for me and hasn't bothered me much ever. Bottom line is, if you suggest people to change their habits then it is close impossible if it is only a single place that likes to do it the other way. -hilmar On Nov 21, 2006, at 12:45 PM, Sendu Bala wrote: > Hi, > > I'd like to propose changing the default reply-to for posts on this > list >> from the current 'reply to the poster' to 'reply to the mailing >> list'. > That way people can just hit 'reply' instead of 'reply to all' in > order > to get a reply back to the list. > > If people then changed the current habit of 'reply to all' to just > 'reply' it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Nov 21 14:41:25 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:41:25 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: I typically run (ran) perl Makefile.PL when I'm forced to, i.e., if someone changed Makefile.PL in the repository and I cvs update. Or if something is just going weird, as a last resort before rebooting ;) On Nov 21, 2006, at 12:41 PM, Sendu Bala wrote: > With the new Build.PL, when it does its check to see if optional > external modules are installed or not, for each module that isn't > installed I can print out details of what Bioperl modules need it and > why and then ask if you'd like to install that module before > proceeding. > > This is obviously very useful for people doing one-off installations >> from CPAN, giving them informed choices and letting them avoid any > problems with particular external modules (vs. having all or > nothing by > installing Bundle::BioPerl). > > But for developers, if you choose not to install a module, you'll keep > getting asked if you want to install it every time you run Build.PL. > > So the question is, would this be too annoying? How often do you run > Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I > run it all the time because I'm developing the thing and trying to > sort > out installation issues, but would it bother anyone else? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Nov 21 14:56:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:56:18 -0500 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4563556A.1050101@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > I don't know if I should hold up release of 1.5.2 for it. Now that > you've > reported on it I'm leaning toward yes, since the new Bio::Species > implementation is one of the major new features of 1.5.2 and it > ought to > work well. I disagree to some extent. This is a developer release, so not everything is expected to work perfectly. What's not desirable is if fixing this required another entire redesign of the API, so that every dev release introduces different API. The thing is, you'll really only get trouble reports once you put it out and people start using it in anger. Don't expect to make it perfect before. > > Anyway, for the memory leak I have some ideas I haven't tried yet; I > don't know if my efforts will solve the speed issue though. The memory leak sounds more concerning to me. Under which circumstances would it crash a script or blow throuhg all of say 1-2GB when it should have taken only a tenth of that. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Tue Nov 21 14:58:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:58:58 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> References: <45633B4A.6060804@sendu.me.uk> <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> Message-ID: <45635A82.6070209@sendu.me.uk> David Messina wrote: >> it would avoid people being replied to getting multiple copies >> of the reply - one direct, a second from the mailing list. > > This behavior can be changed by going to > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > entering your subscribed email address in the last field on the page, > clicking the "unsubscribe or edit options" button to the right of > that field. > > On the next page, enter your password in the password field and click > "Log in". On the options page that you see next, the last option, > called "Avoid duplicate copies of messages?", should be set to "Yes" > if you don't want multiple copies. Ah, thanks for that. Given Hilmar's reply, forget the proposal. I'll just live in misery :( From bosborne11 at verizon.net Tue Nov 21 14:58:00 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 21 Nov 2006 14:58:00 -0500 Subject: [Bioperl-l] Translating alternate start codons In-Reply-To: Message-ID: Amir, I think I understand your question, perhaps not, and I think the recommended solution is to create your own "custom" codon table. See t/CodonTable.t for an example. Brian O. On 11/21/06 11:16 AM, "Amir Karger" wrote: >> From: Brian Osborne [mailto:bosborne11 at verizon.net] >> >> Amir, >> >> The best documentation for translate() is in the online >> Bioperl Tutorial, >> have you checked that? >> >> Brian O. > > Thanks for the quick response. The tutorial is quite informative. > It seems to me that the POD needs to document -complete more thoroughly, > though: > > Or if you expect a complete coding sequence (CDS) > translation, > with inititator at the beginning and terminator at the > end: > > $protein_seq_obj = $cds_seq_obj->translate(-complete > => 1); > > This doesn't really explain what it does. > > I guess -complete was chosen as a compromise between having too many > options and having lots of functionality. In my case, I want to keep the > *, and I don't want warnings about terminators in the middle, because > I've got a bunch of pseudogenes. So I'll just translate the M myself. > > I'm sure you've had many "the documentation is spread out in too many > places" discussions before, and I know keeping docs up to date is Hard. > Oh well. > > -Amir > >> >> >> On 11/21/06 10:21 AM, "Amir Karger" wrote: >> >>> I think this is more a Bio question than a Bioperl question. >>> >>> I did this: >>> >>> ######### >>> #!/usr/local/bin/perl >>> >>> use strict; >>> use warnings; >>> >>> use Bio::Seq; >>> use Bio::Tools::CodonTable; >>> >>> my $seqobj = Bio::PrimarySeq->new ( >>> -seq => 'ATATGATAA', >>> -id => 'GeneFragment-12', >>> -accession_number => 'X78121', >>> -alphabet => 'dna', >>> ); >>> >>> $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); >>> my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; >>> print "ATA $is a valid start codon\n"; >>> print "Table 4: ", $seqobj->translate("-codontable_id" => >> 4)->seq,"\n"; >>> print "Table 1: ", $seqobj->translate("-codontable_id" => >> 1)->seq,"\n"; >>> ########### >>> >>> I got this: >>> ATA is a valid start codon >>> Table 4: IW* >>> Table 1: I** >>> >>> But EMBL tells me that EMBLCDS:AAT64955 starts with an M: >>> >> http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ >> EMBLCDS:'A >>> AT64955']+-qnum+1+-enum+3 >>> >>> So, does Bioperl purposely not translate start codons to M, >> while EMBL >>> does? Am I supposed to just change the I to M explicitly in >> my code? I >>> didn't see an obvious option to translate() to do it. >>> >>> Thanks, >>> >>> - Amir Karger >>> Research Computing >>> Life Sciences Division >>> Harvard University >>> 617-496-0626 >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Tue Nov 21 15:16:18 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 20:16:18 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: <45635E92.7080000@sendu.me.uk> Hilmar Lapp wrote: > > On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > >> Anyway, for the memory leak I have some ideas I haven't tried yet; I >> don't know if my efforts will solve the speed issue though. > > The memory leak sounds more concerning to me. Under which circumstances > would it crash a script or blow throuhg all of say 1-2GB when it should > have taken only a tenth of that. Its been reported as causing problems if you do something like parse a large embl file with many (10s of thousands) sequences in it. So basically any situation that you make lots of Bio::Species objects. IIRC the reporter ran out of memory on a ~40000 sequence embl file. Neither the memory leak fix or speed fix ought to require any API change. I'm fairly certain that the memory leak, at least, is confined to a problem with (as suggested) Bio::Tree* stuff failing to clean up on destruction. There was in fact already an unnoticed problem with Bio::Tree::Node not getting cleaned up (see my #*** comment in the code), but my Bio::Species-related changes exacerbated the problem and also made them noticeable, since you're more likely to create thousands of Bio::Species than you were Bio::Tree::Node. From jason at bioperl.org Tue Nov 21 00:57:54 2006 From: jason at bioperl.org (Jason Stajich) Date: Mon, 20 Nov 2006 21:57:54 -0800 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164070364l.1106082l.0l@psu.edu> References: <1164070364l.1106082l.0l@psu.edu> Message-ID: a specific accession and example code will make it easier for someone to reproduce (and debug) your problem. On Nov 20, 2006, at 4:52 PM, Juan Cristobal Vera wrote: > > > Hi, > I'm writing a simple application to extract various fields from > swissprot objects and I can't access the GO terms found in > "dblink" part of the swiss format flat files. I'm not a > professional programmer and I can't figure out why this is > occuring. All the other "dblink" keys are being > generated as far as I can tell (e.g. embl, pfam, etc). The GO > terms are just skipped over and it's driving me crazy. Not sure if > this is a bug or a deliberate strategy I'm unfamiliar with. I > apologize if this is not the correct forum to ask for this sort of > help and would ask to be directed to the proper one. > > > > Juan Cristobal Vera > > Graduate Student > > Department of Biology > > Penn State University > > 208 Mueller Laboratory > > University Park, PA 16802 > > (814)863-2957 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason at bioperl.org http://jason.open-bio.org/ From stefan.kirov at bms.com Tue Nov 21 15:20:40 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 15:20:40 -0500 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: <45635F98.8030901@bms.com> Hilmar Lapp wrote: > On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > > >> I don't know if I should hold up release of 1.5.2 for it. Now that >> you've >> reported on it I'm leaning toward yes, since the new Bio::Species >> implementation is one of the major new features of 1.5.2 and it >> ought to >> work well. >> > > I disagree to some extent. This is a developer release, so not > everything is expected to work perfectly. > > What's not desirable is if fixing this required another entire > redesign of the API, so that every dev release introduces different API. > > The thing is, you'll really only get trouble reports once you put it > out and people start using it in anger. Don't expect to make it > perfect before. > > >> Anyway, for the memory leak I have some ideas I haven't tried yet; I >> don't know if my efforts will solve the speed issue though. >> > > The memory leak sounds more concerning to me. Under which > circumstances would it crash a script or blow throuhg all of say > 1-2GB when it should have taken only a tenth of that. > > As I was saying, I did pass ref to an array in the classification (wrong parsing): push @classification,'sapiens', 'Homo', 'Hominidae', $arrayref; and my script took 17-18 GB. I am really surprised it stopped getting more RAM and finished successfully. I did not explore further. Stefan > -hilmar > > From gwu at molbio.mgh.harvard.edu Tue Nov 21 15:33:10 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 15:33:10 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> Message-ID: <45636286.6040504@molbio.mgh.harvard.edu> Hi Hilmar, I just rebuilt the Oracle BioSQL database by strictly following the INSTALL doc. You are right that BS-create-Biosql-API.sql must be run to make bioperl-db work with it(the oid columns). But my installation problem was caused by running BS-create-Biosql-API2.sql after it, which rendered the database not compatible with bioperl-db. If I ran only BS-create-Biosql-API.sql, ll bioperl-db tests could pass. Does this mean that the Oracle version is not interoperable between the Bio- projects at this point? Did I miss anything in the INSTALL or README? I only saw a line "-- all others (Biojava, etc)" but did not realize I could not run both BS-create-Biosql-API.sql and BS-create-Biosql-API2.sql. I this is the case, can you please add it to the docs? Thanks very much for your help. Gang Hilmar Lapp wrote: > The Oracle error is > > ORA-00904: "BIODATABASE"."OID": invalid identifier > > and if you look at the accompanying statement, it's the UK select > statement: > > SELECT <*>biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = :p1 > > The column OID must exist in the Biodatabase table (which actually is > a synonym to the SG_BIODATABASE table), if it is the Oracle schema. > > This actually prompts another suggestion, sorry for not asking that > first: did you actually install the BioSQL-API on top of the schema by > running the script BS-create-Biosql-API.sql? (It seems that the > statement it chokes on is also the first statement being prepared, so > this may well be the reason) > > -hilmar > > On Nov 21, 2006, at 3:11 AM, gang wu wrote: > >> Can you show me where it indicates I am actually using the MySQL schema. >> I am pretty sure that I used the sql script files from >> sql/biosql-ora(Has anyone actually tried to install MySQL schema on >> Oracle?). I can reinstall the schema if you think that's the way to >> solve the problem. Thanks very much. >> >> Gang >> >> Hilmar Lapp wrote: >>> It looks like you are using the MySQL schema under Oracle. There are >>> different DDL scripts for each supported RDBMS. The ones for Oracle >>> are in the sql/biosql-ora subdirectory. Note the INSTALL document in >>> that directory. >>> >>> -hilmar >>> >>> >>> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >>> >>> >>>> Hi Hilmar, >>>> >>>> Below is the output. Thanks. >>>> >>>> Gang >>>> ========================================================== >>>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>>> TEST_VERBOSE=1 >>>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >>>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>>> @ARGV;' t/01dbadaptor.t >>>> t/01dbadaptor....1..19 >>>> ok 1 >>>> ok 2 >>>> ok 3 >>>> ok 4 >>>> ok 5 >>>> ok 6 >>>> ok 7 >>>> ok 8 >>>> ok 9 >>>> ok 10 >>>> ok 11 >>>> attempting to load adaptor class for BioNamespace >>>> ok 12 >>>> attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor >>>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>>> ok 13 >>>> ok 14 >>>> attempting to load driver for adaptor class >>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>> attempting to load driver for adaptor class >>>> Bio::DB::BioSQL::BasePersistenceAdaptor >>>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>>> preparing UK select statement: SELECT biodatabase.oid, >>>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >>>> = ? >>>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>>> invalid identifier (DBD ERROR: error possibly near <*> indicator at >>>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>>> Statement "SELECT biodatabase.oid, biodatabase.name, >>>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >>>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>>> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >>>> Can't call method "bind_param" on an undefined value at blib/lib/ >>>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>>> dubious >>>> Test returned status 255 (wstat 65280, 0xff00) >>>> DIED. FAILED tests 15-19 >>>> Failed 5/19 tests, 73.68% okay >>>> Failed Test Stat Wstat Total Fail Failed List of Failed >>>> ---------------------------------------------------------------------- >>>> --------- >>>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>>> okay. >>>> make: *** [test_01dbadaptor] Error 2 >>>> ========================================================= >>>> >>>> >>>> Hilmar Lapp wrote: >>>> >>>>> Hi Gang, >>>>> >>>>> what I wanted to get at was the error message from the driver when >>>>> it fails to generate the prepared statement, but this is not in >>>>> the output. >>>>> >>>>> I believe you need set the HARNESS_VERBOSE environment variable to >>>>> 1 before testing to get what I need: >>>>> >>>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>>> csh/tcsh >>>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>>> >>>>> This will lead to _a lot_ of debugging output. Do not run this for >>>>> the entire test suite. >>>>> >>>>> The errors for mysql I believe are related to the fact that have >>>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>>> (completely empty) instance of BioSQL. >>>>> >>>>> Let me know what you get for the Oracle test above. >>>>> >>>>> -hilmar >>>>> >>>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>>> >>>>> >>>>>> Hi Hilmar, >>>>>> >>>>>> Thanks for your message. Below are several tests for Oracle and >>>>>> MySQL. MySQL actually also has two tests with failed items which >>>>>> may be related to data in BioSQL database. >>>>>> >>>>>> Could it be my Oracle installation/configuration has some issues? >>>>>> >>>>>> Thanks. >>>>>> >>>>>> Gang >>>>>> >>>>> --=========================================================== >>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>>> =========================================================== >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > --=========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > > From jason at bioperl.org Tue Nov 21 11:47:37 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 21 Nov 2006 08:47:37 -0800 Subject: [Bioperl-l] Translating alternate start codons In-Reply-To: References: Message-ID: <8273f6c20611210847q7178025bm8e5367a5ae2138d4@mail.gmail.com> It seem then you don't want to use 'complete' since you don't always expect complete CDSes. Shouldn't you just translate to generate the peptide and then operate on the initial and terminal residues to achieve what you want. substr($peptide,0,1,'M'); chop($peptide) if substr($peptide,-1,1) eq $TERMINATOR; This is a community project so any help in improving apparent deficiencies in documentation are gladly welcomed - the wiki is designed to let everyone contribute. I think that clarifications and better descriptions for modules should reside there so please add your input on the webpages. A dev with write access can migrate updated documentation to the module's POD where appropriate. -jason On 11/21/06, Amir Karger wrote: > > > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > > > Amir, > > > > The best documentation for translate() is in the online > > Bioperl Tutorial, > > have you checked that? > > > > Brian O. > > Thanks for the quick response. The tutorial is quite informative. > It seems to me that the POD needs to document -complete more thoroughly, > though: > > Or if you expect a complete coding sequence (CDS) > translation, > with inititator at the beginning and terminator at the > end: > > $protein_seq_obj = $cds_seq_obj->translate(-complete > => 1); > > This doesn't really explain what it does. > > I guess -complete was chosen as a compromise between having too many > options and having lots of functionality. In my case, I want to keep the > *, and I don't want warnings about terminators in the middle, because > I've got a bunch of pseudogenes. So I'll just translate the M myself. > > I'm sure you've had many "the documentation is spread out in too many > places" discussions before, and I know keeping docs up to date is Hard. > Oh well. > > -Amir > > > > > > > On 11/21/06 10:21 AM, "Amir Karger" wrote: > > > > > I think this is more a Bio question than a Bioperl question. > > > > > > I did this: > > > > > > ######### > > > #!/usr/local/bin/perl > > > > > > use strict; > > > use warnings; > > > > > > use Bio::Seq; > > > use Bio::Tools::CodonTable; > > > > > > my $seqobj = Bio::PrimarySeq->new ( > > > -seq => 'ATATGATAA', > > > -id => 'GeneFragment-12', > > > -accession_number => 'X78121', > > > -alphabet => 'dna', > > > ); > > > > > > $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); > > > my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; > > > print "ATA $is a valid start codon\n"; > > > print "Table 4: ", $seqobj->translate("-codontable_id" => > > 4)->seq,"\n"; > > > print "Table 1: ", $seqobj->translate("-codontable_id" => > > 1)->seq,"\n"; > > > ########### > > > > > > I got this: > > > ATA is a valid start codon > > > Table 4: IW* > > > Table 1: I** > > > > > > But EMBL tells me that EMBLCDS:AAT64955 starts with an M: > > > > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ > > EMBLCDS:'A > > > AT64955']+-qnum+1+-enum+3 > > > > > > So, does Bioperl purposely not translate start codons to M, > > while EMBL > > > does? Am I supposed to just change the I to M explicitly in > > my code? I > > > didn't see an obvious option to translate() to do it. > > > > > > Thanks, > > > > > > - Amir Karger > > > Research Computing > > > Life Sciences Division > > > Harvard University > > > 617-496-0626 > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich jason at bioperl.org http://www.duke.edu/~jes12/ From bosborne11 at verizon.net Tue Nov 21 15:53:39 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 21 Nov 2006 15:53:39 -0500 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: <200611211032.kALAWahR014137@dev.open-bio.org> Message-ID: Bioperl-l, INSTALL has changed in CVS but the Wiki's version has not - you always have to change both versions of the INSTALL instructions, this is how Chris has elected to do it. Brian O. Date: Tue, 21 Nov 2006 10:32:36 +0000 To: Subject: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 Update of /home/repository/bioperl/bioperl-live In directory dev.open-bio.org:/tmp/cvs-serv14112 Modified Files: DEPENDENCIES INSTALL INSTALL.WIN Log Message: clarification for Bundle::BioPerl, updates for Build.PL Index: DEPENDENCIES =================================================================== RCS file: /home/repository/bioperl/bioperl-live/DEPENDENCIES,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** DEPENDENCIES 14 Nov 2006 15:13:24 -0000 1.1 --- DEPENDENCIES 21 Nov 2006 10:32:34 -0000 1.2 *************** *** 5,10 **** The following packages are used by Bioperl. Not all are required for Bioperl to operate properly, however some functionality will be missing ! without them. You can easily install all of these, except srsperl.pm, ! using the Bundle::BioPerl CPAN bundle. The DBD::mysql, DB_File and XML::Parser modules require other applications --- 5,11 ---- The following packages are used by Bioperl. Not all are required for Bioperl to operate properly, however some functionality will be missing ! without them. You can easily install all of these by using CPAN to install ! Bioperl, or if you have installed Bioperl manually (from archive or CVS), ! by using the Bundle::BioPerl CPAN bundle. The DBD::mysql, DB_File and XML::Parser modules require other applications Index: INSTALL =================================================================== RCS file: /home/repository/bioperl/bioperl-live/INSTALL,v retrieving revision 1.57 retrieving revision 1.58 diff -C2 -d -r1.57 -r1.58 *** INSTALL 16 Nov 2006 16:27:49 -0000 1.57 --- INSTALL 21 Nov 2006 10:32:34 -0000 1.58 *************** *** 1,24 **** # $Id$ ! Installing Bioperl for Unix ! * BIOPERL INSTALLATION ! * SYSTEM REQUIREMENTS ! * OPTIONAL ! * ADDITIONAL INSTALLATION INFORMATION ! * THE BIOPERL BUNDLE ! * INSTALLING BIOPERL THE EASY WAY USING CPAN ! * INSTALLING BIOPERL THE EASY WAY USING GNU 'make' ! * WHERE ARE THE MAN PAGES? ! * EXTERNAL PROGRAMS ! * Environment Variables ! * INSTALLING BIOPERL SCRIPTS ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA ! * INSTALLING BIOPERL MODULES THE HARD WAY ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION ! * THE TEST SYSTEM ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE ! * CONFIGURING for BSD and Solaris boxes ! * INSTALLATION BIOPERL INSTALLATION --- 1,24 ---- # $Id$ ! Installing Bioperl for Unix ! * BIOPERL INSTALLATION ! * SYSTEM REQUIREMENTS ! * OPTIONAL ! * ADDITIONAL INSTALLATION INFORMATION ! * THE BIOPERL BUNDLE ! * INSTALLING BIOPERL THE EASY WAY USING CPAN ! * INSTALLING BIOPERL THE EASY WAY USING Build.PL ! * WHERE ARE THE MAN PAGES? ! * EXTERNAL PROGRAMS ! * Environment Variables ! * INSTALLING BIOPERL SCRIPTS ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA ! * INSTALLING BIOPERL MODULES THE HARD WAY ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION ! * THE TEST SYSTEM ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE ! * CONFIGURING for BSD and Solaris boxes ! * INSTALLATION BIOPERL INSTALLATION *************** *** 41,48 **** modules is included in the DEPENDENCIES file. ! The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation of these ! external modules easy. Simply install the bundle using your CPAN shell and ! all necessary modules will be installed. See THE BIOPERL BUNDLE, ! below. OPTIONAL --- 41,49 ---- modules is included in the DEPENDENCIES file. ! When not using CPAN to install Bioperl itself, the CPAN Bioperl Bundle ! (Bundle::BioPerl) makes installation of these external modules easy. Simply ! install the bundle using your CPAN shell and many optional modules will be ! installed. See THE BIOPERL BUNDLE, below. However, it is recommended you use ! CPAN to install Bioperl and not use Bundle::BioPerl. OPTIONAL *************** *** 61,64 **** --- 62,72 ---- THE BIOPERL BUNDLE + You do not need to install Bundle::BioPerl if you will install Bioperl + using CPAN. This is for users manually installing Bioperl from archives + or CVS, who also want an easy way to install the optional external + modules that Bioperl makes use of. + + Bundle::BioPerl does *not* install Bioperl. + You typically need root privileges to install using CPAN. If you don't have these privileges please see INSTALLING BIOPERL IN A PERSONAL *************** *** 86,96 **** CPAN: Storable loaded ok Going to read /home/bosborne/.cpan/Metadata ! Database was generated on Tue, 24 Feb 2004 23:55:23 GMT ! DistributionB/BI/BIRNEY/bioperl-1.2.tar.gz ! DistributionB/BI/BIRNEY/bioperl-1.4.tar.gz Now install: ! cpan>install B/BI/BIRNEY/bioperl-1.4.tar.gz If you've installed everything perfectly and all the network connections --- 94,105 ---- CPAN: Storable loaded ok Going to read /home/bosborne/.cpan/Metadata ! Database was generated on Mon, 20 Nov 2006 05:24:36 GMT ! Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz ! Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz ! Distribution S/SE/SENDU/bioperl-1.5.2_100.tar.gz Now install: ! cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz If you've installed everything perfectly and all the network connections *************** *** 100,105 **** undetected bug in Bioperl, flawed test script, problems with CGI script used for sequence retrieval at public database, and so on. Remember ! that there are over 700 modules in Bioperl and the test suite is running ! more than 9000 individual tests, a few failed tests may not affect your usage of Bioperl. --- 109,114 ---- undetected bug in Bioperl, flawed test script, problems with CGI script used for sequence retrieval at public database, and so on. Remember ! that there are over 800 modules in Bioperl and the test suite is running ! more than 12000 individual tests, a few failed tests may not affect your usage of Bioperl. *************** *** 107,111 **** Bioperl and you'd like to install anyway do: ! cpan>force install B/BI/BIRNEY/bioperl-1.4.tar.gz This is what most experienced Bioperl users would do. However, if you're --- 116,120 ---- Bioperl and you'd like to install anyway do: ! cpan>force install S/SE/SENDU/bioperl-1.5.2_100.tar.gz This is what most experienced Bioperl users would do. However, if you're *************** *** 113,117 **** bioperl-l at bioperl.org. ! INSTALLING BIOPERL THE EASY WAY USING GNU 'make' The advantage of this approach is it's stepwise, so it's easy to stop and --- 122,126 ---- bioperl-l at bioperl.org. ! INSTALLING BIOPERL THE EASY WAY USING Build.PL The advantage of this approach is it's stepwise, so it's easy to stop and *************** *** 120,126 **** Download, then unpack the tar file. For example: ! >gunzip bioperl-1.5.2.tar.gz ! >tar xvf bioperl-1.5.2.tar ! >cd bioperl-1.5.2 Now issue the make commands: --- 129,135 ---- Download, then unpack the tar file. For example: ! >gunzip bioperl-1.5.2_100.tar.gz ! >tar xvf bioperl-1.5.2_100.tar ! >cd bioperl-1.5.2_100 Now issue the make commands: *************** *** 135,141 **** undetected bug in Bioperl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that ! there are over 700 modules in Bioperl and the test suite is running almost ! 9000 individual tests, a few failed tests may not affect your usage of ! Bioperl. If you decide that the failed tests will not affect how you intend to use --- 144,150 ---- undetected bug in Bioperl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that ! there are over 800 modules in Bioperl and the test suite is running more ! than 12000 individual tests, a few failed tests may not affect your usage ! of Bioperl. If you decide that the failed tests will not affect how you intend to use *************** *** 148,154 **** bioperl-l at bioperl.org. ! To 'make install' you need write permission in the perl5/site_perl/source ! area. Usually this will require you becoming root, so you will want to ! talk to your systems manager if you don't have the necessary privileges. It is also straightforward to install the package outside of the this --- 157,164 ---- bioperl-l at bioperl.org. ! To './Build install' you need write permission in the perl5/site_perl/source ! area (or similar, depending on your environment). Usually this will require ! you becoming root, so you will want to talk to your systems manager if you ! don't have the necessary privileges. It is also straightforward to install the package outside of the this *************** *** 158,165 **** WHERE ARE THE MAN PAGES? ! When using Makefile.PL, we had to disable the automatic creation of man ! pages because this step was triggering a "line too long" error on some ! OSs due to shell constraints. If you want man pages installed use the ! Build.PL installation process. EXTERNAL PROGRAMS --- 168,176 ---- WHERE ARE THE MAN PAGES? ! When using Makefile.PL (no longer covered in this documentation), we had ! to disable the automatic creation of man pages because this step was ! triggering a "line too long" error on some OSs due to shell constraints. ! If you want man pages installed use the Build.PL installation process ! discussed above. EXTERNAL PROGRAMS *************** *** 229,234 **** like, simply answer the questions on 'perl Build.PL'. The installation directory can be specified by ! perl Build.PL ! ./Build install --install_path script=/foo/scripts By default they install to /usr/bin or similar, depending on platform. --- 240,245 ---- like, simply answer the questions on 'perl Build.PL'. The installation directory can be specified by ! perl Build.PL ! ./Build install --install_path script=/foo/scripts By default they install to /usr/bin or similar, depending on platform. *************** *** 297,301 **** execute the make commands from the Compile/SW directory. ! If all else fails or are unable to access the perl distribution directories, ask your system administrator to place the files there for you. You can always execute perl scripts in the same directory as the --- 308,312 ---- execute the make commands from the Compile/SW directory. ! If all else fails and you are unable to access the perl distribution directories, ask your system administrator to place the files there for you. You can always execute perl scripts in the same directory as the *************** *** 312,316 **** #!/usr/bin/perl use lib "/home/users/dag/lib/perl5/"; ! use Bio::Seq; #<...insert whizzy perl code here...> --- 323,327 ---- #!/usr/bin/perl use lib "/home/users/dag/lib/perl5/"; ! use Bio::Perl; #<...insert whizzy perl code here...> *************** *** 319,341 **** csh or tcsh: ! setenv PERL5LIB /home/users/dag/lib/perl5// bash or sh: ! export PERL5LIB=/home/users/dag/lib/perl5// THE TEST SYSTEM The Bioperl test system is located in the t/ directory and is ! automatically run whenever you execute the 'make test' command. Alternatively if you want to investigate the behavior of a specific test ! such as the SeqIO test you would type: ! >perl -I. -w t/SeqIO.t ! The -I. tells Perl to use the current directory as the include path - this ! makes sure you are testing the modules in this directory not ones ! installed elsewhere in your PERL5LIB path. The -w tells Perl to print all ! warnings. If you are trying to learn how to use a module, often the test suite is a --- 330,357 ---- csh or tcsh: ! setenv PERL5LIB /home/users/dag/lib/perl5/ bash or sh: ! export PERL5LIB=/home/users/dag/lib/perl5/ THE TEST SYSTEM The Bioperl test system is located in the t/ directory and is ! automatically run whenever you execute the './Build test' command ! (having previously run 'Perl Build.PL'; if you have already installed ! Bioperl answer 'no' to script installation to get nicer test output ! later). Alternatively if you want to investigate the behavior of a specific test ! such as the Seq test you would type: ! >./Build test --test_files t/Seq.t --verbose ! The ./ ensures you are using the Build script in the current directory to ! make sure you are testing the modules in this directory not ones ! installed elsewhere. The --test_files arguement can be used multiple times ! to try a set of test scripts in one go. The --verbose arguement outputs ! the detailed test results, instead of just the summary you see during ! './Build test'. If you are trying to learn how to use a module, often the test suite is a *************** *** 385,388 **** This should install the compiled extension. The Bio::Tools::pSW module will work cleanly now. - - \ No newline at end of file --- 401,402 ---- Index: INSTALL.WIN =================================================================== RCS file: /home/repository/bioperl/bioperl-live/INSTALL.WIN,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -d -r1.23 -r1.24 *** INSTALL.WIN 14 Nov 2006 15:13:24 -0000 1.23 --- INSTALL.WIN 21 Nov 2006 10:32:34 -0000 1.24 *************** *** 80,89 **** 7) Right click the latest version of Bioperl available and choose ! install. ! ! 7a) This package will be sufficient for the main ! functionality of Bioperl. However, if you require ! full functionality, you should also install the ! latest Bundle-BioPerl package. 8) Click the green arrow (Run marked actions) to complete the --- 80,85 ---- 7) Right click the latest version of Bioperl available and choose ! install. (Note for users of previous Bioperl releases: you should ! not have to use the Bundle-BioPerl package anymore.) 8) Click the green arrow (Run marked actions) to complete the _______________________________________________ Bioperl-guts-l mailing list Bioperl-guts-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l ------ End of Forwarded Message From bix at sendu.me.uk Tue Nov 21 16:32:02 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 21:32:02 +0000 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: References: Message-ID: <45637052.4040003@sendu.me.uk> Brian Osborne wrote: > Bioperl-l, > > INSTALL has changed in CVS but the Wiki's version has not - you always have > to change both versions of the INSTALL instructions, this is how Chris has > elected to do it. Yes, I will edit the wiki when I've finished with the INSTALL docs. (I may be changing them further, please don't consider the current information gospel.) From hlapp at gmx.net Tue Nov 21 16:44:50 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 16:44:50 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <45636286.6040504@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> <45636286.6040504@molbio.mgh.harvard.edu> Message-ID: <064D0938-C753-40BD-8A0D-C900985193B8@gmx.net> Yes this needs to be better documented. Note that you can use both APIs if you install them under different users (= schema in Oracle). I'm not 100% sure whether both variants are fully prepared for this; you may have to create synonyms for the schema-owner tables first, i.e., SQL> CREATE SYNONYM sg_biodatabase FOR biosqlowner.sg_biodatabase; etc, assuming that are logged on as the user under which you want to create the API, and biosqlowner is the schema-owner of the BioSQL instance. Did you want to use BioSQL with both bioperl and biojava? -hilmar On Nov 21, 2006, at 3:33 PM, gang wu wrote: > Hi Hilmar, > > I just rebuilt the Oracle BioSQL database by strictly following the > INSTALL doc. You are right that BS-create-Biosql-API.sql must be > run to make bioperl-db work with it(the oid columns). But my > installation problem was caused by running BS-create-Biosql- > API2.sql after it, which rendered the database not compatible with > bioperl-db. If I ran only BS-create-Biosql-API.sql, ll bioperl-db > tests could pass. Does this mean that the Oracle version is not > interoperable between the Bio- projects at this point? > > Did I miss anything in the INSTALL or README? I only saw a line "-- > all others (Biojava, etc)" but did not realize I could not run both > BS-create-Biosql-API.sql and BS-create-Biosql-API2.sql. I this is > the case, can you please add it to the docs? > > Thanks very much for your help. > > Gang > > Hilmar Lapp wrote: >> The Oracle error is >> >> ORA-00904: "BIODATABASE"."OID": invalid identifier >> >> and if you look at the accompanying statement, it's the UK select >> statement: >> >> SELECT <*>biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = :p1 >> >> The column OID must exist in the Biodatabase table (which actually >> is a synonym to the SG_BIODATABASE table), if it is the Oracle >> schema. >> >> This actually prompts another suggestion, sorry for not asking >> that first: did you actually install the BioSQL-API on top of the >> schema by running the script BS-create-Biosql-API.sql? (It seems >> that the statement it chokes on is also the first statement being >> prepared, so this may well be the reason) >> >> -hilmar >> >> On Nov 21, 2006, at 3:11 AM, gang wu wrote: >> >>> Can you show me where it indicates I am actually using the MySQL >>> schema. >>> I am pretty sure that I used the sql script files from >>> sql/biosql-ora(Has anyone actually tried to install MySQL schema on >>> Oracle?). I can reinstall the schema if you think that's the way to >>> solve the problem. Thanks very much. >>> >>> Gang >>> >>> Hilmar Lapp wrote: >>>> It looks like you are using the MySQL schema under Oracle. There >>>> are >>>> different DDL scripts for each supported RDBMS. The ones for Oracle >>>> are in the sql/biosql-ora subdirectory. Note the INSTALL >>>> document in >>>> that directory. >>>> >>>> -hilmar >>>> >>>> >>>> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >>>> >>>> >>>>> Hi Hilmar, >>>>> >>>>> Below is the output. Thanks. >>>>> >>>>> Gang >>>>> ========================================================== >>>>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>>>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>>>> TEST_VERBOSE=1 >>>>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/ >>>>> lib64/ >>>>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>>>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>>>> @ARGV;' t/01dbadaptor.t >>>>> t/01dbadaptor....1..19 >>>>> ok 1 >>>>> ok 2 >>>>> ok 3 >>>>> ok 4 >>>>> ok 5 >>>>> ok 6 >>>>> ok 7 >>>>> ok 8 >>>>> ok 9 >>>>> ok 10 >>>>> ok 11 >>>>> attempting to load adaptor class for BioNamespace >>>>> ok 12 >>>>> attempting to load module >>>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> ok 13 >>>>> ok 14 >>>>> attempting to load driver for adaptor class >>>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> attempting to load driver for adaptor class >>>>> Bio::DB::BioSQL::BasePersistenceAdaptor >>>>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>>>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> preparing UK select statement: SELECT biodatabase.oid, >>>>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE >>>>> name >>>>> = ? >>>>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>>>> invalid identifier (DBD ERROR: error possibly near <*> >>>>> indicator at >>>>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>>>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>>>> Statement "SELECT biodatabase.oid, biodatabase.name, >>>>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/ >>>>> lib/ >>>>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>>>> BioNamespaceAdaptor: binding UK column 1 to >>>>> "__dummy__" (namespace) >>>>> Can't call method "bind_param" on an undefined value at blib/lib/ >>>>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>>>> dubious >>>>> Test returned status 255 (wstat 65280, 0xff00) >>>>> DIED. FAILED tests 15-19 >>>>> Failed 5/19 tests, 73.68% okay >>>>> Failed Test Stat Wstat Total Fail Failed List of Failed >>>>> ------------------------------------------------------------------ >>>>> ---- >>>>> --------- >>>>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>>>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>>>> okay. >>>>> make: *** [test_01dbadaptor] Error 2 >>>>> ========================================================= >>>>> >>>>> >>>>> Hilmar Lapp wrote: >>>>> >>>>>> Hi Gang, >>>>>> >>>>>> what I wanted to get at was the error message from the driver >>>>>> when >>>>>> it fails to generate the prepared statement, but this is not in >>>>>> the output. >>>>>> >>>>>> I believe you need set the HARNESS_VERBOSE environment >>>>>> variable to >>>>>> 1 before testing to get what I need: >>>>>> >>>>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>>>> csh/tcsh >>>>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>>>> >>>>>> This will lead to _a lot_ of debugging output. Do not run this >>>>>> for >>>>>> the entire test suite. >>>>>> >>>>>> The errors for mysql I believe are related to the fact that have >>>>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>>>> (completely empty) instance of BioSQL. >>>>>> >>>>>> Let me know what you get for the Oracle test above. >>>>>> >>>>>> -hilmar >>>>>> >>>>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>>>> >>>>>> >>>>>>> Hi Hilmar, >>>>>>> >>>>>>> Thanks for your message. Below are several tests for Oracle and >>>>>>> MySQL. MySQL actually also has two tests with failed items which >>>>>>> may be related to data in BioSQL database. >>>>>>> >>>>>>> Could it be my Oracle installation/configuration has some >>>>>>> issues? >>>>>>> >>>>>>> Thanks. >>>>>>> >>>>>>> Gang >>>>>>> >>>>>> --=========================================================== >>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>>>> =========================================================== >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> --=========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> >> -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Tue Nov 21 18:54:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 17:54:32 -0600 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164141156l.712786l.0l@psu.edu> References: <1164141156l.712786l.0l@psu.edu> Message-ID: <101BBBA4-391D-4F87-8181-F754A2357DA8@uiuc.edu> You'll want to always reply to the list as well. I would say update to a newer version; many changes have been made to parsing GenBank/ SwissProt/EMBL since rel 1.4, including dblinks. If you're using windows you'll need to follow the instructions on the website for the latest release candidate: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Note that the release candidates are located in a different repository, so you'll need to set that up to find them. chris On Nov 21, 2006, at 2:32 PM, Juan Cristobal Vera wrote: > ok, thanks for responding! > I'm using ActivePerl 5.8.8 build 819 on a windows machine (sorry) > and the bioperl 1.4 PPM3 package. Perhaps this is too old? > Here's part of my code (mostly derived from bioperl docs): > ......................... > #cut > > $seqInObj = $indexObj->get_Seq_by_id($line); #get sequence and > create seq object > > #cut > > if (defined $seqInObj->annotation){ > $annotObj = $seqInObj->annotation; #create annotation object > foreach $key ($annotObj->get_all_annotation_keys){ > @values = $annotObj->get_Annotations($key); > foreach $value (@values){ > if (lc($key) eq "dblink"){ > print $outfh "Annotation: $key\n"; > print $outfh $value->as_text,"\n"; > $dbhash_ref = $value->hash_tree; > for $dbKey (keys %{$dbhash_ref}) { > print $outfh $dbKey,": ",$dbhash_ref-> > {$dbKey},"\n"; #none of these prints produce GO terms > } > } > } > } > } > ......................... > My program searches an indexed database on my machine, creates the > objects, and prints out relevant annotations. > Here are some of the accessions I used for testing: > P19351 TNNT_DROME > P36188 TNNI_DROME > P11147 HSP7D_DROME > .......................................... > the relevant output looks something like this (for debugging) for > P19351: > ...................................................................... > Direct database link to X58188 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: X58188 > optional_id: CAA41171.1 > Annotation: dblink > Direct database link to X59376 in database EMBL > database: EMBL > comment: -; mRNA. > primary_id: X59376 > optional_id: CAA42020.1 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48802.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48803.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48804.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48805.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAN09458.1 > Annotation: dblink > Direct database link to AY122145 in database EMBL > database: EMBL > comment: -; mRNA. > primary_id: AY122145 > optional_id: AAM52657.1 > Annotation: dblink > Direct database link to A40547 in database PIR > database: PIR > primary_id: A40547 > optional_id: A40547 > Annotation: dblink > Direct database link to B38594 in database PIR > database: PIR > primary_id: B38594 > optional_id: B38594 > Annotation: dblink > Direct database link to Dm.1717 in database UniGene > database: UniGene > primary_id: Dm.1717 > optional_id: - > Annotation: dblink > Direct database link to P45379 in database HSSP > database: HSSP > primary_id: P45379 > optional_id: 1J1E > Annotation: dblink > Direct database link to P36188 in database IntAct > database: IntAct > primary_id: P36188 > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PA in database KEGG > database: KEGG > primary_id: dme:CG7178-PA > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PB in database KEGG > database: KEGG > primary_id: dme:CG7178-PB > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PC in database KEGG > database: KEGG > primary_id: dme:CG7178-PC > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PD in database KEGG > database: KEGG > primary_id: dme:CG7178-PD > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PG in database KEGG > database: KEGG > primary_id: dme:CG7178-PG > optional_id: - > Annotation: dblink > Direct database link to FBgn0004028 in database FlyBase > database: FlyBase > primary_id: FBgn0004028 > optional_id: wupA > Annotation: dblink > Direct database link to IPR001978 in database InterPro > database: InterPro > primary_id: IPR001978 > optional_id: Troponin > Annotation: dblink > Direct database link to PF00992 in database Pfam > database: Pfam > comment: 1 > primary_id: PF00992 > optional_id: Troponin > .............................................. > as you can see, no GO terms above > ...................................................... > Vs. the actual content of the flat file from for the dblinks from > P19351: > DR EMBL; X54504; CAA38366.1; -; mRNA. > DR EMBL; AY439172; AAR24583.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24584.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24585.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24586.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24587.1; -; Genomic_DNA. > DR EMBL; AY665838; AAU09446.1; -; mRNA. > DR EMBL; AE014298; AAF48288.2; -; Genomic_DNA. > DR EMBL; AE014298; AAF48289.2; -; Genomic_DNA. > DR EMBL; AE014298; AAF48290.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52491.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52492.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52493.1; -; Genomic_DNA. > DR EMBL; AY051989; AAK93413.1; -; mRNA. > DR EMBL; AY070875; AAL48497.1; ALT_SEQ; mRNA. > DR PIR; S13251; S13251. > DR UniGene; Dm.20472; -. > DR HSSP; P45379; 1J1E. > DR Ensembl; CG7107; Drosophila melanogaster. > DR KEGG; dme:CG7107-PE; -. > DR KEGG; dme:CG7107-PF; -. > DR KEGG; dme:CG7107-PG; -. > DR FlyBase; FBgn0004169; up. > DR GO; GO:0007498; P:mesoderm development; IEP:FlyBase. ...... > where the GO term is last entry in dblink section above. > Any help you could provide would be most welcome. Let me know if > this is insufficient information or if you need a working script. > > > On Tue, 21 Nov 2006 00:19:59 -0600 Chris Fields wrote: > Juan, The DBLink objects should be generated. You'll need to give > us a bit more information to go on, though. We need an example > sequence, your local version of Bioperl, maybe a test script, etc. > This is the right forum for this, yes, if you are using BioPerl. > Chris On Nov 20, 2006, at 6:52 PM, Juan Cristobal Vera wrote: > > > > Hi, > I'm writing a simple application to extract various fields > from > swissprot objects and I can't access the GO terms found in > > "dblink" part of the swiss format flat files. I'm not a > > professional programmer and I can't figure out why this is > > occuring. All the other "dblink" keys are being > > generated as far as I can tell (e.g. embl, pfam, etc). The GO > > terms are just skipped over and it's driving me crazy. Not sure if > > this is a bug or a deliberate strategy I'm unfamiliar with. I > > apologize if this is not the correct forum to ask for this sort of > > help and would ask to be directed to the proper one. > > > > Juan > Cristobal Vera > > Graduate Student > > Department of Biology > > > Penn State University > > 208 Mueller Laboratory > > University > Park, PA 16802 > > (814)863-2957 > > > _______________________________________________ > Bioperl-l mailing > list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/ > mailman/listinfo/bioperl-l Christopher Fields Postdoctoral > Researcher Lab of Dr. Robert Switzer Dept of Biochemistry > University of Illinois Urbana-Champaign > > Juan Cristobal Vera > Graduate Student > Department of Biology > Penn State University > 208 Mueller Laboratory > University Park, PA 16802 > (814)863-2957 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Nov 21 18:56:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 17:56:48 -0600 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: References: Message-ID: On Nov 21, 2006, at 2:53 PM, Brian Osborne wrote: > Bioperl-l, > > INSTALL has changed in CVS but the Wiki's version has not - you > always have > to change both versions of the INSTALL instructions, this is how > Chris has > elected to do it. > > Brian O. Agreed (thanks Brian for pointing that out). I have to update these by hand until I can find a more automated way (which will be hard considering the meta content in the wiki). Chris > > > > Date: Tue, 21 Nov 2006 10:32:36 +0000 > To: > Subject: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 > INSTALL, 1.57, > 1.58 INSTALL.WIN, 1.23, 1.24 > > Update of /home/repository/bioperl/bioperl-live > In directory dev.open-bio.org:/tmp/cvs-serv14112 > > Modified Files: > DEPENDENCIES INSTALL INSTALL.WIN > Log Message: > clarification for Bundle::BioPerl, updates for Build.PL > > Index: DEPENDENCIES > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/DEPENDENCIES,v > retrieving revision 1.1 > retrieving revision 1.2 > diff -C2 -d -r1.1 -r1.2 > *** DEPENDENCIES 14 Nov 2006 15:13:24 -0000 1.1 > --- DEPENDENCIES 21 Nov 2006 10:32:34 -0000 1.2 > *************** > *** 5,10 **** > The following packages are used by Bioperl. Not all are required for > Bioperl to operate properly, however some functionality will be > missing > ! without them. You can easily install all of these, except > srsperl.pm, > ! using the Bundle::BioPerl CPAN bundle. > > The DBD::mysql, DB_File and XML::Parser modules require other > applications > --- 5,11 ---- > The following packages are used by Bioperl. Not all are required for > Bioperl to operate properly, however some functionality will be > missing > ! without them. You can easily install all of these by using CPAN > to install > ! Bioperl, or if you have installed Bioperl manually (from archive > or CVS), > ! by using the Bundle::BioPerl CPAN bundle. > > The DBD::mysql, DB_File and XML::Parser modules require other > applications > > Index: INSTALL > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/INSTALL,v > retrieving revision 1.57 > retrieving revision 1.58 > diff -C2 -d -r1.57 -r1.58 > *** INSTALL 16 Nov 2006 16:27:49 -0000 1.57 > --- INSTALL 21 Nov 2006 10:32:34 -0000 1.58 > *************** > *** 1,24 **** > # $Id$ > > ! Installing Bioperl for Unix > > ! * BIOPERL INSTALLATION > ! * SYSTEM REQUIREMENTS > ! * OPTIONAL > ! * ADDITIONAL INSTALLATION INFORMATION > ! * THE BIOPERL BUNDLE > ! * INSTALLING BIOPERL THE EASY WAY USING CPAN > ! * INSTALLING BIOPERL THE EASY WAY USING GNU 'make' > ! * WHERE ARE THE MAN PAGES? > ! * EXTERNAL PROGRAMS > ! * Environment Variables > ! * INSTALLING BIOPERL SCRIPTS > ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA > ! * INSTALLING BIOPERL MODULES THE HARD WAY > ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION > ! * THE TEST SYSTEM > ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE > ! * CONFIGURING for BSD and Solaris boxes > ! * INSTALLATION > > BIOPERL INSTALLATION > --- 1,24 ---- > # $Id$ > > ! Installing Bioperl for Unix > > ! * BIOPERL INSTALLATION > ! * SYSTEM REQUIREMENTS > ! * OPTIONAL > ! * ADDITIONAL INSTALLATION INFORMATION > ! * THE BIOPERL BUNDLE > ! * INSTALLING BIOPERL THE EASY WAY USING CPAN > ! * INSTALLING BIOPERL THE EASY WAY USING Build.PL > ! * WHERE ARE THE MAN PAGES? > ! * EXTERNAL PROGRAMS > ! * Environment Variables > ! * INSTALLING BIOPERL SCRIPTS > ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA > ! * INSTALLING BIOPERL MODULES THE HARD WAY > ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION > ! * THE TEST SYSTEM > ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE > ! * CONFIGURING for BSD and Solaris boxes > ! * INSTALLATION > > BIOPERL INSTALLATION > *************** > *** 41,48 **** > modules is included in the DEPENDENCIES file. > > ! The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation of > these > ! external modules easy. Simply install the bundle using your CPAN > shell and > ! all necessary modules will be installed. See THE BIOPERL BUNDLE, > ! below. > > OPTIONAL > --- 41,49 ---- > modules is included in the DEPENDENCIES file. > > ! When not using CPAN to install Bioperl itself, the CPAN Bioperl > Bundle > ! (Bundle::BioPerl) makes installation of these external modules easy. > Simply > ! install the bundle using your CPAN shell and many optional > modules will be > ! installed. See THE BIOPERL BUNDLE, below. However, it is > recommended you > use > ! CPAN to install Bioperl and not use Bundle::BioPerl. > > OPTIONAL > *************** > *** 61,64 **** > --- 62,72 ---- > THE BIOPERL BUNDLE > > + You do not need to install Bundle::BioPerl if you will install > Bioperl > + using CPAN. This is for users manually installing Bioperl from > archives > + or CVS, who also want an easy way to install the optional external > + modules that Bioperl makes use of. > + > + Bundle::BioPerl does *not* install Bioperl. > + > You typically need root privileges to install using CPAN. If you > don't > have these privileges please see INSTALLING BIOPERL IN A PERSONAL > *************** > *** 86,96 **** > CPAN: Storable loaded ok > Going to read /home/bosborne/.cpan/Metadata > ! Database was generated on Tue, 24 Feb 2004 23:55:23 GMT > ! DistributionB/BI/BIRNEY/bioperl-1.2.tar.gz > ! DistributionB/BI/BIRNEY/bioperl-1.4.tar.gz > > Now install: > > ! cpan>install B/BI/BIRNEY/bioperl-1.4.tar.gz > > If you've installed everything perfectly and all the network > connections > --- 94,105 ---- > CPAN: Storable loaded ok > Going to read /home/bosborne/.cpan/Metadata > ! Database was generated on Mon, 20 Nov 2006 05:24:36 GMT > ! Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz > ! Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz > ! Distribution S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > Now install: > > ! cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > If you've installed everything perfectly and all the network > connections > *************** > *** 100,105 **** > undetected bug in Bioperl, flawed test script, problems with CGI > script used for sequence retrieval at public database, and so on. > Remember > ! that there are over 700 modules in Bioperl and the test suite is > running > ! more than 9000 individual tests, a few failed tests may not > affect your > usage of Bioperl. > > --- 109,114 ---- > undetected bug in Bioperl, flawed test script, problems with CGI > script used for sequence retrieval at public database, and so on. > Remember > ! that there are over 800 modules in Bioperl and the test suite is > running > ! more than 12000 individual tests, a few failed tests may not > affect your > usage of Bioperl. > > *************** > *** 107,111 **** > Bioperl and you'd like to install anyway do: > > ! cpan>force install B/BI/BIRNEY/bioperl-1.4.tar.gz > > This is what most experienced Bioperl users would do. However, if > you're > --- 116,120 ---- > Bioperl and you'd like to install anyway do: > > ! cpan>force install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > This is what most experienced Bioperl users would do. However, if > you're > *************** > *** 113,117 **** > bioperl-l at bioperl.org. > > ! INSTALLING BIOPERL THE EASY WAY USING GNU 'make' > > The advantage of this approach is it's stepwise, so it's easy to > stop and > --- 122,126 ---- > bioperl-l at bioperl.org. > > ! INSTALLING BIOPERL THE EASY WAY USING Build.PL > > The advantage of this approach is it's stepwise, so it's easy to > stop and > *************** > *** 120,126 **** > Download, then unpack the tar file. For example: > > ! >gunzip bioperl-1.5.2.tar.gz > ! >tar xvf bioperl-1.5.2.tar > ! >cd bioperl-1.5.2 > > Now issue the make commands: > --- 129,135 ---- > Download, then unpack the tar file. For example: > > ! >gunzip bioperl-1.5.2_100.tar.gz > ! >tar xvf bioperl-1.5.2_100.tar > ! >cd bioperl-1.5.2_100 > > Now issue the make commands: > *************** > *** 135,141 **** > undetected bug in Bioperl, flawed test script, problems with CGI > script > using for sequence retrieval at public database, and so on. > Remember that > ! there are over 700 modules in Bioperl and the test suite is > running almost > ! 9000 individual tests, a few failed tests may not affect your > usage of > ! Bioperl. > > If you decide that the failed tests will not affect how you > intend to use > --- 144,150 ---- > undetected bug in Bioperl, flawed test script, problems with CGI > script > using for sequence retrieval at public database, and so on. > Remember that > ! there are over 800 modules in Bioperl and the test suite is > running more > ! than 12000 individual tests, a few failed tests may not affect > your usage > ! of Bioperl. > > If you decide that the failed tests will not affect how you > intend to use > *************** > *** 148,154 **** > bioperl-l at bioperl.org. > > ! To 'make install' you need write permission in the perl5/ > site_perl/source > ! area. Usually this will require you becoming root, so you will > want to > ! talk to your systems manager if you don't have the necessary > privileges. > > It is also straightforward to install the package outside of the > this > --- 157,164 ---- > bioperl-l at bioperl.org. > > ! To './Build install' you need write permission in the > perl5/site_perl/source > ! area (or similar, depending on your environment). Usually this will > require > ! you becoming root, so you will want to talk to your systems > manager if you > ! don't have the necessary privileges. > > It is also straightforward to install the package outside of the > this > *************** > *** 158,165 **** > WHERE ARE THE MAN PAGES? > > ! When using Makefile.PL, we had to disable the automatic creation > of man > ! pages because this step was triggering a "line too long" error on > some > ! OSs due to shell constraints. If you want man pages installed use > the > ! Build.PL installation process. > > EXTERNAL PROGRAMS > --- 168,176 ---- > WHERE ARE THE MAN PAGES? > > ! When using Makefile.PL (no longer covered in this documentation), > we had > ! to disable the automatic creation of man pages because this step was > ! triggering a "line too long" error on some OSs due to shell > constraints. > ! If you want man pages installed use the Build.PL installation > process > ! discussed above. > > EXTERNAL PROGRAMS > *************** > *** 229,234 **** > like, simply answer the questions on 'perl Build.PL'. > The installation directory can be specified by > ! perl Build.PL > ! ./Build install --install_path script=/foo/scripts > By default they install to /usr/bin or similar, depending on > platform. > > --- 240,245 ---- > like, simply answer the questions on 'perl Build.PL'. > The installation directory can be specified by > ! perl Build.PL > ! ./Build install --install_path script=/foo/scripts > By default they install to /usr/bin or similar, depending on > platform. > > *************** > *** 297,301 **** > execute the make commands from the Compile/SW directory. > > ! If all else fails or are unable to access the perl distribution > directories, ask your system administrator to place the files > there for > you. You can always execute perl scripts in the same directory as > the > --- 308,312 ---- > execute the make commands from the Compile/SW directory. > > ! If all else fails and you are unable to access the perl distribution > directories, ask your system administrator to place the files > there for > you. You can always execute perl scripts in the same directory as > the > *************** > *** 312,316 **** > #!/usr/bin/perl > use lib "/home/users/dag/lib/perl5/"; > ! use Bio::Seq; > #<...insert whizzy perl code here...> > > --- 323,327 ---- > #!/usr/bin/perl > use lib "/home/users/dag/lib/perl5/"; > ! use Bio::Perl; > #<...insert whizzy perl code here...> > > *************** > *** 319,341 **** > csh or tcsh: > > ! setenv PERL5LIB /home/users/dag/lib/perl5// > > bash or sh: > > ! export PERL5LIB=/home/users/dag/lib/perl5// > > THE TEST SYSTEM > > The Bioperl test system is located in the t/ directory and is > ! automatically run whenever you execute the 'make test' command. > Alternatively if you want to investigate the behavior of a > specific test > ! such as the SeqIO test you would type: > > ! >perl -I. -w t/SeqIO.t > > ! The -I. tells Perl to use the current directory as the include > path - this > ! makes sure you are testing the modules in this directory not ones > ! installed elsewhere in your PERL5LIB path. The -w tells Perl to > print all > ! warnings. > > If you are trying to learn how to use a module, often the test > suite is a > --- 330,357 ---- > csh or tcsh: > > ! setenv PERL5LIB /home/users/dag/lib/perl5/ > > bash or sh: > > ! export PERL5LIB=/home/users/dag/lib/perl5/ > > THE TEST SYSTEM > > The Bioperl test system is located in the t/ directory and is > ! automatically run whenever you execute the './Build test' command > ! (having previously run 'Perl Build.PL'; if you have already > installed > ! Bioperl answer 'no' to script installation to get nicer test output > ! later). > Alternatively if you want to investigate the behavior of a > specific test > ! such as the Seq test you would type: > > ! >./Build test --test_files t/Seq.t --verbose > > ! The ./ ensures you are using the Build script in the current > directory to > ! make sure you are testing the modules in this directory not ones > ! installed elsewhere. The --test_files arguement can be used > multiple times > ! to try a set of test scripts in one go. The --verbose arguement > outputs > ! the detailed test results, instead of just the summary you see > during > ! './Build test'. > > If you are trying to learn how to use a module, often the test > suite is a > *************** > *** 385,388 **** > This should install the compiled extension. The Bio::Tools::pSW > module will work cleanly now. > - > - > \ No newline at end of file > --- 401,402 ---- > > Index: INSTALL.WIN > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/INSTALL.WIN,v > retrieving revision 1.23 > retrieving revision 1.24 > diff -C2 -d -r1.23 -r1.24 > *** INSTALL.WIN 14 Nov 2006 15:13:24 -0000 1.23 > --- INSTALL.WIN 21 Nov 2006 10:32:34 -0000 1.24 > *************** > *** 80,89 **** > > 7) Right click the latest version of Bioperl available > and > choose > ! install. > ! > ! 7a) This package will be sufficient for > the main > ! functionality of Bioperl. However, if you > require > ! full functionality, you should also > install the > ! latest Bundle-BioPerl package. > > 8) Click the green arrow (Run marked actions) to > complete the > --- 80,85 ---- > > 7) Right click the latest version of Bioperl available > and > choose > ! install. (Note for users of previous Bioperl releases: > you > should > ! not have to use the Bundle-BioPerl package anymore.) > > 8) Click the green arrow (Run marked actions) to > complete the > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l > > ------ End of Forwarded Message > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jcv128 at psu.edu Tue Nov 21 15:53:07 2006 From: jcv128 at psu.edu (Juan Cristobal Vera) Date: Tue, 21 Nov 2006 15:53:07 -0500 Subject: [Bioperl-l] GO terms not present in Swiss annotation object-more details Message-ID: <1164142374l.1118292l.0l@psu.edu> Hi, I'm writing a simple application to extract various fields from swissprot objects and I can't access the GO terms found in dblink part of the swiss format flat files. I'm not a professional programmer and I can't figure out why this is occuring. All the other dblink keys are being generated as far as I can tell (e.g. embl, pfam, etc). The GO terms are just skipped over and it's driving me crazy. Not sure if this is a bug or a deliberate strategy I'm unfamiliar with. I'm using ActivePerl 5.8.8 build 819 on a windows machine (sorry) and the bioperl 1.4 PPM3 package. Perhaps this is too old? Here's part of my code (mostly derived from bioperl docs): ......................... #cut $seqInObj = $indexObj->get_Seq_by_id($line); #get sequence and create seq object #cut if (defined $seqInObj->annotation){ $annotObj = $seqInObj->annotation; #create annotation object foreach $key ($annotObj->get_all_annotation_keys){ @values =$annotObj->get_Annotations($key); foreach $value (@values){ if (lc($key) eq "dblink"){ print $outfh "Annotation: $key\n"; print $outfh $value->as_text,"\n"; $dbhash_ref = $value->hash_tree; for $dbKey (keys %{$dbhash_ref}) { print $outfh $dbKey,":",$dbhash_ref->{$dbKey},"\n"; #none of these prints produce GO terms } } } } } ......................... My program searches an indexed database on my machine, creates the objects, and prints out relevant annotations. Here are some of the accessions I used for testing: P19351 TNNT_DROME P36188 TNNI_DROME P11147 HSP7D_DROME .......................................... the relevant output looks something like this (for debugging) for P19351: ...................................................................... Direct database link to X58188 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: X58188 optional_id: CAA41171.1 Annotation: dblink Direct database link to X59376 in database EMBL database: EMBL comment: -; mRNA. primary_id: X59376 optional_id: CAA42020.1 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48802.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48803.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48804.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48805.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAN09458.1 Annotation: dblink Direct database link to AY122145 in database EMBL database: EMBL comment: -; mRNA. primary_id: AY122145 optional_id: AAM52657.1 Annotation: dblink Direct database link to A40547 in database PIR database: PIR primary_id: A40547 optional_id: A40547 Annotation: dblink Direct database link to B38594 in database PIR database: PIR primary_id: B38594 optional_id: B38594 Annotation: dblink Direct database link to Dm.1717 in database UniGene database: UniGene primary_id: Dm.1717 optional_id: - Annotation: dblink Direct database link to P45379 in database HSSP database: HSSP primary_id: P45379 optional_id: 1J1E Annotation: dblink Direct database link to P36188 in database IntAct database: IntAct primary_id: P36188 optional_id: - Annotation: dblink Direct database link to dme:CG7178-PA in database KEGG database: KEGG primary_id: dme:CG7178-PA optional_id: - Annotation: dblink Direct database link to dme:CG7178-PB in database KEGG database: KEGG primary_id: dme:CG7178-PB optional_id: - Annotation: dblink Direct database link to dme:CG7178-PC in database KEGG database: KEGG primary_id: dme:CG7178-PC optional_id: - Annotation: dblink Direct database link to dme:CG7178-PD in database KEGG database: KEGG primary_id: dme:CG7178-PD optional_id: - Annotation: dblink Direct database link to dme:CG7178-PG in database KEGG database: KEGG primary_id: dme:CG7178-PG optional_id: - Annotation: dblink Direct database link to FBgn0004028 in database FlyBase database: FlyBase primary_id: FBgn0004028 optional_id: wupA Annotation: dblink Direct database link to IPR001978 in database InterPro database: InterPro primary_id: IPR001978 optional_id: Troponin Annotation: dblink Direct database link to PF00992 in database Pfam database: Pfam comment: 1 primary_id: PF00992 optional_id: Troponin .............................................. as you can see, no GO terms above ...................................................... Vs. the actual content of the flat file from for the dblinks from P19351: DR EMBL; X54504; CAA38366.1; -; mRNA. DR EMBL; AY439172; AAR24583.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24584.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24585.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24586.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24587.1; -; Genomic_DNA. DR EMBL; AY665838; AAU09446.1; -; mRNA. DR EMBL; AE014298; AAF48288.2; -; Genomic_DNA. DR EMBL; AE014298; AAF48289.2; -; Genomic_DNA. DR EMBL; AE014298; AAF48290.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52491.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52492.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52493.1; -; Genomic_DNA. DR EMBL; AY051989; AAK93413.1; -; mRNA. DR EMBL; AY070875; AAL48497.1; ALT_SEQ; mRNA. DR PIR; S13251; S13251. DR UniGene; Dm.20472; -. DR HSSP; P45379; 1J1E. DR Ensembl; CG7107; Drosophila melanogaster. DR KEGG; dme:CG7107-PE; -. DR KEGG; dme:CG7107-PF; -. DR KEGG; dme:CG7107-PG; -. DR FlyBase; FBgn0004169; up. DR GO; GO:0007498; P:mesoderm development; IEP:FlyBase. ...... where the GO term is last entry in dblink section above. Any help you could provide would be most welcome. Let me know if this is insufficient information or if you need a working script. Juan Cristobal Vera Graduate Student Department of Biology Penn State University 208 Mueller Laboratory University Park, PA 16802 (814)863-2957 From s.bulashevska at dkfz-heidelberg.de Wed Nov 22 06:20:32 2006 From: s.bulashevska at dkfz-heidelberg.de (Svetlana Bulashevska) Date: Wed, 22 Nov 2006 12:20:32 +0100 Subject: [Bioperl-l] a question on gene retrieval Message-ID: <45643280.3000001@dkfz.de> Dear Sirs, I am very new to bioperl and I would highly appreciate if you could advise me on the following. I have the locations of the sequences (like chr5|-1|102826728|102828399) in the human genome and I would like to retrieve what known genes lay in the close proximity to the sequences (they can also overlap with the sequence). What bioperl modules and classes should I use? Thank you very much, Svetlana Bulashevska. From bosborne11 at verizon.net Wed Nov 22 09:04:35 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 22 Nov 2006 09:04:35 -0500 Subject: [Bioperl-l] a question on gene retrieval In-Reply-To: <45643280.3000001@dkfz.de> Message-ID: Svetlana, There's a page discussing these sorts of questions at the Bioperl Wiki: http://www.bioperl.org/wiki/Getting_Genomic_Sequences It sounds like you just want to compare pairs of coordinates initially, not retrieve sequence, yes? Brian O. On 11/22/06 6:20 AM, "Svetlana Bulashevska" wrote: > Dear Sirs, > I am very new to bioperl and I would highly appreciate if you could > advise me on the following. > I have the locations of the sequences (like chr5|-1|102826728|102828399) > in the human genome > and I would like to retrieve what known genes lay in the close proximity > to the sequences (they can also overlap with the sequence). What bioperl > modules and classes should I use? > Thank you very much, > Svetlana Bulashevska. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Wed Nov 22 11:50:07 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Wed, 22 Nov 2006 11:50:07 -0500 Subject: [Bioperl-l] a question on gene retrieval In-Reply-To: <45643280.3000001@dkfz.de> Message-ID: <18C407FD4FFB424292D769FBD68C1987018123A1@NIHCESMLBX8.nih.gov> You can use LWP to retrieve the following URL http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=5&maps=genes [102826728:104828399]-r&cmd=txt and then parse the HTML. Good luck! Wenwu Cui -----Original Message----- From: Svetlana Bulashevska [mailto:s.bulashevska at dkfz-heidelberg.de] Sent: Wednesday, November 22, 2006 6:21 AM To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] a question on gene retrieval Dear Sirs, I am very new to bioperl and I would highly appreciate if you could advise me on the following. I have the locations of the sequences (like chr5|-1|102826728|102828399) in the human genome and I would like to retrieve what known genes lay in the close proximity to the sequences (they can also overlap with the sequence). What bioperl modules and classes should I use? Thank you very much, Svetlana Bulashevska. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cain at cshl.edu Wed Nov 22 14:09:13 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 14:09:13 -0500 (EST) Subject: [Bioperl-l] Unable to build Module::Build on CentOS Message-ID: Hello, I don't want to throw too much fuel on the Module::Build fire, but I have just discovered that I can't get Module::Build to install on CentOS 4.4. It appears that the developers of MB are aware of the problem, but the currently release ---------------------------------------------------------------------- Scott Cain, Ph. D. cain at cshl.org GMOD Coordinator, http://www.gmod.org/ (216)392-3087 ---------------------------------------------------------------------- From cain at cshl.edu Wed Nov 22 14:59:53 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 14:59:53 -0500 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: References: Message-ID: <1164225594.2639.2.camel@localhost.localdomain> Whoops! That was a half composed message that I thought I canceled. \me blushes Oh well, I was going to write a short note to indicate that in fact, I could not get Module::Build to pass tests on CentOS 4.4 and the authors appear to be aware of the problem, but I have no idea if it is likely to be fixed any time soon. So, if anyone wants to install BioPerl 1.5.2 on any CentOS boxes, they have to force install Module::Build. :-/ Scott On Wed, 2006-11-22 at 14:09 -0500, Scott Cain wrote: > Hello, > > I don't want to throw too much fuel on the Module::Build fire, but I have > just discovered that I can't get Module::Build to install on CentOS 4.4. > It appears that the developers of MB are aware of the problem, but the > currently release > > ---------------------------------------------------------------------- > Scott Cain, Ph. D. cain at cshl.org > GMOD Coordinator, http://www.gmod.org/ (216)392-3087 > ---------------------------------------------------------------------- > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061122/e04ebc5a/attachment-0001.bin From cain at cshl.edu Wed Nov 22 15:04:25 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 15:04:25 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows Message-ID: <1164225865.2639.8.camel@localhost.localdomain> Hello, I just wanted to mention that I made a few minor changes to Build.PL so that I could get `perl Build.PL` to complete successfully. I am using ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't present either. The main thing I did was to have the BioDBGFF test subroutine quit without asking any questions if Build.PL detected that it was running on Windows. There may be a more elegant way of fixing the problem, but I just wanted it to work (as I am also working a release candidate of GBrowse that depends on the release candidate of bioperl). Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061122/220f9b5d/attachment.bin From bix at sendu.me.uk Wed Nov 22 18:16:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 22 Nov 2006 23:16:10 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <1164225594.2639.2.camel@localhost.localdomain> References: <1164225594.2639.2.camel@localhost.localdomain> Message-ID: <4564DA3A.1000601@sendu.me.uk> Scott Cain wrote: > Whoops! That was a half composed message that I thought I canceled. > > \me blushes > > Oh well, I was going to write a short note to indicate that in fact, I > could not get Module::Build to pass tests on CentOS 4.4 and the authors > appear to be aware of the problem, but I have no idea if it is likely to > be fixed any time soon. So, if anyone wants to install BioPerl 1.5.2 on > any CentOS boxes, they have to force install Module::Build. :-/ Thanks for the info. 1.5.2 will come with the old ExtUtils::MakeMaker-based Makefile.PL so it should still be possible to install without a force. From bix at sendu.me.uk Wed Nov 22 18:30:07 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 22 Nov 2006 23:30:07 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164225865.2639.8.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> Message-ID: <4564DD7F.8090301@sendu.me.uk> Scott Cain wrote: > Hello, > > I just wanted to mention that I made a few minor changes to Build.PL so > that I could get `perl Build.PL` to complete successfully. I am using > ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > present either. The main thing I did was to have the BioDBGFF test > subroutine quit without asking any questions if Build.PL detected that > it was running on Windows. Is it completely impossible for it to pass under Windows? I find that quite a shame! I'm surprised it was necessary to make your changes, because it already had to return true from: DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0}) Can Windows pass that test without DBD::mysql installed, and having passed it why does it then fail the actual BioDBSeqFeature_mysql.t script? The cleanest way to do your change would be to make some change to the test_db() sub, eg: sub test_db { eval {require DBI;}; if ($^O =~ /mswin/i) { return "Windows isn't supported"; } unless (DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0})) { return "Could not connect to test database"; } return; } From cjfields at uiuc.edu Wed Nov 22 22:32:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 22 Nov 2006 21:32:34 -0600 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <4564DD7F.8090301@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> Message-ID: On Nov 22, 2006, at 5:30 PM, Sendu Bala wrote: > Scott Cain wrote: >> Hello, >> >> I just wanted to mention that I made a few minor changes to >> Build.PL so >> that I could get `perl Build.PL` to complete successfully. I am >> using >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't >> present either. The main thing I did was to have the BioDBGFF test >> subroutine quit without asking any questions if Build.PL detected >> that >> it was running on Windows. > > Is it completely impossible for it to pass under Windows? I find that > quite a shame! > > I'm surprised it was necessary to make your changes, because it > already > had to return true from: > > DBI->connect('dbi:mysql:test',undef,undef, > {RaiseError=>0,PrintError=>0}) > > Can Windows pass that test without DBD::mysql installed, and having > passed it why does it then fail the actual BioDBSeqFeature_mysql.t > script? I think he means the BioDBGFF.t tests, not BioDBSeqFeature_mysql.t. Myself, I can't get the Build script to detect my local MySQL on WinXP, though the BioDBGFF.t tests passed. I haven't been back to work since last Friday so I can't run updated WinXP tests myself. ... chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From roy at colibase.bham.ac.uk Tue Nov 21 13:51:30 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Tue, 21 Nov 2006 18:51:30 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <45634AB2.1020701@colibase.bham.ac.uk> > I'd like to propose changing the default reply-to for posts on this list > from the current 'reply to the poster' to 'reply to the mailing list'. > That way people can just hit 'reply' instead of 'reply to all' in order > to get a reply back to the list. We did this on our mailing list, and found it to be problematic if the messages still appear to come from an individual rather than the list- people may not realise they are replying to the whole list. This can lead to all sorts of issues- my boss and a collaborator once had a discussion (fortunately nothing too sensitive) that was accidentally copied to everyone in their field. The alternative is to overwrite the from: field as well as reply-to:, but then you rely on people having suitably informative signatures should anyone want to contact them off-list, and it makes the archives less useful. See also this: http://www.unicom.com/pw/reply-to-harmful.html Maybe you could tag a reminder to reply-all on every list message? Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From torsten.seemann at infotech.monash.edu.au Wed Nov 22 21:09:42 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Thu, 23 Nov 2006 13:09:42 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: References: Message-ID: <456502E6.8030409@infotech.monash.edu.au> > I don't want to throw too much fuel on the Module::Build fire, but I have > just discovered that I can't get Module::Build to install on CentOS 4.4. I concur with this problem :-( Most of the errors seem to be due to the large number of environmental variables I have set: "Couldn't run Build.PL: Argument list too long at /root/.cpan/build/Module-Build-0.2805/blib/lib/Module/Build/Compat.pm line 200." I had to "force install" the latest Module::Build to get bioperl-live tested and installed via Build.PL. -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From bix at sendu.me.uk Thu Nov 23 02:44:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 07:44:16 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <456502E6.8030409@infotech.monash.edu.au> References: <456502E6.8030409@infotech.monash.edu.au> Message-ID: <45655150.7090300@sendu.me.uk> Torsten Seemann wrote: >> I don't want to throw too much fuel on the Module::Build fire, but I have >> just discovered that I can't get Module::Build to install on CentOS 4.4. > > I concur with this problem :-( > > Most of the errors seem to be due to the large number of environmental > variables I have set: > > "Couldn't run Build.PL: Argument list too long at > /root/.cpan/build/Module-Build-0.2805/blib/lib/Module/Build/Compat.pm > line 200." > > I had to "force install" the latest Module::Build to get bioperl-live > tested and installed via Build.PL. Did everything with the Bioperl Build.PL script work fine after that? From bix at sendu.me.uk Thu Nov 23 05:48:05 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 10:48:05 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <4564DD7F.8090301@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> Message-ID: <45657C65.50200@sendu.me.uk> Sendu Bala wrote: > Scott Cain wrote: >> Hello, >> >> I just wanted to mention that I made a few minor changes to Build.PL so >> that I could get `perl Build.PL` to complete successfully. I am using >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't >> present either. The main thing I did was to have the BioDBGFF test >> subroutine quit without asking any questions if Build.PL detected that >> it was running on Windows. > > Is it completely impossible for it to pass under Windows? I find that > quite a shame! > > I'm surprised it was necessary to make your changes, because it already > had to return true from: [snip] Sorry, that all made no sense because I didn't pay attention to what changes you actually made. Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if being on mswin still causes a problem, or can the excludes_os restriction on line 78 of Build.PL be lifted now? Cheers, Sendu. From Squig at web.de Thu Nov 23 05:46:30 2006 From: Squig at web.de (Squig at web.de) Date: Thu, 23 Nov 2006 11:46:30 +0100 Subject: [Bioperl-l] Bioperl-ext and Staden Package Message-ID: <914558313@web.de> Hello, I have a short question concerning bioperl-ext and the io_lib from the staden package. Are there plans to fix bioperl-ext so it could be used with the actual version of io_lib (at the moment 1.10.1)? Myself has no experience in evoking externally written c - code from perl. But I think the changes to the io_lib - api are very well documented so a fix shouldn't be to hard for somebody with experience in this field. Please correct me if I'm totally wrong. Here you find the changes, you have to scroll a little bit down to "Changes". https://sourceforge.net/project/shownotes.php?release_id=340318&group_id=100316 If you think I could give a helping hand, please let me know. With kind regards, Stefan _______________________________________________________________________ Viren-Scan f?r Ihren PC! Jetzt f?r jeden. Sofort, online und kostenlos. Gleich testen! http://www.pc-sicherheit.web.de/freescan/?mc=022222 From cjfields at uiuc.edu Thu Nov 23 09:12:20 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 08:12:20 -0600 Subject: [Bioperl-l] Bioperl-ext and Staden Package In-Reply-To: <914558313@web.de> References: <914558313@web.de> Message-ID: On Nov 23, 2006, at 4:46 AM, Squig at web.de wrote: > Hello, > > I have a short question concerning bioperl-ext and the io_lib from > the staden package. > > Are there plans to fix bioperl-ext so it could be used with the > actual version of io_lib (at the moment 1.10.1)? This is one of the things tentatively planned but there have been no volunteers for it. > Myself has no experience in evoking externally written c - code > from perl. But I think the changes to the io_lib - api are very > well documented so a fix shouldn't be to hard for somebody with > experience in this field. Please correct me if I'm totally wrong. > > Here you find the changes, you have to scroll a little bit down to > "Changes". > https://sourceforge.net/project/shownotes.php? > release_id=340318&group_id=100316 > > If you think I could give a helping hand, please let me know. > > > With kind regards, > > Stefan > Any help would be greatly appreciated! There are tests included with bioperl-ext which you can add to or modify if needed. You can post patches for any changed code to bugzilla. Here's a HOWTO: http://www.bioperl.org/wiki/HOWTO:SubmitPatch Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sdavis2 at mail.nih.gov Thu Nov 23 10:43:37 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu, 23 Nov 2006 10:43:37 -0500 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45634AB2.1020701@colibase.bham.ac.uk> References: <45633B4A.6060804@sendu.me.uk> <45634AB2.1020701@colibase.bham.ac.uk> Message-ID: <4565C1A9.4080605@mail.nih.gov> Roy Chaudhuri wrote: >> I'd like to propose changing the default reply-to for posts on this list >> from the current 'reply to the poster' to 'reply to the mailing list'. >> That way people can just hit 'reply' instead of 'reply to all' in order >> to get a reply back to the list. >> > > We did this on our mailing list, and found it to be problematic if the > messages still appear to come from an individual rather than the list- > people may not realise they are replying to the whole list. This can > lead to all sorts of issues- my boss and a collaborator once had a > discussion (fortunately nothing too sensitive) that was accidentally > copied to everyone in their field. The alternative is to overwrite the > from: field as well as reply-to:, but then you rely on people having > suitably informative signatures should anyone want to contact them > off-list, and it makes the archives less useful. > > See also this: > http://www.unicom.com/pw/reply-to-harmful.html > I tend to agree here. I have seen some pretty significant accidents due to this feature. I think less harm is done by simply putting the thread back on list, if appropriate, if the sender happens to send to the original sender and not the entire list. Sean From bix at sendu.me.uk Thu Nov 23 16:18:01 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 21:18:01 +0000 Subject: [Bioperl-l] Please do not commit without testing Message-ID: <45661009.8040303@sendu.me.uk> Developers, Please do not commit changes without testing the test suite first, especially to branches! Note that: perl -I. -w t/test.t is NOT a good enough test, especially for test scripts that still use Test and not Test::More. (The above doesn't capture an incorrect number of tests in the plan.) Always initially do: ./Build test --test_files t/test.t --verbose Then run the entire test suite: ./Build test Thank you, Sendu. From The_Polymorph at rocketmail.com Thu Nov 23 16:30:42 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 23 Nov 2006 13:30:42 -0800 (PST) Subject: [Bioperl-l] Bioperl install question. Message-ID: <541373.13923.qm@web50815.mail.yahoo.com> Hi all. My set-up: WinXP (SP2) ActiveState Perl 5.8.8 I used the perl package manager to download BioPerl 1.2.3 but since that is rather old, I downloaded BioPerl-1.4.zip. Can anyone help me from this point? Where should I unzip the file to? Thanks, ~Katie ____________________________________________________________________________________ Want to start your own business? Learn how on Yahoo! Small Business. http://smallbusiness.yahoo.com/r-index From cjfields at uiuc.edu Thu Nov 23 16:43:30 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 15:43:30 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661009.8040303@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> Message-ID: On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: > Developers, > > Please do not commit changes without testing the test suite first, > especially to branches! > > Note that: > > perl -I. -w t/test.t > > is NOT a good enough test, especially for test scripts that still use > Test and not Test::More. (The above doesn't capture an incorrect > number > of tests in the plan.) > > Always initially do: > > ./Build test --test_files t/test.t --verbose > > Then run the entire test suite: > > ./Build test My bad. As a lousy excuse I have been extremely busy with family this holiday. However, the various changes using Module::Build need to be well-documented both in CVS docs and on the wiki. Your latter example ('./Build test --test_files t/test.t --verbose') is nowhere to be found. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 23 17:07:06 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 22:07:06 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> Message-ID: <45661B8A.9060405@sendu.me.uk> Chris Fields wrote: > > On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: > >> Developers, >> >> Please do not commit changes without testing the test suite first, >> especially to branches! >> >> Note that: >> >> perl -I. -w t/test.t >> >> is NOT a good enough test, especially for test scripts that still use >> Test and not Test::More. (The above doesn't capture an incorrect number >> of tests in the plan.) >> >> Always initially do: >> >> ./Build test --test_files t/test.t --verbose >> >> Then run the entire test suite: >> >> ./Build test [snip] > However, the various changes using Module::Build need to be > well-documented both in CVS docs and on the wiki. Your latter example > ('./Build test --test_files t/test.t --verbose') is nowhere to be found. I posted to the list about it on the 17th in thread 'Testing with Build.PL'. Where would you suggest a good place on the wiki would be to mention something like that? From cjfields at uiuc.edu Thu Nov 23 17:23:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 16:23:12 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> On Nov 23, 2006, at 4:07 PM, Sendu Bala wrote: > Chris Fields wrote: >> ... > [snip] >> However, the various changes using Module::Build need to be well- >> documented both in CVS docs and on the wiki. Your latter example >> ('./Build test --test_files t/test.t --verbose') is nowhere to be >> found. > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would > be to mention something like that? The mail list isn't the best place to document this; very few people (including developers) will take the time to go back digging through old posts except as a last resort. Hence these need to be well- documented AND easily accessible. Relevant changes need to be made everywhere that testing or using make/nmake is mentioned in CVS or the wiki. For the testing case I raised, maybe adding something to the various INSTALL docs and the FAQ would be a good start. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 23 17:36:47 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 22:36:47 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> Message-ID: <4566227F.4060102@sendu.me.uk> Chris Fields wrote: > On Nov 23, 2006, at 4:07 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> ... >> [snip] >>> However, the various changes using Module::Build need to be >>> well-documented both in CVS docs and on the wiki. Your latter >>> example ('./Build test --test_files t/test.t --verbose') is nowhere >>> to be found. >> >> I posted to the list about it on the 17th in thread 'Testing with >> Build.PL'. Where would you suggest a good place on the wiki would be >> to mention something like that? > > The mail list isn't the best place to document this; very few people > (including developers) will take the time to go back digging through old > posts except as a last resort. Hence these need to be well-documented > AND easily accessible. Relevant changes need to be made everywhere that > testing or using make/nmake is mentioned in CVS or the wiki. For the > testing case I raised, maybe adding something to the various INSTALL > docs and the FAQ would be a good start. It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's also on the wiki version of same.) I'm not sure that a developer would think to look in the installation documentation for that kind of information, so I've added the info to http://www.bioperl.org/wiki/Bioperl_Best_Practices#Testing as well. From n.haigh at sheffield.ac.uk Thu Nov 23 17:39:17 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 23 Nov 2006 22:39:17 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <45662315.5090600@sheffield.ac.uk> Sendu Bala wrote: > Chris Fields wrote: > >> On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: >> >> >>> Developers, >>> >>> Please do not commit changes without testing the test suite first, >>> especially to branches! >>> >>> Note that: >>> >>> perl -I. -w t/test.t >>> >>> is NOT a good enough test, especially for test scripts that still use >>> Test and not Test::More. (The above doesn't capture an incorrect number >>> of tests in the plan.) >>> >>> Always initially do: >>> >>> ./Build test --test_files t/test.t --verbose >>> >>> Then run the entire test suite: >>> >>> ./Build test >>> > [snip] > >> However, the various changes using Module::Build need to be >> well-documented both in CVS docs and on the wiki. Your latter example >> ('./Build test --test_files t/test.t --verbose') is nowhere to be found. >> > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would be to > mention something like that? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > I'd possibly put it somewhere like: http://www.bioperl.org/wiki/Developer_Information If there's enough stuff to create a new page? If so, how about a page called "testing" or "test suite" or "running tests"?? Just ensure it's given the "Developer resources" Category to make it that bit easier to locate. Nath From n.haigh at sheffield.ac.uk Thu Nov 23 17:31:58 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 23 Nov 2006 22:31:58 +0000 Subject: [Bioperl-l] Bioperl install question. In-Reply-To: <541373.13923.qm@web50815.mail.yahoo.com> References: <541373.13923.qm@web50815.mail.yahoo.com> Message-ID: <4566215E.9090409@sheffield.ac.uk> Caitlin wrote: > Hi all. > > My set-up: > > WinXP (SP2) > ActiveState Perl 5.8.8 > > > I used the perl package manager to download BioPerl 1.2.3 but since > that is rather old, I downloaded BioPerl-1.4.zip. Can anyone help me > from this point? Where should I unzip the file to? > > Thanks, > > ~Katie > > > Hi Katie, First of all try installing Bioperl 1.5.2 RC2 by following the installation instructions for windows at: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows#Installation_Guide See how you get on with that and let us know if you have troubles, or indeed if you manage to install successfully! Thanks Nathan From bix at sendu.me.uk Thu Nov 23 18:31:59 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 23:31:59 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45662909.3010101@infotech.monash.edu.au> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> <45662909.3010101@infotech.monash.edu.au> Message-ID: <45662F6F.2090700@sendu.me.uk> Torsten Seemann wrote: >>> I had to "force install" the latest Module::Build to get bioperl-live >>> tested and installed via Build.PL. >> >> Did everything with the Bioperl Build.PL script work fine after that? > > Yes. > > However it was much "slower" to install, it initially pauses for a long > time, then eventually does the install. I'm guessing you're describing the period of time that it manifies the documentation? Don't you see lots of output detailing what is going on at each moment in time? From torsten.seemann at infotech.monash.edu.au Thu Nov 23 18:50:30 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 24 Nov 2006 10:50:30 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45662F6F.2090700@sendu.me.uk> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> <45662909.3010101@infotech.monash.edu.au> <45662F6F.2090700@sendu.me.uk> Message-ID: <456633C6.5080109@infotech.monash.edu.au> >>>> I had to "force install" the latest Module::Build to get >>>> bioperl-live tested and installed via Build.PL. >>> >>> Did everything with the Bioperl Build.PL script work fine after that? >> >> Yes. >> >> However it was much "slower" to install, it initially pauses for a >> long time, then eventually does the install. > > I'm guessing you're describing the period of time that it manifies the > documentation? Don't you see lots of output detailing what is going on > at each moment in time? Yes I see all the usual output. The pause is between the following two events:. ... ... Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 . # (no output for 15+ seconds on unloaded server) . Installing /usr/share/man/man1/bp_chaos_plot.pl.1" ... ... -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From torsten.seemann at infotech.monash.edu.au Thu Nov 23 18:04:41 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 24 Nov 2006 10:04:41 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45655150.7090300@sendu.me.uk> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> Message-ID: <45662909.3010101@infotech.monash.edu.au> >> I had to "force install" the latest Module::Build to get bioperl-live >> tested and installed via Build.PL. > > Did everything with the Bioperl Build.PL script work fine after that? Yes. However it was much "slower" to install, it initially pauses for a long time, then eventually does the install. -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From cjfields at uiuc.edu Thu Nov 23 23:04:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 22:04:58 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <4566227F.4060102@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> Message-ID: On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: ... > It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's > also on the wiki version of same.) Okay, but I find the Windows page hasn't been updated (still shows nmake). Everything needs to be changed, not just the UNIX pages > I'm not sure that a developer would think to look in the installation > documentation for that kind of information, so I've added the info to > http://www.bioperl.org/wiki/Bioperl_Best_Practices#Testing as well. Sounds good. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 23 23:09:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 22:09:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45662315.5090600@sheffield.ac.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45662315.5090600@sheffield.ac.uk> Message-ID: On Nov 23, 2006, at 4:39 PM, Nathan S. Haigh wrote: > Sendu Bala wrote: >> >> I posted to the list about it on the 17th in thread 'Testing with >> Build.PL'. Where would you suggest a good place on the wiki would >> be to >> mention something like that? >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > I'd possibly put it somewhere like: > http://www.bioperl.org/wiki/Developer_Information > > If there's enough stuff to create a new page? If so, how about a page > called "testing" or "test suite" or "running tests"?? > > Just ensure it's given the "Developer resources" Category to make it > that bit easier to locate. > > Nath ... I think we need to gear some docs not just towards users but also towards potential developers, so maybe a HOWTO for writing and running tests might be the best way to go. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From The_Polymorph at rocketmail.com Thu Nov 23 23:29:18 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 23 Nov 2006 20:29:18 -0800 (PST) Subject: [Bioperl-l] BioPerl install question (update). Message-ID: <20061124042918.5392.qmail@web50801.mail.yahoo.com> Hi all. Ok. I upgraded my ActiveState perl install from build 817 to build 819 and followed the directions located at the site below to install BioPerl 1.5.2 RC2: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Thanks for the help Nathan! ~Katie ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited From bix at sendu.me.uk Fri Nov 24 02:54:19 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 07:54:19 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> Message-ID: <4566A52B.80304@sendu.me.uk> Chris Fields wrote: > On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: > ... > >> It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's >> also on the wiki version of same.) > > Okay, but I find the Windows page hasn't been updated (still shows > nmake). Everything needs to be changed, not just the UNIX pages I don't know what to say for the windows docs. I can't even get perl -V to work on my Windows machine: &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. The Build.PL scripts fails similarly: &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. Can't locate the perl binary used to run this script in (C:\Perl\bin C:\Perl\bin C:\Perl\bin . C:\Program Files\ActiveState Komodo 3.5 C:\Perl\bin C:\WINDOWS\sy stem32 C:\WINDOWS C:\WINDOWS\System32\Wbem C:\Program Files\ATI Technologies\ATI .ACE) I took it that you had no problems? Should I just make the Windows docs similar to the Unix ones? (Or can you do the appropriate update?) From bix at sendu.me.uk Fri Nov 24 03:56:15 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 08:56:15 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 Message-ID: <4566B3AF.2050305@sendu.me.uk> Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. See http://www.bioperl.org/wiki/Release_1.5.2 for instructions on getting and testing this RC. Everyone: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into. Please try the new Build.PL installation script and report back how you get on. Also try installing using CPAN. Your CPAN mirrors may not be current enough, so you may have delete all entries in your urllist first. Developers: Please experiment with installation, especially via CPAN. If you already have all/most prerequisite external modules installed, try uninstalling some and report how effective the system is at reinstalling them for you. RC5 may form the final release for some of the packages (probably all except for bioperl-run), so any further commits made, even to branch-1-5-2, may not make final release. If you think you've committed an important bug fix that should be part of final release, let me know. Thank you, Sendu. PS. What happened to RC4? I didn't announce it, but it was available on CPAN where I did some testing on it. From n.haigh at sheffield.ac.uk Fri Nov 24 04:35:01 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Fri, 24 Nov 2006 09:35:01 +0000 Subject: [Bioperl-l] Bioperl install question. In-Reply-To: <20061124012953.66815.qmail@web50812.mail.yahoo.com> References: <20061124012953.66815.qmail@web50812.mail.yahoo.com> Message-ID: <4566BCC5.7050003@sheffield.ac.uk> Caitlin wrote: > Hi Nathan, > > Thanks for the quick reply. I wasn't able to locate a Perl Package > Manager GUI from the Start menu. The only options displayed are: > > Documentation > OLE Browser > Perl Package Manager > > Clicking on 'Perl Package Manager' loads ppm in a console window (i.e. > non-GUI environment). Should I re-install ActivePerl? If so, that would > eliminate my installed modules wouldn't it? > > Thanks, > > ~Katie > > It sounds like you probably have a version of ActivePerl < 5.8.8.819. If this is the case, download and install the latest ActivePerl version >= 5.8.8.819. If you do a reinstall into the same location as your current ActivePerl installation you will probably maintain all the currently installed modules - but I can't say for definate. Once you have ActivePerl >= 5.8.8.819 installed, you should be able to follow the instructions in the link I provided previously. Nath From n.haigh at sheffield.ac.uk Fri Nov 24 04:38:54 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Fri, 24 Nov 2006 09:38:54 +0000 Subject: [Bioperl-l] BioPerl install question (update). In-Reply-To: <20061124042918.5392.qmail@web50801.mail.yahoo.com> References: <20061124042918.5392.qmail@web50801.mail.yahoo.com> Message-ID: <4566BDAE.50105@sheffield.ac.uk> Caitlin wrote: > Hi all. > > Ok. I upgraded my ActiveState perl install from build 817 to build 819 > and followed the directions located at the site below to install > BioPerl 1.5.2 RC2: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Thanks for the help Nathan! > > ~Katie > > Ah - have just sent an e-mail to say update to build 819! We should be releasing the proper 1.5.2 release quite soon (hopefully in a week or two) At that stage, you should update the bioperl package. It nice to hear it when things work! Nath From cjfields at uiuc.edu Fri Nov 24 07:15:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 24 Nov 2006 06:15:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <4566A52B.80304@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> <4566A52B.80304@sendu.me.uk> Message-ID: On Nov 24, 2006, at 1:54 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: >> ... >>> It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. >>> (It's >>> also on the wiki version of same.) >> Okay, but I find the Windows page hasn't been updated (still shows >> nmake). Everything needs to be changed, not just the UNIX pages > > I don't know what to say for the windows docs. I can't even get > > perl -V > > to work on my Windows machine: > > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > > The Build.PL scripts fails similarly: > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > Can't locate the perl binary used to run this script in (C:\Perl > \bin C:\Perl\bin > C:\Perl\bin . C:\Program Files\ActiveState Komodo 3.5 C:\Perl\bin > C:\WINDOWS\sy > stem32 C:\WINDOWS C:\WINDOWS\System32\Wbem C:\Program Files\ATI > Technologies\ATI > .ACE) > > I took it that you had no problems? Should I just make the Windows > docs similar to the Unix ones? (Or can you do the appropriate update?) No, everything worked on my machine. I'll try making the necessary changes as soon as I can, but it won't be today. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Fri Nov 24 16:38:07 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 16:38:07 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: Is it possible to add a file to the repository (at least temporarily) called README.Build or something that would contain those examples? I find myself saving your emails which I don't think is the most efficient way for me to have those bits handy when I'll need them. -hilmar On Nov 23, 2006, at 5:07 PM, Sendu Bala wrote: > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would > be to > mention something like that? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Fri Nov 24 17:08:37 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 22:08:37 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <45676D65.6000409@sendu.me.uk> Hilmar Lapp wrote: > Is it possible to add a file to the repository (at least temporarily) > called README.Build or something that would contain those examples? > > I find myself saving your emails which I don't think is the most > efficient way for me to have those bits handy when I'll need them. Given that Makefile.PL is just a stub that prints a message about Build.PL, I can just extend the message to include more tips? From hlapp at gmx.net Fri Nov 24 17:27:43 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 17:27:43 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45676D65.6000409@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> Message-ID: On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: > Hilmar Lapp wrote: >> Is it possible to add a file to the repository (at least temporarily) >> called README.Build or something that would contain those examples? >> >> I find myself saving your emails which I don't think is the most >> efficient way for me to have those bits handy when I'll need them. > > Given that Makefile.PL is just a stub that prints a message about > Build.PL, I can just extend the message to include more tips? You could but that wouldn't substitute. Typing ./Build instead of make is not too hard of a change to make; however, you don't want me to go back and run perl Makefile.PL to get a quick refresher every time I want to use a more advanced feature of the generated Build file, do you? -hilmar > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Fri Nov 24 17:46:49 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 22:46:49 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> Message-ID: <45677659.404@sendu.me.uk> Hilmar Lapp wrote: > > On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: > >> Hilmar Lapp wrote: >>> Is it possible to add a file to the repository (at least temporarily) >>> called README.Build or something that would contain those examples? >>> >>> I find myself saving your emails which I don't think is the most >>> efficient way for me to have those bits handy when I'll need them. >> >> Given that Makefile.PL is just a stub that prints a message about >> Build.PL, I can just extend the message to include more tips? > > You could but that wouldn't substitute. Typing ./Build instead of make > is not too hard of a change to make; however, you don't want me to go > back and run perl Makefile.PL to get a quick refresher every time I want > to use a more advanced feature of the generated Build file, do you? If you can remember at least that it is ./Build you need to do something with, it has lovely in-built help. It's entirely standard stuff so nothing to learn - just remember its there! > ./Build -h No action '-h' defined, try running the 'help' action. ./Build help ./Build help test From hlapp at gmx.net Fri Nov 24 19:08:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 19:08:18 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45677659.404@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> <45677659.404@sendu.me.uk> Message-ID: <965EC1D8-AC7D-491A-BCFE-82776D724161@gmx.net> On Nov 24, 2006, at 5:46 PM, Sendu Bala wrote: > If you can remember at least that it is ./Build you need to do > something > with, it has lovely in-built help. It's entirely standard stuff so > nothing to learn - just remember its there! > >> ./Build -h > No action '-h' defined, try running the 'help' action. > > > > ./Build help > > > > ./Build help test > > Sounds nice & will surely be helpful. I guess what I was trying to say is that you could make the value of the examples you typed up in emails already (including the above) much more lasting by copy&pasting them into a document that's within easy reach of a developer who is losing his/her nerves because somebody from the extended family spilled cranberry sauce across his/her new laptop over Thanksgiving. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Fri Nov 24 19:13:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 24 Nov 2006 18:13:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45677659.404@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> <45677659.404@sendu.me.uk> Message-ID: <9AF9038D-71FD-46AD-A486-5B9472BC29AA@uiuc.edu> On Nov 24, 2006, at 4:46 PM, Sendu Bala wrote: > Hilmar Lapp wrote: >> >> On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: >> >>> Hilmar Lapp wrote: >>>> Is it possible to add a file to the repository (at least >>>> temporarily) >>>> called README.Build or something that would contain those examples? >>>> >>>> I find myself saving your emails which I don't think is the most >>>> efficient way for me to have those bits handy when I'll need them. >>> >>> Given that Makefile.PL is just a stub that prints a message about >>> Build.PL, I can just extend the message to include more tips? >> >> You could but that wouldn't substitute. Typing ./Build instead of >> make >> is not too hard of a change to make; however, you don't want me to go >> back and run perl Makefile.PL to get a quick refresher every time >> I want >> to use a more advanced feature of the generated Build file, do you? > > If you can remember at least that it is ./Build you need to do > something > with, it has lovely in-built help. It's entirely standard stuff so > nothing to learn - just remember its there! > >> ./Build -h > No action '-h' defined, try running the 'help' action. > > > > ./Build help > > > > ./Build help test > > Hilmar's suggestion of collecting these snippets of Build-related commands in a single place seems like a good start, since it doesn't really pertain to installation but is of use for developers and future release pumpkins. As for the help example above, as helpful as it is, I don't think most would know it was even there unless it was pointed out. A few blurbs in the FAQ, maybe in the 'BioPerl in General' or a new developer section, might also help. 'How do I run tests using Module::Build?' or 'Where can I find out more about Module::Build?', for instance. It's also much easier (at least to me) to point out to new users or developers that any relevant information is found in 'document x' vs. 'this post on the mail list, found in the mail archives at this link, just follow the thread...'. chris (still recovering after being dragged out on Black Friday). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Fri Nov 24 18:16:47 2006 From: jason at bioperl.org (Jason Stajich) Date: Fri, 24 Nov 2006 15:16:47 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45635F98.8030901@bms.com> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> Message-ID: <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> Can we just weaken the references with Scalar::Util? This should solve the problem for circular refs. Is Scalar::Util part of the core distro in the min perl we are supporting? I can add this in Bio::Tree::Node and look around to see where else it is a problem. We just need a simple script to verify it is having an effect (i.e. a bug report with this). -jason On Nov 21, 2006, at 12:20 PM, Stefan Kirov wrote: > Hilmar Lapp wrote: >> On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: >> >> >>> I don't know if I should hold up release of 1.5.2 for it. Now that >>> you've >>> reported on it I'm leaning toward yes, since the new Bio::Species >>> implementation is one of the major new features of 1.5.2 and it >>> ought to >>> work well. >>> >> >> I disagree to some extent. This is a developer release, so not >> everything is expected to work perfectly. >> >> What's not desirable is if fixing this required another entire >> redesign of the API, so that every dev release introduces >> different API. >> >> The thing is, you'll really only get trouble reports once you put it >> out and people start using it in anger. Don't expect to make it >> perfect before. >> >> >>> Anyway, for the memory leak I have some ideas I haven't tried yet; I >>> don't know if my efforts will solve the speed issue though. >>> >> >> The memory leak sounds more concerning to me. Under which >> circumstances would it crash a script or blow throuhg all of say >> 1-2GB when it should have taken only a tenth of that. >> >> > As I was saying, I did pass ref to an array in the classification > (wrong > parsing): > push @classification,'sapiens', 'Homo', 'Hominidae', $arrayref; > and my script took 17-18 GB. I am really surprised it stopped getting > more RAM and finished successfully. I did not explore further. > Stefan >> -hilmar >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Sat Nov 25 07:47:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 12:47:28 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> Message-ID: <45683B60.9090402@sendu.me.uk> Jason Stajich wrote: > Can we just weaken the references with Scalar::Util? This should solve > the problem for circular refs. I don't know about Stefan's problem, but I tried weakening refs - it fixed the memory leak I was seeing, but caused other problems. > Is Scalar::Util part of the core distro in the min perl we are supporting? Yes. > I can add this in Bio::Tree::Node and look around to see where else it > is a problem. We just need a simple script to verify it is having an > effect (i.e. a bug report with this). perl -w -MBio::SeqIO -e '$si = new Bio::SeqIO(-file => "5UTR.Pln_nr.dat", -format => "embl"); while ($seq = $si->next_seq) { $seq->id; }' Where 5UTR.Pln_nr.dat is a large embl file with ~50000 sequences. For me this takes ~11mins to parse and ~2GB memory. Once I weakened refs in all the places I could find in Bio::Tree::Node and Bio::Tree::Tree it used a constant 0.3% of memory but still took around 11mins. However lots of the tests in the test suite then fail, because Nodes are often made purely to add into a Tree, with the requirement that the Tree keeps hard refs to them all (else the Tree would fall apart). I think the Tree actually only keeps a ref to its root Node, which means Nodes in general must keep hard refs to their Descendants. With that constraint, I haven't been able to break the deadlock and get these things to clean up. Hopefully I'm missing something obvious; please look into it. From cjfields at uiuc.edu Sat Nov 25 08:32:43 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 25 Nov 2006 07:32:43 -0600 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45683B60.9090402@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> Message-ID: <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: ... > I think the Tree actually only keeps a ref to its root Node, which > means > Nodes in general must keep hard refs to their Descendants. With that > constraint, I haven't been able to break the deadlock and get these > things to clean up. > > Hopefully I'm missing something obvious; please look into it. I'm curious to see if this affects sequence parsing (i.e. SwissProt DB parsing). Does anyone know? It sounds pretty serious. Sendu, could you commit a bug report for this? I don't think this should hold up rel 1.5.2 (it's a dev release) but it would be nice to get it fixed. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Sat Nov 25 08:57:53 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 13:57:53 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> Message-ID: <45684BE1.8010902@sendu.me.uk> Chris Fields wrote: > > On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: > ... > >> I think the Tree actually only keeps a ref to its root Node, which means >> Nodes in general must keep hard refs to their Descendants. With that >> constraint, I haven't been able to break the deadlock and get these >> things to clean up. >> >> Hopefully I'm missing something obvious; please look into it. > > I'm curious to see if this affects sequence parsing (i.e. SwissProt DB > parsing). Does anyone know? It sounds pretty serious. Any time you create lots of Bio::Species objects the memory leak ought to arise. > Sendu, could you commit a bug report for this? I don't think this > should hold up rel 1.5.2 (it's a dev release) but it would be nice to > get it fixed. http://bugzilla.open-bio.org/show_bug.cgi?id=2149 From bix at sendu.me.uk Sat Nov 25 17:08:59 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 22:08:59 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> Message-ID: <4568BEFB.4070201@sendu.me.uk> Jason Stajich wrote: > > The circular ref is from Bio::Species when you have > $self->{tree} = Bio::Tree::Tree->new(-root => $self); > > I added a weaken call in Bio::Species code explicitly -- we can't > generally weaken the ref to the root node in Bio::Tree::Tree as that > breaks some other things as you saw. Thanks. Though there's still the issue with Bio::Tree::Node::node_cleanup not doing anything. > I'm not sure I am digging what you've done with Bio::Tree::Tree. Why > didn't you make a specialized Tree object for Taxonomy stuff so that you > can add methods like lineage_node, etc? http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because it's a Tree function. It goes hand in hand with get_lca(), which was already there. I suppose you're saying it would have been more appropriate to have a new Tree-based object that only differed in its new() instead of adding an option to Tree's new()? My thinking was that both the -node option and get_lineage_nodes() are useful for trees in general, not just Bio::Taxon. From jason at bioperl.org Sat Nov 25 16:20:41 2006 From: jason at bioperl.org (Jason Stajich) Date: Sat, 25 Nov 2006 13:20:41 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45684BE1.8010902@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> Message-ID: The circular ref is from Bio::Species when you have $self->{tree} = Bio::Tree::Tree->new(-root => $self); I added a weaken call in Bio::Species code explicitly -- we can't generally weaken the ref to the root node in Bio::Tree::Tree as that breaks some other things as you saw. I'm not sure I am digging what you've done with Bio::Tree::Tree. Why didn't you make a specialized Tree object for Taxonomy stuff so that you can add methods like lineage_node, etc? We'll talk about it in more detail in Dec I guess to see if we can clean up some of the things here. -jason On Nov 25, 2006, at 5:57 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: >> ... >>> I think the Tree actually only keeps a ref to its root Node, >>> which means >>> Nodes in general must keep hard refs to their Descendants. With that >>> constraint, I haven't been able to break the deadlock and get these >>> things to clean up. >>> >>> Hopefully I'm missing something obvious; please look into it. >> I'm curious to see if this affects sequence parsing (i.e. >> SwissProt DB parsing). Does anyone know? It sounds pretty serious. > > Any time you create lots of Bio::Species objects the memory leak > ought to arise. > > >> Sendu, could you commit a bug report for this? I don't think this >> should hold up rel 1.5.2 (it's a dev release) but it would be nice >> to get it fixed. > > http://bugzilla.open-bio.org/show_bug.cgi?id=2149 -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From biology0046 at hotmail.com Sun Nov 26 08:19:45 2006 From: biology0046 at hotmail.com (=?gb2312?B?va0gzsTi/Q==?=) Date: Sun, 26 Nov 2006 13:19:45 +0000 Subject: [Bioperl-l] PAML problem Message-ID: I use scripts at PAML Howto page to caculate M7 or M8 model. but it always report errors: ------------------------------------------------- Error: err: incorrect model for pairwise comparison.check NSsites, alpha, aaDist.. ------------------------------------------------- Can't call method "next_result" on an undefined value at pamtest.txt line 65. ---------------------------------------------------------- use Bio::Tools::Run::Phylo::PAML::Codeml; use Bio::Tools::Run::Alignment::Clustalw; # for projecting alignments from protein to R/DNA space use Bio::Align::Utilities qw(aa_to_dna_aln); # for input of the sequence data use Bio::SeqIO; use Bio::AlignIO; my $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new; #my $seqdata = shift || 'cds.fa'; my $seqio = new Bio::SeqIO(-file =>"CG4686.cds", -format => 'fasta'); my %seqs; my @prots; # process each sequence while ( my $seq = $seqio->next_seq ) { $seqs{$seq->display_id} = $seq; # translate them into protein my $protein = $seq->translate(); my $pseq = $protein->seq(); if( $pseq =~ /\*/ && $pseq !~ /\*$/ ) { warn("provided a CDS sequence with a stop codon, PAML will choke!"); #exit(0); } # Tcoffee can't handle '*' even if it is trailing $pseq =~ s/\*//g; $protein->seq($pseq); push @prots, $protein; } if( @prots < 2 ) { warn("Need at least 2 CDS sequences to proceed"); exit(0); } open(OUT, ">align_output.txt") || die("cannot open output align_output for writing"); # Align the sequences with clustalw my $aa_aln = $aln_factory->align(\@prots); # project the protein alignment back to CDS coordinates my $dna_aln = aa_to_dna_aln($aa_aln, \%seqs); my @each = $dna_aln->each_seq(); my $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new ( -params => { 'NSsites' => 7, 'ncatG'=>10, 'seqtype' => 1, } ); #I change the parameters here # set the alignment object $kaks_factory->alignment($dna_aln); # run the KaKs analysis my ($rc,$parser) = $kaks_factory->run(); my $result = $parser->next_result; Seqfile:>D_pseudoobscuraATGATGGACACATTGGACTACATCACCCTCAGCAATCCCGTGAGCAAGGCGGTTATATATTCGGGATCGGCTATCTTCCGAGCCCTTGGGCTGCGTCCGAAACAGTTGGTTCCGAAGGAGACCCAGACAGTGCGTCCGGTAATGACTCAGTACATGTCGCCGGGTGCTGGCTCGCTGCATAATTTGGCCGGCCGGTACTATCATTTCGTGCGACTGGCTGGCCTAGGCGGCGCTTCGGCTATTTTCATGGGAGCCTACTGCAAATACGTCCTGAAGGAGATCAAGAACGAAAAGGAGCAGCTGGACTCGCAGGCCTTTGCCGATGTCGCCAATCGCATACACTTTTTGCATTCGTTTGCACTGATGGCCATGCCACTGGCCCACTATCCCATAATCACGGGCTCTTTGATGACCACTGGCACACTGCTCTTCAGCGGCTGCATGTACTATCGTGCATTGACGGGCGAGAAGCGCTTCCAGCCGTTTGCCACCGTTGGAGGCTTCTGTCTGATAGCCGCTTGGCTGACGCTGATATTT >D_willistoniATGTCAATAGTTGATACATTGGACTATATAACCCTGGGTAATCCAGTGAGTCGCTTGGTCATATCTTCAACATCGGCATTAATGCGTACAATTGGTCTGCGCCCCAAGCAGGTGCCTATAAAGGATACAGAAATAGCTGGATTGCCACAGCAGGTCCATCATTTCGGAAATCCAAATGGCCCATCCTTATATACAATTGCCGGCTCTCATTATAACTTTATTCGTCTAGCTGGAATTGGCGGAGCATCGGCTATATTTATGGGAGCGTATTGTAAATATTTTCTTAAGGATATCAATGATCCCAAGGAACAGTTGGATTCACAAGCCTTTGCCGATGTGGCCAATCGTATACATTTTCTCCACTCATTTGCATTAATGGCGATGCCCTTGGCTCATTATCCAGTTTTTACTGGCGCCCTTATGACCACCGGCACATTACTTTTCAGTGGGTGTATGTACTATCGCGCTTTAACCGGTGATAAGAGACTTCAACATTATGCCACAATTGGTGGCTTCTGTCTAATGGCTGCTTGGTTATCCTTGGTTTTG >D_melanogasterATGTCAGTCGCTGACACCATTGAATACGTGACCCTGGGCAATCCTGTCAGCAAGATGGTAGCCTCGTCCGCATCCGCCCTGCTCCGCACGCTTGGTCTGCGTCCCAAGAAGGTGCCGGTGCAGGAGACGAGTATGGCGGTGCTCCCTGCCGCCCACAGCTACGCGCATTCACACGGATCACTCTATCGACTGGCCGGCTGCCATTACCACTTCATTCGGCTGGCCGGGATCGTCGGCGCGTCGGCCATCTTTATGGGCGCCTACTGCAAGTACGTCCTGAAGGACGTCAGCGATCCCAAGGAGCAGGTGGACTCGCAGGCCTTTGCTGATGTGGCCAATCGCATCCACTTTCTGCACTCCTTTGCCATGATGGCCATGCCTCTGGCCCACTATCCCGTATTCACTGGCACTTTGATGATTACGGGCATGATGCTTTTCAGCGGCTGCATGTACTACCGCGCTTTGACTGGCGAGAAGCGTCTGCAACCGTACGCGACCGTCGGAGGATTCTGCCTGATGGCCGCGTGGCTGTCGCTGGTCCTG _________________________________________________________________ ???????????????????????????? MSN Messenger: http://messenger.msn.com/cn From chhalling at verizon.net Sun Nov 26 16:00:18 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 26 Nov 2006 16:00:18 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456A0062.6080103@verizon.net> I attempted to use CPAN to install BioPerl 1.5.2 RC5 into a fresh installation of Perl 5.8.8 under Mac OS X 10.4.8 with all dependencies installed. The tests fail for t/SearchIO. An edited record of the output is shown below. cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz [*snip*] *** Optional dependencies section *** All dependencies are installed [*snip*] Running make test PERL_DL_NONLAZY=1 /test/perl/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t [*snip*] t/SearchIO...................ok 1/1340 -------------------- WARNING --------------------- MSG: XML::SAX::Expat not currently supported; must have local copies of NCBI DTD docs! --------------------------------------------------- -------------------- WARNING --------------------- MSG: error in parsing a report: 404 File `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/NCBI_BlastOutput.dtd' does not exist file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/NCBI_BlastOutput.dtd Handler couldn't resolve external entity at line 2, column 82, byte 104 error in processing external entity reference at line 2, column 82, byte 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm line 187 --------------------------------------------------- t/SearchIO...................NOK 5/1340 # Failed test 'The object isa Bio::Search::Result::ResultI' # in t/SearchIO.t at line 65. # The object isn't defined Can't call method "database_name" on an undefined value at t/SearchIO.t line 66. # Looks like you planned 1340 tests but only ran 5. # Looks like you failed 1 test of 5 run. # Looks like your test died just after 5. t/SearchIO...................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-1340 Failed 1336/1340 tests, 0.30% okay [*snip*] Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/SearchIO.t 255 65280 1340 2671 5-1340 2 tests and 126 subtests skipped. Failed 1/235 test scripts. 1336/11940 subtests failed. Files=235, Tests=11940, 321 wallclock secs (154.44 cusr + 24.28 csys = 178.72 CPU) Failed 1/235 test programs. 1336/11940 subtests failed. make: *** [test_dynamic] Error 255 /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Everyone: > Even though 1.5.2 is a 'developer' release, we consider it the most > stable and capable version of Bioperl, and recommend that you use > it in all but the most critical production environments. Please > try it out and let us know of any problems or difficulties you run > into. > > Please try the new Build.PL installation script and report back how > you get on. Also try installing using CPAN. Your CPAN mirrors may > not be current enough, so you may have delete all entries in your > urllist first. > > > Developers: > Please experiment with installation, especially via CPAN. If you > already have all/most prerequisite external modules installed, > try uninstalling some and report how effective the system is at > reinstalling them for you. > > RC5 may form the final release for some of the packages (probably > all except for bioperl-run), so any further commits made, even to > branch-1-5-2, may not make final release. If you think you've > committed an important bug fix that should be part of final release, > let me know. > > > Thank you, > Sendu. > > > PS. What happened to RC4? I didn't announce it, but it was available on > CPAN where I did some testing on it. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Conrad Halling chhalling at verizon.net From cjfields at uiuc.edu Sun Nov 26 17:04:59 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 16:04:59 -0600 Subject: [Bioperl-l] EntrezGene test failures Message-ID: I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ Build test --test_files t/entrezgene.t --verbose': .. ok 1367 ok 1368 - correct number of loops for T18 # Looks like you planned 1417 tests but only ran 1368. # Looks like you failed 22 tests of 1368 run. dubious Test returned status 22 (wstat 5632, 0x1600) DIED. FAILED tests 56, 162, 182, 184, 367, 512, 603, 631, 667, 711, 766, 920, 998, 1107, 1140, 1192, 1225, 1248, 1270, 1297, 1320, 1345, 1369-1417 Failed 71/1417 tests, 94.99% okay Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------ ------- t/entrezgene.t 22 5632 1417 120 56 162 182 184 367 512 603 631 667 711 766 920 998 1107 1140 1192 1225 1248 1270 1297 1320 1345 1369-1417 Failed 1/1 test scripts. 71/1417 subtests failed. Files=1, Tests=1417, 3 wallclock secs ( 3.06 cusr + 0.09 csys = 3.15 CPU) Failed 1/1 test programs. 71/1417 subtests failed. Looks like not all tests are run. Of the tests that fail, all are from unmatched values. A few examples: # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '14' # expected: '16' not ok 56 - correct number of loops for T15 ... # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '28' # expected: '30' ... not ok 162 - correct number of loops for T15 # Failed test in t/entrezgene.t at line 456. # got: '0' # expected: '1' # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '6' # expected: '5' chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Sun Nov 26 17:17:30 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 16:17:30 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456A0062.6080103@verizon.net> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> Message-ID: <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: > I attempted to use CPAN to install BioPerl 1.5.2 RC5 into a fresh > installation of Perl 5.8.8 under Mac OS X 10.4.8 with all dependencies > installed. > > The tests fail for t/SearchIO. An edited record of the output is shown > below. > > > cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz > > [*snip*] > > *** Optional dependencies section *** > All dependencies are installed > > [*snip*] > > Running make test > PERL_DL_NONLAZY=1 /test/perl/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > > [*snip*] > > t/SearchIO...................ok > 1/1340 > -------------------- WARNING --------------------- > MSG: XML::SAX::Expat not currently supported; must have local > copies of > NCBI DTD docs! > --------------------------------------------------- > > -------------------- WARNING --------------------- > MSG: error in parsing a report: > > 404 File > `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ > NCBI_BlastOutput.dtd' > does not exist > file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ > NCBI_BlastOutput.dtd > Handler couldn't resolve external entity at line 2, column 82, byte > 104 > error in processing external entity reference at line 2, column 82, > byte > 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm > line 187 > > --------------------------------------------------- > t/SearchIO...................NOK > 5/1340 > # Failed test 'The object isa Bio::Search::Result::ResultI' > # in t/SearchIO.t at line 65. > # The object isn't defined > Can't call method "database_name" on an undefined value at t/ > SearchIO.t > line 66. > # Looks like you planned 1340 tests but only ran 5. > # Looks like you failed 1 test of 5 run. > # Looks like your test died just after 5. > t/SearchIO...................dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-1340 > Failed 1336/1340 tests, 0.30% okay > > [*snip*] > > Failed Test Stat Wstat Total Fail List of Failed > ---------------------------------------------------------------------- > --------- > t/SearchIO.t 255 65280 1340 2671 5-1340 > 2 tests and 126 subtests skipped. > Failed 1/235 test scripts. 1336/11940 subtests failed. > Files=235, Tests=11940, 321 wallclock secs (154.44 cusr + 24.28 csys = > 178.72 CPU) > Failed 1/235 test programs. 1336/11940 subtests failed. > make: *** [test_dynamic] Error 255 > /usr/bin/make test -- NOT OK > Running make install > make test had returned bad status, won't install without force > ... There is an eval{} block set up to catch that error but apparently it doesn't work. I'll have a look at it. Like the warning states, XML::SAX::Expat is not supported for BLASTXML parsing unless you have the NCBI DTDs installed as well (blame this on NCBI since their BLAST DTDs don't have the explicit web address). Saying that I don't recommend using XML::SAX::Expat at all (it is no longer actively maintained). Pretty much any other XML::SAX backend works; I recommend using XML::SAX::ExpatXS or XML::LibXML for speedier parsing, though XML::SAX::PurePerl also works. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Sun Nov 26 17:56:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 26 Nov 2006 22:56:28 +0000 Subject: [Bioperl-l] EntrezGene test failures In-Reply-To: References: Message-ID: <456A1B9C.5000105@sendu.me.uk> Chris Fields wrote: > I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ > Build test --test_files t/entrezgene.t --verbose': Yes, Stefan is in the middle of bug fixing/ improvements. I changed the test script recently to highlight the problems. From cjfields at uiuc.edu Sun Nov 26 18:48:23 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 17:48:23 -0600 Subject: [Bioperl-l] EntrezGene test failures In-Reply-To: <2ac232dd4a.2dd4a2ac23@bms.com> References: <2ac232dd4a.2dd4a2ac23@bms.com> Message-ID: On Nov 26, 2006, at 5:44 PM, Stefan Kirov wrote: > I thought Sendu rolled back some changes I've made. I was planning to > commit changes both to the module and the tests, but I am not done > yet. > Stefan Not a problem, just wanted to check. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Sun Nov 26 18:44:29 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Sun, 26 Nov 2006 18:44:29 -0500 Subject: [Bioperl-l] EntrezGene test failures Message-ID: <2ac232dd4a.2dd4a2ac23@bms.com> I thought Sendu rolled back some changes I've made. I was planning to commit changes both to the module and the tests, but I am not done yet. Stefan ----- Original Message ----- From: Chris Fields Date: Sunday, November 26, 2006 5:04 pm Subject: [Bioperl-l] EntrezGene test failures > I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ > Build test --test_files t/entrezgene.t --verbose': > > .. > ok 1367 > ok 1368 - correct number of loops for T18 > # Looks like you planned 1417 tests but only ran 1368. > # Looks like you failed 22 tests of 1368 run. > dubious > Test returned status 22 (wstat 5632, 0x1600) > DIED. FAILED tests 56, 162, 182, 184, 367, 512, 603, 631, 667, 711, > > 766, 920, 998, 1107, 1140, 1192, 1225, 1248, 1270, 1297, 1320, > 1345, > 1369-1417 > Failed 71/1417 tests, 94.99% okay > Failed Test Stat Wstat Total Fail List of Failed > -------------------------------------------------------------------- > ---- > ------- > t/entrezgene.t 22 5632 1417 120 56 162 182 184 367 512 603 > 631 > 667 711 > 766 920 998 1107 1140 1192 > 1225 1248 1270 > 1297 1320 1345 1369-1417 > Failed 1/1 test scripts. 71/1417 subtests failed. > Files=1, Tests=1417, 3 wallclock secs ( 3.06 cusr + 0.09 csys = > 3.15 CPU) > Failed 1/1 test programs. 71/1417 subtests failed. > > > > Looks like not all tests are run. Of the tests that fail, all are > from unmatched values. A few examples: > > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '14' > # expected: '16' > not ok 56 - correct number of loops for T15 > > ... > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '28' > # expected: '30' > > ... > > not ok 162 - correct number of loops for T15 > > # Failed test in t/entrezgene.t at line 456. > # got: '0' > # expected: '1' > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '6' > # expected: '5' > > > > chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at uiuc.edu Sun Nov 26 23:14:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 22:14:32 -0600 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4568BEFB.4070201@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> <4568BEFB.4070201@sendu.me.uk> Message-ID: <34BAD635-8C9F-4A22-B114-B3EFB5B544DD@uiuc.edu> On Nov 25, 2006, at 4:08 PM, Sendu Bala wrote: > Jason Stajich wrote: >> >> The circular ref is from Bio::Species when you have >> $self->{tree} = Bio::Tree::Tree->new(-root => $self); >> >> I added a weaken call in Bio::Species code explicitly -- we can't >> generally weaken the ref to the root node in Bio::Tree::Tree as that >> breaks some other things as you saw. > > Thanks. Though there's still the issue with > Bio::Tree::Node::node_cleanup not doing anything. > > >> I'm not sure I am digging what you've done with Bio::Tree::Tree. Why >> didn't you make a specialized Tree object for Taxonomy stuff so >> that you >> can add methods like lineage_node, etc? > > http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree > > get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because > it's > a Tree function. It goes hand in hand with get_lca(), which was > already > there. > > I suppose you're saying it would have been more appropriate to have a > new Tree-based object that only differed in its new() instead of > adding > an option to Tree's new()? > > My thinking was that both the -node option and get_lineage_nodes() are > useful for trees in general, not just Bio::Taxon. Jason's fixes seem to fix the problem (I tested on Mac OS X). However, does Scalar::Utils come as core with perl 5.6.1? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Sun Nov 26 23:58:14 2006 From: jason at bioperl.org (Jason Stajich) Date: Sun, 26 Nov 2006 20:58:14 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4568BEFB.4070201@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> <4568BEFB.4070201@sendu.me.uk> Message-ID: On Nov 25, 2006, at 2:08 PM, Sendu Bala wrote: > Jason Stajich wrote: >> The circular ref is from Bio::Species when you have >> $self->{tree} = Bio::Tree::Tree->new(-root => $self); >> I added a weaken call in Bio::Species code explicitly -- we can't >> generally weaken the ref to the root node in Bio::Tree::Tree as >> that breaks some other things as you saw. > > Thanks. Though there's still the issue with > Bio::Tree::Node::node_cleanup not doing anything. > right - well I am not sure that it is going to get called if you have to remove the cleanup_methods from the object (or does this mean at all?). I don't have any time to debug it any more so we'll just have to wait till later to figure it out. I'd really like to re-visit the tree bjects to see about making them faster anyways so maybe the memory cycle issue can be revisited as well. > >> I'm not sure I am digging what you've done with Bio::Tree::Tree. >> Why didn't you make a specialized Tree object for Taxonomy stuff >> so that you can add methods like lineage_node, etc? > > http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree > > get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because > it's a Tree function. It goes hand in hand with get_lca(), which > was already there. > > I suppose you're saying it would have been more appropriate to have > a new Tree-based object that only differed in its new() instead of > adding an option to Tree's new()? > > My thinking was that both the -node option and get_lineage_nodes() > are useful for trees in general, not just Bio::Taxon. > I guess I was talking about this code in new() - seems like a Tree::Taxon object could have been made to deal with the special case, but probably I am just not seeing the whole picture so no worries. # to stop us pulling in entire database of a Bio::Taxon when we later do # get_nodes() or similar, specifically set ancestor() for each node if ($node->isa('Bio::Taxon')) { push(@lineage, $node) unless $node eq $root; my $ancestor = $root; foreach my $lineage_node (@lineage) { $lineage_node->ancestor($ancestor); } continue { $ancestor = $lineage_node; } } -- Jason Stajich jason at bioperl.org http://jason.open-bio.org/ From anhthu.tieu at gsf.de Mon Nov 27 03:38:36 2006 From: anhthu.tieu at gsf.de (Anh-Thu Tieu) Date: Mon, 27 Nov 2006 09:38:36 +0100 Subject: [Bioperl-l] exention files for bioperl1.5.2 Message-ID: <456AA40C.3050207@gsf.de> Hi, I noticed there has been a new release for bioperl1.5.2 and I wondered whether there is/ will also be an extension file for this version also (as for version 1.4 or 1.5.1). Until now I have only found the core, network, db and the run files. Is it sufficient to install those four packages (+ various additional perl modules) to make bioperl1.5.2 run or do I need any exention files. Thank you. Best regards, Anh Thu From n.haigh at sheffield.ac.uk Mon Nov 27 04:52:39 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 09:52:39 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456AB567.2010601@sheffield.ac.uk> I just checked out RC5 and ran "perl Build.PL" I get: Can't locate object method "new" via package "Module::Build::Notes" (perhaps you forgot to load "Module::Build::Notes"?) at /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. Nath From bix at sendu.me.uk Mon Nov 27 09:50:08 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 14:50:08 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456AB567.2010601@sheffield.ac.uk> References: <4566B3AF.2050305@sendu.me.uk> <456AB567.2010601@sheffield.ac.uk> Message-ID: <456AFB20.4050102@sendu.me.uk> Nathan Haigh wrote: > I just checked out RC5 and ran "perl Build.PL" I get: > > Can't locate object method "new" via package "Module::Build::Notes" > (perhaps you forgot to load "Module::Build::Notes"?) at > /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. What version of Module::Build do you have installed? Does your Module/Build/Base.pm not 'use Modules::Build::Notes' somewhere near the top? Try upgrading to v0.2805 of Module::Build and let me know if that solves the problem. (If you don't have Module::Build installed at all, didn't you get some kind of prompt to install it?) Thank you, Sendu. From bix at sendu.me.uk Mon Nov 27 11:01:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 16:01:16 +0000 Subject: [Bioperl-l] exention files for bioperl1.5.2 In-Reply-To: <456AA40C.3050207@gsf.de> References: <456AA40C.3050207@gsf.de> Message-ID: <456B0BCC.2020202@sendu.me.uk> Anh-Thu Tieu wrote: > Hi, > > I noticed there has been a new release for bioperl1.5.2 and I wondered > whether there is/ will also be an extension file for this version also > (as for version 1.4 or 1.5.1). Until now I have only found the core, > network, db and the run files. Is it sufficient to install those four > packages (+ various additional perl modules) to make bioperl1.5.2 run or > do I need any exention files. What do you mean by 'extension' file? If you mean the bioperl-ext package then hopefully whatever old version you have will still work. It hasn't been tested, nor will it be updated for 1.5.2 From n.haigh at sheffield.ac.uk Mon Nov 27 11:05:40 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 16:05:40 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456AFB20.4050102@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456AB567.2010601@sheffield.ac.uk> <456AFB20.4050102@sendu.me.uk> Message-ID: <456B0CD4.1060602@sheffield.ac.uk> Sendu Bala wrote: > Nathan Haigh wrote: >> I just checked out RC5 and ran "perl Build.PL" I get: >> >> Can't locate object method "new" via package "Module::Build::Notes" >> (perhaps you forgot to load "Module::Build::Notes"?) at >> /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. > > What version of Module::Build do you have installed? Does your > Module/Build/Base.pm not 'use Modules::Build::Notes' somewhere near > the top? > > Try upgrading to v0.2805 of Module::Build and let me know if that > solves the problem. > > (If you don't have Module::Build installed at all, didn't you get some > kind of prompt to install it?) > > > Thank you, > Sendu. I have v0.2612 installed. Upgrading to Module::Build 0.2805 fixed the problem. Nath From bix at sendu.me.uk Mon Nov 27 11:18:35 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 16:18:35 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> Message-ID: <456B0FDB.9020208@sendu.me.uk> Chris Fields wrote: > On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: [snip] >> t/SearchIO...................ok >> 1/1340 >> -------------------- WARNING --------------------- >> MSG: XML::SAX::Expat not currently supported; must have local >> copies of >> NCBI DTD docs! >> --------------------------------------------------- >> >> -------------------- WARNING --------------------- >> MSG: error in parsing a report: >> >> 404 File >> `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >> NCBI_BlastOutput.dtd' >> does not exist >> file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >> NCBI_BlastOutput.dtd >> Handler couldn't resolve external entity at line 2, column 82, byte >> 104 >> error in processing external entity reference at line 2, column 82, >> byte >> 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm >> line 187 [snip] > There is an eval{} block set up to catch that error but apparently it > doesn't work. I'll have a look at it. The test script has nothing to catch in the eval because blastxml.pm catches the error and emits a warning. You'll either have to make blastxml.pm throw (instead of returning undef + warn), or figure something else out. It's a behaviour change, but would anyone care if it threw thanks to this problem? From cjfields at uiuc.edu Mon Nov 27 11:41:53 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 27 Nov 2006 10:41:53 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B0FDB.9020208@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> <456B0FDB.9020208@sendu.me.uk> Message-ID: On Nov 27, 2006, at 10:18 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: > [snip] >>> t/SearchIO...................ok >>> 1/1340 >>> -------------------- WARNING --------------------- >>> MSG: XML::SAX::Expat not currently supported; must have local >>> copies of >>> NCBI DTD docs! >>> --------------------------------------------------- >>> >>> -------------------- WARNING --------------------- >>> MSG: error in parsing a report: >>> >>> 404 File >>> `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >>> NCBI_BlastOutput.dtd' >>> does not exist >>> file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >>> NCBI_BlastOutput.dtd >>> Handler couldn't resolve external entity at line 2, column 82, >>> byte 104 >>> error in processing external entity reference at line 2, column >>> 82, byte >>> 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/ >>> Parser.pm line 187 > > [snip] > >> There is an eval{} block set up to catch that error but apparently >> it doesn't work. I'll have a look at it. > > The test script has nothing to catch in the eval because > blastxml.pm catches the error and emits a warning. You'll either > have to make blastxml.pm throw (instead of returning undef + warn), > or figure something else out. > > It's a behaviour change, but would anyone care if it threw thanks > to this problem? Ah, that's my fault. I had changed that to a throw but didn't commit it. In a nutshell, we can't/won't support XML::SAX::Expat for a number of reasons. One is the problem with the BLAST DTDs (no explicit web address, so XML validation fails). There may be a way to turn validation off. However, the other, more serious issue is that it is no longer maintained (it hasn't been updated in three years). There were plans a year ago for XML::SAX::ExpatXS to take over the XML::SAX::Expat namespace but no one has bothered to make the changeover, apparently. I have committed the change from warn to throw and made the error message more explicit. You can look it over and merge to 1.5.2 at your discretion. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cain.cshl at gmail.com Mon Nov 27 12:39:09 2006 From: cain.cshl at gmail.com (Scott Cain) Date: Mon, 27 Nov 2006 12:39:09 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <45657C65.50200@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> Message-ID: <1164649150.2575.57.camel@localhost.localdomain> Hi Sendu, I won't have time to do testing on Windows until much later in the day, but I at least want to throw out a little more information. In ActivePerl 819, DBI appears to be installed by default, but the method 'available_drivers' doesn't appear to be available (not implemented? returns something invalid when there are none? not sure at the moment). Anyway, as a result, when I run perl Build.PL and there are no drivers installed, it crashes. I'll try to tease out what is going on later tonight. Scott On Thu, 2006-11-23 at 10:48 +0000, Sendu Bala wrote: > Sendu Bala wrote: > > Scott Cain wrote: > >> Hello, > >> > >> I just wanted to mention that I made a few minor changes to Build.PL so > >> that I could get `perl Build.PL` to complete successfully. I am using > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > >> present either. The main thing I did was to have the BioDBGFF test > >> subroutine quit without asking any questions if Build.PL detected that > >> it was running on Windows. > > > > Is it completely impossible for it to pass under Windows? I find that > > quite a shame! > > > > I'm surprised it was necessary to make your changes, because it already > > had to return true from: > [snip] > > Sorry, that all made no sense because I didn't pay attention to what > changes you actually made. > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > being on mswin still causes a problem, or can the excludes_os > restriction on line 78 of Build.PL be lifted now? > > > Cheers, > Sendu. -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain.cshl at gmail.com GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061127/70151d62/attachment.bin From n.haigh at sheffield.ac.uk Mon Nov 27 12:48:59 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 17:48:59 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456B250B.4050607@sheffield.ac.uk> When running ./Build test for bioperl-run, the tests for DrawGram and DrawTree require me to manually close the window that is opened and press return in the console in order for the test to complete. Nath From bix at sendu.me.uk Mon Nov 27 12:54:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 17:54:58 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B250B.4050607@sheffield.ac.uk> References: <4566B3AF.2050305@sendu.me.uk> <456B250B.4050607@sheffield.ac.uk> Message-ID: <456B2672.5030405@sendu.me.uk> Nathan Haigh wrote: > When running ./Build test for bioperl-run, the tests for DrawGram and > DrawTree require me to manually close the window that is opened and > press return in the console in order for the test to complete. Hasn't that always been the case in the past? Or did you only recently install some optional pre-req? Does anyone know a way around this? From n.haigh at sheffield.ac.uk Mon Nov 27 13:31:18 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 18:31:18 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B2672.5030405@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456B250B.4050607@sheffield.ac.uk> <456B2672.5030405@sendu.me.uk> Message-ID: <456B2EF6.10808@sheffield.ac.uk> Sendu Bala wrote: > Nathan Haigh wrote: >> When running ./Build test for bioperl-run, the tests for DrawGram and >> DrawTree require me to manually close the window that is opened and >> press return in the console in order for the test to complete. > > Hasn't that always been the case in the past? Or did you only recently > install some optional pre-req? > > Does anyone know a way around this? I've always had Phylip installed, and I know I've run the tests remotely without X11 forwarding - which obviously wouldn't allow the windows to appear (tests were still successful). I'm also sure I've run the test locally previously - but I've not noticed it before - starting to think I'm going mad! :-P Nath From cjfields at uiuc.edu Mon Nov 27 16:47:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 27 Nov 2006 15:47:12 -0600 Subject: [Bioperl-l] DBSOURCE parsing Message-ID: Jason, I am working on stockholm and GenPept format parsing, both which have DBLink objects. I have a couple of questions. First, (not a huge issue really, more like a curiosity), is it possible to pass a callback to Annotation objects for the overloaded operators? I'm just thinking of situations where the data is displayed differently in other formats (like Stockholm). Also, would it be feasible to have DBLink objects also contain annotations (comments, other DBLink objects, etc) for more complex data? In particular this regards GenPept stuff, like the following examples: DBSOURCE swissprot: locus BRCA1_HUMAN, accession P38398; class: standard. created: Oct 1, 1994. sequence updated: Feb 1, 1995. annotation updated: Nov 14, 2006. xrefs: U14680.1, AAA73985.1, L78833.1, AAC37594.1, AY273801.1, AAP12647.1, A58881, 1JM7A, 1JNXX, 1N5OX, 1OQAA, 1T15A, 1T29A, 1T2UA, 1T2VA, 1T2VB, 1T2VC, 1T2VD, 1T2VE, 1Y98A xrefs (non-sequence databases): UniGene:Hs.194143, IntAct:P38398, TRANSFAC:T04074, Ensembl:ENSG00000012048, KEGG:hsa:672, HGNC:1100, MIM:113705, MIM:114480, Reactome:P38398, ArrayExpress:P38398, GO:0031436, GO:0008274, GO:0005634, GO:0000151, GO:0050681, GO:0003677, GO:0019899, GO:0003713, GO:0015631, GO:0008270, GO:0030521, GO:0007059, GO:0006978, GO:0008630, GO:0042759, GO:0046600, GO:0016481, GO:0045739, GO:0031398, GO:0045893, GO:0016567, GO:0042981, GO:0042127, GO:0006357, GO:0006359, InterPro:IPR011364, InterPro:IPR001357, InterPro:IPR002378, InterPro:IPR001841, PANTHER:PTHR13763, Pfam:PF00533, Pfam:PF00097, PIRSF:PIRSF001734, PRINTS:PR00493, SMART:SM00292, SMART:SM00184, PROSITE:PS50172, PROSITE:PS00518, PROSITE:PS50089 ... DBSOURCE pdb: molecule 1T2U, chain 65, release Apr 22, 2004; deposition: Apr 22, 2004; class: Antitumor Protein; source: Mol_id: 1; Organism_scientific: Homo Sapiens; Organism_common: Human; Gene: Brca1; Expression_system: Escherichia Coli; Expression_system_common: Bacteria; Exp. method: X-Ray Diffraction. ... DBSOURCE pir: locus I49350; summary: #length 1812 #molecular-weight 198788 #checksum 8813 ; genetic: #gene Brca1 ; superfamily: transcriptional regulator, BRCA1 type; RING finger homology ; PIR dates: 02-Jul-1996 #sequence_revision 02-Jul-1996 #text_change 09-May-2004 . ... DBSOURCE prf: locus 2202221A; state: hepatoma/colonic tumor; taxonomy: Mammalia. My thought is, the first line would be the main DBLink object data, with all subsequent lines as annotation objects (comments, DBLinks, etc) in an annotation collection contained within the main DBLink object. I don't think there would be any danger of circular references if handled correctly. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From chhalling at verizon.net Mon Nov 27 22:25:00 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:25:00 -0500 Subject: [Bioperl-l] A procedure for efficient testing of the installation of BioPerl Message-ID: <456BAC0C.10503@verizon.net> I have devised the following procedure that lets me repeatedly install BioPerl release candidates for testing the installation process. I am performing these tests under Mac OS X 10.4.8. I thought it would be useful to document this process for anyone else who is testing the installation process. I downloaded the tarball for Perl 5.8.8 and ran the following commands to set up the code for installation: cd /Volumes/CHHalling/Perl/Perl-5.8.8 tar -xzf perl-5.8.8.tgz cd perl-5.8.8 sh Configure -Dprefix=/test/perl -Dcc=gcc -des make make test For each round of testing, I run the following commands to install a fresh copy of Perl 5.8.8 and then initialize the cpan utility: cd /Volumes/CHHalling/Perl/Perl-5.8.8/perl-5.8.8 sudo rm -rf /test sudo mkdir /test sudo make install sudo rm -rf ~/.cpan export PATH=/test/perl/bin:$PATH sudo cpan Then I run my cpan commands. For installing BioPerl without having installed the dependencies, I enter the command: cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz For installing the dependencies, then installing BioPerl, I enter the commands: cpan> install Bundle::BioPerl cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz For testing modifications to Bundle::BioPerl (the subject of my next post), I execute the following commands (which exit the cpan utility after I have initialized it, create the Bundle subdirectory, copy the BioPerl.pm file that contains the Bundle::BioPerl package to the .cpan/Bundle directory, start the cpan utility, and install Bundle::BioPerl and BioPerl 1.5.2 RC5): cpan> exit $ sudo mkdir ~/.cpan/Bundle $ sudo cp /Volumes/CHHalling/Perl/BioPerl/BioPerl.pm ~/.cpan/Bundle/ $ sudo cpan cpan> install Bundle::BioPerl cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz When I have finished testing the installation, I loop back to step 2, where I remove the /test directory and reinstall Perl 5.8.8. A note: I was going to use the same procedure to test installing BioPerl 1.5.2 under Perl 5.6.1, but I discovered that Perl 5.6.1 is *so old* that there is no Makefile for Mac OS X. -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Mon Nov 27 22:02:59 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:02:59 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456BA6E3.3010908@verizon.net> I compiled and installed Perl 5.8.8 under Mac OS X 10.4.8 into a directory named /test/perl. Then I used the cpan utility to attempt to install BioPerl 1.5.2 RC5 without having installed any of its dependencies. The installation failed because of the following test failures: t/SeqFeature t/SeqHound_DB t/SeqVersion Here are the pertinent details: t/SeqFeature.................IO::String or LWP::UserAgent or HTTP::Request not installed - skipping DB tests... Can't locate URI/Escape.pm in @INC (@INC contains: t /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/arch /test/perl/lib/5.8.8/darwin-2level /test/perl/lib/5.8.8 /test/perl/lib/site_perl/5.8.8/darwin-2level /test/perl/lib/site_perl/5.8.8 /test/perl/lib/site_perl .) at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/SeqFeature/Annotated.pm line 86. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/SeqFeature/Annotated.pm line 86. Compilation failed in require at t/SeqFeature.t line 52. BEGIN failed--compilation aborted at t/SeqFeature.t line 52. t/SeqFeature.................dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/SeqHound_DB................ok 1/14Can't locate LWP/UserAgent.pm in @INC (@INC contains: /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/arch /test/perl/lib/5.8.8/darwin-2level /test/perl/lib/5.8.8 /test/perl/lib/site_perl/5.8.8/darwin-2level /test/perl/lib/site_perl/5.8.8 /test/perl/lib/site_perl .) at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/WebDBSeqI.pm line 78. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/WebDBSeqI.pm line 78. Compilation failed in require at (eval 19) line 3. ...propagated at /test/perl/lib/5.8.8/base.pm line 85. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/SeqHound.pm line 88. Compilation failed in require at t/SeqHound_DB.t line 41. BEGIN failed--compilation aborted at t/SeqHound_DB.t line 41. Use of uninitialized value in -f at t/SeqHound_DB.t line 34. t/SeqHound_DB................dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/SeqVersion.................NOK 1 # Failed test 'use Bio::DB::SeqVersion;' # in t/SeqVersion.t at line 21. # Tried to use 'Bio::DB::SeqVersion'. # Error: Base class package "LWP::UserAgent" is empty. # (Perhaps you need to 'use' the module which defines that package first.) # at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/WebAgent.pm line 90 # BEGIN failed--compilation aborted at t/SeqVersion.t line 21. # Compilation failed in require at (eval 4) line 3. # ...propagated at /test/perl/lib/5.8.8/base.pm line 85. # BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/SeqVersion.pm line 71. # Compilation failed in require at (eval 3) line 2. # BEGIN failed--compilation aborted at (eval 3) line 2. Can't locate object method "new" via package "Bio::DB::SeqVersion" at t/SeqVersion.t line 23. # Looks like you planned 10 tests but only ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test died just after 1. t/SeqVersion.................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-10 Failed 10/10 tests, 0.00% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/SeqFeature.t 2 512 211 0 0.00% ?? t/SeqHound_DB.t 2 512 14 0 0.00% ?? t/SeqVersion.t 255 65280 10 19 190.00% 1-10 9 tests and 228 subtests skipped. Failed 3/235 test scripts, 98.72% okay. 10/11535 subtests failed, 99.91% okay. make: *** [test_dynamic] Error 255 /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > [*snip*] > Thank you, > Sendu. -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Mon Nov 27 22:51:14 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:51:14 -0500 Subject: [Bioperl-l] A new Bundle::BioPerl Message-ID: <456BB232.4020808@verizon.net> After experimenting with the existing Bundle::BioPerl version 2.1.8 under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install all of the BioPerl dependencies unless run multiple times. I edited the the order that the dependencies were listed so I could get all the dependencies to install on the first try. Then I got carried away and ran some grep commands on the bioperl-live source code to identify all of the dependencies that are use'd or require'd, and I added these dependencies to the Bundle::BioPerl package. Many of these dependencies are core Perl modules, which it doesn't hurt to update. After a few rounds of testing during Thanksgiving weekend festivities, I have completed a new Bundle::BioPerl package that installs virtually all of the dependencies on the first try. There are two modules that won't install. The first is Bio::ASN1::EntrezGene, and the second is CORBA::ORBit. Bio::ASN1::EntrezGene won't install because it is dependent on Bio::Index::AbstractSeq, which is part of BioPerl. CORBA::ORBit won't install because its tarball appears to be corrupted. The cpan utility also reports that Math::Trig and Text::Balanced didn't install, but this is an error, because they are installed correctly. The cpan commands for installing the BioPerl dependencies, Bio::ASN1::EntrezGene, and BioPerl 1.5.2 RC5, will become: cpan> install Bundle::BioPerl cpan> force install Bio::ASN1::EntrezGene cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz I have filed a Bugzilla bug report (bug #2153) and attached my Bundle::BioPerl package (attachment #508) to it for consideration. -- Conrad Halling chhalling at verizon.net From DGroskreutz at twt.com Tue Nov 28 02:00:40 2006 From: DGroskreutz at twt.com (DGroskreutz at twt.com) Date: Tue, 28 Nov 2006 01:00:40 -0600 Subject: [Bioperl-l] CN=Deb Groskreutz/OU=MSN/O=TWT is out of the office. Message-ID: I will be out of the office starting 11/27/2006 and will not return until 12/04/2006. NOTICE OF CONFIDENTIALITY: The information contained in this communication, including attachments, is intended for the specific delivery to and use by the individual(s) to whom it is addressed. This email includes confidential information that may be attorney-client privileged. Any review, retransmission, dissemination, or unauthorized use of this communication is strictly prohibited and may be unlawful. If you have received this communication in error, please reply to the sender immediately and delete the original communication and any copy of it from your computer system, including all attachments. From bix at sendu.me.uk Tue Nov 28 05:53:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 10:53:10 +0000 Subject: [Bioperl-l] A new Bundle::BioPerl In-Reply-To: <456BB232.4020808@verizon.net> References: <456BB232.4020808@verizon.net> Message-ID: <456C1516.5050900@sendu.me.uk> Conrad Halling wrote: > After experimenting with the existing Bundle::BioPerl version 2.1.8 > under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install > all of the BioPerl dependencies unless run multiple times. > > I edited the the order that the dependencies were listed so I could get > all the dependencies to install on the first try. Thank you so much for all your hard work. Its extremely valuable. That said, I'm no longer recommending the usage of Bundle::BioPerl. Instead what I'll do is apply your discovered order to the new Build.PL installation system. You're welcome of course to contact Chris Dagdigian to make sure he knows about your new version of Bundle::BioPerl. He can then upload it to CPAN if he's happy with it, and people who choose to still use the Makefile.PL installation process will surely appreciate the new version of Bundle::BioPerl. Thanks again, Sendu. From st537 at york.ac.uk Tue Nov 28 06:02:07 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Tue, 28 Nov 2006 11:02:07 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... Message-ID: <456C172F.4060008@york.ac.uk> Hi, I am trying to learn bioperl and I'm attempting a few basic thing! I seem to be ok with reading in and outputting sequences and files now I am trying to do a simple BLAST search using a sequence (a sequence object in fact). The code I am attempting to run is at the bottom of the message... I am probably making a dumb mistake and don't understand the capabilities of the objects well enough, but the info for the remoteblast->submit_blast function says that it can take sequences as an argument, I've also tried sending the fasta file name containing my sequence as an argument to submit_blast, with the same result.... I have also tried sending $seqio_obj->next_seq........... i.e the following error message displayed on my terminal: Can't call method "submit_blast" on an undefined value at bioptest2.pl line 22, line 1. I haven't got around to figuring out how to process the returned data from this yet, just trying to get the function to run first! Thanks for any help that anyone can offer me with this... Samantha Thompson #******************************** use Bio::Seq; use Bio::SeqIO; use Bio::Tools::Run::RemoteBlast; use Bio::SearchIO; #seq bit $seq_obj = Bio::Seq->new(-format => 'fasta'); $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); $seq_obj = $seqio_obj->next_seq; #blast bit $remote_blast = Bio::Tools::Run::RemoteBlast->new ( -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); #end From bix at sendu.me.uk Tue Nov 28 07:39:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 12:39:29 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C172F.4060008@york.ac.uk> References: <456C172F.4060008@york.ac.uk> Message-ID: <456C2E01.5070805@sendu.me.uk> Samantha Thompson wrote: > Hi, > I am trying to learn bioperl and I'm attempting a few basic thing! I > seem to be ok with reading in and outputting sequences and files now I > am trying to do a simple BLAST search using a sequence (a sequence > object in fact). The code I am attempting to run is at the bottom of the > message... > I am probably making a dumb mistake and don't understand the > capabilities of the objects well enough, but the info for the > remoteblast->submit_blast function says that it can take sequences as an > argument, I've also tried sending the fasta file name containing my > sequence as an argument to submit_blast, with the same result.... I > have also tried sending $seqio_obj->next_seq........... i.e the > following error message displayed on my terminal: > > Can't call method "submit_blast" on an undefined value at bioptest2.pl > line 22, line 1. Always start your perl scripts with 'use strict;'. This will help you find and fix the main problem with your script, that you made a RemoteBlast object and stored it as $remote_blast, but then tried to use submit_blast() on $remoteBlast which doesn't exist. I've rewritten your code below: use strict; > use Bio::Seq; > use Bio::SeqIO; > > use Bio::Tools::Run::RemoteBlast; > use Bio::SearchIO; > > #seq bit > # $seq_obj = Bio::Seq->new(-format => 'fasta'); # above line doesn't do anything, $seq_obj gets overwritten below > my $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > my $seq_obj = $seqio_obj->next_seq; > > > > #blast bit > my $remote_blast = Bio::Tools::Run::RemoteBlast->new(-prog => 'blastp', -db => 'nr', -expect => '1e-15' ); # submit_blast takes the sequence object, not the sequence string my $blastreturn_obj = $remote_blast->submit_blast($seq_obj); From n.haigh at sheffield.ac.uk Tue Nov 28 08:10:45 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 28 Nov 2006 13:10:45 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C172F.4060008@york.ac.uk> References: <456C172F.4060008@york.ac.uk> Message-ID: <456C3555.3040807@sheffield.ac.uk> Samantha Thompson wrote: > Hi, > I am trying to learn bioperl and I'm attempting a few basic thing! I > seem to be ok with reading in and outputting sequences and files now I > am trying to do a simple BLAST search using a sequence (a sequence > object in fact). The code I am attempting to run is at the bottom of the > message... > I am probably making a dumb mistake and don't understand the > capabilities of the objects well enough, but the info for the > remoteblast->submit_blast function says that it can take sequences as an > argument, I've also tried sending the fasta file name containing my > sequence as an argument to submit_blast, with the same result.... I > have also tried sending $seqio_obj->next_seq........... i.e the > following error message displayed on my terminal: > > Can't call method "submit_blast" on an undefined value at bioptest2.pl > line 22, line 1. > > I haven't got around to figuring out how to process the returned data > from this yet, just trying to get the function to run first! > Thanks for any help that anyone can offer me with this... > > Samantha Thompson > > #******************************** > > > use Bio::Seq; > use Bio::SeqIO; > > use Bio::Tools::Run::RemoteBlast; > use Bio::SearchIO; > > #seq bit > > $seq_obj = Bio::Seq->new(-format => 'fasta'); > > $seqio_obj = Bio::SeqIO->new(-file => > "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > > $seq_obj = $seqio_obj->next_seq; > > > > #blast bit > > $remote_blast = Bio::Tools::Run::RemoteBlast->new ( > -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); > > $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); > > > > > #end > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > Hi Samantha, At first glance and without running any code, the first thing I can see that is incorrect is: $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); I believe that submit_blast() would be likely to take the actual sequence object ($seq_obj) as the argument and not the actual sequence string itself (e.g. "ACTGCTG") that you get by calling $seq_obj->seq. So swap this line for: $blastreturn_obj = $remoteBlast->submit_blast($seq_obj); And see how you get on. Nath From hlapp at gmx.net Tue Nov 28 11:20:59 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 28 Nov 2006 11:20:59 -0500 Subject: [Bioperl-l] load_seqdatabase.pl question In-Reply-To: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> Message-ID: <53C6D534-6E36-4061-B955-E74537839265@gmx.net> Hi Derek, first off, I'd recommend to always post such questions to the mailing list; sometimes I may not have a chance to check my email for a while or respond right away but someone else may know the answer too. In your case it looks like you didn't install bioperl-db. You need to install bioperl-db from CVS (using the main trunk). Instructions for how to do this are on the bioperl web site. Let me (and the list) know if you have trouble finding those. Let me know if you did install bioperl-db. (If you did, did you also set PERL5LIB if you installed it in non-standard place, such as your home directory?) -hilmar On Nov 27, 2006, at 12:07 PM, Derek Buchfink wrote: > Hi, I am new to BioSQL and I am looking to use the > load_seqdatabase.pl script to load some data into a PostgreSQL > 8.1.4 database. I am using version 1.24 of the script. However, I > am getting the following error: > > Can't locate Bio/DB/BioDB.pm in @INC (@INC contains: /usr/lib/ > perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/ > perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/ > site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/ > 5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386- > linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread- > multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/ > lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/ > perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/ > site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/ > site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi / > usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/ > perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/ > vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/ > vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/ > vendor_perl .) at load_seqdatabase.pl line 337. > BEGIN failed--compilation aborted at load_seqdatabase.pl line 337. > > Do you know how to solve this issue or do you have any helpful > suggestions? Thank you very much. > > Derek Buchfink -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cain at cshl.edu Tue Nov 28 11:42:23 2006 From: cain at cshl.edu (Scott Cain) Date: Tue, 28 Nov 2006 11:42:23 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164649150.2575.57.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> Message-ID: <1164732143.2584.33.camel@localhost.localdomain> Hi Sendu, It looks like what you've done did the trick--bioperl installed on both ActivePerl 817 and 819 using Module::Build (though I must admit I didn't look at the tests--I just wanted `perl Build.PL` to work). Nice work! Scott On Mon, 2006-11-27 at 12:39 -0500, Scott Cain wrote: > Hi Sendu, > > I won't have time to do testing on Windows until much later in the day, > but I at least want to throw out a little more information. In > ActivePerl 819, DBI appears to be installed by default, but the method > 'available_drivers' doesn't appear to be available (not implemented? > returns something invalid when there are none? not sure at the moment). > Anyway, as a result, when I run perl Build.PL and there are no drivers > installed, it crashes. I'll try to tease out what is going on later > tonight. > > Scott > > > On Thu, 2006-11-23 at 10:48 +0000, Sendu Bala wrote: > > Sendu Bala wrote: > > > Scott Cain wrote: > > >> Hello, > > >> > > >> I just wanted to mention that I made a few minor changes to Build.PL so > > >> that I could get `perl Build.PL` to complete successfully. I am using > > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > > >> present either. The main thing I did was to have the BioDBGFF test > > >> subroutine quit without asking any questions if Build.PL detected that > > >> it was running on Windows. > > > > > > Is it completely impossible for it to pass under Windows? I find that > > > quite a shame! > > > > > > I'm surprised it was necessary to make your changes, because it already > > > had to return true from: > > [snip] > > > > Sorry, that all made no sense because I didn't pay attention to what > > changes you actually made. > > > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > > being on mswin still causes a problem, or can the excludes_os > > restriction on line 78 of Build.PL be lifted now? > > > > > > Cheers, > > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061128/edece4fd/attachment.bin From bix at sendu.me.uk Tue Nov 28 11:56:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 16:56:04 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164732143.2584.33.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> <1164732143.2584.33.camel@localhost.localdomain> Message-ID: <456C6A24.5090105@sendu.me.uk> Scott Cain wrote: > Hi Sendu, > > It looks like what you've done did the trick--bioperl installed on both > ActivePerl 817 and 819 using Module::Build (though I must admit I didn't > look at the tests--I just wanted `perl Build.PL` to work). Nice work! ... I didn't do anything yet :O Can you check on an export of bioperl-release-1-5-2-rc5 and compare to an export of branch-1-5-2 and let me know if you see the bug in the former and no bug in the latter? From gwu at molbio.mgh.harvard.edu Tue Nov 28 16:13:11 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 28 Nov 2006 16:13:11 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <53C6D534-6E36-4061-B955-E74537839265@gmx.net> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> Message-ID: <456CA667.6010609@molbio.mgh.harvard.edu> Hi everyone, I'm using load_seqdatabase.pl to upload some Genbank genome sequences to my Oracle BioSQL database. I saw some errors(See attached warning message) related to seqfeature_qualifier_value (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data type of maximum 4000 bytes. Did anybody mention this issue before? Should I just modify the column to a type being able store more data such as LONG or CLOB? Thanks. Gang Log information: ============================================ load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank /genomeseq/arabidopsis//NC_003070.gbk Loading /genomeseq/arabidopsis//NC_003070.gbk ... -------------------- WARNING --------------------- MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement execution: ORA-01461: can bind a LONG value only for insert into a LONG column (DBD ERROR: error possibly near <*> indicator at char 12 in 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, rank) VALUES (:p1, :p2, :p3, :p4)') name: INSERT ASSOC [2] Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue values: FK[Bio::SeqFeature::Generic]:14898, FK[Bio::Annotation::SimpleValue]:800, value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFVGTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADRGTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEILASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFPWEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERASVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRYIQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEAEDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDINQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDWRLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFALDIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDNQGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRYMRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYTFESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGLVQATYQASAPLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKVHLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAYTDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFVSVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSEKETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLGNFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEVTAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQLEVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTLSVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVTILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRLMLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAVPDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEYTYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVDISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLRVKLDFNFMYASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQSQVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSNTYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCLSIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWDILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSEIAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASVTRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGLHGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSSKPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDFQTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGLHIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVARLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCLLISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRNGRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVENSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPLWLSVGADASVLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVYLTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITNDSYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQESAGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTSDRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSVFSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESWQFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIVRISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMSVQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRVYPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAMSPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDILGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAKSSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLRPYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMGQRKFIPAKDACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQAINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", rank:"1" -------------------------------------------------- ============================================= From cain.cshl at gmail.com Tue Nov 28 15:18:02 2006 From: cain.cshl at gmail.com (Scott Cain) Date: Tue, 28 Nov 2006 15:18:02 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <456C6A24.5090105@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> <1164732143.2584.33.camel@localhost.localdomain> <456C6A24.5090105@sendu.me.uk> Message-ID: <536f21b00611281218v3e6fd7a1ia2c9e81ef7ad678c@mail.gmail.com> Sendu, I've tried exports of both branches and they both work. Scott On 11/28/06, Sendu Bala wrote: > > Scott Cain wrote: > > Hi Sendu, > > > > It looks like what you've done did the trick--bioperl installed on both > > ActivePerl 817 and 819 using Module::Build (though I must admit I didn't > > look at the tests--I just wanted `perl Build.PL` to work). Nice work! > > ... > > I didn't do anything yet :O > > Can you check on an export of bioperl-release-1-5-2-rc5 and compare to > an export of branch-1-5-2 and let me know if you see the bug in the > former and no bug in the latter? > > From lincoln.stein at gmail.com Tue Nov 28 21:15:38 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 28 Nov 2006 21:15:38 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph Message-ID: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> Hi, I had to back out a change I made to Bio/Graphics/Glyph recently (on both live and 1.52 branches). It caused a bizarre problem in which some features had twice the expected height. Lincoln On 11/23/06, Sendu Bala wrote: > > Sendu Bala wrote: > > Scott Cain wrote: > >> Hello, > >> > >> I just wanted to mention that I made a few minor changes to Build.PL so > >> that I could get `perl Build.PL` to complete successfully. I am using > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > >> present either. The main thing I did was to have the BioDBGFF test > >> subroutine quit without asking any questions if Build.PL detected that > >> it was running on Windows. > > > > Is it completely impossible for it to pass under Windows? I find that > > quite a shame! > > > > I'm surprised it was necessary to make your changes, because it already > > had to return true from: > [snip] > > Sorry, that all made no sense because I didn't pay attention to what > changes you actually made. > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > being on mswin still causes a problem, or can the excludes_os > restriction on line 78 of Build.PL be lifted now? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From hlapp at gmx.net Tue Nov 28 23:54:53 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 28 Nov 2006 23:54:53 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <456CA667.6010609@molbio.mgh.harvard.edu> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> Message-ID: These are the protein translations stored in the feature table as tags of features, right? You can change the type of the column (although there may be some issues when you update the column because the NVL() clause won't work if I recall that correctly), but doing so will deprive you of any 'normal' searches against that column. (You can still use functions from the DBMS_LOB package, but they will be much slower and are completely non-standard.) It is up to you whether that is too big of a price to pay for having some redundant protein translations (translating the feature's DNA sequence should give you the same) in the database. I always trimmed those feature tags off (using a custom SeqProcessor). An alternative is to convert these feature tags into actual bioentries (i.e., Bio::Seq objects; again, a custom SeqProcessor will allow you to do that). -hilmar On Nov 28, 2006, at 4:13 PM, gang wu wrote: > Hi everyone, > > I'm using load_seqdatabase.pl to upload some Genbank genome > sequences to > my Oracle BioSQL database. I saw some errors(See attached warning > message) related to seqfeature_qualifier_value > (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data > type of maximum 4000 bytes. Did anybody mention this issue before? > Should I just modify the column to a type being able store more data > such as LONG or CLOB? > > Thanks. > > Gang > > > Log information: > ============================================ > > load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser > biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank > /genomeseq/arabidopsis//NC_003070.gbk > > > Loading /genomeseq/arabidopsis//NC_003070.gbk ... > > > -------------------- WARNING --------------------- > MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement > execution: ORA-01461: can bind a LONG value only for insert into a > LONG > column (DBD ERROR: error possibly near <*> indicator at char 12 in > 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, > rank) VALUES (:p1, :p2, :p3, :p4)') > name: INSERT ASSOC [2] > Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue > values: FK[Bio::SeqFeature::Generic]:14898, > FK[Bio::Annotation::SimpleValue]:800, > value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFV > GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADR > GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEI > LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFP > WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERA > SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRY > IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEA > EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDI > NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDW > RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFAL > DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDN > QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRY > MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYT > FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGL > VQATYQASA! > > PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKV > HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAY > TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFV > SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSE > KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLG > NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEV > TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQL > EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTL > SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVT > ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRL > MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAV > PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEY > TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVD > ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLR > VKLDFNFM! > > YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQS > QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSN > TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCL > SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWD > ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSE > IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASV > TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGL > HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSS > KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDF > QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGL > HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVA > RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCL > LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRN > GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVE > NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPL > WLSVGADAS! > > VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVY > LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITND > SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQES > AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTS > DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSV > FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESW > QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIV > RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMS > VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRV > YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAM > SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDI > LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAK > SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLR > PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMG > QRKFIPAK! > > DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQ > AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", > rank:"1" > -------------------------------------------------- > > > ============================================= > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Wed Nov 29 04:32:24 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 09:32:24 +0000 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> Message-ID: <456D53A8.80800@sendu.me.uk> Lincoln Stein wrote: > Hi, > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > both live and 1.52 branches). It caused a bizarre problem in which some > features had twice the expected height. Exactly which recent commits are the necessary reversion? Just 'fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height'? I'm confused by 'removed debugging warning' since you did different things during that named commit in HEAD (you removed a warn()) vs branch-1-5-2 (you added a bunch of non-warn related stuff). From lincoln.stein at gmail.com Wed Nov 29 09:41:25 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 29 Nov 2006 09:41:25 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <456D53A8.80800@sendu.me.uk> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> Message-ID: <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> There were two branch-1-5-2 commits last night. Both are needed to back out the changes. Lincoln On 11/29/06, Sendu Bala wrote: > > Lincoln Stein wrote: > > Hi, > > > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > > both live and 1.52 branches). It caused a bizarre problem in which some > > features had twice the expected height. > > Exactly which recent commits are the necessary reversion? Just 'fixed > minor bug which caused some features drawn with the "box" glyph to have > an unexpected height'? > > I'm confused by 'removed debugging warning' since you did different > things during that named commit in HEAD (you removed a warn()) vs > branch-1-5-2 (you added a bunch of non-warn related stuff). > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From lincoln.stein at gmail.com Wed Nov 29 09:38:18 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 29 Nov 2006 09:38:18 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <456D53A8.80800@sendu.me.uk> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> Message-ID: <6dce9a0b0611290638h46dc7d95o7ce5f7977fddfc81@mail.gmail.com> Uh oh. Perhaps I made a mistake during the commits. I will check what's up. Lincoln On 11/29/06, Sendu Bala wrote: > > Lincoln Stein wrote: > > Hi, > > > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > > both live and 1.52 branches). It caused a bizarre problem in which some > > features had twice the expected height. > > Exactly which recent commits are the necessary reversion? Just 'fixed > minor bug which caused some features drawn with the "box" glyph to have > an unexpected height'? > > I'm confused by 'removed debugging warning' since you did different > things during that named commit in HEAD (you removed a warn()) vs > branch-1-5-2 (you added a bunch of non-warn related stuff). > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bix at sendu.me.uk Wed Nov 29 10:53:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 15:53:04 +0000 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> Message-ID: <456DACE0.5060401@sendu.me.uk> Lincoln Stein wrote: > There were two branch-1-5-2 commits last night. Both are needed to back > out the changes. I'm not seeing the changes as a true revert. cvs diff -r 1.113.4.6 Bio/Graphics/Glyph.pm Index: Bio/Graphics/Glyph.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph.pm,v retrieving revision 1.113.4.6 retrieving revision 1.113.4.9 diff -r1.113.4.6 -r1.113.4.9 3c3 < # $Id: Glyph.pm,v 1.113.4.6 2006/11/19 17:18:45 lstein Exp $ --- > # $Id: Glyph.pm,v 1.113.4.9 2006/11/29 02:38:33 lstein Exp $ 126a127,128 > my $feature = $self->feature; > return 1 if $feature->can('compound') && $feature->compound; 1636a1639 > cvs diff -r 1.40.2.2 Bio/Graphics/Glyph/generic.pm Index: Bio/Graphics/Glyph/generic.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/generic.pm,v retrieving revision 1.40.2.2 retrieving revision 1.40.2.4 diff -r1.40.2.2 -r1.40.2.4 113,115c113,115 < my $md = $self->SUPER::maxdepth; < return $md if defined $md; < return 0; --- > my $maxdepth = $self->option('maxdepth'); > return $maxdepth if defined $maxdepth; > return 1; cvs diff -r 1.6.8.1 Bio/Graphics/Glyph/box.pm Index: Bio/Graphics/Glyph/box.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/box.pm,v retrieving revision 1.6.8.1 retrieving revision 1.6.8.2 diff -r1.6.8.1 -r1.6.8.2 14a15,21 > sub maxdepth { > my $self = shift; > my $maxdepth = $self->option('maxdepth'); > return $maxdepth if defined $maxdepth; > return 0; > } > Is this intended? Are you sure this is safe to go into final release for 1.5.2? From cjfields at uiuc.edu Wed Nov 29 10:55:33 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 09:55:33 -0600 Subject: [Bioperl-l] URI, Graph, and Module::Build Message-ID: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> Sendu, For the Build.PL dependencies, do we want to use the absolute module requirements (URI::Escape, Graph::Directed, XML::SAX::Base) or the distributions they are in (URI, Graph, XML::SAX)? Or does it really make a difference? Also, you had mentioned that Bundle::Bioperl is no longer needed since you can have them installed via Build. Does that also hold true for Windows (since CPAN is, at best, very testy installing on Windows)? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 29 11:04:07 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 16:04:07 +0000 Subject: [Bioperl-l] URI, Graph, and Module::Build In-Reply-To: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> References: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> Message-ID: <456DAF77.6050609@sendu.me.uk> Chris Fields wrote: > Sendu, > > For the Build.PL dependencies, do we want to use the absolute module > requirements (URI::Escape, Graph::Directed, XML::SAX::Base) or the > distributions they are in (URI, Graph, XML::SAX)? Or does it really > make a difference? It makes a difference right now only where the absolute module doesn't have a version (because in Build.PL we ask for at least version 0, which fails if version in the modules is actually undef). I'll fix that in the future, so it is best to use the absolute module for clarity. > Also, you had mentioned that Bundle::Bioperl is no longer needed since > you can have them installed via Build. Does that also hold true for > Windows (since CPAN is, at best, very testy installing on Windows)? In what way is it testy? I set up a new WinXP machine today and installed ActiveState. My Build.PL script happily offered to install Module::Build for me with CPAN and it almost worked up until CPAN needed nmake. After installing nmake I upgraded CPAN with no problems and then everything worked after that (I only tried to install one optional dep with Build.PL via CPAN, and that worked fine). So yes, I'd say it holds true for Windows. Though I haven't sorted out the ppd stuff yet. From cjfields at uiuc.edu Wed Nov 29 12:06:37 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 11:06:37 -0600 Subject: [Bioperl-l] URI, Graph, and Module::Build In-Reply-To: <456DAF77.6050609@sendu.me.uk> References: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> <456DAF77.6050609@sendu.me.uk> Message-ID: On Nov 29, 2006, at 10:04 AM, Sendu Bala wrote: > Chris Fields wrote: >> Sendu, >> For the Build.PL dependencies, do we want to use the absolute >> module requirements (URI::Escape, Graph::Directed, XML::SAX::Base) >> or the distributions they are in (URI, Graph, XML::SAX)? Or does >> it really make a difference? > > It makes a difference right now only where the absolute module > doesn't have a version (because in Build.PL we ask for at least > version 0, which fails if version in the modules is actually > undef). I'll fix that in the future, so it is best to use the > absolute module for clarity. That sounds fine to me. If I remember correctly, at least one example (XML::SAX::Base) used to be a separate distribution, but it should install XML::SAX now. >> Also, you had mentioned that Bundle::Bioperl is no longer needed >> since you can have them installed via Build. Does that also hold >> true for Windows (since CPAN is, at best, very testy installing on >> Windows)? > > In what way is it testy? I set up a new WinXP machine today and > installed ActiveState. My Build.PL script happily offered to > install Module::Build for me with CPAN and it almost worked up > until CPAN needed nmake. After installing nmake I upgraded CPAN > with no problems and then everything worked after that (I only > tried to install one optional dep with Build.PL via CPAN, and that > worked fine). It all depends on the modules installed. For instance, a few that include C code or required external compiled libraries had generally been much harder to install, or they were historically; I admittedly haven't tried them recently. GD, (I think) DBD::mysql, and anything using precompiled dynamic libraries were the most problematic, but PPMs and Win-compatible dynamic libraries were always available somewhere which made installing them via nmake a non-issue. One thing I noticed (and mentioned previously) is that using 'Build' also generated HTML docs on WinXP (I didn't see this on Mac OS X); I don't know if this still occurs, so I'll give it a run today. This may be a problem since the pod2html-generated formatting differs significantly from the PPM-generated docs. I'm not even sure they install in the same location as the PPM-generated pages or whether this will cause any issues. Do you also see this on your local WinXP? > So yes, I'd say it holds true for Windows. Though I haven't sorted > out the ppd stuff yet. I think recommending PPM for BioPerl installation on Windows is still the best option for now, at least until we are sure about CPAN installation and the HTML issue above. Frankly, there will just be too much demand for it just for the HTML docs alone (they are quite nice). If the prereqs are listed correctly it should install those first, but who knows with PPM4! It will also generate HTML on the fly and install it in the doc tree as expected, which I have tested. As for a new PPD/PPM, I haven't tried generating it yet via Module::Build (I thought maybe Nathan was doing this). I may give it a go today on WinXP with a fresh ActiveState install (most of my important work is now on Mac OS X, so that shouldn't interfere). My guess is the PPD will be in old PPM3 XML format. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From chhalling at verizon.net Wed Nov 29 20:25:45 2006 From: chhalling at verizon.net (Conrad Halling) Date: Wed, 29 Nov 2006 20:25:45 -0500 Subject: [Bioperl-l] A new Bundle::BioPerl In-Reply-To: <456C1516.5050900@sendu.me.uk> References: <456BB232.4020808@verizon.net> <456C1516.5050900@sendu.me.uk> Message-ID: <456E3319.5090703@verizon.net> Sendu Bala wrote: > Conrad Halling wrote: > >> After experimenting with the existing Bundle::BioPerl version 2.1.8 >> under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install >> all of the BioPerl dependencies unless run multiple times. >> >> I edited the the order that the dependencies were listed so I could get >> all the dependencies to install on the first try. >> > > Thank you so much for all your hard work. Its extremely valuable. That > said, I'm no longer recommending the usage of Bundle::BioPerl. Instead > what I'll do is apply your discovered order to the new Build.PL > installation system. > > You're welcome of course to contact Chris Dagdigian to make sure he > knows about your new version of Bundle::BioPerl. He can then upload it > to CPAN if he's happy with it, and people who choose to still use the > Makefile.PL installation process will surely appreciate the new version > of Bundle::BioPerl. > Good. Having Build.PL do all the work is the best solution. -- Conrad -- Conrad Halling chhalling at verizon.net From hlapp at gmx.net Wed Nov 29 23:03:08 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 29 Nov 2006 23:03:08 -0500 Subject: [Bioperl-l] release timetable Message-ID: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Sendu - what is the timetable in your mind for getting the release out? The NESCent phyloinformatics hackathon is impending and if at all possible I'd really like to see the release be out of the way when it starts so that all new code can simply go the main trunk and has no chance of interfering with the release. Do you think this won't be a problem, or should we start thinking about how to expedite the release in a sensible manner? If anyone else on the list has any concerns about that code going right into the main trunk, please let me know. We (the hackathon attendees) may have to relax the must-pass-all- tests rule, so it may take until a couple days after the end of the event until some sharp edges are smoothened out. I would rather not make any guarantees as to what we will not break, and instead focus on getting the work committed. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Wed Nov 29 23:59:50 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 22:59:50 -0600 Subject: [Bioperl-l] release timetable In-Reply-To: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Message-ID: <8BA20ADA-5114-4DAA-A95F-CBD22C80CC26@uiuc.edu> On Nov 29, 2006, at 10:03 PM, Hilmar Lapp wrote: > Sendu - > > what is the timetable in your mind for getting the release out? The > NESCent phyloinformatics hackathon is impending and if at all > possible I'd really like to see the release be out of the way when it > starts so that all new code can simply go the main trunk and has no > chance of interfering with the release. > > Do you think this won't be a problem, or should we start thinking > about how to expedite the release in a sensible manner? > > If anyone else on the list has any concerns about that code going > right into the main trunk, please let me know. > > We (the hackathon attendees) may have to relax the must-pass-all- > tests rule, so it may take until a couple days after the end of the > event until some sharp edges are smoothened out. I would rather not > make any guarantees as to what we will not break, and instead focus > on getting the work committed. > > -hilmar I think most everyone would agree that the final rel. 1.5.2 should be out soon. I vote for a release before the hackathon, essentially for the same reasons you already outlined. This will get the 1.5.2 code out in the wild for testing, which will (hopefully) iron out any kinks with Module::Build and other residual bugs. If needed we could always have another developer release in the spring to clean up anything from the hackathon, fix bugs from this release, etc. Like you mentioned before, this is (and should be considered by all) a developer release, so not all tests need to pass. Saying that, I applaud Sendu and Nathan (and everyone else) for their hard work. I think this is the first time I can remember where all tests pass for all systems (though I only used since rel 1.0). Even if it's for a finite period of time. -chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 30 02:50:06 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 07:50:06 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Message-ID: <456E8D2E.60908@sendu.me.uk> Hilmar Lapp wrote: > Sendu - > > what is the timetable in your mind for getting the release out? The > NESCent phyloinformatics hackathon is impending and if at all possible > I'd really like to see the release be out of the way when it starts so > that all new code can simply go the main trunk and has no chance of > interfering with the release. I'm going to do one final merge from HEAD to branch-1-5-2 and then set the final release tags later today, so a) anything done at the hackathon won't make any difference, and b) the release should go out soon. The release will go ahead when I've sorted out the Windows PPM and the Change Log (neither of which require code changes on the branch). On this schedule I won't be able to implement Conrad's pre-req installation order in Build.PL since that would require a substantial change to ModuleBuildBioperl.pm and another RC. I'll do that after release so that 1.5.3 benefits. From n.haigh at sheffield.ac.uk Thu Nov 30 03:35:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 08:35:08 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E8D2E.60908@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> Message-ID: <456E97BC.9000800@sheffield.ac.uk> Sendu Bala wrote: > Hilmar Lapp wrote: > >> Sendu - >> >> what is the timetable in your mind for getting the release out? The >> NESCent phyloinformatics hackathon is impending and if at all possible >> I'd really like to see the release be out of the way when it starts so >> that all new code can simply go the main trunk and has no chance of >> interfering with the release. >> > > I'm going to do one final merge from HEAD to branch-1-5-2 and then set > the final release tags later today, so a) anything done at the hackathon > won't make any difference, and b) the release should go out soon. > > The release will go ahead when I've sorted out the Windows PPM and the > Change Log (neither of which require code changes on the branch). > > On this schedule I won't be able to implement Conrad's pre-req > installation order in Build.PL since that would require a substantial > change to ModuleBuildBioperl.pm and another RC. I'll do that after > release so that 1.5.3 benefits. > > _______________________________________________ > I've not had the time to test out the new CPAN installation until now. I've just tried it on a clan install of ActivePerl 5.8.8.819 and it didn't install: Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/RemoteBlast.t 9 2304 13 0 0.00% ?? t/rnamotif.t 2 512 72 144 200.00% 1-72 2 tests and 197 subtests skipped. How can I get the test output from CPAN to go to a log file so I can look at the errors more closely? Nath p.s. I think nmake will need to be installed for windows but I'll doublecheck. --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-0, 29/11/2006 Tested on: 30/11/2006 08:35:09 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From bix at sendu.me.uk Thu Nov 30 03:46:44 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 08:46:44 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E97BC.9000800@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> Message-ID: <456E9A74.9020404@sendu.me.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: >> Hilmar Lapp wrote: >> >>> Sendu - >>> >>> what is the timetable in your mind for getting the release out? The >>> NESCent phyloinformatics hackathon is impending and if at all >>> possible I'd really like to see the release be out of the way when it >>> starts so that all new code can simply go the main trunk and has no >>> chance of interfering with the release. >>> >> >> I'm going to do one final merge from HEAD to branch-1-5-2 and then set >> the final release tags later today, so a) anything done at the >> hackathon won't make any difference, and b) the release should go out >> soon. >> >> The release will go ahead when I've sorted out the Windows PPM and the >> Change Log (neither of which require code changes on the branch). >> >> On this schedule I won't be able to implement Conrad's pre-req >> installation order in Build.PL since that would require a substantial >> change to ModuleBuildBioperl.pm and another RC. I'll do that after >> release so that 1.5.3 benefits. >> >> _______________________________________________ >> > > I've not had the time to test out the new CPAN installation until now. > I've just tried it 'it' being RC5? On Windows? > on a clan install of ActivePerl 5.8.8.819 and it > didn't install: > Failed Test Stat Wstat Total Fail Failed List of Failed > ------------------------------------------------------------------------------- > > t/RemoteBlast.t 9 2304 13 0 0.00% ?? > t/rnamotif.t 2 512 72 144 200.00% 1-72 > 2 tests and 197 subtests skipped. > > How can I get the test output from CPAN to go to a log file so I can > look at the errors more closely? I don't know about log files, but you can configure the cmd window to have a large history and then just copy/paste the results. You can also go into the directory that CPAN extracted the archive to and run the tests there manually. Please send me the results of those tests. From n.haigh at sheffield.ac.uk Thu Nov 30 04:28:36 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 09:28:36 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456EA444.1010705@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sendu Bala wrote: >>> Hilmar Lapp wrote: >>> >>>> Sendu - >>>> >>>> what is the timetable in your mind for getting the release out? The >>>> NESCent phyloinformatics hackathon is impending and if at all >>>> possible I'd really like to see the release be out of the way when >>>> it starts so that all new code can simply go the main trunk and has >>>> no chance of interfering with the release. >>>> >>> >>> I'm going to do one final merge from HEAD to branch-1-5-2 and then >>> set the final release tags later today, so a) anything done at the >>> hackathon won't make any difference, and b) the release should go >>> out soon. >>> >>> The release will go ahead when I've sorted out the Windows PPM and >>> the Change Log (neither of which require code changes on the branch). >>> >>> On this schedule I won't be able to implement Conrad's pre-req >>> installation order in Build.PL since that would require a >>> substantial change to ModuleBuildBioperl.pm and another RC. I'll do >>> that after release so that 1.5.3 benefits. >>> >>> _______________________________________________ >>> >> >> I've not had the time to test out the new CPAN installation until >> now. I've just tried it > > 'it' being RC5? On Windows? > > >> on a clan install of ActivePerl 5.8.8.819 and it didn't install: >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ------------------------------------------------------------------------------- >> >> t/RemoteBlast.t 9 2304 13 0 0.00% ?? >> t/rnamotif.t 2 512 72 144 200.00% 1-72 >> 2 tests and 197 subtests skipped. >> >> How can I get the test output from CPAN to go to a log file so I can >> look at the errors more closely? > > I don't know about log files, but you can configure the cmd window to > have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the archive to > and run the tests there manually. > > Please send me the results of those tests. > > While I figure this out, I've come across the following: The version of CPAN that ships with ActivePerl 5.8.8.819 is 1.7602 and the first version of CPAN to support setting the preference of Module::Build over MakeMaker with "o conf prefer_installer MB" is 1.81 according to their change log. As a result, the default installation of Bioperl on ActivePerl 5.8.8.819 will always use Makefile.PL if it's available. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-0, 29/11/2006 Tested on: 30/11/2006 09:28:37 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From n.haigh at sheffield.ac.uk Thu Nov 30 07:50:57 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 12:50:57 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456ED3B1.9060208@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sendu Bala wrote: >>> Hilmar Lapp wrote: >>> >>>> Sendu - >>>> >>>> what is the timetable in your mind for getting the release out? The >>>> NESCent phyloinformatics hackathon is impending and if at all >>>> possible I'd really like to see the release be out of the way when >>>> it starts so that all new code can simply go the main trunk and has >>>> no chance of interfering with the release. >>>> >>> >>> I'm going to do one final merge from HEAD to branch-1-5-2 and then >>> set the final release tags later today, so a) anything done at the >>> hackathon won't make any difference, and b) the release should go >>> out soon. >>> >>> The release will go ahead when I've sorted out the Windows PPM and >>> the Change Log (neither of which require code changes on the branch). >>> >>> On this schedule I won't be able to implement Conrad's pre-req >>> installation order in Build.PL since that would require a >>> substantial change to ModuleBuildBioperl.pm and another RC. I'll do >>> that after release so that 1.5.3 benefits. >>> >>> _______________________________________________ >>> >> >> I've not had the time to test out the new CPAN installation until >> now. I've just tried it > > 'it' being RC5? On Windows? > > >> on a clan install of ActivePerl 5.8.8.819 and it didn't install: >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ------------------------------------------------------------------------------- >> >> t/RemoteBlast.t 9 2304 13 0 0.00% ?? >> t/rnamotif.t 2 512 72 144 200.00% 1-72 >> 2 tests and 197 subtests skipped. >> >> How can I get the test output from CPAN to go to a log file so I can >> look at the errors more closely? > > I don't know about log files, but you can configure the cmd window to > have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the archive to > and run the tests there manually. > > Please send me the results of those tests. > > > Hi Sendu, Installation on a clean install of ActivePerl 5.8.8.819 n WindowsXP: 1) nmake is required for CPAN installations 2) I updated CPAN to the latest version 3) Restarted CPAN and did "o conf prefer_installer MB" and "o conf commit" 4) Restarted CPAN and tried the install of bioperl 1.5.2 RC5. I still get the message saying it's using Makefile.PL and not Build.PL - not sure why! I'm going to see if updating Module::Build helps. For the time being I installed anyway..... 5) towards the end of dependency checking I get this: -- snip -- Checking if your kit is complete... Looks good Warning: prerequisite DB_File 0 not found. Writing Makefile for Bio ---- Unsatisfied dependencies detected during [S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz] ----- DB_File Shall I follow them and prepend them to the queue of modules we are processing right now? [yes] -- snip -- 6) When running the install, DB_File fails to install and that appears to be the root of the rnamotif test failing: -- snip -- t/rnamotif...................Can't locate DB_File.pm in @INC (@INC contains: t/lib C:\Perl\cpan \build\bioperl-1.5.2_005-RC\blib\lib C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\arch C:/Perl/ site/lib C:/Perl/lib .) at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SeqFeature/Coll ection.pm line 133. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SeqFe ature/Collection.pm line 133. Compilation failed in require at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Tools/RNA Motif.pm line 145. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Tools /RNAMotif.pm line 145. Compilation failed in require at t/rnamotif.t line 27. BEGIN failed--compilation aborted at t/rnamotif.t line 27. t/rnamotif...................dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-72 Failed 72/72 tests, 0.00% okay -- snip -- 7) The RemoteBlast seems to fail due to XML/SAX not being installed: --s nip t/RemoteBlast................ok 10/13Bio::SearchIO: blastxml cannot be found Exception ------------- EXCEPTION ------------- MSG: Failed to load module Bio::SearchIO::blastxml. Can't locate XML/SAX.pm in @INC (@INC conta ins: t C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib C:\Perl\cpan\build\bioperl-1.5.2_005-RC \blib\arch C:/Perl/site/lib C:/Perl/lib .) at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/ Bio\SearchIO\blastxml.pm line 112. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio\Searc hIO\blastxml.pm line 112. Compilation failed in require at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Root/Root .pm line 425. STACK Bio::Root::Root::_load_module C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Root/R oot.pm:427 STACK (eval) C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm:397 STACK Bio::SearchIO::_load_format_module C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/S earchIO.pm:396 STACK Bio::SearchIO::new C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm:176 STACK Bio::Tools::Run::RemoteBlast::retrieve_blast C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib \lib/Bio/Tools/Run/RemoteBlast.pm:603 STACK toplevel t/RemoteBlast.t:185 -------------------------------------- For more information about the SearchIO system please see the SearchIO docs. This includes ways of checking for formats at compile time, not run time Use of uninitialized value in numeric lt (<) at t/RemoteBlast.t line 187. Can't locate object method "new" via package "Bio::SearchIO::blastxml" at C:\Perl\cpan\build\bi operl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm line 177. t/RemoteBlast................dubious Test returned status 9 (wstat 2304, 0x900) after all the subtests completed successfully -- snip -- HTH, Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-1, 30/11/2006 Tested on: 30/11/2006 12:50:59 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From n.haigh at sheffield.ac.uk Thu Nov 30 07:58:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 12:58:08 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456ED560.1020001@sheffield.ac.uk> More updates: After the failed install I updating Module::Build, and re-ran the install, I get: -- snip -- Creating new 'Build' script for 'bioperl' version '1.005002005' Warning: while trying to determine prerequisites for S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi th the help of Module::Build the following error occurred: 'Failed to re-load 'ModuleBuildBiope rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: _build\lib C:\Perl\site\lib C:\ Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. ' Falling back to META.yml for prerequisites 'YAML' not installed, cannot parse 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' -- snip -- Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-1, 30/11/2006 Tested on: 30/11/2006 12:58:09 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From djupiter at tamu.edu Thu Nov 30 01:22:57 2006 From: djupiter at tamu.edu (Daniel Jupiter) Date: Thu, 30 Nov 2006 00:22:57 -0600 Subject: [Bioperl-l] Large databases Message-ID: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> Hi all. I'm new to this list, so if my question is misdirected, or inappropriate, please let me know. The question concerns databases/hashes. I would like to have a rather large hash file. Say 10,000 keys, each with a data field containing roughly 50,000 integers. For whatever reason, the dbm implementation on Mac OSX does not seem to like things of this size. Several strange things happen. First, file size seem to increase exponentially, as I increase the data field size. Additionally, in certain situations, I am returned a rather strange error concerning an uninitialized variable, which has in fact been initialized. In great confusion, I'm just curious as to whether there is a work around for dealing with such large amounts of data, or somewhere with good documentation on using hashes. Thanks. Daniel C. Jupiter, Ph.D. Postdoctoral Research Associate Department of Systems Biology and Translational Medicine College of Medicine Texas A&M University Health Science Center 702 SW H.K. Dodgen Loop Temple, TX 76504 979.997.2106 | Fax 254.742.7145 djupitern at tamu.edu | www.tamhsc.edu ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061130/af6c95e9/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: -1.jpeg Type: image/jpeg Size: 19402 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061130/af6c95e9/attachment.jpeg From cjfields at uiuc.edu Thu Nov 30 11:13:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 10:13:58 -0600 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> Message-ID: <01b801c7149a$8a9777d0$15327e82@pyrimidine> > Nathan S. Haigh wrote: ... > > How can I get the test output from CPAN to go to a log file > so I can > > look at the errors more closely? > > I don't know about log files, but you can configure the cmd > window to have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the > archive to and run the tests there manually. > > Please send me the results of those tests. Like Sendu, I usually copy from the buffer in the terminal window when running from CPAN (you can set the buffer size for Windows cmd.exe). When running tests manually, I may redirect all output to a temp file, which is a bit easier to scan through since it doesn't wrap text like a cut&paste from the terminal: # Mac OS X ./Build tests &> results.txt # WinXP Build tests > results.txt 2>&1 With Windows I find it sometimes easier to just redirect STDOUT, to avoid all of the 'Subroutine x redefined' warnings. If the CPAN tests go to STDERR you could try redirectly only that stream to a temp file. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Thu Nov 30 11:29:51 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 11:29:51 -0500 Subject: [Bioperl-l] Large databases In-Reply-To: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> References: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> Message-ID: You are aware that you are getting close (or possibly beyond, depending on the exact numbers and if there is any overhead for each integer) the 2GB signed int boundary? Did you make sure that your dbm version is 64-bit enabled and supports 64 bit for filesize? -hilmar On Nov 30, 2006, at 1:22 AM, Daniel Jupiter wrote: > Hi all. > > I'm new to this list, so if my question is misdirected, or > inappropriate, please let me know. > > The question concerns databases/hashes. I would like to have a > rather large hash file. Say 10,000 keys, each with a data field > containing roughly 50,000 integers. For whatever reason, the dbm > implementation on Mac OSX does not seem to like things of this size. > > Several strange things happen. First, file size seem to increase > exponentially, as I increase the data field size. Additionally, in > certain situations, I am returned a rather strange error concerning > an uninitialized variable, which has in fact been initialized. > > In great confusion, I'm just curious as to whether there is a work > around for dealing with such large amounts of data, or somewhere > with good documentation on using hashes. > > Thanks. > > > > Daniel C. Jupiter, Ph.D. > Postdoctoral Research Associate > Department of Systems Biology and Translational Medicine > College of Medicine > Texas A&M University Health Science Center > 702 SW H.K. Dodgen Loop > Temple, TX 76504 > > 979.997.2106 | Fax 254.742.7145 > djupitern at tamu.edu | www.tamhsc.edu > > > <-1.jpeg> > > > > > > > <-1.jpeg> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From st537 at york.ac.uk Thu Nov 30 11:52:27 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Thu, 30 Nov 2006 16:52:27 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C2E01.5070805@sendu.me.uk> References: <456C172F.4060008@york.ac.uk> <456C2E01.5070805@sendu.me.uk> Message-ID: <456F0C4B.2000502@york.ac.uk> Hi, Thanks for helping me with the BLAST code, when I made the corections in ran fine, I'm assuming the returned object $blast_result is a kind of searchio object, although I'm not sure. I tried the code on the bioperl tutorial page for processing a searchio object returned from blast.... http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FASTA_reports_with_Search_and_SearchIO this seems to be the next stage after blasting in the bioperl tutorial but I'm sure how to process it correctly to get hit and alignment information regards, Samantha Thompson Sendu Bala wrote: >Samantha Thompson wrote: > > >>Hi, >>I am trying to learn bioperl and I'm attempting a few basic thing! I >>seem to be ok with reading in and outputting sequences and files now I >>am trying to do a simple BLAST search using a sequence (a sequence >>object in fact). The code I am attempting to run is at the bottom of the >>message... >>I am probably making a dumb mistake and don't understand the >>capabilities of the objects well enough, but the info for the >>remoteblast->submit_blast function says that it can take sequences as an >>argument, I've also tried sending the fasta file name containing my >>sequence as an argument to submit_blast, with the same result.... I >>have also tried sending $seqio_obj->next_seq........... i.e the >>following error message displayed on my terminal: >> >>Can't call method "submit_blast" on an undefined value at bioptest2.pl >>line 22, line 1. >> >> > >Always start your perl scripts with 'use strict;'. This will help you >find and fix the main problem with your script, that you made a >RemoteBlast object and stored it as $remote_blast, but then tried to use >submit_blast() on $remoteBlast which doesn't exist. > >I've rewritten your code below: > >use strict; > > >>use Bio::Seq; >>use Bio::SeqIO; >> >>use Bio::Tools::Run::RemoteBlast; >>use Bio::SearchIO; >> >>#seq bit >> >> >> ># $seq_obj = Bio::Seq->new(-format => 'fasta'); ># above line doesn't do anything, $seq_obj gets overwritten below > > >my $seqio_obj = Bio::SeqIO->new(-file => >"/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > > >my $seq_obj = $seqio_obj->next_seq; > > >> >>#blast bit >> >> >> >my $remote_blast = Bio::Tools::Run::RemoteBlast->new(-prog => 'blastp', >-db => 'nr', -expect => '1e-15' ); > ># submit_blast takes the sequence object, not the sequence string >my $blastreturn_obj = $remote_blast->submit_blast($seq_obj); > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at uiuc.edu Thu Nov 30 12:12:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 11:12:32 -0600 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456F0C4B.2000502@york.ac.uk> Message-ID: <01ba01c714a2$b9659c10$15327e82@pyrimidine> > Hi, > Thanks for helping me with the BLAST code, when I made the > corections in ran fine, I'm assuming the returned object > $blast_result is a kind of searchio object, although I'm not > sure. I tried the code on the bioperl tutorial page for > processing a searchio object returned from blast.... > http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FA > STA_reports_with_Search_and_SearchIO > this seems to be the next stage after blasting in the bioperl > tutorial but I'm sure how to process it correctly to get hit > and alignment information regards, > > Samantha Thompson It is a SearchIO object. FYI, you also have the option of saving the raw BLAST output to a file if needed (it should be described in the RemoteBlast POD). There is also a great HOWTO which goes into more detail about hits/HSPs and how to get alignments: http://www.bioperl.org/wiki/HOWTO:SearchIO chris From bix at sendu.me.uk Thu Nov 30 12:44:38 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 17:44:38 +0000 Subject: [Bioperl-l] Please help with the change log Message-ID: <456F1886.2090708@sendu.me.uk> I'm hoping someone out there is willing to help add summaries for each release to the Change Log: http://bioperl.org/wiki/Change_log Basically, just add a few bullet points about what was new or especially interesting in each release. Thank you, Sendu. From cjfields at uiuc.edu Thu Nov 30 12:50:03 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 11:50:03 -0600 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <438954.89098.qm@web50815.mail.yahoo.com> Message-ID: <000001c714a7$f6ee1300$15327e82@pyrimidine> Katie, Make sure you keep the posts on the mail list, just in case I can't respond but someone else can. > Hi all. > > I just ran the following test script: > > use strict; > use Bio::SearchIO; > my $in = new Bio::SearchIO(-format => 'blast', > -file => 'report.bls'); > while( my $result = $in->next_result ) { > while( my $hit = $result->next_hit ) { > while( my $hsp = $hit->next_hsp ) { > if( $hsp->length('total') > 100 ) { > if ( $hsp->percent_identity >= 75 ) { > print "Hit= ", $hit->name, > ",Length=", $hsp->length('total'), > ",Percent_id=", $hsp->percent_identity, "\n"; > } > } > } > } > } > > and saw the following output: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Could not open report.bls: No such file or directory > STACK: Error::throw > STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:350 > STACK: Bio::Root::IO::_initialize_io > C:/Perl/site/lib/Bio/Root/IO.pm:310 > STACK: Bio::Root::IO::new C:/Perl/site/lib/Bio/Root/IO.pm:223 > STACK: Bio::SearchIO::new C:/Perl/site/lib/Bio/SearchIO.pm:145 > STACK: Bio::SearchIO::new C:/Perl/site/lib/Bio/SearchIO.pm:177 > STACK: test.pl:3 > ----------------------------------------------------------- > > I'm using BioPerl 1.5.2 RC2 > Perl 5.8.8 (Build 819). > WinXP (SP2) > > Thanks, > > ~Katie Is there a BLAST report file named 'report.bls' in the same directory as your script? That's what the error indicates. Chris From n.haigh at sheffield.ac.uk Thu Nov 30 13:24:59 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 18:24:59 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456F2017.8000008@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> <456F2017.8000008@sendu.me.uk> Message-ID: <456F21FB.7090702@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> More updates: >> >> After the failed install I updating Module::Build, and re-ran the >> install, I get: >> >> -- snip -- >> Creating new 'Build' script for 'bioperl' version '1.005002005' >> Warning: while trying to determine prerequisites for >> S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi >> th the help of Module::Build the following error occurred: 'Failed to >> re-load 'ModuleBuildBiope >> rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: >> _build\lib C:\Perl\site\lib C:\ >> Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. >> ' >> >> Falling back to META.yml for prerequisites >> 'YAML' not installed, cannot parse >> 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' >> -- snip -- > > I had that problem fleetingly and it drove me crazy because later I > couldn't reproduce it. Is it reproducible on your end? > I've seen it several time and i'm sure I could reproduce it....give me a few mins and i'll see what I can report. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 18:25:01 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From bix at sendu.me.uk Thu Nov 30 13:16:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 18:16:55 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456ED560.1020001@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> Message-ID: <456F2017.8000008@sendu.me.uk> Nathan S. Haigh wrote: > More updates: > > After the failed install I updating Module::Build, and re-ran the > install, I get: > > -- snip -- > Creating new 'Build' script for 'bioperl' version '1.005002005' > Warning: while trying to determine prerequisites for > S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi > th the help of Module::Build the following error occurred: 'Failed to > re-load 'ModuleBuildBiope > rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: > _build\lib C:\Perl\site\lib C:\ > Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. > ' > > Falling back to META.yml for prerequisites > 'YAML' not installed, cannot parse > 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' > -- snip -- I had that problem fleetingly and it drove me crazy because later I couldn't reproduce it. Is it reproducible on your end? From cjfields at uiuc.edu Thu Nov 30 14:11:47 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 13:11:47 -0600 Subject: [Bioperl-l] Intermittent MySQL problems on BioPerl wiki Message-ID: <000201c714b3$6198e4e0$15327e82@pyrimidine> I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and WinXP): Database error >From BioPerl Jump to: navigation, search A database query syntax error has occurred. This may indicate a bug in the software. The last attempted database query was: (SQL query hidden) from within function "MediaWikiBagOStuff::_doquery". MySQL returned error "1205: Lock wait timeout exceeded; try restarting transaction (localhost)". This occurs intermittently when editting pages, logging in, etc. Also, pages loading to the browser seem much slower. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 30 14:19:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 13:19:34 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl5.8.8.819 In-Reply-To: <456F2017.8000008@sendu.me.uk> Message-ID: <000301c714b4$7846e790$15327e82@pyrimidine> > Nathan S. Haigh wrote: > > More updates: > > > > After the failed install I updating Module::Build, and re-ran the > > install, I get: > > > > -- snip -- > > Creating new 'Build' script for 'bioperl' version '1.005002005' > > Warning: while trying to determine prerequisites for > > S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi th the help of > > Module::Build the following error occurred: 'Failed to re-load > > 'ModuleBuildBiope > > rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: > > _build\lib C:\Perl\site\lib C:\ > > Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. > > ' > > > > Falling back to META.yml for prerequisites 'YAML' not installed, > > cannot parse 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' > > -- snip -- > > I had that problem fleetingly and it drove me crazy because > later I couldn't reproduce it. Is it reproducible on your end? During Module::Build installation I see this: ... t\metadata........ok 8/43 skipped: YAML_support feature is not enabled t\metadata2.......ok 4/18 skipped: YAML_support feature is not enabled t\moduleinfo......ok t\notes...........ok t\parents.........ok t\pod_parser......ok t\ppm.............skipped all skipped: C_support not enabled t\runthrough......ok 7/32 skipped: YAML_support feature is not enabled t\signature.......skipped all skipped: $ENV{TEST_SIGNATURE} is not set t\tilde...........ok t\versions........ok t\xs..............skipped all skipped: C_support not enabled All tests successful, 3 tests and 27 subtests skipped. Files=21, Tests=679, 262 wallclock secs ( 0.00 cusr + 0.00 csys = 0.00 CPU) C:\WINDOWS\nmake.EXE test -- OK Running make install ... Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From st537 at york.ac.uk Thu Nov 30 13:50:17 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Thu, 30 Nov 2006 18:50:17 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <01ba01c714a2$b9659c10$15327e82@pyrimidine> References: <01ba01c714a2$b9659c10$15327e82@pyrimidine> Message-ID: <456F27E9.70205@york.ac.uk> Chris Fields wrote: >>Hi, >>Thanks for helping me with the BLAST code, when I made the >>corections in ran fine, I'm assuming the returned object >>$blast_result is a kind of searchio object, although I'm not >>sure. I tried the code on the bioperl tutorial page for >>processing a searchio object returned from blast.... >>http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FA >>STA_reports_with_Search_and_SearchIO >>this seems to be the next stage after blasting in the bioperl >>tutorial but I'm sure how to process it correctly to get hit >>and alignment information regards, >> >>Samantha Thompson >> >> > >It is a SearchIO object. FYI, you also have the option of saving the raw >BLAST output to a file if needed (it should be described in the RemoteBlast >POD). > >There is also a great HOWTO which goes into more detail about hits/HSPs and >how to get alignments: > >http://www.bioperl.org/wiki/HOWTO:SearchIO > > >chris > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/bioper > > Hi, OK, I tried the code at the SearchIO HOWTO, I've pasted it below, you can see where I've added the SearchIO handling part I've changed $in to the $blast_report as this is returned from the submit_blast ... what happens when I run this however is that I get the following error: Can't call method "next_result" without a package or object reference at bioptest2.pl line 31, line 1. Line 31 being: while( my $result = $blast_report->next_result ) { Not sure why this is happening. Thanks for any help... Samantha Thompson use strict; use Bio::Perl; use Bio::Seq; use Bio::SeqIO; use Bio::Tools::Run::RemoteBlast; use Bio::SearchIO; #seq bit #$seq_obj = Bio::Seq->new(-format => 'fasta'); my $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); my $seq_obj = $seqio_obj->next_seq; #blast bit my $remote_blast = Bio::Tools::Run::RemoteBlast->new ( -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); my $blast_report = $remote_blast->submit_blast($seq_obj); #new part for SearchIO... while( my $result = $blast_report->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { if( $hsp->length('total') > 100 ) { if ( $hsp->percent_identity >= 75 ) { print "Hit= ", $hit->name, ",Length=", $hsp->length('total'), ",Percent_id=", $hsp->percent_identity, "\n"; } } } } } From dag at sonsorol.org Thu Nov 30 14:25:16 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 30 Nov 2006 14:25:16 -0500 Subject: [Bioperl-l] [Root-l] Intermittent MySQL problems on BioPerl wiki In-Reply-To: <000201c714b3$6198e4e0$15327e82@pyrimidine> References: <000201c714b3$6198e4e0$15327e82@pyrimidine> Message-ID: Reports like this need to go to support at helpdesk.open-bio.org so that they enter our RT helpdesk queue -- the main reason is that sometimes emails to the root-l at open-bio.org administrators mailing list can get lost in the shuffle. I am going to bounce this message into RT and will restart mysql on the portal box. This is probably something we should be doing anyway to free up memory -- the wikis in particular seem to be pretty hard on mysql and free memory. -Chris On Nov 30, 2006, at 2:11 PM, Chris Fields wrote: > I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and > WinXP): > > Database error >> From BioPerl > Jump to: navigation, search > A database query syntax error has occurred. This may indicate a bug > in the > software. The last attempted database query was: > > (SQL query hidden) > > from within function "MediaWikiBagOStuff::_doquery". MySQL returned > error > "1205: Lock wait timeout exceeded; try restarting transaction > (localhost)". > > > This occurs intermittently when editting pages, logging in, etc. > Also, > pages loading to the browser seem much slower. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > _______________________________________________ > Root-l mailing list > Root-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/root-l From n.haigh at sheffield.ac.uk Thu Nov 30 15:07:24 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 20:07:24 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456F21FB.7090702@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> <456F2017.8000008@sendu.me.uk> <456F21FB.7090702@sheffield.ac.uk> Message-ID: <456F39FC.9070805@sheffield.ac.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: > >> Nathan S. Haigh wrote: >> >>> More updates: >>> >>> After the failed install I updating Module::Build, and re-ran the >>> install, I get: >>> >>> -- snip -- >>> Creating new 'Build' script for 'bioperl' version '1.005002005' >>> Warning: while trying to determine prerequisites for >>> S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi >>> th the help of Module::Build the following error occurred: 'Failed to >>> re-load 'ModuleBuildBiope >>> rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: >>> _build\lib C:\Perl\site\lib C:\ >>> Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. >>> ' >>> >>> Falling back to META.yml for prerequisites >>> 'YAML' not installed, cannot parse >>> 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' >>> -- snip -- >>> >> I had that problem fleetingly and it drove me crazy because later I >> couldn't reproduce it. Is it reproducible on your end? >> >> > > I've seen it several time and i'm sure I could reproduce it....give me a > few mins and i'll see what I can report. > > Nath > > > --- > avast! Antivirus: Outbound message clean. > Virus Database (VPS): 0652-2, 30/11/2006 > Tested on: 30/11/2006 18:25:01 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > --- > avast! Antivirus: Inbound message clean. > Virus Database (VPS): 0652-2, 30/11/2006 > Tested on: 30/11/2006 18:50:39 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > > Reproduce: 1) clean install of ActivePerl 5.8.8.819 on WinXP 2) Install nmake in path 3) run "cpan CPAN" to install the latest version of CPAN module 4) ran cpan, accepted default for new CPAN configuration, ran "o conf prefer_installer MB" and "o conf commit" then "q" 5) run "cpan Module::Build" to install the latest version of Module::Build 6) run "cpan" and then "install S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" 7) Choose not to install optional modules 8) Error shows here Installing all optional modules doesn't produce the error. However, It produces the problem i've told you about missing "scripts" dir (actually, it's not just the scripts dir - it's all but the base dir it was unpacked into). Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 20:07:25 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From cjfields at uiuc.edu Thu Nov 30 15:48:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 14:48:26 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXPActivePerl 5.8.8.819 In-Reply-To: <456F39FC.9070805@sheffield.ac.uk> Message-ID: <000801c714c0$e26eff70$15327e82@pyrimidine> > Nathan S. Haigh wrote: > Reproduce: > 1) clean install of ActivePerl 5.8.8.819 on WinXP > 2) Install nmake in path > 3) run "cpan CPAN" to install the latest version of CPAN module > 4) ran cpan, accepted default for new CPAN configuration, ran > "o conf prefer_installer MB" and "o conf commit" then "q" > 5) run "cpan Module::Build" to install the latest version of > Module::Build > 6) run "cpan" and then "install > S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" > 7) Choose not to install optional modules > 8) Error shows here > > Installing all optional modules doesn't produce the error. > However, It produces the problem i've told you about missing > "scripts" dir (actually, it's not just the scripts dir - it's > all but the base dir it was unpacked into). > > Nath Confirmed, using same setup as Nathan. chris From cjfields at uiuc.edu Thu Nov 30 16:27:17 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 15:27:17 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <000801c714c0$e26eff70$15327e82@pyrimidine> Message-ID: <002401c714c6$53f65080$15327e82@pyrimidine> > > Nathan S. Haigh wrote: > > Reproduce: > > 1) clean install of ActivePerl 5.8.8.819 on WinXP > > 2) Install nmake in path > > 3) run "cpan CPAN" to install the latest version of CPAN module > > 4) ran cpan, accepted default for new CPAN configuration, > ran "o conf > > prefer_installer MB" and "o conf commit" then "q" > > 5) run "cpan Module::Build" to install the latest version of > > Module::Build > > 6) run "cpan" and then "install > > S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" > > 7) Choose not to install optional modules > > 8) Error shows here > > > > Installing all optional modules doesn't produce the error. > > However, It produces the problem i've told you about > missing "scripts" > > dir (actually, it's not just the scripts dir - it's all but > the base > > dir it was unpacked into). > > > > Nath > > Confirmed, using same setup as Nathan. > > chris Okay, revise that. I get the message you mentioned, but installation only fails after tests are run. The single failed test (rnamotif.t) is due to DB_File not being installed, which Sendu has corrected in CVS and (I think) the 1.5.2 branch. However, I can't get DB_File to install via CPAN (I have VC++ Express Edition installed). I think XML::SAX and a few others fail as well. Chris From n.haigh at sheffield.ac.uk Thu Nov 30 16:41:30 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 21:41:30 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <002401c714c6$53f65080$15327e82@pyrimidine> References: <002401c714c6$53f65080$15327e82@pyrimidine> Message-ID: <456F500A.7010707@sheffield.ac.uk> Chris Fields wrote: >>> Nathan S. Haigh wrote: >>> Reproduce: >>> 1) clean install of ActivePerl 5.8.8.819 on WinXP >>> 2) Install nmake in path >>> 3) run "cpan CPAN" to install the latest version of CPAN module >>> 4) ran cpan, accepted default for new CPAN configuration, >>> >> ran "o conf >> >>> prefer_installer MB" and "o conf commit" then "q" >>> 5) run "cpan Module::Build" to install the latest version of >>> Module::Build >>> 6) run "cpan" and then "install >>> S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" >>> 7) Choose not to install optional modules >>> 8) Error shows here >>> >>> Installing all optional modules doesn't produce the error. >>> However, It produces the problem i've told you about >>> >> missing "scripts" >> >>> dir (actually, it's not just the scripts dir - it's all but >>> >> the base >> >>> dir it was unpacked into). >>> >>> Nath >>> >> Confirmed, using same setup as Nathan. >> >> chris >> > > Okay, revise that. I get the message you mentioned, but installation only > fails after tests are run. The single failed test (rnamotif.t) is due to > DB_File not being installed, which Sendu has corrected in CVS and (I think) > the 1.5.2 branch. However, I can't get DB_File to install via CPAN (I have > VC++ Express Edition installed). I think XML::SAX and a few others fail as > well. > > Chris > > > Yes that's correct, I get the message but things then seem to proceed normally (not that I know what normal is!). I had to install DB_File via PPM and install XML::SAX explicitly in CPAN. That then seems to have cleared things up and the tests pass and bioperl core is installed. However, there are other optional dependencies that didn't install successfully - I suppose I should investigate those tomorrow. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 21:41:31 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From gwu at molbio.mgh.harvard.edu Thu Nov 30 17:08:08 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Thu, 30 Nov 2006 17:08:08 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> Message-ID: <456F5648.6070207@molbio.mgh.harvard.edu> Thanks Hilmar. Do you mean the NVL() clause will make load_seqdatabase.pl not work when update? I have problem with updating. Seems load_seqdatabase.pl only tries to insert instead of update. I used one of the test genbank file coming whith bioperl-db. Please take a look at the attached output. Thanks. Gang ========================================= >perl load_seqdatabase.pl -lookup -host elegans -driver Oracle -dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank -namespace test /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/AP000868.gb Loading /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/AP000868.gb ... -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("This sequence was reannotated via the Ensembl system. Please visit the Ensembl web site, http://www.ensembl.org/ for more information. ","1") FKs (389109) ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) violated (DBD ERROR: OCIStmtExecute) --------------------------------------------------- -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("The /gene indicates a unique id for a gene, /cds a unique id for a translation and a /exon a unique id for an exon. These ids are maintained wherever possible between versions. For more information on how to interpret the feature table, please visit http://www.ensembl.org/Docs/embl.html. ","2") FKs (389109) ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) violated (DBD ERROR: OCIStmtExecute) --------------------------------------------------- ... ... ========================================================== Hilmar Lapp wrote: > These are the protein translations stored in the feature table as > tags of features, right? > > You can change the type of the column (although there may be some > issues when you update the column because the NVL() clause won't work > if I recall that correctly), but doing so will deprive you of any > 'normal' searches against that column. (You can still use functions > from the DBMS_LOB package, but they will be much slower and are > completely non-standard.) > > It is up to you whether that is too big of a price to pay for having > some redundant protein translations (translating the feature's DNA > sequence should give you the same) in the database. I always trimmed > those feature tags off (using a custom SeqProcessor). An alternative > is to convert these feature tags into actual bioentries (i.e., > Bio::Seq objects; again, a custom SeqProcessor will allow you to do > that). > > -hilmar > > On Nov 28, 2006, at 4:13 PM, gang wu wrote: > > >> Hi everyone, >> >> I'm using load_seqdatabase.pl to upload some Genbank genome >> sequences to >> my Oracle BioSQL database. I saw some errors(See attached warning >> message) related to seqfeature_qualifier_value >> (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data >> type of maximum 4000 bytes. Did anybody mention this issue before? >> Should I just modify the column to a type being able store more data >> such as LONG or CLOB? >> >> Thanks. >> >> Gang >> >> >> Log information: >> ============================================ >> >> load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser >> biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank >> /genomeseq/arabidopsis//NC_003070.gbk >> >> >> Loading /genomeseq/arabidopsis//NC_003070.gbk ... >> >> >> -------------------- WARNING --------------------- >> MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement >> execution: ORA-01461: can bind a LONG value only for insert into a >> LONG >> column (DBD ERROR: error possibly near <*> indicator at char 12 in >> 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, >> rank) VALUES (:p1, :p2, :p3, :p4)') >> name: INSERT ASSOC [2] >> Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue >> values: FK[Bio::SeqFeature::Generic]:14898, >> FK[Bio::Annotation::SimpleValue]:800, >> value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFV >> GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADR >> GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEI >> LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFP >> WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERA >> SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRY >> IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEA >> EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDI >> NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDW >> RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFAL >> DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDN >> QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRY >> MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYT >> FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGL >> VQATYQASA! >> >> PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKV >> HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAY >> TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFV >> SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSE >> KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLG >> NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEV >> TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQL >> EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTL >> SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVT >> ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRL >> MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAV >> PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEY >> TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVD >> ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLR >> VKLDFNFM! >> >> YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQS >> QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSN >> TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCL >> SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWD >> ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSE >> IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASV >> TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGL >> HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSS >> KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDF >> QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGL >> HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVA >> RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCL >> LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRN >> GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVE >> NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPL >> WLSVGADAS! >> >> VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVY >> LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITND >> SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQES >> AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTS >> DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSV >> FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESW >> QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIV >> RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMS >> VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRV >> YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAM >> SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDI >> LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAK >> SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLR >> PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMG >> QRKFIPAK! >> >> DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQ >> AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", >> rank:"1" >> -------------------------------------------------- >> >> >> ============================================= >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > From cjfields at uiuc.edu Thu Nov 30 17:16:02 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 16:16:02 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <456F500A.7010707@sheffield.ac.uk> References: <002401c714c6$53f65080$15327e82@pyrimidine> <456F500A.7010707@sheffield.ac.uk> Message-ID: <202B1F50-E905-46DE-9EB5-5F206AC04523@uiuc.edu> On Nov 30, 2006, at 3:41 PM, Nathan S. Haigh wrote: > ... >> >> Okay, revise that. I get the message you mentioned, but >> installation only >> fails after tests are run. The single failed test (rnamotif.t) is >> due to >> DB_File not being installed, which Sendu has corrected in CVS and >> (I think) >> the 1.5.2 branch. However, I can't get DB_File to install via >> CPAN (I have >> VC++ Express Edition installed). I think XML::SAX and a few >> others fail as >> well. >> >> Chris >> >> >> > > Yes that's correct, I get the message but things then seem to > proceed normally (not that I know what normal is!). > I had to install DB_File via PPM and install XML::SAX explicitly in > CPAN. That then seems to have cleared things up and the tests pass > and bioperl core is installed. However, there are other optional > dependencies that didn't install successfully - I suppose I should > investigate those tomorrow. > > Nath The DB_File failure is due to compilation problems. BTW, I can get XML::SAX to install, so that shouldn't be an issue. I know that setting up the PPM is a pain, but I have to say it is much faster, and all required PPMs are available. Which makes me curious: why bother with trying out a CPAN installation process at this point, especially when you have to use PPM to install some of the prereqs properly anyway? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From pelikan at cs.pitt.edu Thu Nov 30 17:19:29 2006 From: pelikan at cs.pitt.edu (pelikan at cs.pitt.edu) Date: Thu, 30 Nov 2006 17:19:29 -0500 (EST) Subject: [Bioperl-l] Error with supplied lineages importing uniprot data Message-ID: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> Hello all, I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows, without Cygwin. The "make test"s have all completed without error. This is my first time dealing with bioperl, so bear with me. I've successfully loaded the most recent taxonomy information using the biosql-schema scripts. After this, I attempted to load the most recent release of the uniprot flat file dataset with the following command: load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat I am subsequently greeted by many of the following errors: Could not store Q7N3Q6: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: The supplied lineage does not start near 'Photorhabdus luminescens subsp. laumondii' STACK: Error::throw STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio\Root\Root.pm:359 STACK: Bio::Species::classification C:/Perl/site/lib/Bio\Species.pm:166 STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:55 STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row C:/Perl/site/lib/Bio\DB\BioSQL\SpeciesAdaptor.pm:281 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key C:/Perl/site/lib/Bio/DB/BioSQL/BasePersisten STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenc STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: STACK: Bio::DB::Persistent::PersistentObject::create C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:244 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:2 STACK: Bio::DB::Persistent::PersistentObject::store C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:271 STACK: C:\DATA\MYSQL\cvs\src\bioperl\bioperl-db-1.5.2_005-RC\scripts\biosql\load_seqdatabase.pl:620 ----------------------------------------------------------- Can someone shed some light on why this may be taking place? -Richard From hlapp at gmx.net Thu Nov 30 18:28:40 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 18:28:40 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <456F5648.6070207@molbio.mgh.harvard.edu> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> <456F5648.6070207@molbio.mgh.harvard.edu> Message-ID: <70B28FBB-0250-4EB8-8775-CD0537369A3D@gmx.net> Right. You need to tell it to lookup sequences first if you know that you are loading sequences which may be in the database already (see the POD of load_seqdatabase.pl, switch --lookup; there are several other command line options that control what will happen if a sequence entry is already present in the database.). The messages in you report are warnings, not errors. It looks like some of the comments are duplicated for a sequence, it doesn't look like reason for concern. Is not so good if you get errors thrown. -hilmar On Nov 30, 2006, at 5:08 PM, gang wu wrote: > Thanks Hilmar. Do you mean the NVL() clause will make > load_seqdatabase.pl not work when update? > > I have problem with updating. Seems load_seqdatabase.pl only tries > to insert instead of update. I used one of the test genbank file > coming whith bioperl-db. Please take a look at the attached output. > > Thanks. > > Gang > > ========================================= > >perl load_seqdatabase.pl -lookup -host elegans -driver Oracle - > dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank - > namespace test /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/ > biosql/data/AP000868.gb > Loading /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/ > AP000868.gb ... > > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, > values were ("This sequence was reannotated via the Ensembl system. > Please visit the Ensembl web site, http://www.ensembl.org/ for more > information. ","1") FKs (389109) > ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) > violated (DBD ERROR: OCIStmtExecute) > --------------------------------------------------- > > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, > values were ("The /gene indicates a unique id for a gene, /cds a > unique id for a translation and a /exon a unique id for an exon. > These ids are maintained wherever possible between versions. For > more information on how to interpret the feature table, please > visit http://www.ensembl.org/Docs/embl.html. ","2") FKs (389109) > ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) > violated (DBD ERROR: OCIStmtExecute) > --------------------------------------------------- > ... > ... > ========================================================== > Hilmar Lapp wrote: >> These are the protein translations stored in the feature table as >> tags of features, right? You can change the type of the column >> (although there may be some issues when you update the column >> because the NVL() clause won't work if I recall that correctly), >> but doing so will deprive you of any 'normal' searches against >> that column. (You can still use functions >from the DBMS_LOB >> package, but they will be much slower and are completely non- >> standard.) It is up to you whether that is too big of a price to >> pay for having some redundant protein translations (translating >> the feature's DNA sequence should give you the same) in the >> database. I always trimmed those feature tags off (using a custom >> SeqProcessor). An alternative is to convert these feature tags >> into actual bioentries (i.e., Bio::Seq objects; again, a custom >> SeqProcessor will allow you to do that). -hilmar On Nov 28, 2006, >> at 4:13 PM, gang wu wrote: >>> Hi everyone, I'm using load_seqdatabase.pl to upload some Genbank >>> genome sequences to my Oracle BioSQL database. I saw some errors >>> (See attached warning message) related to >>> seqfeature_qualifier_value (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE >>> column), which has Varchar2 data type of maximum 4000 bytes. Did >>> anybody mention this issue before? Should I just modify the >>> column to a type being able store more data such as LONG or CLOB? >>> Thanks. Gang Log information: >>> ============================================ load_seqdatabase.pl - >>> host elegans -driver Oracle -dbname sparc -dbuser biosqldb- >>> sgowner -dbpass PASS -format genbank -namespace genbank / >>> genomeseq/arabidopsis//NC_003070.gbk Loading /genomeseq/ >>> arabidopsis//NC_003070.gbk ... -------------------- WARNING >>> --------------------- MSG: SimpleValueAdaptor::add_assoc: >>> unexpected failure of statement execution: ORA-01461: can bind a >>> LONG value only for insert into a LONG column (DBD ERROR: error >>> possibly near <*> indicator at char 12 in 'INSERT INTO >>> <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, rank) >>> VALUES (:p1, :p2, :p3, :p4)') name: INSERT ASSOC [2] >>> Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue values: FK >>> [Bio::SeqFeature::Generic]:14898, FK >>> [Bio::Annotation::SimpleValue]:800, >>> value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSG >>> FV >>> GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASA >>> DR >>> GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSS >>> EI >>> LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNS >>> FP >>> WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFE >>> RA >>> SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYT >>> RY >>> IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRT >>> EA >>> EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIV >>> DI >>> NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENI >>> DW >>> RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRF >>> AL >>> DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGS >>> DN >>> QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPT >>> RY >>> MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYL >>> YT >>> FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLR >>> GL VQATYQASA! >>> PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGG >>> KV >>> HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDED >>> AY >>> TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSD >>> FV >>> SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSD >>> SE >>> KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGT >>> LG >>> NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQ >>> EV >>> TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLG >>> QL >>> EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVP >>> TL >>> SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRT >>> VT >>> ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEM >>> RL >>> MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRIL >>> AV >>> PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGID >>> EY >>> TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDG >>> VD >>> ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKL >>> LR VKLDFNFM! >>> YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNL >>> QS >>> QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAV >>> SN >>> TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVY >>> CL >>> SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSG >>> WD >>> ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADD >>> SE >>> IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEA >>> SV >>> TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLD >>> GL >>> HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQ >>> SS >>> KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDED >>> DF >>> QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAK >>> GL >>> HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKG >>> VA >>> RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNG >>> CL >>> LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSM >>> RN >>> GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPK >>> VE >>> NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSK >>> PL WLSVGADAS! >>> VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRP >>> VY >>> LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWIT >>> ND >>> SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQ >>> ES >>> AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNM >>> TS >>> DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPF >>> SV >>> FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSE >>> SW >>> QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKN >>> IV >>> RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILY >>> MS >>> VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDL >>> RV >>> YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSM >>> AM >>> SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGV >>> DI >>> LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEG >>> AK >>> SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSL >>> LR >>> PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNI >>> MG QRKFIPAK! >>> DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAI >>> DQ AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", >>> rank:"1" -------------------------------------------------- >>> ============================================= >>> _______________________________________________ Bioperl-l mailing >>> list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/ >>> mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Nov 30 18:31:41 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 18:31:41 -0500 Subject: [Bioperl-l] Error with supplied lineages importing uniprot data In-Reply-To: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> References: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> Message-ID: <24C694D6-1124-48A9-8C7C-FA58AB598F01@gmx.net> Maybe Sendu can shed light on what might be happening here? On Nov 30, 2006, at 5:19 PM, pelikan at cs.pitt.edu wrote: > Hello all, > > I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows, > without Cygwin. The "make test"s have all completed without error. > This > is my first time dealing with bioperl, so bear with me. > > I've successfully loaded the most recent taxonomy information > using the > biosql-schema scripts. After this, I attempted to load the most recent > release of the uniprot flat file dataset with the following command: > > load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass > ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat > > I am subsequently greeted by many of the following errors: > > Could not store Q7N3Q6: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: The supplied lineage does not start near 'Photorhabdus > luminescens > subsp. laumondii' > STACK: Error::throw > STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio\Root\Root.pm:359 > STACK: Bio::Species::classification C:/Perl/site/lib/Bio\Species.pm: > 166 > STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:55 > STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row > C:/Perl/site/lib/Bio\DB\BioSQL\SpeciesAdaptor.pm:281 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersisten > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenc > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: > STACK: Bio::DB::Persistent::PersistentObject::create > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:244 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:2 > STACK: Bio::DB::Persistent::PersistentObject::store > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:271 > STACK: > C:\DATA\MYSQL\cvs\src\bioperl\bioperl-db-1.5.2_005-RC\scripts\biosql > \load_seqdatabase.pl:620 > ----------------------------------------------------------- > > Can someone shed some light on why this may be taking place? > > -Richard > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From The_Polymorph at rocketmail.com Thu Nov 30 18:58:22 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 30 Nov 2006 15:58:22 -0800 (PST) Subject: [Bioperl-l] Upgrading my BioPerl RC via ppm? In-Reply-To: <000001c714a7$f6ee1300$15327e82@pyrimidine> Message-ID: <519167.29410.qm@web50804.mail.yahoo.com> Hi all. I'm currently using BioPerl 1.5.2 RC2 but I've seen multiple references to 1.5.2 RC5. Can anyone tell me how to upgrade to the latest version? The ppm GUI (ActivePerl Build 819) doesn't include any BioPerl packages among those deemed upgradable. Thanks, ~Katie "Be who you are and say what you feel because those who mind don't matter and those who matter don't mind." - Dr. Seuss, "Oh the Places You'll Go" ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com From arareko at campus.iztacala.unam.mx Thu Nov 30 19:56:02 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Thu, 30 Nov 2006 18:56:02 -0600 Subject: [Bioperl-l] [Root-l] Intermittent MySQL problems on BioPerl wiki In-Reply-To: References: <000201c714b3$6198e4e0$15327e82@pyrimidine> Message-ID: <456F7DA2.7000408@campus.iztacala.unam.mx> Chris & Chris, I've run the maintenance scripts for MediaWiki (just in case they weren't run in the upgrade to 1.8.2), restarted Apache (with no significant changes on website response), then rebooted the machine (seems like MySQL restart didn't do the trick) and apparently its behaving much better. Please check if the reported error still happens. Regards, Mauricio. Chris Dagdigian wrote: > Reports like this need to go to support at helpdesk.open-bio.org so that > they enter our RT helpdesk queue -- the main reason is that > sometimes emails to the root-l at open-bio.org administrators mailing > list can get lost in the shuffle. > > I am going to bounce this message into RT and will restart mysql on > the portal box. This is probably something we should be doing anyway > to free up memory -- the wikis in particular seem to be pretty hard > on mysql and free memory. > > -Chris > > On Nov 30, 2006, at 2:11 PM, Chris Fields wrote: > >> I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and >> WinXP): >> >> Database error >>> From BioPerl >> Jump to: navigation, search >> A database query syntax error has occurred. This may indicate a bug >> in the >> software. The last attempted database query was: >> >> (SQL query hidden) >> >> from within function "MediaWikiBagOStuff::_doquery". MySQL returned >> error >> "1205: Lock wait timeout exceeded; try restarting transaction >> (localhost)". >> >> >> This occurs intermittently when editting pages, logging in, etc. >> Also, >> pages loading to the browser seem much slower. >> >> Christopher Fields >> Postdoctoral Researcher - Switzer Lab >> Dept. of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> _______________________________________________ >> Root-l mailing list >> Root-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/root-l > > _______________________________________________ > Root-l mailing list > Root-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/root-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From huangyi1 at hkusua.hku.hk Wed Nov 1 03:25:10 2006 From: huangyi1 at hkusua.hku.hk (Huang Yi) Date: Wed, 1 Nov 2006 16:25:10 +0800 Subject: [Bioperl-l] bioperl1.5 and GD2.35 - solved In-Reply-To: <1A4207F8295607498283FE9E93B775B4023B5F3C@EX02.asurite.ad.asu.edu> Message-ID: <200611010825.kA18PGWu022850@hkusua.hku.hk> The problem was solved. I re-emerged gd-2.0.33 with png USE flag. Thanks again! Huang Yi -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Kevin Brown Sent: Tuesday, October 31, 2006 11:35 PM To: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] bioperl1.5 and GD2.35 Not really a Bioperl issue per se, but sounds like when you had Gentoo emerge GD it didn't include libpng and so didn't build the needed parts to create PNG type graphics. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Huang Yi > Sent: Monday, October 30, 2006 10:46 PM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] bioperl1.5 and GD2.35 > > Hi, > > > > I just installed bioperl 1.4 from CPAN to my Gentoo linux > computer. But the > installation was failed. I had to install by force. > > > > However, the GD module couldn't be installed for some unknown reasons. > > > > I therefore use "emerge" tool of Gentoo to get bioperl and GD > again. They > are fine. The version of bioperl became upgrade to1.5 and GD was 2.35. > > > > However, when I tested it by using the program in HOWTO wiki page > (http://www.bioperl.org/wiki/HOWTO:Graphics), it always told me: > > > > Can't locate object method "png" via package "GD::Image" at > /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Panel.pm line > 799, <> line 9. > > > > In my other computer, bioperl1.4 and GD2.34 work fine. I > therefore want to > remove the CPAN bioperl from the system and re-install it, > but it seems to > be impossible. > > > > Would you please give me some advices on how to let my GD and > bioperl work. > > > > Thanks! > > > > Huang Yi > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/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 nhansen at nhgri.nih.gov Wed Nov 1 08:43:32 2006 From: nhansen at nhgri.nih.gov (Nancy Hansen) Date: Wed, 1 Nov 2006 08:43:32 -0500 (EST) Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: References: Message-ID: On Tue, 31 Oct 2006, Brian Osborne wrote: > It looks like a good place to start would be the get_header() and > _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that > the author, at some point, wanted get_header to return meaningful > information but stepping through the test shows it returning a lot of UNDEF. > Now I don't know if this is due to the method or the source SCF file, but > you might be able to get these methods to work yourself. > > But to answer your questions, yes, it certainly sounds reasonable that these > values would be extracted by Bio::SeqIO::scf. Sounds great! So, if I make these changes, is there someone I should run them by before checking them into CVS? Is Chad Matsalla still involved in bioperl? I've never contributed to the project, so I'm not sure how things work... Thanks! --Nancy ************************************* Nancy F. Hansen, PhD nhansen at nhgri.nih.gov Bioinformatics Group NIH Intramural Sequencing Center (NISC) 5625 Fishers Lane Rockville, MD 20852 Phone: (301) 435-1560 Fax: (301) 435-6170 From arareko at campus.iztacala.unam.mx Wed Nov 1 09:30:34 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed, 01 Nov 2006 08:30:34 -0600 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: References: Message-ID: <4548AF8A.6090205@campus.iztacala.unam.mx> The usual way is to send your modifications as an 'enhancement' through the Bugzilla system (please add your patches as attachments after creating the report, not into the description field): http://bugzilla.open-bio.org/ Thanks for contributing! Regards, Mauricio. Nancy Hansen wrote: > On Tue, 31 Oct 2006, Brian Osborne wrote: > >> It looks like a good place to start would be the get_header() and >> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that >> the author, at some point, wanted get_header to return meaningful >> information but stepping through the test shows it returning a lot of UNDEF. >> Now I don't know if this is due to the method or the source SCF file, but >> you might be able to get these methods to work yourself. >> >> But to answer your questions, yes, it certainly sounds reasonable that these >> values would be extracted by Bio::SeqIO::scf. > > Sounds great! So, if I make these changes, is there someone I should run > them by before checking them into CVS? Is Chad Matsalla still involved in > bioperl? I've never contributed to the project, so I'm not sure how > things work... > > Thanks! > --Nancy > > ************************************* > Nancy F. Hansen, PhD nhansen at nhgri.nih.gov > Bioinformatics Group > NIH Intramural Sequencing Center (NISC) > 5625 Fishers Lane > Rockville, MD 20852 > Phone: (301) 435-1560 Fax: (301) 435-6170 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From cjfields at uiuc.edu Wed Nov 1 09:39:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 1 Nov 2006 08:39:38 -0600 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: Message-ID: <000c01c6fdc3$8ed54770$15327e82@pyrimidine> > On Tue, 31 Oct 2006, Brian Osborne wrote: > >> It looks like a good place to start would be the get_header() and >> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can >> see that the author, at some point, wanted get_header to return >> meaningful information but stepping through the test shows it >> returning a lot of UNDEF. Now I don't know if this is due to the >> method or the source SCF file, but you might be able to get these >> methods to work yourself. >> >> But to answer your questions, yes, it certainly sounds reasonable >> that these values would be extracted by Bio::SeqIO::scf. > > Sounds great! So, if I make these changes, is there someone > I should run them by before checking them into CVS? Is Chad > Matsalla still involved in bioperl? I've never contributed > to the project, so I'm not sure how things work... > > Thanks! > --Nancy You can check them into Bugzilla as a patch to a bug: http://bugzilla.open-bio.org/ There is a HOWTO for patch submission here: http://www.bioperl.org/wiki/HOWTO:SubmitPatch You could also send them to Brian or me. Bugzilla is probably your best bet as anyone with a developer account can check in the fix. You should also write up some tests for your code changes. You can use the test file mentioned above (t/scf.t) as a start. -chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Wed Nov 1 08:00:53 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 01 Nov 2006 09:00:53 -0400 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: Message-ID: Nancy, I suggest doing this through Bugzilla, http://bugzilla.open-bio.org. First add your proposal as a bug or as an enhancement, sounds like it could be either but I'd say it doesn't matter. Then contribute patches to the "bug" as you work, some one will apply them. Also add tests to t/scf.t, if you're working on scf.pm. Thank you in advance for your contributions. As for Chad, I have no idea but strictly speaking no one "owns" a module in Bioperl. Brian O. On 11/1/06 9:43 AM, "Nancy Hansen" wrote: > Sounds great! So, if I make these changes, is there someone I should run > them by before checking them into CVS? Is Chad Matsalla still involved in > bioperl? I've never contributed to the project, so I'm not sure how > things work... From keithplayer at hotmail.com Wed Nov 1 19:22:07 2006 From: keithplayer at hotmail.com (Keith Player) Date: Thu, 2 Nov 2006 00:22:07 +0000 (UTC) Subject: [Bioperl-l] Article Message-ID: Sorry I didn't attach the article link originally. You can view the full-text for free: http://www.genome.org/cgi/content/abstract/12/10/1599 When I was talking about the R-tree I was talking about the current implementation. I should point out that I didn't actually try the perl module directly but implemented the binning schema straight in mysql. I found that by using the SQL I mentioned previously the database performed better compared to using the binning schema, I assume because of less disk seeks. I tested on a dataset of around 30k records and another the same size as the paper. The binning outperformed the queries as described in the paper, but the SQL I mentioned in the first post outperformed the binning schema by around a factor of 3. The new binning schema might make all this moot, especially if it removes layers so that groups/features next to each other are saved on the same/adjacent pages. The only question then would be whether database optimization is effected by the binning. Also does needing to know the largest length of a group/feature make the SQL statement I created impractical? From limericksean at gmail.com Wed Nov 1 11:28:58 2006 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 1 Nov 2006 17:28:58 +0100 Subject: [Bioperl-l] Can't locate object method "new_instance" via package "Bio::DB::SeqFeature::Store::dbi::mysql" at /project/gbrowse/httpd_perllib_new/Bio/DB/SeqFeature/Store.pm line 336. Message-ID: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> Hi, I am currently in the process of trying testing Gbrowse with the (relatively new) Bio::DB::SeqFeature::Store adaptor method. A couple of teething problems, just wondering if anyone else had encountered the message above. Any insight appreciated. Also the package called (Bio::DB::SeqFeature::Store::dbi::mysql) had to be copied into the lowercase 'dbi' from its original DBI form - don't know if this was a previously reported bug. Thanks, Sean. From ybolo001 at student.ucr.edu Wed Nov 1 19:15:57 2006 From: ybolo001 at student.ucr.edu (Eugene Bolotin) Date: Wed, 1 Nov 2006 16:15:57 -0800 Subject: [Bioperl-l] Check sequence format, question Message-ID: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> Dear bioperl mailing list, I trying to get sequence from a file using Bio::SeqIO, before I do anything, I want to make sure that the file is in a correct Fasta sequence format. I want it to spit out an error message if it is in any other format. What is the easiest way to do it? Thanks, Eugene Bolotin Sladek Lab. From cjfields at uiuc.edu Wed Nov 1 23:28:11 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 1 Nov 2006 22:28:11 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> References: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> Message-ID: <24DED46C-4630-4E95-94D0-87810183F191@uiuc.edu> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: > Dear bioperl mailing list, > I trying to get sequence from a file using Bio::SeqIO, before I do > anything, > I want to make sure that the file is in a correct Fasta sequence > format. I > want it to spit out an error message if it is in any other format. > What is the easiest way to do it? > Thanks, > Eugene Bolotin > Sladek Lab. There is no formal FASTA definition that is universally accepted beyond having the first line start with '>' and an optional description, with the sequence in subsequent lines. http://www.bioperl.org/wiki/FASTA_sequence_format Bio::SeqIO isn't currently set up to validate sequence formats directly, but you could try preparsing the data using Bio::Tools::GuessSeqFormat. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Wed Nov 1 21:21:35 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 1 Nov 2006 21:21:35 -0500 Subject: [Bioperl-l] Can't locate object method "new_instance" via package "Bio::DB::SeqFeature::Store::dbi::mysql" at /project/gbrowse/httpd_perllib_new/Bio/DB/SeqFeature/Store.pm line 336. In-Reply-To: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> References: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> Message-ID: <6dce9a0b0611011821l45cd7f8enb2e77f286f7cf6f5@mail.gmail.com> Hi, DBI should be uppercased in the gbrowse config file: [GENERAL] description = C. elegans GFF3 Database db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn ws164_gff3 You shouldn't have to change anything to lowercase. Lincoln On 11/1/06, Sean O'Keeffe wrote: > > Hi, > I am currently in the process of trying testing Gbrowse with the > (relatively new) Bio::DB::SeqFeature::Store adaptor method. A couple > of teething problems, just wondering if anyone else had encountered > the message above. Any insight appreciated. > Also the package called (Bio::DB::SeqFeature::Store::dbi::mysql) had > to be copied into the lowercase 'dbi' from its original DBI form - > don't know if this was a previously reported bug. > > Thanks, > Sean. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From Bernhard.Schmalhofer at biomax.com Thu Nov 2 03:53:14 2006 From: Bernhard.Schmalhofer at biomax.com (Bernhard Schmalhofer) Date: Thu, 02 Nov 2006 09:53:14 +0100 Subject: [Bioperl-l] Is it possible to parse BLAST output using IO:String? In-Reply-To: <716af09c0610301244q1c6d4cd6y23e72371dda4fa4d@mail.gmail.com> References: <00e301c6fc5f$a36de9e0$e6028a0a@GOLHARMOBILE1> <716af09c0610301244q1c6d4cd6y23e72371dda4fa4d@mail.gmail.com> Message-ID: <4549B1FA.1020506@biomax.com> Bernd Web wrote: > Hi Ryan, > > I parse blastn output using IO::String w/o problems: > > my $stringfh = new IO::String($input); > my $in = new Bio::SearchIO(-format => 'blast', -fh => $stringfh); I do the same with implicitly using IO::String. Works like a charm at leaset with Perl 5.8.0. # get $blast_report from MySQL open my $blast_report_fh, '<', \$blast_report; my $in = Bio::SearchIO->new( -format => 'blast', -fh => $blast_report_fh ); Regards, Bernhard -- ************************************************** Dipl.-Physiker Bernhard Schmalhofer Senior Developer Biomax Informatics AG Lochhamer Str. 11 82152 Martinsried, Germany Tel: +49 89 895574-839 Fax: +49 89 895574-825 eMail: Bernhard.Schmalhofer at biomax.com Website: www.biomax.com ************************************************** From cjfields at uiuc.edu Thu Nov 2 10:11:01 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 09:11:01 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <85304914-322B-46BA-BED2-09722FE08D57@uiuc.edu> Brian, I think the validation issue is worthwhile but I can see logistical nightmares having every SeqIO parser validate sequence while parsing; GenBank and EMBL do this to some extent already but it isn't foolproof. Much of SeqIO (e.g. GenBank/EMBL/Swiss parsing) is already in dire need of an overhaul as is w/o adding validation. I wonder if it would be better if SeqIO has-a validator object instead of acting as a validator itself, i.e. SeqIO would focus on parsing and writing, the validator would focus on validation. It might be easier from the maintenance aspect. It's probably worthwhile exploring using Bio::Tools::GuessSeqFormat within SeqIO, or setting up a new system altogether. Validation using the sequence validator could then be enabled by having a validation option when instantiating SeqIO. We could even enable XML format validation using the DTD/Schema, which should be fairly straightforward. Of course, this all depends on someone writing it up... Chris On Nov 2, 2006, at 6:49 AM, Brian Osborne wrote: > Chris et al., > > As you know the question of whether SeqIO should or should not > validate or > check the given format is still an open one. In fact, some SeqIO > modules do > validate to some extent. See: > > http://bugzilla.open-bio.org/show_bug.cgi?id=1508 > > I can see that you've commented on this enhancement, I'm replying > just to > bring this to the attention of others. > > Brian O. > > > On 11/2/06 12:28 AM, "Chris Fields" wrote: > >> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: >> >>> Dear bioperl mailing list, >>> I trying to get sequence from a file using Bio::SeqIO, before I do >>> anything, >>> I want to make sure that the file is in a correct Fasta sequence >>> format. I >>> want it to spit out an error message if it is in any other format. >>> What is the easiest way to do it? >>> Thanks, >>> Eugene Bolotin >>> Sladek Lab. >> >> There is no formal FASTA definition that is universally accepted >> beyond having the first line start with '>' and an optional >> description, with the sequence in subsequent lines. >> >> http://www.bioperl.org/wiki/FASTA_sequence_format >> >> Bio::SeqIO isn't currently set up to validate sequence formats >> directly, but you could try preparsing the data using >> Bio::Tools::GuessSeqFormat. >> >> Chris >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Thu Nov 2 09:38:36 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 10:38:36 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <85304914-322B-46BA-BED2-09722FE08D57@uiuc.edu> Message-ID: Chris, Yes, and validation should always be optional. SeqIO is not always as fast as some want it to be and sometimes you're certain that your files don't need to be validated. Brian O. On 11/2/06 11:11 AM, "Chris Fields" wrote: > Brian, > > I think the validation issue is worthwhile but I can see logistical > nightmares having every SeqIO parser validate sequence while parsing; > GenBank and EMBL do this to some extent already but it isn't > foolproof. Much of SeqIO (e.g. GenBank/EMBL/Swiss parsing) is > already in dire need of an overhaul as is w/o adding validation. > > I wonder if it would be better if SeqIO has-a validator object > instead of acting as a validator itself, i.e. SeqIO would focus on > parsing and writing, the validator would focus on validation. It > might be easier from the maintenance aspect. It's probably > worthwhile exploring using Bio::Tools::GuessSeqFormat within SeqIO, > or setting up a new system altogether. Validation using the sequence > validator could then be enabled by having a validation option when > instantiating SeqIO. We could even enable XML format validation > using the DTD/Schema, which should be fairly straightforward. > > Of course, this all depends on someone writing it up... > > Chris > > On Nov 2, 2006, at 6:49 AM, Brian Osborne wrote: > >> Chris et al., >> >> As you know the question of whether SeqIO should or should not >> validate or >> check the given format is still an open one. In fact, some SeqIO >> modules do >> validate to some extent. See: >> >> http://bugzilla.open-bio.org/show_bug.cgi?id=1508 >> >> I can see that you've commented on this enhancement, I'm replying >> just to >> bring this to the attention of others. >> >> Brian O. >> >> >> On 11/2/06 12:28 AM, "Chris Fields" wrote: >> >>> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: >>> >>>> Dear bioperl mailing list, >>>> I trying to get sequence from a file using Bio::SeqIO, before I do >>>> anything, >>>> I want to make sure that the file is in a correct Fasta sequence >>>> format. I >>>> want it to spit out an error message if it is in any other format. >>>> What is the easiest way to do it? >>>> Thanks, >>>> Eugene Bolotin >>>> Sladek Lab. >>> >>> There is no formal FASTA definition that is universally accepted >>> beyond having the first line start with '>' and an optional >>> description, with the sequence in subsequent lines. >>> >>> http://www.bioperl.org/wiki/FASTA_sequence_format >>> >>> Bio::SeqIO isn't currently set up to validate sequence formats >>> directly, but you could try preparsing the data using >>> Bio::Tools::GuessSeqFormat. >>> >>> Chris >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > From bosborne11 at verizon.net Thu Nov 2 07:49:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 08:49:01 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <24DED46C-4630-4E95-94D0-87810183F191@uiuc.edu> Message-ID: Chris et al., As you know the question of whether SeqIO should or should not validate or check the given format is still an open one. In fact, some SeqIO modules do validate to some extent. See: http://bugzilla.open-bio.org/show_bug.cgi?id=1508 I can see that you've commented on this enhancement, I'm replying just to bring this to the attention of others. Brian O. On 11/2/06 12:28 AM, "Chris Fields" wrote: > On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: > >> Dear bioperl mailing list, >> I trying to get sequence from a file using Bio::SeqIO, before I do >> anything, >> I want to make sure that the file is in a correct Fasta sequence >> format. I >> want it to spit out an error message if it is in any other format. >> What is the easiest way to do it? >> Thanks, >> Eugene Bolotin >> Sladek Lab. > > There is no formal FASTA definition that is universally accepted > beyond having the first line start with '>' and an optional > description, with the sequence in subsequent lines. > > http://www.bioperl.org/wiki/FASTA_sequence_format > > Bio::SeqIO isn't currently set up to validate sequence formats > directly, but you could try preparsing the data using > Bio::Tools::GuessSeqFormat. > > Chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Thu Nov 2 13:07:45 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 12:07:45 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <93F383D1-6DDF-4238-954A-96CE1218C641@uiuc.edu> On Nov 2, 2006, at 8:38 AM, Brian Osborne wrote: > Chris, > > Yes, and validation should always be optional. SeqIO is not always > as fast > as some want it to be and sometimes you're certain that your files > don't > need to be validated. > > Brian O. Agreed. We could use the original Bugzilla bug (1508?) to track this and maybe gather ideas, but the wiki is probably a better place... Chris > On 11/2/06 11:11 AM, "Chris Fields" wrote: > >> ... Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Thu Nov 2 13:08:45 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 14:08:45 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <93F383D1-6DDF-4238-954A-96CE1218C641@uiuc.edu> Message-ID: Chris, Yes, in the Project priority list page. Speaking of this page, why is all of the text on the bottom half of this page crossed out? Many of these items have _not_ been done. Brian O. On 11/2/06 2:07 PM, "Chris Fields" wrote: > Agreed. We could use the original Bugzilla bug (1508?) to track this > and maybe gather ideas, but the wiki is probably a better place... From cjfields at uiuc.edu Thu Nov 2 14:22:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 13:22:48 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <0DA38665-F4CB-4000-974F-47915F0524A2@uiuc.edu> On Nov 2, 2006, at 12:08 PM, Brian Osborne wrote: > Chris, > > Yes, in the Project priority list page. > > Speaking of this page, why is all of the text on the bottom half of > this > page crossed out? Many of these items have _not_ been done. > > Brian O. You're right; they shouldn't be crossed out unless they are completed. If someone takes on a project then they attach their signature to it, not cross it off the list. I'll change that and add a disclaimer to the top of the page. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stewarta at nmrc.navy.mil Thu Nov 2 15:26:08 2006 From: stewarta at nmrc.navy.mil (Andrew Stewart) Date: Thu, 2 Nov 2006 15:26:08 -0500 Subject: [Bioperl-l] Bio::DB::GFF and feature order Message-ID: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> In attempting to determine some statistics on the distances between CDS features in my Bio::DB::GFF database, I ran a query on all CDS features as follows... my @CDS = $segment->features('CDS'); ...only to find that the features returned are not in order. Is there a way of returning the features in order or sorting them through some internal Bio::DB::GFF related method, aside from the more obvious path of sorting through the array itself (somehow)? -A -- Andrew Stewart Research Assistant, Genomics Team Navy Medical Research Center (NMRC) Biological Defense Research Directorate (BDRD) BDRD Annex 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 email: stewarta at nmrc.navy.mil phone: 301-231-6700 Ext 270 From lincoln.stein at gmail.com Thu Nov 2 15:41:06 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 2 Nov 2006 15:41:06 -0500 Subject: [Bioperl-l] [Gmod-gbrowse] Bio::DB::GFF and feature order In-Reply-To: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> References: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> Message-ID: <6dce9a0b0611021241i35f602f2q6ca59f23738d1013@mail.gmail.com> How do you want them sorted? To sort them by their start positions: my @CDS = sort {$a->start<=>$b->start} $segment->features('CDS'); Other people may want to sort features by end position, length, name, or who knows what. Lincoln On 11/2/06, Andrew Stewart wrote: > > In attempting to determine some statistics on the distances between CDS > features in my Bio::DB::GFF database, I ran a query on all CDS features as > follows... > my @CDS = $segment->features('CDS'); > > ...only to find that the features returned are not in order. Is there a > way of returning the features in order or sorting them through some internal > Bio::DB::GFF related method, aside from the more obvious path of sorting > through the array itself (somehow)? > > > -A > > -- > Andrew Stewart > Research Assistant, Genomics Team > Navy Medical Research Center (NMRC) > Biological Defense Research Directorate (BDRD) > BDRD Annex > 12300 Washington Avenue, 2nd Floor > Rockville, MD 20852 > > email: stewarta at nmrc.navy.mil > phone: 301-231-6700 Ext 270 > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From n.haigh at sheffield.ac.uk Thu Nov 2 17:12:28 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 02 Nov 2006 22:12:28 +0000 Subject: [Bioperl-l] $Bio::Root::Version:VERSION Message-ID: <454A6D4C.3020605@sheffield.ac.uk> When does $Bio::Root::Version::VERSION get incremented? immediately prior to a tag or straight after a tag so that CVS code is seen as more recent than an official release? For example, $VERSION is currently set to 1.52_01 but the code in CVS HEAD is passed 1.5.2 RC2 now so should is read 1.52_02 or be 1.52_03 for the upcoming 1.52 RC3? Cheers Nath From bix at sendu.me.uk Thu Nov 2 18:14:57 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 02 Nov 2006 23:14:57 +0000 Subject: [Bioperl-l] $Bio::Root::Version:VERSION In-Reply-To: <454A6D4C.3020605@sheffield.ac.uk> References: <454A6D4C.3020605@sheffield.ac.uk> Message-ID: <454A7BF1.1060705@sendu.me.uk> Nathan S. Haigh wrote: > When does $Bio::Root::Version::VERSION get incremented? immediately > prior to a tag or straight after a tag so that CVS code is seen as more > recent than an official release? Normally nothing happens. > For example, $VERSION is currently set to 1.52_01 but the code in CVS > HEAD is passed 1.5.2 RC2 now so should is read 1.52_02 or be 1.52_03 for > the upcoming 1.52 RC3? Once I've decided what to do based on the discussion we had, I'll update it. I'll currently leaning toward the 'clean break', pugs-style suggestion from Chris. If you've strong views in another direction, post in that thread. From bernd.web at gmail.com Fri Nov 3 07:57:03 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 3 Nov 2006 13:57:03 +0100 Subject: [Bioperl-l] Bio::DB::Query::GenBank Message-ID: <716af09c0611030457p678f4d30v935215ba3c4dd5dc@mail.gmail.com> Hi, In contrast to the doc of Bio::DB::Query::GenBank at http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Query/GenBank.html this following seems not the case: "If you provide an array reference of IDs in -ids, the query will be ignored and the list of IDs will be used when the query is passed to a Bio::DB::GenBank object's get_Stream_by_query() method" I used # $Id: GenBank.pm,v 1.19 2006/09/26 22:03:07 sendu Exp $ It looks like query always overrules the array(ref) given in -ids. bernd From staffa at niehs.nih.gov Fri Nov 3 11:29:19 2006 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Fri, 03 Nov 2006 12:29:19 -0400 Subject: [Bioperl-l] Bio::Tools::RestrictionEnzyme Message-ID: The module Bio::Tools::RestrictionEnzyme Uses the perl split function to generate the fragments of a digestion, Using the recognition pattern as the delimiter. It then glues onto the resulting strings that part of the pattern representing the sequence before and after the cut. This is fine for non-ambiguous patterns, but starts looking funny for patterns having ambiguities. Worse that in doing a double digest, one enzyme after another, the ambiguity code character can mask a true cut site. I was using BsaHI [GRCGYC] followed by HpaII [CCGG] Below is the example of the CCGG pattern being masked by a Y And the different results of the digestion. CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAA As opposed to the real thing: CGCCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAA Which when cut by HpaII [CCGG] really yields first A_B_frag : CGC Instead of : first A_B_frag = CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAAG ACTTGCTAGTGCTGTTGGGTCTCC TTGACTCTGAGACAATGATAACAATGTTGAAGGTGGTCTAGGCATTTGGGTGCTGTGGAGTTATAAAGAGGAAAAG AAAAGATAAAACAAAAAAAAATAG GAAACAAATGATTAAGCCACTACTAAGGGGTCTAGTCTAATGCCAACTGGGTAAATTCATGGGAACAATGTGTGCC AGTCTTTAGAAACACTGTTTCATA TTGCATATATTATGGCATGGTATTACATTGATTAATTTTACTTTAGAGATGAAGAAGCTGAGATTTGGGGTGAATA GCAATTATCCCAAAGTCTCTCAGA TAGCTGGAGGCAGCAGGGTCTGGGGTATTCACAGTCCCTACTCCATATTGTGTGGTCAGAACCAAATGAGACAGAT AAAGGGCAGACAAAAGAGAAAGTG GGGAGTATGATTTGAAAATGATGGTGTGACCCAGATTTCTGATGGAAATATCTAATGGCTGCAGACTGGATAGCTG TGACCATTTTAGTTACTGAATTCA GGAGATCTTATCTCAATGGAGGCATGTTGTCAACCAAAAGCCAGGATAAGCAAGGGTCAGTGTCTAGACATTGGAG TAAGGTTTGCCTGGATATTTCCAC AGGGAACCAAGTGTCATGGAGTCTTATTCATTGGGAGGTTATCTTTGTTACACACATGGACATATCATCAAGCCAG CAATTCAGCAAAACTGTCAACACA CAAATAGAGATGTATTGACAACGGGGAACCACAAGTCATGCTTATTCCAAGCTAAAGCCCTCATGTGGAACTTGTT TTGTATGGCATTTGTCTCATCTAC ACATTGATGGGAAGGGTAAAAGGAAGTCTTTGGTGGGATTACAGAAGTCAGTAAAAAAGCAAAAGGAAAGATTTAG AAAACAAAGAAAAAGAAAAGGGAG GAAAGGAAAAGAAAAAAGATTTCAGAGATCTCAACATCAATTCAGACCAAGGGTGCCTCTTATACTATGTCCAAGC CAGTAAGTGGGGTTGTTCTTGTTA ACTACAGCCATGTATAGAGGTGAACTTCAGGCTCCTGACTGATCCTCTGAGGTAGAAAGTAAACAGTACTCTTATG ACACACGCAGTTGTTCAGTGCTGA CATGAAAATGTCATTGCTTACAGCGCTAGGAGAC This subroutine yields, I believe, the true sequence, Although I don't know how efficient it is. I'm thinking it must be more efficient than having to turn each fragment from the first digestion into a BioPerl Sequence Object before applying the cut_seq method. sub cut_seq { my $number= 0; my @frags = (); my $bigline = shift @_; my $recognition_site = shift @_; my $cutsite = shift @_; my $pat = &expanded_string($recognition_site); while ($bigline){ #my $offset = index $bigline, $pat; if ($bigline =~/($pat)/){ my $first = substr $&,0,$cutsite; my $last = substr $&,$cutsite; my $frag = $`.$first; push @frags, $frag; $number++; #print "fragment # $number:\n$frag\n"; my $rest_of_bigline = $last.$'; $bigline = $rest_of_bigline;} else {push @frags, $bigline; #Last one $number++; #print "fragment # $number:\n$bigline\n"; $bigline = "";} } return @frags; } Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Information Technology Support Services Contract (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov ) National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From cjfields at uiuc.edu Fri Nov 3 13:28:53 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 3 Nov 2006 12:28:53 -0600 Subject: [Bioperl-l] Bio::Tools::RestrictionEnzyme In-Reply-To: References: Message-ID: <915FE028-7F12-4BCE-AD9D-7D8D7D74AD6F@uiuc.edu> Nick, Could you file this as a bug? Chris On Nov 3, 2006, at 10:29 AM, Staffa, Nick (NIH/NIEHS) wrote: > The module Bio::Tools::RestrictionEnzyme > Uses the perl split function to generate the fragments of a digestion, > Using the recognition pattern as the delimiter. It then glues onto > the > resulting strings that part of the pattern representing the > sequence before > and after the cut. This is fine for non-ambiguous patterns, but > starts > looking funny for patterns having ambiguities. > Worse that in doing a double digest, one enzyme after another, the > ambiguity > code character can mask a true cut site. > I was using BsaHI [GRCGYC] followed by HpaII [CCGG] > Below is the example of the CCGG pattern being masked by a Y > And the different results of the digestion. > > > CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAA > As opposed to the real thing: > CGCCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAA > > Which when cut by HpaII [CCGG] really yields > first A_B_frag : > CGC > > Instead of : > first A_B_frag = > > CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAAG > ACTTGCTAGTGCTGTTGGGTCTCC > TTGACTCTGAGACAATGATAACAATGTTGAAGGTGGTCTAGGCATTTGGGTGCTGTGGAGTTATAAAGAG > GAAAAG > AAAAGATAAAACAAAAAAAAATAG > GAAACAAATGATTAAGCCACTACTAAGGGGTCTAGTCTAATGCCAACTGGGTAAATTCATGGGAACAATG > TGTGCC > AGTCTTTAGAAACACTGTTTCATA > TTGCATATATTATGGCATGGTATTACATTGATTAATTTTACTTTAGAGATGAAGAAGCTGAGATTTGGGG > TGAATA > GCAATTATCCCAAAGTCTCTCAGA > TAGCTGGAGGCAGCAGGGTCTGGGGTATTCACAGTCCCTACTCCATATTGTGTGGTCAGAACCAAATGAG > ACAGAT > AAAGGGCAGACAAAAGAGAAAGTG > GGGAGTATGATTTGAAAATGATGGTGTGACCCAGATTTCTGATGGAAATATCTAATGGCTGCAGACTGGA > TAGCTG > TGACCATTTTAGTTACTGAATTCA > GGAGATCTTATCTCAATGGAGGCATGTTGTCAACCAAAAGCCAGGATAAGCAAGGGTCAGTGTCTAGACA > TTGGAG > TAAGGTTTGCCTGGATATTTCCAC > AGGGAACCAAGTGTCATGGAGTCTTATTCATTGGGAGGTTATCTTTGTTACACACATGGACATATCATCA > AGCCAG > CAATTCAGCAAAACTGTCAACACA > CAAATAGAGATGTATTGACAACGGGGAACCACAAGTCATGCTTATTCCAAGCTAAAGCCCTCATGTGGAA > CTTGTT > TTGTATGGCATTTGTCTCATCTAC > ACATTGATGGGAAGGGTAAAAGGAAGTCTTTGGTGGGATTACAGAAGTCAGTAAAAAAGCAAAAGGAAAG > ATTTAG > AAAACAAAGAAAAAGAAAAGGGAG > GAAAGGAAAAGAAAAAAGATTTCAGAGATCTCAACATCAATTCAGACCAAGGGTGCCTCTTATACTATGT > CCAAGC > CAGTAAGTGGGGTTGTTCTTGTTA > ACTACAGCCATGTATAGAGGTGAACTTCAGGCTCCTGACTGATCCTCTGAGGTAGAAAGTAAACAGTACT > CTTATG > ACACACGCAGTTGTTCAGTGCTGA > CATGAAAATGTCATTGCTTACAGCGCTAGGAGAC > > > This subroutine yields, I believe, the true sequence, > Although I don't know how efficient it is. > I'm thinking it must be more efficient than having to turn each > fragment > from the first digestion into a BioPerl Sequence Object before > applying the > cut_seq method. > > sub cut_seq { > my $number= 0; > my @frags = (); > my $bigline = shift @_; > my $recognition_site = shift @_; > my $cutsite = shift @_; > my $pat = &expanded_string($recognition_site); > while ($bigline){ > #my $offset = index $bigline, $pat; > if ($bigline =~/($pat)/){ > my $first = substr $&,0,$cutsite; > my $last = substr $&,$cutsite; > my $frag = $`.$first; > push @frags, $frag; > $number++; > #print "fragment # $number:\n$frag\n"; > my $rest_of_bigline = $last.$'; > $bigline = $rest_of_bigline;} > else {push @frags, $bigline; #Last one > $number++; > #print "fragment # $number:\n$bigline\n"; > $bigline = "";} > } > return @frags; > } > > > > > Nick Staffa > Telephone: 919-316-4569 (NIEHS: 6-4569) > Scientific Computing Support Group > NIEHS Information Technology Support Services Contract > (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov ) > National Institute of Environmental Health Sciences > National Institutes of Health > Research Triangle Park, North Carolina > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From johnson.biotech at gmail.com Fri Nov 3 11:47:56 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Fri, 3 Nov 2006 11:47:56 -0500 Subject: [Bioperl-l] BioSQL load_seqdatabase.pl -pipeline option Message-ID: Hello guys, I'm populating biosql database using "load_seqdatabase.pl" from genbank release files for primates. However, I only need sequences that belong to humans (taxon id: 9606). I assume that best way to filter the necessary sequences is to use '-pipeline' option of the script. The documentation seems a little vague to me on how to create my own processor to accomplish the task. Can anyone clarify the steps??? -- Best Regards, Seth Johnson Senior Bioinformatics Associate From er at xs4all.nl Fri Nov 3 14:59:47 2006 From: er at xs4all.nl (Erik) Date: Fri, 3 Nov 2006 20:59:47 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error Message-ID: <10596.156.83.1.241.1162583987.squirrel@webmail.xs4all.nl> Hi all, I noticed the parsing is borked with newest swisprot files: UniProt Knowledgebase Release 9 consists of: UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines in swissprot/trembl according to the new specification (see http://expasy.org/sprot/relnotes/sp_news.html). Basically, the change is as follows: ID EntryName DataClass; MoleculeType; SequenceLength. is changed to: ID EntryName DataClass; SequenceLength. The change I made was only in the regex capturing the entry name: method next_seq (Bio/SeqIO/swiss.pm) : =============== unless( m/ ^ ID \s+ # (\S+) \s+ # $1 entryname ([^\s;]+); \s+ # $2 DataClass [0-9]+[ ]AA \. # Sequencelength (capture?) $ /ox ) { $self->throw("swissprot stream with no ID. Not swissprot in my book"); } =============== I tested this (=entry parsable and SeqIO created) against several hundred Swissprot and Trembl entries. Of course, files with the older format are now broken - it may be better to leave old and new format, and try both (newest first). hth, Erik From er at xs4all.nl Fri Nov 3 15:56:47 2006 From: er at xs4all.nl (Erik) Date: Fri, 3 Nov 2006 21:56:47 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error - Message-ID: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> I should have mentioned two more changes needed in Bio/SeqIO/swiss.pm for the new Swissprot format: In Bio/SeqIO/swiss.pm, next_seq(): =============== $params{'-namespace'} = ($2 eq 'Reviewed' ) ? 'Swiss-Prot' : ($2 eq 'Unreviewed' ) ? 'TrEMBL' : # ($2 eq 'STANDARD' ) ? 'Swiss-Prot' : # ($2 eq 'PRELIMINARY') ? 'TrEMBL' : $2; =============== and in Bio/SeqIO/swiss.pm, write_seq(): =============== $div = ($ns eq 'Swiss-Prot') ? 'Reviewed' : ($ns eq 'TrEMBL') ? 'Unreviewed' : # ($ns eq 'Swiss-Prot') ? 'STANDARD' : # ($ns eq 'TrEMBL') ? 'PRELIMINARY' : $ns; =============== above, the old lines are shown as outcommented. again, hth, Erik From pllv_shrm at yahoo.com Fri Nov 3 16:14:14 2006 From: pllv_shrm at yahoo.com (pallavi sharma) Date: Fri, 3 Nov 2006 13:14:14 -0800 (PST) Subject: [Bioperl-l] need help Message-ID: <20061103211414.56111.qmail@web31712.mail.mud.yahoo.com> hii could ny one plz tell me how to convert bioperl module like Bio::SearchIO n Bio::alignIO module into perl lang --------------------------------- Check out the New Yahoo! Mail - Fire up a more powerful email and get things done faster. From hlapp at gmx.net Fri Nov 3 17:54:08 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 3 Nov 2006 17:54:08 -0500 Subject: [Bioperl-l] BioSQL load_seqdatabase.pl -pipeline option In-Reply-To: References: Message-ID: Close. It's not the --pipeline option you want to use for this purpose but the --seqfilter option. For example, to retain only sequence with taxon id 9606 you would say --seqfilter 'sub {my $s=shift->{"-species"}; return 1 unless $s; return 1 unless $s->ncbi_taxid; return 1 if $s->ncbi_taxid == 9606; return 0;}' Note that when formulating the conditions upon which to accept or reject the object you need to take into account that the closure may be called multiple times for one object, at various stages of completion of the properties hash. So, the above sequence of logic says, accept the object if there is no species attached (yet), or if the species doesn't have a taxon ID (yet; in Genbank format, the taxon ID is actually in the feature table, and hence will only be populated later, after parsing the organism lines), or if the taxon ID is 9606. Otherwise (i.e., there is a species object, it has a taxon ID defined, and the taxon ID is not 9606) reject the object. (Note that --seqfilter will read and parse a file if the argument refers to an existing and readable file. So if you are going to use this construct often, you may want to put into a file.) -hilmar On Nov 3, 2006, at 11:47 AM, Seth Johnson wrote: > Hello guys, > > I'm populating biosql database using "load_seqdatabase.pl" from > genbank release files for primates. However, I only need sequences > that belong to humans (taxon id: 9606). I assume that best way to > filter the necessary sequences is to use '-pipeline' option of the > script. The documentation seems a little vague to me on how to create > my own processor to accomplish the task. Can anyone clarify the > steps??? > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From akozik at atgc.org Fri Nov 3 17:29:49 2006 From: akozik at atgc.org (Alexander Kozik) Date: Fri, 03 Nov 2006 14:29:49 -0800 Subject: [Bioperl-l] SCF files Message-ID: <454BC2DD.5050405@atgc.org> Hi all, There is a contradiction in opinions (I have used google search) what type of data SCF files (sequencing chromatograms) carry. Could you help to clarify following topics: are these statements true or false: 1. SCF files can be generated by Phred program only. 2. new version of Phred can read SCF files produced by older version of Phred and re-do basecalling with new quality scores [new quality scores could be different because of the improvements/changes in a basecalling algorithm] 3. SCF files contain no less information as original AB1 files [in other words, no information lost during conversion of AB1 to SCF] Thanks, -Alex ======================================== Alexander Kozik Bioinformatics Specialist Genome and Biomedical Sciences Facility 451 East Health Sciences Drive University of California Davis, CA 95616-8816 Phone: (530) 754-9127 email: akozik at atgc.org web: http://www.atgc.org/ ======================================== From cjfields at uiuc.edu Sun Nov 5 16:56:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 5 Nov 2006 15:56:08 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error - In-Reply-To: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> References: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> Message-ID: <73A15B2C-A8FE-4F1B-B17E-B43A46B82140@uiuc.edu> We'll try to get these in. THe problem is we need to try and make this backwards compatible. I'll post this as a bug for now as a reminder. Chris On Nov 3, 2006, at 2:56 PM, Erik wrote: > > I should have mentioned two more changes needed > in Bio/SeqIO/swiss.pm for the new Swissprot > format: > > In Bio/SeqIO/swiss.pm, next_seq(): > =============== > $params{'-namespace'} = ($2 eq 'Reviewed' ) ? 'Swiss-Prot' : > ($2 eq 'Unreviewed' ) ? 'TrEMBL' : > # ($2 eq 'STANDARD' ) ? 'Swiss-Prot' : > # ($2 eq 'PRELIMINARY') ? 'TrEMBL' : > $2; > =============== > > > and in Bio/SeqIO/swiss.pm, write_seq(): > =============== > $div = ($ns eq 'Swiss-Prot') ? 'Reviewed' : > ($ns eq 'TrEMBL') ? 'Unreviewed' : > # ($ns eq 'Swiss-Prot') ? 'STANDARD' : > # ($ns eq 'TrEMBL') ? 'PRELIMINARY' : > $ns; > =============== > > above, the old lines are shown as outcommented. > > > again, hth, > > Erik > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From adsj at novozymes.com Mon Nov 6 08:03:21 2006 From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=) Date: Mon, 06 Nov 2006 14:03:21 +0100 Subject: [Bioperl-l] Subclassing Bio::Seq ? Extending Bio::Perl References: <934F95E71B6C9347A873C42AE3C196191299DFBF@NZT0004E.dknz.nzcorp.n et> <934F95E71B6C9347A873C42AE3C196190B84C5FC@NZT0004E.dknz.nzcorp.net> Message-ID: <87zmb4ohgm.fsf@topper.koldfront.dk> On Tue, 24 Oct 2006 14:57:02 -0400, Hilmar wrote: > On Oct 24, 2006, at 1:59 PM, JK ((Jesper Agerbo Krogh)) wrote: >>> The reason that this is a Bio::PrimarySeq and not a Bio::Seq or your >>> extension of the latter is that the Perl garbage collector can't deal >>> with circular references. >> Doesn't Scalar::Util::weaken solve that? > You're welcome to test and try. It should be a simple change in > Bio::Seq::add_SeqFeature(). You will see that it is this method and > not the feature object that makes sure the wrapped primarySeq gets > passed as sequence reference. Just change that to creating a new > reference to the sequence object and make it a weak reference before > passing it to the feature object. > (The feature object has no requirement (or knowledge) that the > referenced sequence object is a PrimarySeq.) I've tried implementing this approach - the only test that failed was FootPrinter.t, which I "solved" by not weakening if the object is a Bio::PrimarySeq. I am not sure how fragile this approach is; any comments (patch attached)? [...] > I'm not following you why this would make any difference (it would be > $seq->message_digest() compared to $seqCompute->message_digest > ($seq)), unless what you are saying is that you would like to cache > the result of the computation. You would have to create, or pass around, a $seqCompute object everywhere your $seq-object's digest was needed, which would be a bit of a pain? Best regards, Adam -- Adam Sj?gren adsj at novozymes.com -------------- next part -------------- A non-text attachment was scrubbed... Name: feature_seq_weaken.patch Type: text/x-patch Size: 3675 bytes Desc: not available URL: From n.haigh at sheffield.ac.uk Mon Nov 6 10:12:37 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 15:12:37 +0000 Subject: [Bioperl-l] return undef Message-ID: <454F50E5.3030702@sheffield.ac.uk> Is there any reason why a "return undef" can't simply be swapped over to just "return"? Cheers Nath From n.haigh at sheffield.ac.uk Mon Nov 6 11:19:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 16:19:08 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F5BED.6040406@sendu.me.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> Message-ID: <454F607C.5020808@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Is there any reason why a "return undef" can't simply be swapped over to >> just "return"? > > No, in fact if you see any 'return undef's, please change them to > 'return' since the former can lead to subtle bugs. We did do an audit > earlier to fix most of those; presumably there was some kind of issue > with the remainder (or they just weren't caught), so check that no > problems arise when you make the change. > Just been checking the bioperl-run modules and changed the ones I found. Running "make test" doesn't seem to show up any errors so I'll commit them shortly. On a similar note, is it safe to simply substitute "use vars" for "our" and correctly commenting the list of variables if qw() was previously used? e.g.: use vars qw($variable1 @array1 %hash1); # to: our ($variable1, @array1, %hash1); If so, there are 340+ "use vars" in the bioperl-run......any wise ideas on a generic script that can do an intelligent search and replace. Bearing in mind that these lists can span multiple lines? I set up the following page a couple of days ago to house some scripts that can be used to do audit checks of code: http://www.bioperl.org/wiki/Auditing If anyone has any scripts, Perl, shell or otherwise fell free to add them! :-) Cheers Nath -- > A: Yes. >> Q: Are you sure? >> >>> A: Because it reverses the logical flow of conversation. >>> >>>> Q: Why is top posting frowned upon? >>>> Get Thunderbird From bix at sendu.me.uk Mon Nov 6 10:59:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 15:59:41 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F50E5.3030702@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> Message-ID: <454F5BED.6040406@sendu.me.uk> Nathan S. Haigh wrote: > Is there any reason why a "return undef" can't simply be swapped over to > just "return"? No, in fact if you see any 'return undef's, please change them to 'return' since the former can lead to subtle bugs. We did do an audit earlier to fix most of those; presumably there was some kind of issue with the remainder (or they just weren't caught), so check that no problems arise when you make the change. From cjfields at uiuc.edu Mon Nov 6 11:35:52 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 10:35:52 -0600 Subject: [Bioperl-l] AlignIO::stockholm write_aln() Message-ID: I have added some experimental write_aln() support for Stockholm format to CVS along with some basic tests to AlignIO.t. I plan on cleaning it up a bit and adding more tests, along with possibly adding a builder option (similar to SeqIO::genbank) to have annotation parsing optional. Right now it is always on by default. It doesn't print meta data yet but does parse and store it; I'll probably add that in the next day or two. Be forewarned if testing this: I haven't tried clustal/msf/etc- >stockholm conversions yet so don't know if that works, but it should (it just won't print annotations). I'll add tests for that when I get time. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 6 11:55:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 16:55:55 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F607C.5020808@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> Message-ID: <454F691B.3090900@sendu.me.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: >> Nathan S. Haigh wrote: >>> Is there any reason why a "return undef" can't simply be swapped over to >>> just "return"? >> >> No, in fact if you see any 'return undef's, please change them to >> 'return' since the former can lead to subtle bugs. We did do an audit >> earlier to fix most of those; presumably there was some kind of issue >> with the remainder (or they just weren't caught), so check that no >> problems arise when you make the change. > > Just been checking the bioperl-run modules and changed the ones I found. > Running "make test" doesn't seem to show up any errors so I'll commit > them shortly. Thanks. > On a similar note, is it safe to simply substitute "use vars" for "our" > and correctly commenting the list of variables if qw() was previously used? Should be. But note that we didn't officially agree on having the Run package require Perl 5.6... Is there a particular person who maintains the Run package, or does that fall to the pumpkin of Core? > If so, there are 340+ "use vars" in the bioperl-run......any wise ideas > on a generic script that can do an intelligent search and replace. > Bearing in mind that these lists can span multiple lines? It'll need a little futzing, just be very careful it is working perfectly before applying it to everything. All of Core and the other packages need the same work done on them... > I set up the following page a couple of days ago to house some scripts > that can be used to do audit checks of code: > http://www.bioperl.org/wiki/Auditing > > If anyone has any scripts, Perl, shell or otherwise fell free to add > them! :-) I created a one-off for the conversion to 'use base', but its a bit of delirium-induced hack. I'll add it when I get the chance; its essentially a more complex version of what you want to do. It also ought to be applied to all the other Bioperl packages... (You should make mention of the existing audit scripts in CVS for bioperl-live in maintenance/) From cjfields at uiuc.edu Mon Nov 6 12:58:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 11:58:27 -0600 Subject: [Bioperl-l] return undef In-Reply-To: <454F691B.3090900@sendu.me.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> <454F691B.3090900@sendu.me.uk> Message-ID: <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> >> On a similar note, is it safe to simply substitute "use vars" for >> "our" >> and correctly commenting the list of variables if qw() was >> previously used? > > Should be. But note that we didn't officially agree on having the Run > package require Perl 5.6... Is there a particular person who maintains > the Run package, or does that fall to the pumpkin of Core? I believe Albert Vilella was taking care of bioperl-run, but I'm not absolutely sure. I think we can assume that, if core rel. 1.5.2 requires perl 5.6.1, anything that requires bioperl rel. 1.5.2 should likewise require perl 5.6.1 as well. Probably should make that explicitly stated somewhere. >> If so, there are 340+ "use vars" in the bioperl-run......any wise >> ideas >> on a generic script that can do an intelligent search and replace. >> Bearing in mind that these lists can span multiple lines? > > It'll need a little futzing, just be very careful it is working > perfectly before applying it to everything. All of Core and the other > packages need the same work done on them... I have gone through a few and manually switched 'use vars' over to 'our'. You can always try making the necessary changes globally but I think you'll see a lot of failed tests. >> I set up the following page a couple of days ago to house some >> scripts >> that can be used to do audit checks of code: >> http://www.bioperl.org/wiki/Auditing >> >> If anyone has any scripts, Perl, shell or otherwise fell free to add >> them! :-) > > I created a one-off for the conversion to 'use base', but its a bit of > delirium-induced hack. I'll add it when I get the chance; its > essentially a more complex version of what you want to do. It also > ought > to be applied to all the other Bioperl packages... > > (You should make mention of the existing audit scripts in CVS for > bioperl-live in maintenance/) Not sure how much more global code auditing should be done before the 1.5.2 final release, but if it passes tests then I don't have a problem. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 6 13:08:38 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 18:08:38 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> <454F691B.3090900@sendu.me.uk> <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> Message-ID: <454F7A26.9090800@sendu.me.uk> Chris Fields wrote: >>> I set up the following page a couple of days ago to house some scripts >>> that can be used to do audit checks of code: >>> http://www.bioperl.org/wiki/Auditing >>> >>> If anyone has any scripts, Perl, shell or otherwise fell free to add >>> them! :-) >> >> I created a one-off for the conversion to 'use base', but its a bit of >> delirium-induced hack. I'll add it when I get the chance; its >> essentially a more complex version of what you want to do. It also ought >> to be applied to all the other Bioperl packages... >> >> (You should make mention of the existing audit scripts in CVS for >> bioperl-live in maintenance/) > > Not sure how much more global code auditing should be done before the > 1.5.2 final release None; I won't add any to the branch (bug fixes and documentation only, for the most part). It is still valuable to do for the next release though! From n.haigh at sheffield.ac.uk Mon Nov 6 15:29:23 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 20:29:23 +0000 Subject: [Bioperl-l] StandAloneFasta::version Message-ID: <454F9B23.8010302@sheffield.ac.uk> Hi Sendu, I've written a version method for StandAloneFasta.pm. However, because of the way in which FASTA is versioned, it makes for difficult version comparisons i.e. they contain non-numeric characters e.g. 3.4t26. I have employed a private function that does a conversion of the non-numeric characters into their ascii value representation to build a float. e.g. the above version would result in: 3.411626 which can then be compared easily. At the moment, this is accessed via $factory->version like other modules as this will give access to a version number that is easily comparable. However, should there be a different function to return the unconverted version string e.g. 3.4t26? Or should there be a function that does a compare internally so it can be accessed something like: print "we have met the min version requirement\n" if $factory->at_least_version('3.4t26'); Ideas welcome! Nath From cjfields at uiuc.edu Mon Nov 6 16:21:10 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 15:21:10 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <454F9B23.8010302@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> Message-ID: <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> Nathan, Weren't the problems with the reported StandAloneFasta.pm test fails due to differences in the returned order of the Hits/HSPs in the FASTA reports from the different versions? The test results you posted on the wiki (where I commented on this) seem to indicate that: not ok 11 # Test 11 got: "0" (t/StandAloneFasta.t at line 75) # Expected: "994" # t/StandAloneFasta.t line 75 is: ok $hsp->num_identical, 994; not ok 12 # Test 12 got: "1977" (t/StandAloneFasta.t at line 76) # Expected: "994" # t/StandAloneFasta.t line 76 is: ok $hsp->length, 994; ok 13 not ok 14 # Test 14 got: "0" (t/StandAloneFasta.t at line 88) # Expected: "994" # t/StandAloneFasta.t line 88 is: ok $hsp->num_identical, 994; not ok 15 # Test 15 got: "1977" (t/StandAloneFasta.t at line 89) # Expected: "994" # t/StandAloneFasta.t line 89 is: ok $hsp->length, 994; It looks like a value is returned for the tests, so parsing isn't broken. They just aren't returned in the order specified, so the tests are faulty, not the parsing. The tests could be fixed by using id/score key/value pairs in a hash or something similar. We probably shouldn't limit to a specific version unless parsing is actually broken. Chris On Nov 6, 2006, at 2:29 PM, Nathan S. Haigh wrote: > Hi Sendu, > > I've written a version method for StandAloneFasta.pm. However, because > of the way in which FASTA is versioned, it makes for difficult version > comparisons i.e. they contain non-numeric characters e.g. 3.4t26. > > I have employed a private function that does a conversion of the > non-numeric characters into their ascii value representation to > build a > float. e.g. the above version would result in: 3.411626 which can then > be compared easily. At the moment, this is accessed via > $factory->version like other modules as this will give access to a > version number that is easily comparable. However, should there be a > different function to return the unconverted version string e.g. > 3.4t26? > Or should there be a function that does a compare internally so it can > be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26'); > > Ideas welcome! > Nath > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From torsten.seemann at infotech.monash.edu.au Mon Nov 6 15:41:24 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Tue, 07 Nov 2006 07:41:24 +1100 Subject: [Bioperl-l] return undef In-Reply-To: <454F607C.5020808@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> Message-ID: <454F9DF4.80702@infotech.monash.edu.au> > I set up the following page a couple of days ago to house some scripts > that can be used to do audit checks of code: > http://www.bioperl.org/wiki/Auditing Your 'grep' patterns should probably have "\s+" rather than " " between keywords as often coders have used multiple spaces or tabs. Your 'die/confess/...' patterns require a "(" after them. I'd say those functions are used without parentheses about half the time, eg. die "ech!"; Explicit "return undef" aren't too hard to find. It's the hidden ones where it's "my $value; ...lots of code...; return $value;" which are hard to identify. -- Torsten Seemann Victorian Bioinformatics Consortium, Monash University, Australia From n.appleby at uq.edu.au Mon Nov 6 21:11:06 2006 From: n.appleby at uq.edu.au (Nikki Appleby) Date: Tue, 7 Nov 2006 12:11:06 +1000 Subject: [Bioperl-l] go-perl error: ')' missing Message-ID: <005d01c70211$fbaf55a0$1b776682@IMBPC.AD> Thanks for being there when things go wrong. I have installed required modules as listed in Chris' instructions, then get stuck on this. C:\Perl\go-perl\go-perl-0.05>perl Makefile.PL The system cannot find the path specified. NOTICE: ** You do not have xsltproc ** This tool is not required for go-perl, but it is useful for for certain kinds of format conversion (eg converting to OWL format). You will also need this tool if you are installing go-db-perl You can safely ignore this notification message; Even if you do intend to use go-db-perl later, you can install xsltproc at a later date xsltproc is available as part of libxslt. See http://xmlsoft.org/XSLT/ for details Writing Makefile for GO C:\Perl\go-perl\go-perl-0.05>nmake Microsoft (R) Program Maintenance Utility Version 1.50 Copyright (c) Microsoft Corp 1988-94. All rights reserved. makefile(1706) : fatal error U1000: syntax error : ')' missing in macro invocati on Stop. Nikki Appleby. 07 334 62634 From n.haigh at sheffield.ac.uk Tue Nov 7 02:05:40 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 07 Nov 2006 07:05:40 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> Message-ID: <45503044.30000@sheffield.ac.uk> Chris Fields wrote: > Nathan, > > Weren't the problems with the reported StandAloneFasta.pm test fails > due to differences in the returned order of the Hits/HSPs in the FASTA > reports from the different versions? The test results you posted on > the wiki (where I commented on this) seem to indicate that: > > not ok 11 > # Test 11 got: "0" (t/StandAloneFasta.t at line 75) > # Expected: "994" > # t/StandAloneFasta.t line 75 is: ok $hsp->num_identical, 994; > not ok 12 > # Test 12 got: "1977" (t/StandAloneFasta.t at line 76) > # Expected: "994" > # t/StandAloneFasta.t line 76 is: ok $hsp->length, 994; > ok 13 > not ok 14 > # Test 14 got: "0" (t/StandAloneFasta.t at line 88) > # Expected: "994" > # t/StandAloneFasta.t line 88 is: ok $hsp->num_identical, 994; > not ok 15 > # Test 15 got: "1977" (t/StandAloneFasta.t at line 89) > # Expected: "994" > # t/StandAloneFasta.t line 89 is: ok $hsp->length, 994; > > It looks like a value is returned for the tests, so parsing isn't > broken. They just aren't returned in the order specified, so the > tests are faulty, not the parsing. The tests could be fixed by using > id/score key/value pairs in a hash or something similar. We probably > shouldn't limit to a specific version unless parsing is actually broken. > > Chris > Chris, I agree, I was going to update the tests later this morning :-P Any thoughts about version() or should I just leave it be for now? Cheers Nath From bix at sendu.me.uk Tue Nov 7 04:15:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 09:15:41 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45503044.30000@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> Message-ID: <45504EBD.2000708@sendu.me.uk> Nathan S. Haigh wrote: > I agree, I was going to update the tests later this morning :-P Any > thoughts about version() or should I just leave it be for now? If its no trouble, go ahead with a version() method. Its nice to have in any case. I'd suggest your latter option of 'there be a function that does a compare internally so it can be accessed something like: print "we have met the min version requirement\n" if $factory->at_least_version('3.4t26');' In fact, it ought to work with '34t26b3' as well (I guess the method would try what it was given, and on failure, try again with the last 2 characters removed, then try both cases again with a decimal added if there wasn't one). From n.haigh at sheffield.ac.uk Tue Nov 7 04:50:52 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 07 Nov 2006 09:50:52 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45504EBD.2000708@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> Message-ID: <455056FC.90608@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> I agree, I was going to update the tests later this morning :-P Any >> thoughts about version() or should I just leave it be for now? > > If its no trouble, go ahead with a version() method. Its nice to have > in any case. I'd suggest your latter option of 'there be a function > that does a compare internally so it can be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26');' > In fact, it ought to work with '34t26b3' as well (I guess the method > would try what it was given, and on failure, try again with the last 2 > characters removed, then try both cases again with a decimal added if > there wasn't one). I've contacted Bill Pearson to clarify his versioning scheme. Ideally, we could do as you say, compare variants of '34t26b3'. However, the software doesn't report the b3 part of the version string only 3.4t26 followed by a date. Therefore, I'm not sure it's possible to distinguish between 3.4t26b1 and 3.4t26b3 - unless we consider the date also returned by the software :-( . Bill said he is currently busy with a course at Cold Spring Harbor but will respond in full later. Therefore, until he's informed me of how he versions his releases, I'll hold off with the version() method for the time being. Nath From cjfields at uiuc.edu Tue Nov 7 10:58:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 09:58:48 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45504EBD.2000708@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> Message-ID: <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> On Nov 7, 2006, at 3:15 AM, Sendu Bala wrote: > Nathan S. Haigh wrote: >> I agree, I was going to update the tests later this morning :-P Any >> thoughts about version() or should I just leave it be for now? > > If its no trouble, go ahead with a version() method. Its nice to > have in > any case. I'd suggest your latter option of 'there be a function that > does a compare internally so it can be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26');' > In fact, it ought to work with '34t26b3' as well (I guess the method > would try what it was given, and on failure, try again with the last 2 > characters removed, then try both cases again with a decimal added if > there wasn't one). Is it possible to have the interface base class contain an abstract program_version() (or similar) method? One that could be implemented to just grab the current version of the program? I was thinking about something like this for the RNA-based wrappers I want to add but it seems to be something that most Run modules would benefit from. Just haven't had time to look into it with much detail. Almost wonder if it would be easier to have all bioperl-run modules have a Run-specific Root object for common methods, regardless of the other interfaces used. Maybe something inheriting Bio::Root::Root... chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Nov 7 11:54:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 10:54:48 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550AF3B.8000807@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> Message-ID: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: ... >> Is it possible to have the interface base class contain an >> abstract program_version() (or similar) method? One that could be >> implemented to just grab the current version of the program? I >> was thinking about something like this for the RNA-based wrappers >> I want to add but it seems to be something that most Run modules >> would benefit from. Just haven't had time to look into it with >> much detail. > > What's wrong with version() ? Didn't realize there was a version() already. >> Almost wonder if it would be easier to have all bioperl-run >> modules have a Run-specific Root object for common methods, >> regardless of the other interfaces used. Maybe something >> inheriting Bio::Root::Root... > > What's wrong with Bio::Tools::Run::WrapperBase ? I agree that WrapperBase fulfills most of this functionality. However, don't a few bioperl-run wrappers 'roll their own', i.e. not implement WrapperBase? Requiring all bioperl-run module inherit the same Run-specific base object would integrate them a bit more and distinguish them from the core modules (which would inherit Bio::Root::Root). Anyway, it's just a suggestion. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Tue Nov 7 10:54:06 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 07 Nov 2006 10:54:06 -0500 Subject: [Bioperl-l] Bio::SeqIO::gcg bug Message-ID: <4550AC1E.2070500@bms.com> Bio::SeqIO::gcg is checking the checksum against the GCG generated one. There is a problem with the way this is done: 1. Bio::SeqIO::gcg removes all characters, except [A-Za-z] (which by the way is always wrong). 2. GCG calculates the checksum on uppercase I assume Hilmar removed the $_ = uc($_); line for a very good reason, but the call to validate should be: _validate_checksum(uc($sequence),$chksum)) Also I believe the regexp for checking the alphabet should remove explicitly numbers and whitespaces. Removing everything else is not a good idea because gaps, end of translation are removed also and possible parsing errors might be suppressed incorrectly. Let me know if I am missing some other considerations here. If not I will commit these changes. Stefan From bix at sendu.me.uk Tue Nov 7 12:25:22 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 17:25:22 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> Message-ID: <4550C182.3000308@sendu.me.uk> Chris Fields wrote: > > On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: > >>> Almost wonder if it would be easier to have all bioperl-run modules >>> have a Run-specific Root object for common methods, regardless of the >>> other interfaces used. Maybe something inheriting Bio::Root::Root... >> >> What's wrong with Bio::Tools::Run::WrapperBase ? > > I agree that WrapperBase fulfills most of this functionality. However, > don't a few bioperl-run wrappers 'roll their own', i.e. not implement > WrapperBase? Requiring all bioperl-run module inherit the same > Run-specific base object would integrate them a bit more and distinguish > them from the core modules (which would inherit Bio::Root::Root). > Anyway, it's just a suggestion. Well, how would you 'require' them to use anything at all? There's not even anything 'requiring' that a core module inherit from Bio::Root::Root(I). We just (very strongly) advise that you inherit from there. So we can also advise that bioperl-run wrappers do not roll their own but use Bio::Tools::Run::WrapperBase. From cjfields at uiuc.edu Tue Nov 7 12:40:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 11:40:32 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C182.3000308@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> Message-ID: <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> > Well, how would you 'require' them to use anything at all? There's not > even anything 'requiring' that a core module inherit from > Bio::Root::Root(I). We just (very strongly) advise that you inherit > from > there. So we can also advise that bioperl-run wrappers do not roll > their > own but use Bio::Tools::Run::WrapperBase. Like I said, it's a suggestion. No need to get snippy. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Tue Nov 7 11:07:23 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 16:07:23 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> Message-ID: <4550AF3B.8000807@sendu.me.uk> Chris Fields wrote: > > On Nov 7, 2006, at 3:15 AM, Sendu Bala wrote: > >> Nathan S. Haigh wrote: >>> I agree, I was going to update the tests later this morning :-P Any >>> thoughts about version() or should I just leave it be for now? >> >> If its no trouble, go ahead with a version() method. Its nice to have in >> any case. I'd suggest your latter option of 'there be a function that >> does a compare internally so it can be accessed something like: >> print "we have met the min version requirement\n" if >> $factory->at_least_version('3.4t26');' >> In fact, it ought to work with '34t26b3' as well (I guess the method >> would try what it was given, and on failure, try again with the last 2 >> characters removed, then try both cases again with a decimal added if >> there wasn't one). > > Is it possible to have the interface base class contain an abstract > program_version() (or similar) method? One that could be implemented to > just grab the current version of the program? I was thinking about > something like this for the RNA-based wrappers I want to add but it > seems to be something that most Run modules would benefit from. Just > haven't had time to look into it with much detail. What's wrong with version() ? > Almost wonder if it would be easier to have all bioperl-run modules have > a Run-specific Root object for common methods, regardless of the other > interfaces used. Maybe something inheriting Bio::Root::Root... What's wrong with Bio::Tools::Run::WrapperBase ? From n.haigh at sheffield.ac.uk Tue Nov 7 12:48:56 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 07 Nov 2006 17:48:56 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> Message-ID: <4550C708.5060209@sheffield.ac.uk> Chris Fields wrote: > On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: > ... > > >>> Is it possible to have the interface base class contain an >>> abstract program_version() (or similar) method? One that could be >>> implemented to just grab the current version of the program? I >>> was thinking about something like this for the RNA-based wrappers >>> I want to add but it seems to be something that most Run modules >>> would benefit from. Just haven't had time to look into it with >>> much detail. >>> >> What's wrong with version() ? >> > > Didn't realize there was a version() already. > > >>> Almost wonder if it would be easier to have all bioperl-run >>> modules have a Run-specific Root object for common methods, >>> regardless of the other interfaces used. Maybe something >>> inheriting Bio::Root::Root... >>> >> What's wrong with Bio::Tools::Run::WrapperBase ? >> > > I agree that WrapperBase fulfills most of this functionality. > However, don't a few bioperl-run wrappers 'roll their own', i.e. not > implement WrapperBase? Requiring all bioperl-run module inherit the > same Run-specific base object would integrate them a bit more and > distinguish them from the core modules (which would inherit > Bio::Root::Root). Anyway, it's just a suggestion. > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > >From what i've seen of Bioperl-run there is not a whole lot of consistency between modules. I think it would be a good idea to have all run modules inherit WrapperBase - would this be a big change?? Nath From bix at sendu.me.uk Tue Nov 7 12:49:09 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 17:49:09 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> Message-ID: <4550C715.5090608@sendu.me.uk> Chris Fields wrote: >> Well, how would you 'require' them to use anything at all? There's not >> even anything 'requiring' that a core module inherit from >> Bio::Root::Root(I). We just (very strongly) advise that you inherit from >> there. So we can also advise that bioperl-run wrappers do not roll their >> own but use Bio::Tools::Run::WrapperBase. > > Like I said, it's a suggestion. No need to get snippy. You took that completely the wrong way. I am applying absolutely no value judgment on your suggestion. It may be an excellent one. I was simply explaining we have no programmatic way of requiring that modules use other modules - we rely on people following the advice/ status quo. Given that, are you still suggesting that it would be better to advise people to use Bio::Root::SomeNewRunThing, or is Bio::Tools::Run::WrapperBase satisfactory? From hlapp at gmx.net Tue Nov 7 12:55:12 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 7 Nov 2006 12:55:12 -0500 Subject: [Bioperl-l] Bio::SeqIO::gcg bug In-Reply-To: <4550AC1E.2070500@bms.com> References: <4550AC1E.2070500@bms.com> Message-ID: On Nov 7, 2006, at 10:54 AM, Stefan Kirov wrote: > I assume Hilmar removed the $_ = uc($_); line for a very good reason, > but the call to validate should be: > _validate_checksum(uc($sequence),$chksum)) I agree. The case of the sequence letters should remain untouched though for other purposes. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Tue Nov 7 12:55:22 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 11:55:22 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C708.5060209@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C708.5060209@sheffield.ac.uk> Message-ID: <8132EB4F-2FE0-4A46-A96D-E406CCB0F047@uiuc.edu> On Nov 7, 2006, at 11:48 AM, Nathan Haigh wrote: ... > From what i've seen of Bioperl-run there is not a whole lot of > consistency between modules. I think it would be a good idea to > have all > run modules inherit WrapperBase - would this be a big change?? > > Nath We really have no idea how many wrappers don't implement WrapperBase at the moment; until then we don't know how much work it would take. This might be a job for a maintenance script... Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From natalia.grabar at club-internet.fr Tue Nov 7 12:48:53 2006 From: natalia.grabar at club-internet.fr (natalia.grabar at club-internet.fr) Date: Tue, 7 Nov 2006 18:48:53 +0100 Subject: [Bioperl-l] perl conference in Paris Message-ID: hi all, are you fine? next 25 & 26 November there will be a Perl conference in Paris http://conferences.mongueurs.net/fpw2006/ I wonder if it would be possible to have a presentation (tutorial?) of the bioperl package during this conference. thanks have a nice day natalia From cjfields at uiuc.edu Tue Nov 7 14:49:47 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 13:49:47 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C715.5090608@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> <4550C715.5090608@sendu.me.uk> Message-ID: <4AC53CE6-20EC-4841-A28C-E083823F8487@uiuc.edu> On Nov 7, 2006, at 11:49 AM, Sendu Bala wrote: >> Like I said, it's a suggestion. No need to get snippy. > > You took that completely the wrong way. I am applying absolutely no > value judgment on your suggestion. It may be an excellent one. I > was simply explaining we have no programmatic way of requiring that > modules use other modules - we rely on people following the advice/ > status quo. There may not be a programmatic way of enforcing one to use WrapperBase or other base classes beyond using maintenance scripts. However, if we as a community agree on following a basic set of bioperl coding standards (Best Practices, using Bio::Root::Root/ RootI, POD, etc), then anyone should reasonably expect that their code may be changed to conform more with those standards, at least within reason. We recently enforced this with Bio::Root::Root/RootI, 'return undef', 'use base', and others, so I don't see the problem with doing so here. There will always be some controversial or grey areas (use of AUTOLOAD comes to mind), but in my opinion it is very reasonable to require that new modules use a particular base class or implement a specific interface if the new code is expected to interact properly with other BioPerl classes/objects. One could always use the mail list to express their opinions if they disagree or want some clarification or guidance. Sorry, Election Day in the States. Lots of snippiness around on this end (overdosed of negative ads)! > Given that, are you still suggesting that it would be better to > advise people to use Bio::Root::SomeNewRunThing, or is > Bio::Tools::Run::WrapperBase satisfactory? Either way will work, but.... I was thinking of something like this: Run-based |---WrapperBase Root class---| |---Non-WrapperBase (web apps and others) Bio::Root::Root works in this capacity already, but I was thinking of a base class unique to bioperl-run classes which could integrate similar methods from WrapperBase and non-WrapperBase'd modules. I suppose we could also have it as a simple interface; modules which implement it could be distinguished from core if needed. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Tue Nov 7 14:58:10 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 7 Nov 2006 11:58:10 -0800 Subject: [Bioperl-l] (no subject) Message-ID: Lincoln - I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql which call $sth->finish in the offset_boundary call and the fetch_sequence method as my code which does GFF3 -> CDS dumping was getting lots of " statement handle DBI::st=HASH(0x189bf8c) still Active at" Changes are here: http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/Bio/DB/ SeqFeature/Store/DBI/mysql.pm.diff?r1=1.25&r2=1.26 These changes should be migrated to the branch before the release if all is okay. Please let me know. -jason From jason at bioperl.org Tue Nov 7 13:27:27 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 7 Nov 2006 10:27:27 -0800 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C708.5060209@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C708.5060209@sheffield.ac.uk> Message-ID: <4A984083-23FA-42F6-8C73-901FD87DB5F6@bioperl.org> i think it is important - we just have not had a dedicated developer who enforced these requirements by auditing the code. I had tried to establish a standard through WrapperBase but some contributions ignored this and some modules had grown up before the wrapperbase was in place. I also think the ontology of applications is a bit screwed up so people were putting modules in directories willy-nilly. I think bioperl-run is even more cat-herding than the other aspects of the project because applications change and there are very many combinations of parameters and version of applications. There was a flurry of contributions and no good way to marshall them initially. So what to do - I guess make do with how it is but not rename anything at this point but try and standardize things - it will depend on your desire to really take this on. The PISE modules may need to be re-evaluated to insure they are still working - there was hope that some of them could be simplified through some automated class generation from the XML they are based on, but that was never developed. We will try and a have an open-bio linux server available as a platform where we can have a consistent testing environment but I am not sure if we want this to represent every possible version of apps or just the most recent. -jason On Nov 7, 2006, at 9:48 AM, Nathan Haigh wrote: > Chris Fields wrote: >> On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: >> ... >> >> >>>> Is it possible to have the interface base class contain an >>>> abstract program_version() (or similar) method? One that could be >>>> implemented to just grab the current version of the program? I >>>> was thinking about something like this for the RNA-based wrappers >>>> I want to add but it seems to be something that most Run modules >>>> would benefit from. Just haven't had time to look into it with >>>> much detail. >>>> >>> What's wrong with version() ? >>> >> >> Didn't realize there was a version() already. >> >> >>>> Almost wonder if it would be easier to have all bioperl-run >>>> modules have a Run-specific Root object for common methods, >>>> regardless of the other interfaces used. Maybe something >>>> inheriting Bio::Root::Root... >>>> >>> What's wrong with Bio::Tools::Run::WrapperBase ? >>> >> >> I agree that WrapperBase fulfills most of this functionality. >> However, don't a few bioperl-run wrappers 'roll their own', i.e. not >> implement WrapperBase? Requiring all bioperl-run module inherit the >> same Run-specific base object would integrate them a bit more and >> distinguish them from the core modules (which would inherit >> Bio::Root::Root). Anyway, it's just a suggestion. >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> From what i've seen of Bioperl-run there is not a whole lot of > consistency between modules. I think it would be a good idea to > have all > run modules inherit WrapperBase - would this be a big change?? > > Nath > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Wed Nov 8 05:24:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 08 Nov 2006 10:24:41 +0000 Subject: [Bioperl-l] (no subject) Message-ID: <4551B069.6060305@sendu.me.uk> [forwarded on behalf of Dave Howorth] Jason Stajich wrote: > Lincoln - > I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql > which call $sth->finish in the offset_boundary call and the > fetch_sequence method as my code which does GFF3 -> CDS dumping was > getting lots of " statement handle DBI::st=HASH(0x189bf8c) still > Active at" What version of DBD::mysql are you using? It sounds like this: http://rt.cpan.org/Public/Bug/Display.html?id=20464 Cheers, Dave From bix at sendu.me.uk Wed Nov 8 06:12:12 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 08 Nov 2006 11:12:12 +0000 Subject: [Bioperl-l] Bioperl versioning In-Reply-To: <6dce9a0b0610311224x79256b29sf102eb5c35865caf@mail.gmail.com> References: <453E309B.9090007@sendu.me.uk> <000001c6f78b$d1c65a30$15327e82@pyrimidine> <6dce9a0b0610311224x79256b29sf102eb5c35865caf@mail.gmail.com> Message-ID: <4551BB8C.5040606@sendu.me.uk> Lincoln Stein wrote: > Are you going to go ahead with 1.52_XX ? If so, I will code GBrowse to > look for 1.52 or higher. You should do the equivalent of use Bio::Root::Version 1.5.2; Eg. unless (eval{"require $Bio::Root::Version;" || ${Bio::Root::Version::VERSION'} < 1.005002) { #complain } Since most core modules get their version from Bio::Root::Version, you could also check the core module you're actually using in GBrowse, instead of asking Bio::Root::Version itself. So, if you do actually need to use Bio::Whatever in your module, the best thing to do is say: use Bio::Whatever 1.5.2; From jason at bioperl.org Wed Nov 8 10:56:55 2006 From: jason at bioperl.org (Jason Stajich) Date: Wed, 8 Nov 2006 07:56:55 -0800 Subject: [Bioperl-l] (no subject) In-Reply-To: <4551B069.6060305@sendu.me.uk> References: <4551B069.6060305@sendu.me.uk> Message-ID: <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> sounds like it. I am running 3.0006 The added sth->finish did take care of it for now since I assume a fair number of people are stuck with these vers? On Nov 8, 2006, at 2:24 AM, Sendu Bala wrote: > [forwarded on behalf of Dave Howorth] > > > Jason Stajich wrote: >> Lincoln - >> I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql >> which call $sth->finish in the offset_boundary call and the >> fetch_sequence method as my code which does GFF3 -> CDS dumping was >> getting lots of " statement handle DBI::st=HASH(0x189bf8c) still >> Active at" > > What version of DBD::mysql are you using? It sounds like this: > > http://rt.cpan.org/Public/Bug/Display.html?id=20464 > > Cheers, Dave > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California Dept of Plant and Microbial Biology 321 Koshland Hall #3102 Berkeley, CA 94720-3102 lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From dhoworth at mrc-lmb.cam.ac.uk Wed Nov 8 11:16:05 2006 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Wed, 08 Nov 2006 16:16:05 +0000 Subject: [Bioperl-l] (no subject) In-Reply-To: <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> References: <4551B069.6060305@sendu.me.uk> <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> Message-ID: <455202C5.9060609@mrc-lmb.cam.ac.uk> Jason Stajich wrote: > sounds like it. > > I am running 3.0006 > > The added sth->finish did take care of it for now since I assume a fair > number of people are stuck with these vers? Well, the current version on CPAN is fixed and the bug breaks lots of applications so upgrading DBD::mysql is a better cure. Or even downgrading to the one before it broke :) Cheers, Dave From bix at sendu.me.uk Thu Nov 9 05:28:34 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 10:28:34 +0000 Subject: [Bioperl-l] bptutorial.pl 0 In-Reply-To: <000601c6fc4a$c3e43450$15327e82@pyrimidine> References: <000601c6fc4a$c3e43450$15327e82@pyrimidine> Message-ID: <455302D2.1000901@sendu.me.uk> Chris Fields wrote: > What version of Bioperl are you running? > > As a warning, the bptutorial.pl script has been removed from CVS and will > not be included in future versions of Bioperl. It can be found on the > bioperl wiki instead: > > http://www.bioperl.org/wiki/Bptutorial It hasn't been removed, but should it be? AFAIK there was still a request from at least one person to keep it. But is it still out of date wrt the wiki version? From bix at sendu.me.uk Thu Nov 9 05:31:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 10:31:16 +0000 Subject: [Bioperl-l] bptutorial.pl 0 In-Reply-To: <455302D2.1000901@sendu.me.uk> References: <000601c6fc4a$c3e43450$15327e82@pyrimidine> <455302D2.1000901@sendu.me.uk> Message-ID: <45530374.1010001@sendu.me.uk> Sendu Bala wrote: > Chris Fields wrote: >> What version of Bioperl are you running? >> As a warning, the bptutorial.pl script has been removed from CVS and will >> not be included in future versions of Bioperl. It can be found on the >> bioperl wiki instead: >> >> http://www.bioperl.org/wiki/Bptutorial > > It hasn't been removed, but should it be? AFAIK there was still a > request from at least one person to keep it. But is it still out of date > wrt the wiki version? Scratch that, it was still in the 1.5.2 branch but I've removed it. From bix at sendu.me.uk Thu Nov 9 07:04:56 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 12:04:56 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 Message-ID: <45531968.6080607@sendu.me.uk> Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. See http://www.bioperl.org/wiki/Release_1.5.2 for instructions on getting and testing this RC. Developers: Once again I'm hopeful that this is the last RC. If all goes well expect final release in about a weeks time. Please check and update documentation. Users: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into. Thank you, Sendu. From avilella at gmail.com Thu Nov 9 07:15:20 2006 From: avilella at gmail.com (Albert Vilella) Date: Thu, 9 Nov 2006 12:15:20 +0000 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln Message-ID: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> Hi, I am musing on how to add trees to the AlignIO::Nexus objects. In PAML we have this "add_tree" method, and "get_rst_trees", which we could also apply to this case. I also would like to hear some feedback on how to write_aln nexus files that contain one or more trees in the object instance. Do we want this by default? Only if a "with_trees" parameter is set? Cheers, Albert. From n.haigh at sheffield.ac.uk Thu Nov 9 08:55:59 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Thu, 09 Nov 2006 13:55:59 +0000 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> Message-ID: <4553336F.2000000@sheffield.ac.uk> Albert Vilella wrote: > Hi, > > I am musing on how to add trees to the AlignIO::Nexus objects. > > In PAML we have this "add_tree" method, and "get_rst_trees", which we > could also apply to this case. > > I also would like to hear some feedback on how to write_aln nexus > files that contain one or more trees in the object instance. Do we > want this by default? Only if a "with_trees" parameter is set? > > Cheers, > > Albert. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > Hi Albert, I don't know if you are aware of this resource, so here it is: http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all I would suggest that if there are trees in the object instance, then write_aln should print them by default and then have a "no_trees" option. Nath From cjfields at uiuc.edu Thu Nov 9 09:13:09 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 08:13:09 -0600 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <4553336F.2000000@sheffield.ac.uk> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> <4553336F.2000000@sheffield.ac.uk> Message-ID: <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> On Nov 9, 2006, at 7:55 AM, Nathan Haigh wrote: > Albert Vilella wrote: >> Hi, >> >> I am musing on how to add trees to the AlignIO::Nexus objects. >> >> In PAML we have this "add_tree" method, and "get_rst_trees", which we >> could also apply to this case. >> >> I also would like to hear some feedback on how to write_aln nexus >> files that contain one or more trees in the object instance. Do we >> want this by default? Only if a "with_trees" parameter is set? >> >> Cheers, >> >> Albert. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > Hi Albert, > > I don't know if you are aware of this resource, so here it is: > http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all > > I would suggest that if there are trees in the object instance, then > write_aln should print them by default and then have a "no_trees" > option. > > Nath Another option is to store them in the SimpleAlign object as a queue of Tree objects. Stockholm format allows trees in the annotation section, so it makes sense that if some alignments contain this data then we should have a way of parsing and storing it, as long as we read/write support the particular tree format. Something like: my $aln = $alnin->next_aln(); # iterate... while (my $tree = $aln->next_tree()) { ... } # or SimpleAlign-like for my $tree ($aln->each_tree()) { ... } # all trees @trees = $aln->each_tree(); etc. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 9 10:28:45 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 09:28:45 -0600 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> <4553336F.2000000@sheffield.ac.uk> <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> Message-ID: <112C051C-0868-4933-A1CE-87E773B7FD05@uiuc.edu> On Nov 9, 2006, at 8:13 AM, Chris Fields wrote: > On Nov 9, 2006, at 7:55 AM, Nathan Haigh wrote: > >> Albert Vilella wrote: >>> Hi, >>> >>> I am musing on how to add trees to the AlignIO::Nexus objects. >>> >>> In PAML we have this "add_tree" method, and "get_rst_trees", >>> which we >>> could also apply to this case. >>> >>> I also would like to hear some feedback on how to write_aln nexus >>> files that contain one or more trees in the object instance. Do we >>> want this by default? Only if a "with_trees" parameter is set? >>> >>> Cheers, >>> >>> Albert. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> Hi Albert, >> >> I don't know if you are aware of this resource, so here it is: >> http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all >> >> I would suggest that if there are trees in the object instance, then >> write_aln should print them by default and then have a "no_trees" >> option. >> >> Nath > > Another option is to store them in the SimpleAlign object as a queue > of Tree objects. Stockholm format allows trees in the annotation > section, so it makes sense that if some alignments contain this data > then we should have a way of parsing and storing it, as long as we > read/write support the particular tree format. .... Forgot to mention the option of using a builder object, analogous to the one used for Bio::SeqIO::genbank (Bio::Seq::SeqBuilder); this would be similar to Nathan's suggestion but would tell the parser what data you want parsed (alignment annotation, tree data, sequences, accession/id, etc) based on 'slots' and particular conditions, and therefore determines what data is stored in SimpleAlign objects. I planned on setting one up for Bio::AlignIO::stockholm in the near future for optional annotation parsing, but tree parsing could be included as well. Were you thinking of something along those lines? Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bernd.web at gmail.com Thu Nov 9 18:07:48 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 10 Nov 2006 00:07:48 +0100 Subject: [Bioperl-l] Blast Writer Message-ID: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> Hi, I am using Bio::SearchIO and Bio::SearchIO::Writer::HTMLResultWriter and its filter, as my $writer = new Bio::SearchIO::Writer::HTMLResultWriter(); $writer->filter('hsp', \&hsp_filter); Can I change the contents of the HSP objects (apart from true/false filtering)? I would like to change some HSP values. Would it be possible to do so with HTMLResultWriter's filters? And if so, how to access the Hit/HSP objects in the filter? I'd be grateful for any suggestions. Best regards, Bernd From jason at bioperl.org Thu Nov 9 18:21:34 2006 From: jason at bioperl.org (Jason Stajich) Date: Thu, 9 Nov 2006 15:21:34 -0800 Subject: [Bioperl-l] Blast Writer In-Reply-To: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> References: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> Message-ID: <15C2FE1E-F0C8-43DD-96E7-FADA3421AA82@bioperl.org> You can always do this before you pass the Result object to the writer. The for loop will pass back the actual hit or hsp objects and so any updates should be stored. for my $hit ( $result->hits ) { for my $hsp ( $hit->hsps ) { # change the HSP } } -jason On Nov 9, 2006, at 3:07 PM, Bernd Web wrote: > Hi, > > I am using Bio::SearchIO and Bio::SearchIO::Writer::HTMLResultWriter > and its filter, as > my $writer = new Bio::SearchIO::Writer::HTMLResultWriter(); > $writer->filter('hsp', \&hsp_filter); > > Can I change the contents of the HSP objects (apart from true/ > false filtering)? > I would like to change some HSP values. Would it be possible to do so > with HTMLResultWriter's filters? And if so, how to access the Hit/HSP > objects in the filter? > > I'd be grateful for any suggestions. > > Best regards, > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California Dept of Plant and Microbial Biology 321 Koshland Hall #3102 Berkeley, CA 94720-3102 lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From James.Rose at UCHSC.edu Thu Nov 9 17:56:00 2006 From: James.Rose at UCHSC.edu (James.Rose at UCHSC.edu) Date: Thu, 9 Nov 2006 15:56:00 -0700 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI Message-ID: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Hi- apologies if this subject has been addressed before, but I can't seem to find a way to search prior threads short of downloading the entire archives. I'm trying to use Bioperl to do something I thought would be fairly simple: Ingredients: one file containing a list of GI numbers for various proteins 1) Read GI number from file. 2) run a remote tblastn search against the sequenced Spermophilus tridecemlineatus genome with the GI number as query. 3) save resultant BLAST file to disk for later parsing. As it stands, several hours of browsing and scripting has failed to turn up anything that might be useful in this regard. Any advice is very much appreciated. Thanks, James From ak at ebi.ac.uk Thu Nov 9 19:01:55 2006 From: ak at ebi.ac.uk (Andreas Kahari) Date: Fri, 10 Nov 2006 00:01:55 +0000 Subject: [Bioperl-l] Archive searching (was Re: Remote tblastn against a sequenced genome at NCBI) In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: <20061110000155.GA27524@ebi.ac.uk> On Thu, Nov 09, 2006 at 03:56:00PM -0700, James.Rose at UCHSC.edu wrote: > > > Hi- apologies if this subject has been addressed before, but I can't > seem to find a way to search prior threads short of downloading the > entire archives. [cut] See here: http://www.bioperl.org/wiki/Mailing_lists -- Andreas K?h?ri :: Ensembl Software Developer European Bioinformatics Institute (EMBL-EBI) -------------------------------------------- contentsofsignaturemightsettleduringtransfer From cjfields at uiuc.edu Thu Nov 9 19:46:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 18:46:35 -0600 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: <43D47332-B9A9-4D01-87FD-433D86B68853@uiuc.edu> > Hi- apologies if this subject has been addressed before, but I > can't seem to find a way to search prior threads short of > downloading the entire archives. I'm trying to use Bioperl to do > something I thought would be fairly simple: > > Ingredients: one file containing a list of GI numbers for various > proteins > > 1) Read GI number from file. > 2) run a remote tblastn search against the sequenced Spermophilus > tridecemlineatus genome with the GI number as query. > 3) save resultant BLAST file to disk for later parsing. > > As it stands, several hours of browsing and scripting has failed to > turn up anything that might be useful in this regard. > > Any advice is very much appreciated. > > Thanks, > > James NCBI has a little-known (but very useful) list of databases available for remote BLAST searches: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastdblist.html If you replace the database parameter with the exact string listed under the table, then it should work. 'Trace/ Spermophilus_tridecemlineatus_WGS' for the WGS sequences is probably what you want. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 9 19:49:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 18:49:24 -0600 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: On Nov 9, 2006, at 4:56 PM, wrote: > > > Hi- apologies if this subject has been addressed before, but I > can't seem to find a way to search prior threads short of > downloading the entire archives. I'm trying to use Bioperl to do > something I thought would be fairly simple: > > Ingredients: one file containing a list of GI numbers for various > proteins > > 1) Read GI number from file. > 2) run a remote tblastn search against the sequenced Spermophilus > tridecemlineatus genome with the GI number as query. > 3) save resultant BLAST file to disk for later parsing. > > As it stands, several hours of browsing and scripting has failed to > turn up anything that might be useful in this regard. > > Any advice is very much appreciated. > > Thanks, > > James Oops, sent you an old page. Here's the more up-to-date one: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/ remote_accessible_blastdblist.html Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sayali_salodkar at persistent.co.in Fri Nov 10 00:10:35 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Fri, 10 Nov 2006 10:40:35 +0530 Subject: [Bioperl-l] Bioperl parser for PolyPhred? Message-ID: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> Hi, I want to parse the output of polyphred http://droog.gs.washington.edu/PolyPhred.html. Is there a parser already available in Bioperl which would help me in doing the same. Thanks, Sayali DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From bix at sendu.me.uk Fri Nov 10 05:15:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 10:15:41 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) Message-ID: <4554514D.2020001@sendu.me.uk> Hi all, Since I'm seeing inadequacies with the current Makefile.PL scripts we have, I'm thinking of converting from ExtUtils::MakeMaker and the Makefile.PL scripts to Module::Build Build.PL scripts. The advantages this will bring would be creation and installation of documentation, sane handling of required and optional dependencies, and hopefully good META.yml output, for CPAN compatibility wrt version numbers. I'll be able to use Module::Build::Compat to automatically generate Makefile.PL scripts in 'passthrough' style (if an end-user tries to use Makefile.PL without having Module::Build installed, it will offer to install Module::Build for them) when it comes time to make distributions, but Makefile.PL would no longer be in CVS. One thing I'm not clear on with the current situation is what is supposed to happen when the user chooses to install scripts. Where are they supposed to get installed to, and where do end-users normally run them from and how? How does this compare to expectations from other perl module distributions that have installable scripts? Please comment and discuss, but I'd like to get this done for the 1.5.2 release so that the CPAN distribution will be happy. From Derek.Fairley at bll.n-i.nhs.uk Fri Nov 10 05:15:52 2006 From: Derek.Fairley at bll.n-i.nhs.uk (Fairley, Derek) Date: Fri, 10 Nov 2006 10:15:52 -0000 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: James, Try the nabble.com mirror of this forum for easy searching of prior threads: http://www.nabble.com/BioPerl-f13596.html Derek. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of James.Rose at UCHSC.edu Sent: 09 November 2006 22:56 To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI Hi- apologies if this subject has been addressed before, but I can't seem to find a way to search prior threads short of downloading the entire archives. I'm trying to use Bioperl to do something I thought would be fairly simple: Ingredients: one file containing a list of GI numbers for various proteins 1) Read GI number from file. 2) run a remote tblastn search against the sequenced Spermophilus tridecemlineatus genome with the GI number as query. 3) save resultant BLAST file to disk for later parsing. As it stands, several hours of browsing and scripting has failed to turn up anything that might be useful in this regard. Any advice is very much appreciated. Thanks, James _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Fri Nov 10 07:31:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 12:31:29 +0000 Subject: [Bioperl-l] Distribution files, versions Message-ID: <45547121.6040904@sendu.me.uk> Does anyone know what the following files are supposed to do and if they still used/needed? bioperl.lisp maintenance/symlink_scripts.pl maintenance/symlink_scripts.PLS doc/makedoc.PL scripts/install_bioperl_scripts.pl Most modules in the distribution take their version from Bio::Root::Version, but some do not. Is there some reason they must keep the version they currently have, or can they be made like the others? These are the modules that seem to define their own version (based on a quick grep): Bio/DB/NCBIHelper.pm Bio/DB/Expression/geo.pm Bio/DB/EUtilities/elink.pm Bio/SeqIO/tinyseq.pm Bio/Graphics/Glyph/cds.pm Bio/Graphics/Glyph/translation.pm Bio/Graphics/Glyph/so_transcript.pm Bio/Index/Blast.pm Bio/Index/Hmmer.pm Bio/Tools/WebBlat.pm Bio/Tools/HMM.pm Bio/Tools/dpAlign.pm From JK at novozymes.com Fri Nov 10 07:41:19 2006 From: JK at novozymes.com (JK (Jesper Agerbo Krogh)) Date: Fri, 10 Nov 2006 13:41:19 +0100 Subject: [Bioperl-l] Bio::SeqIO::fasta patch. Message-ID: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> Hi. Just a small patch for outputting stuff on the descriptionline i fasta format. Stuff like: DE test DE test2 DE test3 converted to fasta becomes: > testtest2test3 and not > test test2 test3 Index: fasta.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/fasta.pm,v retrieving revision 1.60 diff -r1.60 fasta.pm 203c203 < $desc =~ s/\n//g; --- > $desc =~ s/\n/ /g; Should probably be applied to the stable-branch . Jesper From arareko at campus.iztacala.unam.mx Fri Nov 10 10:14:18 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Fri, 10 Nov 2006 09:14:18 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: <4554974A.4010206@campus.iztacala.unam.mx> Sendu Bala wrote: > Does anyone know what the following files are supposed to do and if they > still used/needed? > > bioperl.lisp This a module template for Emacs users. > maintenance/symlink_scripts.pl > maintenance/symlink_scripts.PLS The 1st is created by Makefile.PL (basically its a rename of the 2nd) and is run during 'make install'. From the POD: "This script will create a symlink in the 'installscript' directory (as defined during install) to a script in that same directory. It was written to create a symlink with the name 'bp_pg_bulk_load_gff.pl' that targeted 'bp_bulk_load_gff.pl' but can be extended by adding files to the %symlink_scripts hash. Perl function 'symlink' is used to keep the script from crashing on systems that don't allow symbolic linking." > doc/makedoc.PL I have no idea :) > scripts/install_bioperl_scripts.pl This is also run automatically on 'make install'. Cheers, Mauricio. -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From aaron.j.mackey at gsk.com Fri Nov 10 08:59:55 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Fri, 10 Nov 2006 08:59:55 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> Message-ID: > bioperl.lisp This is a set of convenience macros for developers who use Emacs, but it's pretty out of date. Some may still use it, though. It's of no use being in the package distribution, however. > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must keep > the version they currently have, or can they be made like the others? if their current version is greater than the bioperl version, then they must keep it for backwards compatibility (as otherwise a "require" statement for a certain version of Bio::SeqIO::tinyseq won't work properly). -Aaron From dmessina at wustl.edu Fri Nov 10 09:55:44 2006 From: dmessina at wustl.edu (David Messina) Date: Fri, 10 Nov 2006 08:55:44 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: <256AAE6A-2ACC-4CFE-B66E-F94C536FA8C5@wustl.edu> > bioperl.lisp This is the emacs template for bioperl module writing. Should be kept I think. http://www.bioperl.org/wiki/Emacs_template > maintenance/symlink_scripts.pl > maintenance/symlink_scripts.PLS Don't know if they're still needed, but Makefile.PL still refers to them. > doc/makedoc.PL I think this does similar to what you propose below, namely redefining modules' version strings to be the same as Bio::Root::Version's. I don't see any reason to remove it, but I like your suggestion to have all the modules get their version from Bio::Root::Version. > scripts/install_bioperl_scripts.pl Does what it says. Don't know if it's still needed; I think Makefile.PL handles script installation. Re your other post about switching over to Build.PL, I think scripts go into /usr/local/bin by default, or wherever specified if PREFIX or the like is set when the user runs 'perl Makefile.PL'. That seems to fit with other CPAN distros' model, and is what I (as an end-user) would expect. Dave > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must > keep > the version they currently have, or can they be made like the others? > > These are the modules that seem to define their own version (based > on a > quick grep): > Bio/DB/NCBIHelper.pm > Bio/DB/Expression/geo.pm > Bio/DB/EUtilities/elink.pm > Bio/SeqIO/tinyseq.pm > Bio/Graphics/Glyph/cds.pm > Bio/Graphics/Glyph/translation.pm > Bio/Graphics/Glyph/so_transcript.pm > Bio/Index/Blast.pm > Bio/Index/Hmmer.pm > Bio/Tools/WebBlat.pm > Bio/Tools/HMM.pm > Bio/Tools/dpAlign.pm From cjfields at uiuc.edu Fri Nov 10 10:50:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 09:50:58 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > Hi all, > > Since I'm seeing inadequacies with the current Makefile.PL scripts we > have, I'm thinking of converting from ExtUtils::MakeMaker and the > Makefile.PL scripts to Module::Build Build.PL scripts. > > The advantages this will bring would be creation and installation of > documentation, sane handling of required and optional dependencies, > and > hopefully good META.yml output, for CPAN compatibility wrt version > numbers. > > I'll be able to use Module::Build::Compat to automatically generate > Makefile.PL scripts in 'passthrough' style (if an end-user tries to > use > Makefile.PL without having Module::Build installed, it will offer to > install Module::Build for them) when it comes time to make > distributions, but Makefile.PL would no longer be in CVS. > > > One thing I'm not clear on with the current situation is what is > supposed to happen when the user chooses to install scripts. Where are > they supposed to get installed to, and where do end-users normally run > them from and how? How does this compare to expectations from other > perl > module distributions that have installable scripts? > > > Please comment and discuss, but I'd like to get this done for the > 1.5.2 > release so that the CPAN distribution will be happy. I don't have a problem with this as long as it works for all systems. It sounds like a good long-term solution, esp. for CPAN developer releases. However, we've already had three RC's using the regular old Makefile.PL setup, which seems to work fine for now. It also sounds like we will need to update all relevant installation documentation (since we can't run 'perl Makefile.PL' w/o Makefile.PL, unless I'm missing something). Hence I'm a bit worried about adding something new like this after three RCs and just before a final release. I think it's something we should do, but I'm not sure we should have it for this release. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From dmessina at wustl.edu Fri Nov 10 10:40:21 2006 From: dmessina at wustl.edu (David Messina) Date: Fri, 10 Nov 2006 09:40:21 -0600 Subject: [Bioperl-l] Bioperl parser for PolyPhred? In-Reply-To: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> References: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> Message-ID: Sayali, I don't believe there is a BioPerl polyphred parser yet. This question came up on the list previously, however, and there was mention of a Perl script that appears to parse polyphred output: http://portal.open-bio.org/pipermail/bioperl-l/2003-December/014206.html Dave From bix at sendu.me.uk Fri Nov 10 10:59:54 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 15:59:54 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> Message-ID: <4554A1FA.6080003@sendu.me.uk> Chris Fields wrote: > On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > >> Hi all, >> >> Since I'm seeing inadequacies with the current Makefile.PL scripts we >> have, I'm thinking of converting from ExtUtils::MakeMaker and the >> Makefile.PL scripts to Module::Build Build.PL scripts. [snip] > I don't have a problem with this as long as it works for all systems. > It sounds like a good long-term solution, esp. for CPAN developer releases. > > However, we've already had three RC's using the regular old Makefile.PL > setup, which seems to work fine for now. It also sounds like we will > need to update all relevant installation documentation (since we can't > run 'perl Makefile.PL' w/o Makefile.PL, unless I'm missing something). > Hence I'm a bit worried about adding something new like this after three > RCs and just before a final release. > > I think it's something we should do, but I'm not sure we should have it > for this release. Now that I'm looking into it, it seems like quite a job, and yes, especially with all the documentation updates that need to be carefully looked at. Though to answer your question, Makefile.PL would be auto-generated by Build.PL immediately prior to a release and included in the distribution file for end users to use, but it wouldn't be in CVS. Such a Makefile.PL is essentially a front-end to the Build.PL for backwards-compatibility. For 1.5.2 I may just manually create a META.yml (the one generated via Makefile.PL isn't good enough) which only affects CPAN behaviour and nothing else we've been testing in the RCs. From bix at sendu.me.uk Fri Nov 10 11:03:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 16:03:04 +0000 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554974A.4010206@campus.iztacala.unam.mx> References: <45547121.6040904@sendu.me.uk> <4554974A.4010206@campus.iztacala.unam.mx> Message-ID: <4554A2B8.4010207@sendu.me.uk> Mauricio Herrera Cuadra wrote: > Sendu Bala wrote: >> Does anyone know what the following files are supposed to do and if >> they still used/needed? >> >> bioperl.lisp > > This a module template for Emacs users. I propose moving it to the wiki and removing it from CVS. >> maintenance/symlink_scripts.pl >> maintenance/symlink_scripts.PLS > The 1st is created by Makefile.PL (basically its a rename of the 2nd) > and is run during 'make install'. From the POD: > > "This script will create a symlink in the 'installscript' directory (as > defined during install) to a script in that same directory. It was > written to create a symlink with the name 'bp_pg_bulk_load_gff.pl' that > targeted 'bp_bulk_load_gff.pl' but can be extended by adding files to > the %symlink_scripts hash. > > Perl function 'symlink' is used to keep the script from crashing on > systems that don't allow symbolic linking." The question is, do we need this symlink? Is the bulk_load_gff stuff still relevant? Why was it needed in the first place? For me, it doesn't seem to do anything useful; it just creates a broken symlink in PREFIX/bin. >> scripts/install_bioperl_scripts.pl > This is also run automatically on 'make install'. Not any more it isn't. Makefile.PL has (some of, at least) this script's methods. Does anyone use it manually? I propose removing it from CVS. AFAICT, Makefile.PL only ever installs to scripts_temp? How would people normally expect to define the script installation directory? Maybe it used to install scripts to user-defined or typical places (eg. /usr/local/bin as David Messina suggests) but that got broken in a recent commit? Can anyone confirm if script installation works properly for them, and how they got it to work? From cjfields at uiuc.edu Fri Nov 10 11:11:17 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:11:17 -0600 Subject: [Bioperl-l] Bio::SeqIO::fasta patch. In-Reply-To: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> References: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> Message-ID: <7BBF2CEB-B012-4145-9818-6B69D10C7E8F@uiuc.edu> On Nov 10, 2006, at 6:41 AM, JK ((Jesper Agerbo Krogh)) wrote: > Hi. > > Just a small patch for outputting stuff on the descriptionline i > fasta format. > > Stuff like: > > DE test > DE test2 > DE test3 > > converted to fasta becomes: > >> testtest2test3 > > and not > >> test test2 test3 ... Actually, this should be fixed in the original input parser, not in fasta.pm. Was this from EMBL format? Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Fri Nov 10 11:16:24 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Fri, 10 Nov 2006 11:16:24 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> Message-ID: <4554A5D8.8000700@bms.com> I personally like the idea. Why not have both for this release to ensure smooth transition? Sendu, would having Makefile.PL (I mean the old one) along with the build script be a problem? I am not very familiar with both modules, but from the pdoc it seems it should not be too hard: Note that if you want to provide both a Makefile.PL and a Build.PL for your distribution, you probably want to add the following to "WriteMakefile" in your Makefile.PL so that MakeMaker doesn?t try to run your Build.PL as a nor? mal .PL file: PL_FILES => {}, Stefan Chris Fields wrote: > On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > > >> Hi all, >> >> Since I'm seeing inadequacies with the current Makefile.PL scripts we >> have, I'm thinking of converting from ExtUtils::MakeMaker and the >> Makefile.PL scripts to Module::Build Build.PL scripts. >> >> The advantages this will bring would be creation and installation of >> documentation, sane handling of required and optional dependencies, >> and >> hopefully good META.yml output, for CPAN compatibility wrt version >> numbers. >> >> I'll be able to use Module::Build::Compat to automatically generate >> Makefile.PL scripts in 'passthrough' style (if an end-user tries to >> use >> Makefile.PL without having Module::Build installed, it will offer to >> install Module::Build for them) when it comes time to make >> distributions, but Makefile.PL would no longer be in CVS. >> >> >> One thing I'm not clear on with the current situation is what is >> supposed to happen when the user chooses to install scripts. Where are >> they supposed to get installed to, and where do end-users normally run >> them from and how? How does this compare to expectations from other >> perl >> module distributions that have installable scripts? >> >> >> Please comment and discuss, but I'd like to get this done for the >> 1.5.2 >> release so that the CPAN distribution will be happy. >> > > I don't have a problem with this as long as it works for all > systems. It sounds like a good long-term solution, esp. for CPAN > developer releases. > > However, we've already had three RC's using the regular old > Makefile.PL setup, which seems to work fine for now. It also sounds > like we will need to update all relevant installation documentation > (since we can't run 'perl Makefile.PL' w/o Makefile.PL, unless I'm > missing something). Hence I'm a bit worried about adding something > new like this after three RCs and just before a final release. > > I think it's something we should do, but I'm not sure we should have > it for this release. > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at uiuc.edu Fri Nov 10 11:21:07 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:21:07 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: ... > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must > keep > the version they currently have, or can they be made like the others? > > These are the modules that seem to define their own version (based > on a > quick grep): > Bio/DB/NCBIHelper.pm > Bio/DB/Expression/geo.pm > Bio/DB/EUtilities/elink.pm > Bio/SeqIO/tinyseq.pm > Bio/Graphics/Glyph/cds.pm > Bio/Graphics/Glyph/translation.pm > Bio/Graphics/Glyph/so_transcript.pm > Bio/Index/Blast.pm > Bio/Index/Hmmer.pm > Bio/Tools/WebBlat.pm > Bio/Tools/HMM.pm > Bio/Tools/dpAlign.pm They probably shouldn't have their own unless there is a good reason (and I can't really think of one). The elink $VERSION is for the NCBI elink DTD, not the bioperl version, but that should be changed in elinks to something else beside $VERSION (my bad). The same reasoning may be relevant for the other modules; we'll just have to check them one-by-one. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Nov 10 11:29:42 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:29:42 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554A5D8.8000700@bms.com> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> Message-ID: On Nov 10, 2006, at 10:16 AM, Stefan Kirov wrote: > I personally like the idea. Why not have both for this release to > ensure smooth transition? Sendu, would having Makefile.PL (I mean > the old one) along with the build script be a problem? I am not > very familiar with both modules, but from the pdoc it seems it > should not be too hard: > > Note that if you want to provide both a Makefile.PL and a > Build.PL for your distribution, you probably want to add > the following to "WriteMakefile" in your Makefile.PL so > that MakeMaker doesn?t try to run your Build.PL as a nor > mal .PL file: > > PL_FILES => {}, > > > Stefan ... Sounds like a good compromise to me. Like I said, the only problem I had is introducing something drastically new after three RCs (and just prior to a final release; I think Sendu wanted to release the final 1.5.2 next week, just before Thanksgiving here.). There is no problem though if we have the old Makefile.PL to fall back to for this release. In fact, you could remove it from HEAD when needed; the file still exists on the 1.5.2 branch, right? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bernd.web at gmail.com Fri Nov 10 12:39:30 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 10 Nov 2006 18:39:30 +0100 Subject: [Bioperl-l] Bio::Graphics Message-ID: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> Hi, Lincoln made an excellent help on Graphics. Thanks for that!(http://www.bioperl.org/wiki/HOWTO:Graphics) I am just looking at the imagemap creation with my $map=$panel->create_web_map('mapname',\&linkrule,'bbb'); and would like to connect the PNG from a blast report to the blast results. I just realize that this likely has been done many times. Does someone have a pointer to code for creating an imagemap from a BLAST report and also write the blast results with links? Bernd From bosborne11 at verizon.net Fri Nov 10 13:10:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Fri, 10 Nov 2006 13:10:01 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554A2B8.4010207@sendu.me.uk> Message-ID: Sendu, No, no scripts installed either by bioperl-live or by 1.5.2-RC3 (Mac OS X, Perl 5.8.6). But yes, bioperl-live has certainly been capable of installing scripts in the past. Brian O. On 11/10/06 11:03 AM, "Sendu Bala" wrote: > Can anyone confirm if script installation works properly for them, and > how they got it to work? From hlapp at gmx.net Fri Nov 10 18:33:48 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:33:48 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: On Nov 10, 2006, at 7:31 AM, Sendu Bala wrote: > bioperl.lisp This is the macros file for emacs. Do not delete it from the repository ... -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Nov 10 18:37:32 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:37:32 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: References: Message-ID: <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: >> bioperl.lisp > > This is a set of convenience macros for developers who use Emacs, > but it's > pretty out of date. What is out of date in there? > Some may still use it, though. E.g., dinosaurs like me. > It's of no use being in the package distribution, however. I agree. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Nov 10 18:40:40 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:40:40 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554A2B8.4010207@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> <4554974A.4010206@campus.iztacala.unam.mx> <4554A2B8.4010207@sendu.me.uk> Message-ID: <2E617B21-BBFA-4865-AC50-6D6694B6CE2F@gmx.net> On Nov 10, 2006, at 11:03 AM, Sendu Bala wrote: >>> bioperl.lisp >> >> This a module template for Emacs users. > > I propose moving it to the wiki and removing it from CVS. This is not a good idea because the wiki is a bad platform for version controlling source code files, and this is a source code file. I don't have a problem with putting it up on the wiki, too. Better yet, link to the version in CVS. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Nov 10 19:35:06 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 19:35:06 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: Sounds like a good thing to do to me - I'd just be hesitant to do this for the 1.5.2 release. But I'm not the release master. -hilmar On Nov 10, 2006, at 5:15 AM, Sendu Bala wrote: > Hi all, > > Since I'm seeing inadequacies with the current Makefile.PL scripts we > have, I'm thinking of converting from ExtUtils::MakeMaker and the > Makefile.PL scripts to Module::Build Build.PL scripts. > > The advantages this will bring would be creation and installation of > documentation, sane handling of required and optional dependencies, > and > hopefully good META.yml output, for CPAN compatibility wrt version > numbers. > > I'll be able to use Module::Build::Compat to automatically generate > Makefile.PL scripts in 'passthrough' style (if an end-user tries to > use > Makefile.PL without having Module::Build installed, it will offer to > install Module::Build for them) when it comes time to make > distributions, but Makefile.PL would no longer be in CVS. > > > One thing I'm not clear on with the current situation is what is > supposed to happen when the user chooses to install scripts. Where are > they supposed to get installed to, and where do end-users normally run > them from and how? How does this compare to expectations from other > perl > module distributions that have installable scripts? > > > Please comment and discuss, but I'd like to get this done for the > 1.5.2 > release so that the CPAN distribution will be happy. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From kaboroev at sfu.ca Fri Nov 10 17:51:21 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Fri, 10 Nov 2006 14:51:21 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical Message-ID: <45550269.9050407@sfu.ca> Hi, I am attempting to add a few methods (ie. matching_bands_list) to the fpc map class but I am having a hard time inheriting the class properly. My first attempt was to inherit the "Bio::Map::Physical" class but the "next_map" package is not found. So I tried inheriting "Bio::MapIO" instead, and get a cannot find "matching_bands_list" via package "Bio::Map::Physical" The only way I can get it to work is with no inheritance and passing the map class variable to the function, but this isn't very elegant. Is there a correct way to inherit these classes that will allow me to execute this properly? keith From bernd.web at gmail.com Fri Nov 10 18:10:09 2006 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 11 Nov 2006 00:10:09 +0100 Subject: [Bioperl-l] POD HTML ResultWriter Message-ID: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> Hi, I just found the POD for HTMLResultWriter is truncated in Internet Explorer. http://doc.bioperl.org/bioperl-live/Bio/SearchIO/Writer/HTMLResultWriter.html. It stops with start_report. I think this is due to the tag (and , <BODY> tags in the text of start_report. In Firefox the page is rendered OK. Bernd From bix at sendu.me.uk Sat Nov 11 03:38:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 11 Nov 2006 08:38:27 +0000 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45550269.9050407@sfu.ca> References: <45550269.9050407@sfu.ca> Message-ID: <45558C03.8020903@sendu.me.uk> Keith Anthony Boroevich wrote: > Hi, > > I am attempting to add a few methods (ie. matching_bands_list) to the > fpc map class but I am having a hard time inheriting the class properly. > > My first attempt was to inherit the "Bio::Map::Physical" class but the > "next_map" package is not found. > So I tried inheriting "Bio::MapIO" instead, and get a cannot find > "matching_bands_list" via package "Bio::Map::Physical" > The only way I can get it to work is with no inheritance and passing the > map class variable to the function, but this isn't very elegant. Is > there a correct way to inherit these classes that will allow me to > execute this properly? It's hard to diagnose the problem without knowing exactly what you've tried. Please post some relevant code. Also, what version of Bioperl are you using? From bernd.web at gmail.com Sat Nov 11 08:53:55 2006 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 11 Nov 2006 14:53:55 +0100 Subject: [Bioperl-l] Bio::DB::Fasta index Message-ID: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Hi, A maybe strange question: is it possible to force Bio::DB::Fasta NOT to index the fasta file at any time (if there is already an index)? In the doc (http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Fasta.html), I read: " If one of the source fasta files is updated, the module reindexes just that one file. (You can also force reindexing manually)." Can I also switch off reindexing? (I realize that with Bio::Index::Fasta indexing can be separated). bernd From mkiwala at watson.wustl.edu Sat Nov 11 10:54:55 2006 From: mkiwala at watson.wustl.edu (mkiwala at watson.wustl.edu) Date: Sat, 11 Nov 2006 09:54:55 -0600 (CST) Subject: [Bioperl-l] Bio::DB::Fasta index In-Reply-To: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> References: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Message-ID: <58605.24.107.18.143.1163260495.squirrel@gscmail.wustl.edu> > A maybe strange question: is it possible to force Bio::DB::Fasta NOT > to index the fasta file at any time (if there is already an index)? I don't think so, but you could set the time stamp on the index file just before you run your script that uses the index. On a unix-like machine you would use the touch command. From cjfields at uiuc.edu Sat Nov 11 11:26:31 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 11 Nov 2006 10:26:31 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> References: <OF981FA506.80BA9953-ON85257222.004C99FF-85257222.004CE6C4@gsk.com> <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> Message-ID: <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> On Nov 10, 2006, at 5:37 PM, Hilmar Lapp wrote: > > On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: > >>> bioperl.lisp >> >> This is a set of convenience macros for developers who use Emacs, >> but it's >> pretty out of date. > > What is out of date in there? > >> Some may still use it, though. > > E.g., dinosaurs like me. > >> It's of no use being in the package distribution, however. > > I agree. > > -hilmar Maybe move it to it's own folder? It would be convenient if anyone else has helper macros (Komodo, vim, etc) or other developer stuff donated that we don't want included in the package distribution. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Sat Nov 11 11:31:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 11 Nov 2006 10:31:26 -0600 Subject: [Bioperl-l] POD HTML ResultWriter In-Reply-To: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> References: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> Message-ID: <27593A76-29AE-4295-A229-36A92F9F92F6@uiuc.edu> Bernd, Could you submit this as a bug? It likely has to do with PDOC. Include the IE version etc. Chris On Nov 10, 2006, at 5:10 PM, Bernd Web wrote: > Hi, > > I just found the POD for HTMLResultWriter is truncated in Internet > Explorer. > http://doc.bioperl.org/bioperl-live/Bio/SearchIO/Writer/ > HTMLResultWriter.html. > It stops with start_report. > I think this is due to the <HTML> tag (and <TITLE>, <BODY> tags in the > text of start_report. In Firefox the page is rendered OK. > > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Sat Nov 11 13:02:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 11 Nov 2006 13:02:18 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> References: <OF981FA506.80BA9953-ON85257222.004C99FF-85257222.004CE6C4@gsk.com> <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> Message-ID: <6E07DFB4-4D2A-4D66-9FAA-FEC20F6DE1B2@gmx.net> On Nov 11, 2006, at 11:26 AM, Chris Fields wrote: > > On Nov 10, 2006, at 5:37 PM, Hilmar Lapp wrote: > >> >> On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: >> >>>> bioperl.lisp >> >>> It's of no use being in the package distribution, however. >> >> I agree. >> >> -hilmar > > Maybe move it to it's own folder? It would be convenient if anyone > else has helper macros (Komodo, vim, etc) or other developer stuff > donated that we don't want included in the package distribution. Good idea, I agree. -hilmar > > chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From chhalling at verizon.net Sun Nov 12 13:11:54 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 12 Nov 2006 13:11:54 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC Message-ID: <455763EA.8080300@verizon.net> Quick summary: 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but not by Bio::Restriction::Enzyme. Should 'X' be removed from Bio::Tools::IUPAC or should it be added to Bio::Restriction::Enzyme? Detailed explanation: I tried to use the Bio::Restriction modules to perform a simple restriction analysis of some sequences I'm using at work, and I found the documentation and code confusing. So I'm volunteering to overhaul and redocument these modules. As part of this effort, I am also volunteering to fix the Bio::Restriction::IO::bairoch module. I have begun writing a test suite, RestrictionEnzyme.t, for the Bio::Restriction::Enzyme module. For one of the tests, I created a Bio::Restriction::Enzyme object with a recognition sequence that includes all of the IUPAC base symbols along with the caret ('^') symbol. A code excerpt is: use Bio::Tools::IUPAC; my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); ok $enzyme = Bio::Restriction::Enzyme->new( -name => 'IUPAC-IUB', -site => $site ); This test fails because Bio::Tools::IUPAC module includes 'X' as a valid base symbol, whereas Bio::Restriction::Enzyme does not. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 STACK: t/RestrictionEnzyme.t:184 ----------------------------------------------------------- The symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC need to be synchronized. Since 'X' is not recommended by "Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences" (see http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it stands for xanthine), I am in favor of removing it as a valid symbol. But I have a feeling that if 'X' is removed as a valid symbol from Bio::Tools::IUPAC, this will break a lot of existing code. So the simplest solution seems to be to add 'X' to the symbols recognized by Bio::Restriction::Enzyme. Does anyone have a recommendation? -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Sun Nov 12 17:21:06 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 12 Nov 2006 17:21:06 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> References: <455763EA.8080300@verizon.net> Message-ID: <45579E52.3010606@verizon.net> A followup: Bio::Tools::IUPAC::iupac_iub() also returns 'U' as a valid base. My idea of getting an authoritative set of base symbols from Bio::Tools::IUPAC does not work well. I will leave the valid bases in Bio::Restriction::Enzyme set to what is already used in the module ('ABCDGHKMNRSTVWY'). -- Conrad Conrad Halling wrote: > Quick summary: > > 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but not by > Bio::Restriction::Enzyme. Should 'X' be removed from Bio::Tools::IUPAC > or should it be added to Bio::Restriction::Enzyme? > > Detailed explanation: > > I tried to use the Bio::Restriction modules to perform a simple > restriction analysis of some sequences I'm using at work, and I found > the documentation and code confusing. So I'm volunteering to overhaul > and redocument these modules. As part of this effort, I am also > volunteering to fix the Bio::Restriction::IO::bairoch module. > > I have begun writing a test suite, RestrictionEnzyme.t, for the > Bio::Restriction::Enzyme module. For one of the tests, I created a > Bio::Restriction::Enzyme object with a recognition sequence that > includes all of the IUPAC base symbols along with the caret ('^') > symbol. A code excerpt is: > > use Bio::Tools::IUPAC; > my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); > my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); > ok $enzyme = > Bio::Restriction::Enzyme->new( > -name => 'IUPAC-IUB', > -site => $site ); > > This test fails because Bio::Tools::IUPAC module includes 'X' as a valid > base symbol, whereas Bio::Restriction::Enzyme does not. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 > STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 > STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 > STACK: t/RestrictionEnzyme.t:184 > ----------------------------------------------------------- > > The symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC > need to be synchronized. Since 'X' is not recommended by "Nomenclature > for Incompletely Specified Bases in Nucleic Acid Sequences" (see > http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it > stands for xanthine), I am in favor of removing it as a valid symbol. > > But I have a feeling that if 'X' is removed as a valid symbol from > Bio::Tools::IUPAC, this will break a lot of existing code. So the > simplest solution seems to be to add 'X' to the symbols recognized by > Bio::Restriction::Enzyme. > > Does anyone have a recommendation? > > -- Conrad Halling chhalling at verizon.net From dmessina at wustl.edu Sun Nov 12 17:30:59 2006 From: dmessina at wustl.edu (David Messina) Date: Sun, 12 Nov 2006 16:30:59 -0600 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> References: <455763EA.8080300@verizon.net> Message-ID: <C5C56BF0-8135-4CBE-BF30-B931E79B39C7@wustl.edu> > The symbols recognized by Bio::Restriction::Enzyme and > Bio::Tools::IUPAC > need to be synchronized. Since 'X' is not recommended by "Nomenclature > for Incompletely Specified Bases in Nucleic Acid Sequences" (see > http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it > stands for xanthine), I am in favor of removing it as a valid symbol. > > But I have a feeling that if 'X' is removed as a valid symbol from > Bio::Tools::IUPAC, this will break a lot of existing code. So the > simplest solution seems to be to add 'X' to the symbols recognized by > Bio::Restriction::Enzyme. How about adding a -strict option which would require valid IUPAC symbols (i.e. not 'X')? And the permissive, 'X'-okay behavior would be the default. Dave From cjfields at uiuc.edu Sun Nov 12 19:15:37 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 12 Nov 2006 18:15:37 -0600 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <45579E52.3010606@verizon.net> References: <455763EA.8080300@verizon.net> <45579E52.3010606@verizon.net> Message-ID: <59337785-5E63-4FD3-A490-FA9AC4715BBE@uiuc.edu> On Nov 12, 2006, at 4:21 PM, Conrad Halling wrote: > A followup: > > Bio::Tools::IUPAC::iupac_iub() also returns 'U' as a valid base. My > idea > of getting an authoritative set of base symbols from Bio::Tools::IUPAC > does not work well. > > I will leave the valid bases in Bio::Restriction::Enzyme set to > what is > already used in the module ('ABCDGHKMNRSTVWY'). > > -- Conrad Conrad, You could grab a hash of DNA/RNA codes from Bio::Tools::IUPAC using iupac_iub(), then modify that for internal use in Bio::Restriction modules by adding/deleting what you want. Or add a method to Bio::Tools::IUPAC that adds/deletes key-value pairs in the object to your specifications. If there are non-IUPAC symbols present in the module we should consider the reasons why they are there. Were they added as a quick fix, or for other reasons? Strictly speaking, I would say a module named Bio::Tools::IUPAC should not contain non-IUPAC symbols, and modifications should be made on a case-by-case basis (in objects), vs. universally (in classes). You could always remove any non- standard symbols and see what breaks. By the way, I think I can speak for many here by saying that we are happy you will take up the Bio::Restriction classes. They definitely need some work! Chris > Conrad Halling wrote: >> Quick summary: >> >> 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but >> not by >> Bio::Restriction::Enzyme. Should 'X' be removed from >> Bio::Tools::IUPAC >> or should it be added to Bio::Restriction::Enzyme? >> >> Detailed explanation: >> >> I tried to use the Bio::Restriction modules to perform a simple >> restriction analysis of some sequences I'm using at work, and I found >> the documentation and code confusing. So I'm volunteering to overhaul >> and redocument these modules. As part of this effort, I am also >> volunteering to fix the Bio::Restriction::IO::bairoch module. >> >> I have begun writing a test suite, RestrictionEnzyme.t, for the >> Bio::Restriction::Enzyme module. For one of the tests, I created a >> Bio::Restriction::Enzyme object with a recognition sequence that >> includes all of the IUPAC base symbols along with the caret ('^') >> symbol. A code excerpt is: >> >> use Bio::Tools::IUPAC; >> my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); >> my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); >> ok $enzyme = >> Bio::Restriction::Enzyme->new( >> -name => 'IUPAC-IUB', >> -site => $site ); >> >> This test fails because Bio::Tools::IUPAC module includes 'X' as a >> valid >> base symbol, whereas Bio::Restriction::Enzyme does not. >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 >> STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 >> STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 >> STACK: t/RestrictionEnzyme.t:184 >> ----------------------------------------------------------- >> >> The symbols recognized by Bio::Restriction::Enzyme and >> Bio::Tools::IUPAC >> need to be synchronized. Since 'X' is not recommended by >> "Nomenclature >> for Incompletely Specified Bases in Nucleic Acid Sequences" (see >> http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it >> stands for xanthine), I am in favor of removing it as a valid symbol. >> >> But I have a feeling that if 'X' is removed as a valid symbol from >> Bio::Tools::IUPAC, this will break a lot of existing code. So the >> simplest solution seems to be to add 'X' to the symbols recognized by >> Bio::Restriction::Enzyme. >> >> Does anyone have a recommendation? >> >> > > -- > Conrad Halling > chhalling at verizon.net > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Mon Nov 13 04:59:34 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 13 Nov 2006 09:59:34 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 Message-ID: <45584206.2040506@sheffield.ac.uk> I've done a test of the bioperl-run 1.5.2 RC3. I've posted results etc to the wiki. I have quite a lot of changes to commit regarding changing "return undef" to "return" and other issues about "bioperl best practices" - they are mainly only obvious changes. I also, moved some tests over to Test::More and added a few further tests for those modules. The test suite passes OK for me (other than the same issues for 1.5.2 RC3). Should It be OK to commit the to HEAD? or shall I wait till after the 1.5.2 release? Cheers Nath From avilella at gmail.com Mon Nov 13 08:25:44 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 13 Nov 2006 13:25:44 +0000 Subject: [Bioperl-l] new methods -- wiki or bugzilla? Message-ID: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Hi, Should the new methods/features be declared as ENH bugs in bugzilla or using the wiki? Cheers, Albert. From cjfields at uiuc.edu Mon Nov 13 10:10:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 09:10:27 -0600 Subject: [Bioperl-l] new methods -- wiki or bugzilla? In-Reply-To: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Message-ID: <013f01c70735$dbc09140$15327e82@pyrimidine> > Hi, > > Should the new methods/features be declared as ENH bugs in > bugzilla or using the wiki? > > Cheers, > > Albert. Historically we have used Bugzilla so we can keep track of them (the enhancement tag is also available there for that reason). You could use the wiki, but I personally think the wiki better serves as primarily a documentation site, both for current code and for the direction we plan on taking Bioperl. We could add a code requests page, though. We already have a Projects Priority page that details what we think are the top issues with Bioperl that need to be addressed; there have been a number of things added to that page that should be separated out into a code request page. However, I don't know how much will be implemented unless someone interested takes it up. Frankly, there are quite a number of requests in bugzilla that haven't been added b/c of lack of interest/time by the other developers. Either that, or we have a lack of knowledge about a certain format or program, as I had with the XMFA and ARP AlignIO parsers (see the POD for my comments; the parsing is pretty minimal). Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Mon Nov 13 10:17:03 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 09:17:03 -0600 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <45584206.2040506@sheffield.ac.uk> Message-ID: <014001c70736$c6e20c80$15327e82@pyrimidine> > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Nathan S. Haigh > Sent: Monday, November 13, 2006 4:00 AM > To: bioperl-l; sendu Bala > Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 > > I've done a test of the bioperl-run 1.5.2 RC3. I've posted > results etc to the wiki. > > I have quite a lot of changes to commit regarding changing > "return undef" to "return" and other issues about "bioperl > best practices" - they are mainly only obvious changes. I > also, moved some tests over to Test::More and added a few > further tests for those modules. The test suite passes OK for > me (other than the same issues for 1.5.2 RC3). > Should It be OK to commit the to HEAD? or shall I wait till after the > 1.5.2 release? > > Cheers > Nath I would say, if the tests pass, commit away. As an aside, I'm not sure how versioning works in the other bioperl distributions. We generally package them up at the same time but I don't remember them getting a specific version number upon release. For instance, bioperl-db was considered at version 0.1 for a long time, but I can't remember if it was officially assigned that. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 13 10:18:43 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 15:18:43 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <014001c70736$c6e20c80$15327e82@pyrimidine> References: <014001c70736$c6e20c80$15327e82@pyrimidine> Message-ID: <45588CD3.5020407@sendu.me.uk> Chris Fields wrote: > > As an aside, I'm not sure how versioning works in the other bioperl > distributions. We generally package them up at the same time but I don't > remember them getting a specific version number upon release. For instance, > bioperl-db was considered at version 0.1 for a long time, but I can't > remember if it was officially assigned that. I'm making their versions match that of core, which seems appropriate. From avilella at gmail.com Mon Nov 13 08:36:44 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 13 Nov 2006 13:36:44 +0000 Subject: [Bioperl-l] new methods -- wiki or bugzilla? In-Reply-To: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> References: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Message-ID: <358f4d650611130536sd99bc51u9df42f8bd71cb3a8@mail.gmail.com> and related to the previous question: can an email (presumably with a certain template format) be sent somewhere so that either one or the other system create a new feature ticket somewhere? I've been told that it can be done with wikis, but never seen it done. On 11/13/06, Albert Vilella <avilella at gmail.com> wrote: > Hi, > > Should the new methods/features be declared as ENH bugs in bugzilla or > using the wiki? > > Cheers, > > Albert. > From cjfields at uiuc.edu Mon Nov 13 11:51:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 10:51:24 -0600 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <45588CD3.5020407@sendu.me.uk> Message-ID: <000001c70743$f45b5ce0$15327e82@pyrimidine> > Chris Fields wrote: > > > > As an aside, I'm not sure how versioning works in the other bioperl > > distributions. We generally package them up at the same time but I > > don't remember them getting a specific version number upon > release. > > For instance, bioperl-db was considered at version 0.1 for a long > > time, but I can't remember if it was officially assigned that. > > I'm making their versions match that of core, which seems appropriate. Sounds good to me. We could at least state that run, db, and network 1.5.2 releases require bioperl rel. 1.5.2 (i.e. they are not guaranteed to work with older bioperl core versions), since that's what they were tested against. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 13 11:52:15 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 16:52:15 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <000001c70743$f45b5ce0$15327e82@pyrimidine> References: <000001c70743$f45b5ce0$15327e82@pyrimidine> Message-ID: <4558A2BF.7000405@sendu.me.uk> Chris Fields wrote: >> Chris Fields wrote: >>> As an aside, I'm not sure how versioning works in the other bioperl >>> distributions. We generally package them up at the same time but I >>> don't remember them getting a specific version number upon >> release. >>> For instance, bioperl-db was considered at version 0.1 for a long >>> time, but I can't remember if it was officially assigned that. >> I'm making their versions match that of core, which seems appropriate. > > Sounds good to me. We could at least state that run, db, and network 1.5.2 > releases require bioperl rel. 1.5.2 (i.e. they are not guaranteed to work > with older bioperl core versions), since that's what they were tested > against. Yes, they will (do already) require core 1.5.2 for Makefile.PL (Build.PL) to succeed. From alessandro.botton at unipd.it Mon Nov 13 13:10:36 2006 From: alessandro.botton at unipd.it (Alessandro Botton) Date: Mon, 13 Nov 2006 19:10:36 +0100 Subject: [Bioperl-l] Installation problems... Message-ID: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Sorry to disturb you... I tried to install BioPerl by means of cpan. I have previously installed Bundle::BioPerl and everything was ok, and then tried to force the Bioperl installation. Anyway, I attach the "make test" part taken from my shell during Bioperl installation and the result of the second test (tut1.pl, also in attachment) suggested to detect a good installation of Biopelr (the first one was ok). if you need further information please ask me. Thank you in advance for your precious help. Best wishes, A.Botton ??? ======================================= ALESSANDRO BOTTON, PhD student Department of Environmental Agronomy and Crop Science University of Padova AGRIPOLIS - V.le dell'Universit?, 16 35020 Legnaro (PD)-ITALY Fax ++39 049 8272850 Phone ++39 049 8272889 E-mail: alessandro.botton at unipd.it _______________________________________ Doctorate School of Crop Science www.daapv.unipd.it/spv _______________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0008.html> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: make_test_part.txt URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0004.txt> -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0009.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: tut1.pl Type: text/x-perl-script Size: 137 bytes Desc: not available URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0002.bin> -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0010.html> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: test_tut1.pl.txt URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0005.txt> -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0011.html> From bix at sendu.me.uk Mon Nov 13 14:16:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 19:16:58 +0000 Subject: [Bioperl-l] Installation problems... In-Reply-To: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> References: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Message-ID: <4558C4AA.6020004@sendu.me.uk> Alessandro Botton wrote: > Sorry to disturb you... > I tried to install BioPerl by means of cpan. I have previously installed > Bundle::BioPerl and everything was ok, and then tried to force the > Bioperl installation. Anyway, I attach the "make test" part taken from > my shell during Bioperl installation and the result of the second test > (tut1.pl, also in attachment) suggested to detect a good installation of > Biopelr (the first one was ok). if you need further information please > ask me. Unfortunately Bioperl 1.4 (the latest 'stable' edition in CPAN) is very old and yes, you're likely to get all sorts of failures. tut1.pl tries to do something that indeed no longer works in 1.4. We have a 'developer' release called 1.5.2 soon to be released which should in fact be suitable for use by everyone and everything should work. You can download a pre-release version and install it manually: http://bioperl.org/wiki/Release_1.5.2 Or wait a week or two and you'll be able to find the final release on CPAN. Hope that helps, Sendu. From n.haigh at sheffield.ac.uk Mon Nov 13 14:50:53 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 13 Nov 2006 19:50:53 +0000 Subject: [Bioperl-l] Installation problems... In-Reply-To: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> References: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Message-ID: <4558CC9D.2050507@sheffield.ac.uk> Alessandro Botton wrote: > Sorry to disturb you... > I tried to install BioPerl by means of cpan. I have previously > installed Bundle::BioPerl and everything was ok, and then tried to > force the Bioperl installation. Anyway, I attach the "make test" part > taken from my shell during Bioperl installation and the result of the > second test (tut1.pl, also in attachment) suggested to detect a good > installation of Biopelr (the first one was ok). if you need further > information please ask me. > Thank you in advance for your precious help. > Best wishes, > A.Botton > Hi Alessandro, The Bioperl 1.4 release is now somewhat out-of-date and you might be better to install the latest 1.5.x developer release. We are currently working towards a 1.5.2 release, which should be out within the next week or so. The latest version is 1.5.2 release candidate 3 - it should be installable via CPAN. I will refer you to what has been said about the 1.5.2 RC3 release: "Users: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into." At the moment CPAN doesn't see 1.5.x as a developer release (which should be fixed shortly). Therefore you should still be able to install it with: prompt> perl -MCPAN -e shell CPAN> install Bioperl Once the 1.5.2 RC3 distribution file is fixed, the above will not work. Let me know how you get on and if you get 1.5.2 RC3 installed. Cheers Nathan From jdw at ou.edu Mon Nov 13 18:50:15 2006 From: jdw at ou.edu (James D. White) Date: Mon, 13 Nov 2006 17:50:15 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> Message-ID: <455904B7.50504@ou.edu> "Erik" <er at xs4all.nl> wrote: >Hi all, > >I noticed the parsing is borked with newest swisprot files: > UniProt Knowledgebase Release 9 consists of: > UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 > UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 > > >I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines >in swissprot/trembl according to the new specification (see >http://expasy.org/sprot/relnotes/sp_news.html). > >Basically, the change is as follows: > ID EntryName DataClass; MoleculeType; SequenceLength. >is changed to: > ID EntryName DataClass; SequenceLength. > > > >The change I made was only in the regex capturing the entry name: >method next_seq (Bio/SeqIO/swiss.pm) : > >=============== > > unless( m/ > ^ > ID \s+ # > (\S+) \s+ # $1 entryname > ([^\s;]+); \s+ # $2 DataClass > [0-9]+[ ]AA \. # Sequencelength (capture?) > $ > /ox ) > { > $self->throw("swissprot stream with no ID. Not swissprot in my book"); > } > >=============== > > How about something like the following to recognize both old and new formats =============== unless( m/ ^ ID \s+ # (\S+) \s+ # $1 entryname ( (: [^\s;]+; \s+ )? ) # $2 DataClass (including ";\s+") [0-9]+[ ]AA \. # Sequencelength (capture?) $ /ox ) { $self->throw("swissprot stream with no ID. Not swissprot in my book"); } # Because $2 now contains a trailing ";\s+" in the new format, it needs to be fixed $DataClass = $2 || 'default DataClass'; # provide default for old file format $DataClass =~ s/;\s+$//; # remove trailing ";\s+" =============== The code trailing the unless block should be modified to use the appropriate variable names. This is provided only to show what post-match modification is needed. > >I tested this (=entry parsable and SeqIO created) against several >hundred Swissprot and Trembl entries. > >Of course, files with the older format are now broken - it may be better >to leave old and new format, and try both (newest first). > >hth, > >Erik > > > > > > From lincoln.stein at gmail.com Mon Nov 13 12:43:50 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 13 Nov 2006 12:43:50 -0500 Subject: [Bioperl-l] Bio::DB::Fasta index In-Reply-To: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> References: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Message-ID: <6dce9a0b0611130943n28600d66xb3fa37f7bb4a68b6@mail.gmail.com> You can always remove write permissions from the index file, in which case the attempted reindexing will fail quickly. Lincoln On 11/11/06, Bernd Web <bernd.web at gmail.com> wrote: > > Hi, > > A maybe strange question: is it possible to force Bio::DB::Fasta NOT > to index the fasta file at any time (if there is already an index)? In > the doc ( > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Fasta.html > ), > I read: " If one of the source fasta files is updated, the module > reindexes just that one file. (You can also force reindexing > manually)." > > Can I also switch off reindexing? (I realize that with > Bio::Index::Fasta indexing can be separated). > > bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Mon Nov 13 23:44:09 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 22:44:09 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <455904B7.50504@ou.edu> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> Message-ID: <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> On Nov 13, 2006, at 5:50 PM, James D. White wrote: > "Erik" <er at xs4all.nl> wrote: > >> Hi all, >> >> I noticed the parsing is borked with newest swisprot files: >> UniProt Knowledgebase Release 9 consists of: >> UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 >> UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 >> >> >> I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines >> in swissprot/trembl according to the new specification (see >> http://expasy.org/sprot/relnotes/sp_news.html). >> >> Basically, the change is as follows: >> ID EntryName DataClass; MoleculeType; SequenceLength. >> is changed to: >> ID EntryName DataClass; SequenceLength. >> >> >> >> The change I made was only in the regex capturing the entry name: >> method next_seq (Bio/SeqIO/swiss.pm) : >> >> =============== >> >> unless( m/ >> ^ >> ID \s+ # >> (\S+) \s+ # $1 entryname >> ([^\s;]+); \s+ # $2 DataClass >> [0-9]+[ ]AA \. # Sequencelength >> (capture?) >> $ >> /ox ) >> { >> $self->throw("swissprot stream with no ID. Not swissprot in my >> book"); >> } >> >> =============== >> >> > > How about something like the following to recognize both old and > new formats > > =============== > > unless( m/ > ^ > ID \s+ # > (\S+) \s+ # $1 entryname > ( (: [^\s;]+; \s+ )? ) # $2 DataClass > (including ";\s+") > [0-9]+[ ]AA \. # > Sequencelength (capture?) > $ > /ox ) > { > $self->throw("swissprot stream with no ID. Not swissprot in my > book"); > } > # Because $2 now contains a trailing ";\s+" in the new format, it > needs to be fixed > $DataClass = $2 || 'default DataClass'; # provide default > for old file format > $DataClass =~ s/;\s+$//; # remove trailing "; > \s+" > > =============== > > The code trailing the unless block should be modified to use the > appropriate > variable names. This is provided only to show what post-match > modification is > needed. > >> >> I tested this (=entry parsable and SeqIO created) against several >> hundred Swissprot and Trembl entries. >> >> Of course, files with the older format are now broken - it may be >> better >> to leave old and new format, and try both (newest first). >> >> hth, >> >> Erik This has been fixed to match old and new formats in CVS and passes all tests so far. You can try it out if you want. The regex is made to match up to (but not include) the ';', so there is no need to remove the extra space. ... unless( m{^ ID \s+ # (\S+) \s+ # $1 entryname ([^\s;]+); \s+ # $2 DataClass (?:PRT;)? \s+ # Molecule Type (optional) [0-9]+[ ]AA \. # Sequencelength (capture?) $ }ox ) { ... The molecule type was always PRT and was a carryover from EMBL format divisions. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From kaboroev at sfu.ca Tue Nov 14 00:55:46 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Mon, 13 Nov 2006 21:55:46 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45558C03.8020903@sendu.me.uk> References: <45550269.9050407@sfu.ca> <45558C03.8020903@sendu.me.uk> Message-ID: <45595A62.7090704@sfu.ca> Hi, I am using an up-to-date bioperl-live. The precise code is insignificant so I wrote some additional (shorter) code to attempt to explain my problem. What I want to do is the following. I want to add some functionality to the Bio::Map::Physical module so i created a module that inherits Physical module, Extended::FPC.pm. #----Test.pl-BEGIN---# use strict; use diagnostics; use Extended::FPC; my $mapio = new Extended::FPC(-format => "fpc",-file => $ARGV[0],-readcor => 1); my $map = $mapio->next_map(); $map->fpc_test(); exit 0; #---Test.pl-END------# #----Extended::FPC.pm-BEGIN---# package Extended::FPC; use strict; use base qw(Bio::Map::Physical Bio::MapIO); sub fpc_test { print STDERR "testing\n"; return 0; } 1; #----Extended::FPC.pm-END-----# The execution of test.pl results in a "Can't locate object method "next_map" via package "Extended::FPC"" error; Then I added the "Bio::MapIO" module to the "use base qw(Bio::Map::Physical Bio::MapIO);", because that is the module in which next_map is declared. When I again execute test.pl I now get the exception: Uncaught exception from user code: #-------- EXCEPTION ------- # ------------- EXCEPTION: Bio::Root::NotImplemented ------------- MSG: Abstract method "Bio::Factory::MapFactoryI::next_map" is not implemented by package Extended::FPC. This is not your fault - author of Extended::FPC should be blamed! STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.7/Bio/Root/Root.pm:359 STACK: Bio::Root::RootI::throw_not_implemented /usr/lib/perl5/site_perl/5.8.7/Bio/Root/RootI.pm:522 STACK: Bio::Factory::MapFactoryI::next_map /usr/lib/perl5/site_perl/5.8.7/Bio/Factory/MapFactoryI.pm:84 STACK: ./fpc.pl:12 ---------------------------------------------------------------- at /usr/lib/perl5/site_perl/5.8.7/Error.pm line 187 Error::throw('Bio::Root::NotImplemented', '-class', 'Bio::Root::NotImplemented', '-object', 'Extended::FPC=HASH(0x109ce10)', '-text', 'Abstract method "Bio::Factory::MapFactoryI::next_map" is not ...') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Root/Root.pm line 359 Bio::Root::Root::throw('Extended::FPC=HASH(0x109ce10)', '-text', 'Abstract method "Bio::Factory::MapFactoryI::next_map" is not ...', '-class', 'Bio::Root::NotImplemented') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Root/RootI.pm line 522 Bio::Root::RootI::throw_not_implemented('Extended::FPC=HASH(0x109ce10)') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Factory/MapFactoryI.pm line 84 Bio::Factory::MapFactoryI::next_map('Extended::FPC=HASH(0x109ce10)') called at ./fpc.pl line 12 #---- EXCEPTION END ----# This is where I am now and have no real idea of where to begin. I suppose the easiest way is to pass the $map variable to the function of interest and not to bother with inheriting any modules. Sendu Bala wrote: > Keith Anthony Boroevich wrote: > >> Hi, >> >> I am attempting to add a few methods (ie. matching_bands_list) to the >> fpc map class but I am having a hard time inheriting the class properly. >> >> My first attempt was to inherit the "Bio::Map::Physical" class but the >> "next_map" package is not found. >> So I tried inheriting "Bio::MapIO" instead, and get a cannot find >> "matching_bands_list" via package "Bio::Map::Physical" >> The only way I can get it to work is with no inheritance and passing the >> map class variable to the function, but this isn't very elegant. Is >> there a correct way to inherit these classes that will allow me to >> execute this properly? >> > > It's hard to diagnose the problem without knowing exactly what you've > tried. Please post some relevant code. Also, what version of Bioperl are > you using? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- ><)))?> -cGRASP- <?(((>< Keith Anthony Boroevich Simon Fraser University Tel: 604-268-7276 From bix at sendu.me.uk Tue Nov 14 03:49:52 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 14 Nov 2006 08:49:52 +0000 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45595A62.7090704@sfu.ca> References: <45550269.9050407@sfu.ca> <45558C03.8020903@sendu.me.uk> <45595A62.7090704@sfu.ca> Message-ID: <45598330.20400@sendu.me.uk> Keith Anthony Boroevich wrote: > Hi, > > I am using an up-to-date bioperl-live. The precise code is > insignificant so I wrote some additional (shorter) code to attempt to > explain my problem. What I want to do is the following. I want to add > some functionality to the Bio::Map::Physical module so i created a > module that inherits Physical module, Extended::FPC.pm. > > #----Test.pl-BEGIN---# > use strict; > use diagnostics; > use Extended::FPC; > my $mapio = new Extended::FPC(-format => "fpc",-file => > $ARGV[0],-readcor => 1); > my $map = $mapio->next_map(); > $map->fpc_test(); > exit 0; > #---Test.pl-END------# > > #----Extended::FPC.pm-BEGIN---# > package Extended::FPC; > use strict; > use base qw(Bio::Map::Physical Bio::MapIO); > > sub fpc_test { > print STDERR "testing\n"; > return 0; > } > > 1; > #----Extended::FPC.pm-END-----# > > The execution of test.pl results in a "Can't locate object method > "next_map" via package "Extended::FPC"" error; > Then I added the "Bio::MapIO" module to the "use base > qw(Bio::Map::Physical Bio::MapIO);", because that is the module in which > next_map is declared. Well I think alarm bells should have been ringing at that point. I think you're trying to inherit from the wrong module to do whatever it is you want to do. Bio::Map::Physical has no next_map() because it isn't a Map::IO module. It represents a /single/ map (only), and is the sort of object you might /receive/ as the result of calling next_map() on an actual Map::IO module. So perhaps you should take another look at the various Map modules and figure out the correct thing to inherit from, or you just need to correct your usage (only call next_map() on a Map::IO). From er at xs4all.nl Tue Nov 14 04:40:20 2006 From: er at xs4all.nl (Erik) Date: Tue, 14 Nov 2006 10:40:20 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> Message-ID: <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> Btw and FYI: I have run this regex through SwissProt and Trembl and a previous version of those two files (to be version-precise: swissprot 51 and 50; trembl 33 and 34). It matched all ID lines. Thanks :) Erik > ... > unless( m{^ > ID \s+ # > (\S+) \s+ # $1 entryname > ([^\s;]+); \s+ # $2 DataClass > (?:PRT;)? \s+ # Molecule Type (optional) > [0-9]+[ ]AA \. # Sequencelength (capture?) > $ > }ox ) { > ... > > The molecule type was always PRT and was a carryover from EMBL format > divisions. From cjfields at uiuc.edu Tue Nov 14 07:35:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 14 Nov 2006 06:35:24 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> Message-ID: <B5AD2308-6CC0-4250-ABFA-1E728196693F@uiuc.edu> On Nov 14, 2006, at 3:40 AM, Erik wrote: > Btw and FYI: > > I have run this regex through SwissProt and Trembl and a previous > version > of those two files (to be version-precise: swissprot 51 and 50; > trembl 33 > and 34). > > It matched all ID lines. > > Thanks :) > > Erik ... Thanks for letting us know. We like success stories! Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From gcarbajosa at cnio.es Tue Nov 14 05:39:41 2006 From: gcarbajosa at cnio.es (guillermo) Date: Tue, 14 Nov 2006 11:39:41 +0100 Subject: [Bioperl-l] Error while indexing whole genbank Message-ID: <80337800c106ece5f0c78ed0b098b8f8@cnio.es> Hello, I am trying to index the whole of genbank nucleotide (release number 156, October 15 2006), with the script (which uses Bio::Index::GenBank) that is attached at the end of this message the process crashes with this error message: sdbm store returned -1, errno 9, key "BF460808" at /usr/local/lib/perl5/site_perl/5.8.8/Bio/Index/Abstract.pm line 714, <GenBank> line 164732819. why could this be? Thanks, Guillermo #!/usr/local/bin/perl -w # Perl pragma to restrict unsafe constructs use strict; # Issue warnings about suspicious programming. use warnings; # Use the code module that contains BioPerl Services. use Bio::Index::GenBank; # Use to index GenBank file use Bio::SeqIO; # be prepare for command-line options/arguments use Getopt::Std; sub help { return<<"END_HELP"; Description: Make index from GenBank database Usage: createGenBankIndex.pl -d {index file} -g {GenBank database} -d path and file name of index database -g GenBank database path END_HELP } BEGIN { # Determines the options with values from program use vars qw/$opt_d $opt_g/; # these are switches taking an argument (a value) my $switches = 'dg'; # Get the switches getopt($switches); # If the user does not write nothing, skip to help unless (defined($opt_d) || defined($opt_g)){ print help; exit 0; } } ######################################################################## ####### # # DESCRIPTION: The next program creates an BioPerl index aside GenBank database. # # INPUT (BY CONSOLE): - (-d) Path where the Uniprot index is going to store. # - (-g) Path where GenBank database is located # # OUTPUT: - O => The program has finished sucessfully # - 1 => Some of database files has not founded # - 2 => There was an error while the process was running # # AUTHOR: Jos?? Manuel Rodr??guez Carrasco -jmrc at cnb.uam.es- (INB-CNB) ######################################################################## ####### # Check if the path of GenBank database is able to read unless (-f $opt_g && -r $opt_g) { # The GenBank database has not been found print "Error of createGenBankIndex program: The GenBank database has not been found\n"; # Return an error exit 1; } # Store the database paths my @DBList = ($opt_g); # Create new instance to index file. It is used the option my $indexSW = Bio::Index::GenBank->new ('-filename' => $opt_d, '-write_flag' => 1); # Make the index my $numFiles = $indexSW->make_index(@DBList); # Check how many databases have been indexed if ($numFiles == 1) { # There has been not exist error. print "\nThe creation of GenBank index has been executed successfully\n"; exit 0; } else { # There has been exist an process error print "\nThere was a problem while the creation of GenBank index was running\n"; exit 2; } **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From gcarbajosa at cnio.es Tue Nov 14 05:57:01 2006 From: gcarbajosa at cnio.es (guillermo) Date: Tue, 14 Nov 2006 11:57:01 +0100 Subject: [Bioperl-l] indexing with several processors Message-ID: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> Hello, While using the Bio::Index::GenBank module for indexing Genbank, is there any option to run the process with more than one processor. Thanks **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From lincoln.stein at gmail.com Tue Nov 14 11:08:55 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 14 Nov 2006 11:08:55 -0500 Subject: [Bioperl-l] Bio::Graphics In-Reply-To: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> References: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> Message-ID: <6dce9a0b0611140808md4edbe7ye2632714621da52d@mail.gmail.com> I don't think the dots have been connected on this. It should be straightforward following the example in the BioGraphics HOWTO. Lincoln On 11/10/06, Bernd Web <bernd.web at gmail.com> wrote: > > Hi, > > Lincoln made an excellent help on Graphics. Thanks for > that!(http://www.bioperl.org/wiki/HOWTO:Graphics) > I am just looking at the imagemap creation with > my $map=$panel->create_web_map('mapname',\&linkrule,'bbb'); > and would like to connect the PNG from a blast report to the blast > results. > > I just realize that this likely has been done many times. Does someone > have a pointer to code for creating an imagemap from a BLAST report > and also write the blast results with links? > > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bosborne11 at verizon.net Tue Nov 14 16:54:25 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 14 Nov 2006 16:54:25 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> Message-ID: <C17FA541.B55D%bosborne11@verizon.net> Conrad, The typical solution is to declare an alphabet, as in: my $seq = Bio::Seq->new(-seq => "xxxx", -alphabet => "dna") Then Bioperl will not check your sequence. This works since you'll know that the alphabet, in this case, has to be "dna". Brian O. On 11/12/06 1:11 PM, "Conrad Halling" <chhalling at verizon.net> wrote: > This test fails because Bio::Tools::IUPAC module includes 'X' as a valid > base symbol, whereas Bio::Restriction::Enzyme does not. From stewarta at nmrc.navy.mil Tue Nov 14 17:47:26 2006 From: stewarta at nmrc.navy.mil (Andrew Stewart) Date: Tue, 14 Nov 2006 17:47:26 -0500 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast Message-ID: <8AF15F1F-0C81-4506-97C4-D25A12804731@nmrc.navy.mil> Anyone have any opinions as to how easy/difficult it would be to incorporate mpiblast into Bio::Tools::Run::StandAloneBlast? It runs essentially the same way as blastall, and its output is nearly identical. -A -- Andrew Stewart Research Assistant, Genomics Team Navy Medical Research Center (NMRC) Biological Defense Research Directorate (BDRD) BDRD Annex 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 email: stewarta at nmrc.navy.mil phone: 301-231-6700 Ext 270 From bosborne11 at verizon.net Tue Nov 14 22:10:00 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 14 Nov 2006 22:10:00 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <45531968.6080607@sendu.me.uk> Message-ID: <C17FEF38.B565%bosborne11@verizon.net> Sendu, RC3 can't be released as it doesn't install its scripts and some of these scripts are critical (e.g. the bp_*load_gff.pl and bp_process*.pl scripts, used by GMOD and chado users). I believe I've fixed this though, the problem was in Makefile.PL, no surprise. BIO On 11/9/06 7:04 AM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Developers: > Once again I'm hopeful that this is the last RC. If all goes well > expect final release in about a weeks time. Please check and update > documentation. > > Users: > Even though 1.5.2 is a 'developer' release, we consider it the most > stable and capable version of Bioperl, and recommend that you use > it in all but the most critical production environments. Please > try it out and let us know of any problems or difficulties you run > into. > > > Thank you, > Sendu. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sayali_salodkar at persistent.co.in Wed Nov 15 09:15:52 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Wed, 15 Nov 2006 19:45:52 +0530 Subject: [Bioperl-l] Help needed urgently Message-ID: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> I wish to fetch consensus sequence and the names of the trace (chromat) files used in the assembly from the .ace file For this purpose, I am using Bio::Assembly::IO. But I am unable to find the appropriate methods which would enable me to fetch this information. Note: The BS line (base segment) in the .ace file indicates which read phrap has chosen to be the consensus at a particular position. For example: BS 1 515 K26-572c gives BS <padded start consensus position> <padded end consensus position> <read name> respectively. How do I retrieve this information contig wise? Kindly help. Regards, Sayali D Salodkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From cjfields at uiuc.edu Wed Nov 15 09:22:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 08:22:38 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <C17FEF38.B565%bosborne11@verizon.net> Message-ID: <000a01c708c1$80d37300$15327e82@pyrimidine> > Sendu, > > RC3 can't be released as it doesn't install its scripts and > some of these scripts are critical (e.g. the bp_*load_gff.pl > and bp_process*.pl scripts, used by GMOD and chado users). I > believe I've fixed this though, the problem was in > Makefile.PL, no surprise. > > BIO ... This is definitely something to think about with Sendu's proposed changeover to Module::Build, which would obviate having a Makefile.PL. The issue with broken script installation was raised previously, but there were few responses (probably b/c itr came up somewhat indirectly in relation to other files in CVS). Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 09:24:25 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 08:24:25 -0600 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast In-Reply-To: <8AF15F1F-0C81-4506-97C4-D25A12804731@nmrc.navy.mil> Message-ID: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> > Anyone have any opinions as to how easy/difficult it would be > to incorporate mpiblast into > Bio::Tools::Run::StandAloneBlast? It runs essentially the > same way as blastall, and its output is nearly identical. > > > -A > > -- > Andrew Stewart > Research Assistant, Genomics Team > Navy Medical Research Center (NMRC) > Biological Defense Research Directorate (BDRD) BDRD Annex > 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 > > email: stewarta at nmrc.navy.mil > phone: 301-231-6700 Ext 270 I think plans were to rewrite StandAloneBlast and RemoteBlast to make them more 'generic' (i.e. capable of running other BLAST-related programs), though I'm not sure at what stage everything is. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From sayali_salodkar at persistent.co.in Wed Nov 15 09:15:52 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Wed, 15 Nov 2006 19:45:52 +0530 Subject: [Bioperl-l] Help needed urgently Message-ID: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> I wish to fetch consensus sequence and the names of the trace (chromat) files used in the assembly from the .ace file For this purpose, I am using Bio::Assembly::IO. But I am unable to find the appropriate methods which would enable me to fetch this information. Note: The BS line (base segment) in the .ace file indicates which read phrap has chosen to be the consensus at a particular position. For example: BS 1 515 K26-572c gives BS <padded start consensus position> <padded end consensus position> <read name> respectively. How do I retrieve this information contig wise? Kindly help. Regards, Sayali D Salodkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From bix at sendu.me.uk Wed Nov 15 10:35:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 15:35:29 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: <455B33C1.1010800@sendu.me.uk> Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I propose removing it from CVS. Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL when a user does a normal install of Bioperl? Or can it safely be ignored, only run manually by people who want to install Deobfuscator? From nhansen at nhgri.nih.gov Wed Nov 15 10:52:05 2006 From: nhansen at nhgri.nih.gov (Nancy Hansen) Date: Wed, 15 Nov 2006 10:52:05 -0500 (EST) Subject: [Bioperl-l] Inheritance Bio::Map::Physical Message-ID: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Keith Anthony Boroevich wrote: > > I am using an up-to-date bioperl-live. The precise code is > insignificant so I wrote some additional (shorter) code to attempt to > explain my problem. What I want to do is the following. I want to add > some functionality to the Bio::Map::Physical module so i created a > module that inherits Physical module, Extended::FPC.pm. > > #----Test.pl-BEGIN---# > use strict; > use diagnostics; > use Extended::FPC; > my $mapio = new Extended::FPC(-format => "fpc",-file => > $ARGV[0],-readcor => 1); > my $map = $mapio->next_map(); > $map->fpc_test(); > exit 0; > #---Test.pl-END------# You're right that your Extended::FPC should inherit from Bio::Map::Physical, but you really don't want to use it to parse the fpc file (Bio::MapIO does that just fine, and gets all the data you need into the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical object using Bio::MapIO, then forcing it to be an Extended::FPC, which will allow it to use your method(s): my $mapio = Bio::MapIO->new(-format => 'fpc', -file => $ARGV[0], -readcor => 1); my $fpc_map = $mapio->next_map(); bless $fpc_map, Extended::FPC; my $ra_bands = $fpc_map->my_new_extended_method(); I've actually written my own method to return the band sizes as well, so it would probably make a good enhancement to Bio::Map::Physical, which already has a "matching_bands" method that returns the (scalar) number of bands that match at a given tolerance. If that method were "enhanced" to return an array of matching band sizes rather than the scalar number of bands, it would still return the number in scalar context, but give you the matching band info in list context. I'd be happy to submit a patch for this if others think it's backwardly-compatible enough. --Nancy ************************************* Nancy F. Hansen, PhD nhansen at nhgri.nih.gov Bioinformatics Group NIH Intramural Sequencing Center (NISC) 5625 Fishers Lane Rockville, MD 20852 Phone: (301) 435-1560 Fax: (301) 435-6170 From cjfields at uiuc.edu Wed Nov 15 11:24:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 10:24:57 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> Message-ID: <000001c708d2$97c9d610$15327e82@pyrimidine> > Does anyone know what purpose Bio/DB/Makefile.PL serves? If > none, I propose removing it from CVS. > > Dave: Do you need anything to happen with > doc/Deobfuscator/Makefile.PL when a user does a normal > install of Bioperl? Or can it safely be ignored, only run > manually by people who want to install Deobfuscator? The Bio/DB/Makefile.PL and MANIFEST could be GMOD- or Chado-related (they are both related to Bio::DB::GFF). I'm not sure though; I'm cc'ing this to Lincoln to see if they are still needed. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From arareko at campus.iztacala.unam.mx Wed Nov 15 11:23:45 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed, 15 Nov 2006 10:23:45 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> Message-ID: <455B3F11.6070102@campus.iztacala.unam.mx> I think Deobfuscator code should be manually installed only. Mauricio. Sendu Bala wrote: > Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I > propose removing it from CVS. > > Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL > when a user does a normal install of Bioperl? Or can it safely be > ignored, only run manually by people who want to install Deobfuscator? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From kaboroev at sfu.ca Wed Nov 15 12:14:14 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Wed, 15 Nov 2006 09:14:14 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> References: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Message-ID: <455B4AE6.509@sfu.ca> Thanks, this is exactly what I was looking for. I didn't know how to get Bio::MapIO to return "my" class and I was unaware that bless could be used in such a manner. Not to nit-pick, but just in case anyone else has such a problem, quotes are required around the class. bless $fpc_map "Extended::FPC"; Nancy Hansen wrote: > > > You're right that your Extended::FPC should inherit from > Bio::Map::Physical, but you really don't want to use it to parse the fpc > file (Bio::MapIO does that just fine, and gets all the data you need into > the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical > object using Bio::MapIO, then forcing it to be an Extended::FPC, which > will allow it to use your method(s): > > my $mapio = Bio::MapIO->new(-format => 'fpc', > -file => $ARGV[0], > -readcor => 1); > > my $fpc_map = $mapio->next_map(); > > bless $fpc_map, Extended::FPC; > my $ra_bands = $fpc_map->my_new_extended_method(); > -- ><)))?> -cGRASP- <?(((>< Keith Anthony Boroevich Simon Fraser University Tel: 604-268-7276 From pmiguel at purdue.edu Wed Nov 15 12:00:50 2006 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 15 Nov 2006 12:00:50 -0500 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <455B47C2.8020400@purdue.edu> Sayali wrote: > I wish to fetch consensus sequence and the names of the trace (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar > Hi Sayali, I don't think there is a pre-rolled bioperl method to do what you ask. (But it seems like one is under construction?) You can extract the contig sequences from a phrap .ace file with the following plain perl code: my $print_it = 0; while (<>){ $print_it = /^CO / ? 1 : /^$/ ? 0 : $print_it ; s/^CO />/; s/\*//g; #removes "pads"--optional print if $print_it; } To find the reads that went into each contig, you do *not* want the BS tagged records. My understanding is that BS is just what consed uses to populate its consensus line from the ace file. The simplest way is: egrep '^CO|AF' acefilename if you are on a unix system. Or with perl while (<>) { print if (/^CO|AF/); } -- Phillip Purdue Genomics Core Facility From cjfields at uiuc.edu Wed Nov 15 12:00:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:00:05 -0600 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> > I wish to fetch consensus sequence and the names of the trace > (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to > find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read > phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus > position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar It looks like the relevant part of the Bio::Assembly::IO::ace parser responsible for parsing this is commented out: # Loading base segments definitions (Base Segment field) # /^BS (\d+) (\d+) (\S+)/ && do { # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} {'segments'})) { # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . " " . $2; # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = $1 . " " . $2 } # }; I'm not sure why to be honest as I'm not very familiar with the Bio::Assembly. Have you tried removing the comments to see what happens? You could file a bug report noting this using Bugzilla: http://bugzilla.open-bio.org/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 12:00:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:00:05 -0600 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> > I wish to fetch consensus sequence and the names of the trace > (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to > find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read > phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus > position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar It looks like the relevant part of the Bio::Assembly::IO::ace parser responsible for parsing this is commented out: # Loading base segments definitions (Base Segment field) # /^BS (\d+) (\d+) (\S+)/ && do { # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} {'segments'})) { # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . " " . $2; # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = $1 . " " . $2 } # }; I'm not sure why to be honest as I'm not very familiar with the Bio::Assembly. Have you tried removing the comments to see what happens? You could file a bug report noting this using Bugzilla: http://bugzilla.open-bio.org/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 12:37:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:37:35 -0600 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> References: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Message-ID: <D7DFA98D-2107-4C4C-9BBA-8B029DD9CC41@uiuc.edu> On Nov 15, 2006, at 9:52 AM, Nancy Hansen wrote: > Keith Anthony Boroevich wrote: >> >> I am using an up-to-date bioperl-live. The precise code is >> insignificant so I wrote some additional (shorter) code to attempt to >> explain my problem. What I want to do is the following. I want >> to add >> some functionality to the Bio::Map::Physical module so i created a >> module that inherits Physical module, Extended::FPC.pm. >> >> #----Test.pl-BEGIN---# >> use strict; >> use diagnostics; >> use Extended::FPC; >> my $mapio = new Extended::FPC(-format => "fpc",-file => >> $ARGV[0],-readcor => 1); >> my $map = $mapio->next_map(); >> $map->fpc_test(); >> exit 0; >> #---Test.pl-END------# > > You're right that your Extended::FPC should inherit from > Bio::Map::Physical, but you really don't want to use it to parse > the fpc > file (Bio::MapIO does that just fine, and gets all the data you > need into > the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical > object using Bio::MapIO, then forcing it to be an Extended::FPC, which > will allow it to use your method(s): > > my $mapio = Bio::MapIO->new(-format => 'fpc', > -file => $ARGV[0], > -readcor => 1); > > my $fpc_map = $mapio->next_map(); > > bless $fpc_map, Extended::FPC; > my $ra_bands = $fpc_map->my_new_extended_method(); > > I've actually written my own method to return the band sizes as > well, so > it would probably make a good enhancement to Bio::Map::Physical, which > already has a "matching_bands" method that returns the (scalar) > number of > bands that match at a given tolerance. If that method were > "enhanced" to > return an array of matching band sizes rather than the scalar > number of > bands, it would still return the number in scalar context, but give > you > the matching band info in list context. I'd be happy to submit a > patch > for this if others think it's backwardly-compatible enough. > > --Nancy Keith, Nancy, Sendu Bala has taken over maintenance of the Bio::Map modules. I have cc'd him this in case he has missed it (he's in the middle of getting a bioperl developer release put together). In general we are more than happy to take new modules and patches for current ones. There is a HOWTO on submitting patches and new code: http://www.bioperl.org/wiki/HOWTO:SubmitPatch If you plan on submitting a patch, you should also consider adding some tests as well. I think the relevant tests for Bio::Map modules are in t/Map.t and t/MapIO.t. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 13:15:48 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 18:15:48 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> Message-ID: <455B5954.1080209@sendu.me.uk> Chris Fields wrote: > On Nov 10, 2006, at 10:16 AM, Stefan Kirov wrote: > >> I personally like the idea. Why not have both for this release to >> ensure smooth transition? Sendu, would having Makefile.PL (I mean >> the old one) along with the build script be a problem? [snip] > Sounds like a good compromise to me. Like I said, the only problem I > had is introducing something drastically new after three RCs (and > just prior to a final release; I think Sendu wanted to release the > final 1.5.2 next week, just before Thanksgiving here.). There is no > problem though if we have the old Makefile.PL to fall back to for > this release. In fact, you could remove it from HEAD when needed; > the file still exists on the 1.5.2 branch, right? I think the compromise isn't worth it. The old Makefile.PL is just too inadequate and I don't want to support it. Build.pl is simply far too superior and I really want all users to be using it. I've now made the changeover in HEAD for core only (so far). Can people please try it out, especially wrt to installation in default and user-specified locations? First, clean out your system of the old Makefile.PL stuff: perl Makefile.PL make clean rm Makefile.PL Makefile.old cvs update -d -P Now try out the new Build.PL: perl Build.PL ./Build test ./Build install Try out other things: http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm You'll notice you don't have a Makefile.PL anymore. Distributions will include one, and as a cvs user you can generate one by: ./Build manifest ./Build distmeta Now you can try out the things you used to be able to do: make test make install Please let me know how you get on, Sendu. From bosborne11 at verizon.net Wed Nov 15 13:33:06 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 13:33:06 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> Message-ID: <C180C792.B596%bosborne11@verizon.net> Sendu, I see: 175 ~/bioperl-live>perl Build.PL Checking prerequisites... ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Which is incorrect since there no "modules indicated above". Brian O. On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Please let me know how you get on, From gcarbajosa at cnio.es Wed Nov 15 12:43:10 2006 From: gcarbajosa at cnio.es (guillermo) Date: Wed, 15 Nov 2006 18:43:10 +0100 Subject: [Bioperl-l] Fwd: Error while indexing whole genbank Message-ID: <68874599fabff74a65fcc62568022288@cnio.es> Hello, I just indexed BCT without problems and now I am going to do it in parts, different indexes for each one, for PLN, PRI, ROD, etc. Anyways, I??l try to do it for the whole genbank and if it works I?ll let you know. Thanks for the support, Guille Inicio mensaje reenviado: > De: guillermo <gcarbajosa at cnio.es> > Fecha: 14 de noviembre de 2006 11:39:41 GMT+01:00 > Para: bioperl-l at bioperl.org > Asunto: Error while indexing whole genbank > > Hello, > > I am trying to index the whole of genbank nucleotide (release number > 156, October 15 2006), with the script (which uses > Bio::Index::GenBank) that is attached at the end of this message the > process crashes with this error message: > > sdbm store returned -1, errno 9, key "BF460808" at > /usr/local/lib/perl5/site_perl/5.8.8/Bio/Index/Abstract.pm line 714, > <GenBank> line 164732819. > > why could this be? > > Thanks, > Guillermo > > > #!/usr/local/bin/perl -w > > # Perl pragma to restrict unsafe constructs > use strict; > > # Issue warnings about suspicious programming. > use warnings; > > # Use the code module that contains BioPerl Services. > use Bio::Index::GenBank; # Use to index GenBank file > use Bio::SeqIO; > > # be prepare for command-line options/arguments > use Getopt::Std; > > sub help { > return<<"END_HELP"; > Description: Make index from GenBank database > Usage: > > createGenBankIndex.pl -d {index file} -g {GenBank database} > -d path and file name of index database > -g GenBank database path > > END_HELP > > } > > > BEGIN { > > # Determines the options with values from program > use vars qw/$opt_d $opt_g/; > > # these are switches taking an argument (a value) > my $switches = 'dg'; > > # Get the switches > getopt($switches); > > # If the user does not write nothing, skip to help > unless (defined($opt_d) || defined($opt_g)){ > print help; > exit 0; > } > > } > > ####################################################################### > ######## > # > # DESCRIPTION: The next program creates an BioPerl index aside GenBank > database. > # > # INPUT (BY CONSOLE): - (-d) Path where the Uniprot index is going to > store. > # - (-g) Path where GenBank database is located > # > # OUTPUT: - O => The program has finished sucessfully > # - 1 => Some of database files has not founded > # - 2 => There was an error while the process was running > # > # AUTHOR: Jos?? Manuel Rodr??guez Carrasco -jmrc at cnb.uam.es- (INB-CNB) > ####################################################################### > ######## > > > # Check if the path of GenBank database is able to read > unless (-f $opt_g && -r $opt_g) { > > # The GenBank database has not been found > print "Error of createGenBankIndex program: The GenBank database has > not been found\n"; > > # Return an error > exit 1; > } > > > # Store the database paths > my @DBList = ($opt_g); > > # Create new instance to index file. It is used the option > my $indexSW = Bio::Index::GenBank->new ('-filename' => $opt_d, > '-write_flag' => 1); > > # Make the index > my $numFiles = $indexSW->make_index(@DBList); > > # Check how many databases have been indexed > if ($numFiles == 1) { > > # There has been not exist error. > print "\nThe creation of GenBank index has been executed > successfully\n"; > exit 0; > > > } else { > > # There has been exist an process error > print "\nThere was a problem while the creation of GenBank index was > running\n"; > exit 2; > } > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3585 bytes Desc: not available URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061115/64a3cab3/attachment-0002.bin> From cain at cshl.edu Wed Nov 15 12:45:52 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 15 Nov 2006 12:45:52 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <000001c708d2$97c9d610$15327e82@pyrimidine> References: <000001c708d2$97c9d610$15327e82@pyrimidine> Message-ID: <1163612752.2599.2.camel@localhost.localdomain> I didn't even know those files were in the repository. I suspect they are leftovers from original Bio::DB::GFF development. Given that the last time they were touched was over five years ago, and neither GBrowse nor any other GMOD project use them (that I know of), I think they can be safely removed. Scott On Wed, 2006-11-15 at 10:24 -0600, Chris Fields wrote: > > Does anyone know what purpose Bio/DB/Makefile.PL serves? If > > none, I propose removing it from CVS. > > > > Dave: Do you need anything to happen with > > doc/Deobfuscator/Makefile.PL when a user does a normal > > install of Bioperl? Or can it safely be ignored, only run > > manually by people who want to install Deobfuscator? > > The Bio/DB/Makefile.PL and MANIFEST could be GMOD- or Chado-related (they > are both related to Bio::DB::GFF). I'm not sure though; I'm cc'ing this to > Lincoln to see if they are still needed. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061115/e5f0620c/attachment-0002.bin> From pabignone at gmail.com Wed Nov 15 09:51:43 2006 From: pabignone at gmail.com (Paola Bignone) Date: Wed, 15 Nov 2006 14:51:43 +0000 Subject: [Bioperl-l] reverse complement - and features Message-ID: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Hi all, do you know of an easy way to reverse complement the sequence of an embl entry and the features associated with that sequence. I'm looking at genomic syntenic regions, and in some organisms the gene is in the plus strand while in others is in the minus. Thanks in advance, PAB From cjfields at uiuc.edu Wed Nov 15 14:16:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:16:34 -0600 Subject: [Bioperl-l] Fwd: Error while indexing whole genbank In-Reply-To: <68874599fabff74a65fcc62568022288@cnio.es> References: <68874599fabff74a65fcc62568022288@cnio.es> Message-ID: <E99B3889-1800-4A69-9F40-FEED774FD653@uiuc.edu> On Nov 15, 2006, at 11:43 AM, guillermo wrote: > Hello, > > I just indexed BCT without problems and now I am going to do it in > parts, different indexes for each one, for PLN, PRI, ROD, etc. > Anyways, I??l try to do it for the whole genbank and if it works I > ?ll let you know. > > Thanks for the support, > Guille My guess is that the full genbank file was way too large, so breaking them up by division is probably the way to go. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 14:18:18 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:18:18 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> <455B5954.1080209@sendu.me.uk> Message-ID: <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> On Nov 15, 2006, at 12:15 PM, Sendu Bala wrote: > ... > I think the compromise isn't worth it. The old Makefile.PL is just too > inadequate and I don't want to support it. Build.pl is simply far too > superior and I really want all users to be using it. > > I've now made the changeover in HEAD for core only (so far). > > Can people please try it out, especially wrt to installation in > default > and user-specified locations? > > First, clean out your system of the old Makefile.PL stuff: > perl Makefile.PL > make clean > rm Makefile.PL Makefile.old > cvs update -d -P > > Now try out the new Build.PL: > perl Build.PL > ./Build test > ./Build install > > Try out other things: > http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm > > You'll notice you don't have a Makefile.PL anymore. Distributions will > include one, and as a cvs user you can generate one by: > ./Build manifest > ./Build distmeta > > Now you can try out the things you used to be able to do: > make test > make install > > > Please let me know how you get on, > Sendu. Will do. We'll need to change all docs in CVS/wiki to conform with the new install routine. You'll probably want to post another interim RC before a final release just to make sure any residual bugs are worked out, unless you are just doing this in CVS HEAD. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 14:22:08 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:22:08 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> <455B5954.1080209@sendu.me.uk> <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> Message-ID: <455B68E0.9090308@sendu.me.uk> Chris Fields wrote: > Will do. We'll need to change all docs in CVS/wiki to conform with the > new install routine. You'll probably want to post another interim RC > before a final release just to make sure any residual bugs are worked > out, unless you are just doing this in CVS HEAD. There needs to be another RC for 1.5.2 for the remaining run package problems, so what I'll do is wait a little while longer for Build.PL feedback and when all seems well it'll go into 1.5.2 branch and become part of RC4. From bix at sendu.me.uk Wed Nov 15 14:33:33 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:33:33 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <OFAAF39FAB.9EB9DA23-ON85257227.00675002-85257227.00676C9E@gsk.com> References: <OFAAF39FAB.9EB9DA23-ON85257227.00675002-85257227.00676C9E@gsk.com> Message-ID: <455B6B8D.30508@sendu.me.uk> Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: > What actual needs prompted the change from ExtUtils::MakeMaker to > Module::Build? For the old Makefile.PL: At the time I started, script installation was broken. Documentation installation hasn't worked in a very long time. Handling of true requirements and optional pre-requisites is completely inadequate. It can't generate a suitable META.yml, and leaves the package non-ideal for distribution on CPAN. It was also a nightmare keeping the Makefile.PL scripts in each cvs module (live, run, db, network) in sync with each other. Now they can have simple module-specific Build.PL scripts, with all the advanced functionality in a rarely-updated and unchanged-between-modules ModuleBuildBioperl.pm. > It seems that the switch was made without a complete understanding of > all the bits and bobs in the existing Makefile.PL I hope that's not the case; I tried to understand everything. Please let me know if I've missed something. (To tidy up a question I asked about the symlink script, I've resolved that and the symlink should also work given the proviso outlined in the POD for maintenance/symlink_script.pl) > For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered > by the main Makefile.PL) such that users can choose whether to test > the install vs. a live database or not. The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such functionality. Letting the user choose to do live database tests was a function of the main Makefile.PL, which I have carried over to the new Build.PL. (And made it better in the process.) > This is an example of encapsulation: the specializied testing/install > process for a module is kept with the module, and not in the > monolithic main script. From a maintenance point of view, it seems to me to be much easier if all install-related things are in one place rather than scattered where you might miss things. > For two, it seems that the ability to install bp_*.pl scripts was > "lost" in the transition. What makes you say that? It certainly shouldn't be. What should happen is you get asked what scripts you'd like to install (the same question as before), but again its done in a much nicer way. (The major difference, I suppose, is that scripts_temp is no longer generated; prior to "./Build install" you'll find the scripts in blib/script/) > For three, there's certainly a lot more that I can't remember right > now. Please try and remember. I spent a lot of time trying to make sure that Build.PL does everything Makefile.PL did, but much much better. Thank you, Sendu. From bix at sendu.me.uk Wed Nov 15 14:09:01 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:09:01 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180CA3A.B599%bosborne11@verizon.net> References: <C180CA3A.B599%bosborne11@verizon.net> Message-ID: <455B65CD.3020400@sendu.me.uk> Brian Osborne wrote: > Sendu, > > 177 ~/bioperl-live>./Build test > scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Can't copy('scripts/utilities/bp_sreformat.PLS', > 'blib/script/bp_sreformat.PLS'): Permission denied at > /Library/Perl/5.8.6/Module/Build/Base.pm line 3977. That's an odd one. Did you first start out with a clean bioperl-live (ie. one without a blib directory made by something else)? Is it consistent? If you run ./Build test again, does it keep happening? Does blib/script/bp_sreformat.PLS exist and what are its permissions? Did it manage to put anything at all in blib? Is ~/bioperl-live writable? From bix at sendu.me.uk Wed Nov 15 14:09:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:09:41 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <455B65F5.1030207@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > > Which is incorrect since there no "modules indicated above". Thanks, I'll look into it. Just to confirm, do you suppose that you have all pre-reqs installed? From cjfields at uiuc.edu Wed Nov 15 14:36:11 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:36:11 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <0FCFCA18-8FDC-4463-BF3B-1586145743CE@uiuc.edu> On Nov 15, 2006, at 12:33 PM, Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this > installation > > > Which is incorrect since there no "modules indicated above". > > > Brian O. > > > On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > >> Please let me know how you get on, Same here (Mac OS X). All tests pass, though (setting BIOPERLDEBUG=1): All tests successful, 6 subtests skipped. Files=236, Tests=12817, 398 wallclock secs (86.03 cusr + 14.12 csys = 100.15 CPU) I'll give WinXP a test to see how it fares. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Wed Nov 15 11:44:19 2006 From: jason at bioperl.org (Jason Stajich) Date: Wed, 15 Nov 2006 08:44:19 -0800 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> Message-ID: <1965DDC8-DC2E-4895-A6C9-BD7A15FACDF1@bioperl.org> On Nov 15, 2006, at 7:35 AM, Sendu Bala wrote: > Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I > propose removing it from CVS. this was from when Lincoln imported Bio::DB::GFF into Bioperl from a separate code base. I don't know that it serves any purpose but I would get an okay from Lincoln first. > > Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL > when a user does a normal install of Bioperl? Or can it safely be > ignored, only run manually by people who want to install Deobfuscator? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From bosborne11 at verizon.net Wed Nov 15 13:44:26 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 13:44:26 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> Message-ID: <C180CA3A.B599%bosborne11@verizon.net> Sendu, 177 ~/bioperl-live>./Build test scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Can't copy('scripts/utilities/bp_sreformat.PLS', 'blib/script/bp_sreformat.PLS'): Permission denied at /Library/Perl/5.8.6/Module/Build/Base.pm line 3977. Brian O. On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Please let me know how you get on, From bix at sendu.me.uk Wed Nov 15 15:20:26 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 20:20:26 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <455B768A.8060009@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > > Which is incorrect since there no "modules indicated above". Should be fixed now. From bix at sendu.me.uk Wed Nov 15 15:23:22 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 20:23:22 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C180E071.B5B0%bosborne11@verizon.net> References: <C180E071.B5B0%bosborne11@verizon.net> Message-ID: <455B773A.5080608@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I just looked at the most recent bioperl-db and bioperl-run, I don't see any > Build.pl there. Are you suggesting that the Bioperl core build should be > mediated by Build.pl yet all other packages are built by some Makefile.PL? No, once it seems like Build.PL is ok in core, I'll convert db, run and network over to it as well. From bosborne11 at verizon.net Wed Nov 15 14:24:12 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 14:24:12 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B65F5.1030207@sendu.me.uk> Message-ID: <C180D38C.B5A4%bosborne11@verizon.net> Sendu, According to my install of 1.5.2 RC3 I have all of the dependencies installed: *** Optional dependencies section *** All dependencies are installed So that line "ERRORS/WARNINGS FOUND IN PREREQUISITES.." shouldn't appear. Brian O. On 11/15/06 2:09 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Brian Osborne wrote: >> Sendu, >> >> I see: >> >> 175 ~/bioperl-live>perl Build.PL >> Checking prerequisites... >> >> ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the >> versions >> of the modules indicated above before proceeding with this installation >> >> >> Which is incorrect since there no "modules indicated above". > > Thanks, I'll look into it. Just to confirm, do you suppose that you have > all pre-reqs installed? From cjfields at uiuc.edu Wed Nov 15 15:52:23 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 14:52:23 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B68E0.9090308@sendu.me.uk> Message-ID: <001601c708f7$f441dd50$15327e82@pyrimidine> > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Sendu Bala > Sent: Wednesday, November 15, 2006 1:22 PM > To: bioperl-l > Subject: Re: [Bioperl-l] No more Makefile.PL (MakeMaker -> > Module::Build) > > Chris Fields wrote: > > Will do. We'll need to change all docs in CVS/wiki to conform with > > the new install routine. You'll probably want to post > another interim > > RC before a final release just to make sure any residual bugs are > > worked out, unless you are just doing this in CVS HEAD. > > There needs to be another RC for 1.5.2 for the remaining run > package problems, so what I'll do is wait a little while > longer for Build.PL feedback and when all seems well it'll go > into 1.5.2 branch and become part of RC4. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l All tests pass for WinXP. If anyone wants to install from CVS using WinXP we'll need to get them to install Module::Build, as it doesn't come standard with ActivePerl (although a PPM is available). I'm guessing make/nmake is still required, though not explicitly. One oddity I noticed is if you use: perl Build.PL Build On Mac it manifies the POD; on WinXP it manify's and HTMLifies the POD. No idea why there is a difference between the two. I would suggest that we make this optional, though; not everybody wants the HTML/man pages. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 16:10:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 21:10:27 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <001601c708f7$f441dd50$15327e82@pyrimidine> References: <001601c708f7$f441dd50$15327e82@pyrimidine> Message-ID: <455B8243.4080809@sendu.me.uk> Chris Fields wrote: > All tests pass for WinXP. If anyone wants to install from CVS using > WinXP we'll need to get them to install Module::Build, as it doesn't > come standard with ActivePerl (although a PPM is available). I'm > guessing make/nmake is still required, though not explicitly. I think one of the benefits of Module::Build is that it is more cross-platform, and doesn't rely on a make-like thing. If you tried to install without Module::Build on WinXP, did you get some kind of meaningful error message? > One oddity I noticed is if you use: > > perl Build.PL Build > > On Mac it manifies the POD; on WinXP it manify's and HTMLifies the > POD. Nothing to do with me. I guess WinXP people like HTML docs :) > I would suggest that we make this optional, though; not everybody > wants the HTML/man pages. I disagree with making it optional, default off. I've never been aware of having the option to not install man pages for things that had man pages to install. It just happens and I'm glad of it. Its telling that there doesn't seem to be command line arg to turn doc installation off in Module::Build. Its a new functionality I'd have to add, I think. Is there actually any significant value in not installing docs? From bosborne11 at verizon.net Wed Nov 15 15:19:13 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 15:19:13 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <C180E071.B5B0%bosborne11@verizon.net> Sendu, I just looked at the most recent bioperl-db and bioperl-run, I don't see any Build.pl there. Are you suggesting that the Bioperl core build should be mediated by Build.pl yet all other packages are built by some Makefile.PL? Brian O. On 11/15/06 2:33 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: >> What actual needs prompted the change from ExtUtils::MakeMaker to >> Module::Build? > > For the old Makefile.PL: > At the time I started, script installation was broken. Documentation > installation hasn't worked in a very long time. Handling of true > requirements and optional pre-requisites is completely inadequate. It > can't generate a suitable META.yml, and leaves the package non-ideal for > distribution on CPAN. > > It was also a nightmare keeping the Makefile.PL scripts in each cvs > module (live, run, db, network) in sync with each other. Now they can > have simple module-specific Build.PL scripts, with all the advanced > functionality in a rarely-updated and unchanged-between-modules > ModuleBuildBioperl.pm. > > >> It seems that the switch was made without a complete understanding of >> all the bits and bobs in the existing Makefile.PL > > I hope that's not the case; I tried to understand everything. Please let > me know if I've missed something. (To tidy up a question I asked about > the symlink script, I've resolved that and the symlink should also work > given the proviso outlined in the POD for maintenance/symlink_script.pl) > > >> For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered >> by the main Makefile.PL) such that users can choose whether to test >> the install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such > functionality. Letting the user choose to do live database tests was a > function of the main Makefile.PL, which I have carried over to the new > Build.PL. (And made it better in the process.) > > >> This is an example of encapsulation: the specializied testing/install >> process for a module is kept with the module, and not in the >> monolithic main script. > > From a maintenance point of view, it seems to me to be much easier if > all install-related things are in one place rather than scattered where > you might miss things. > > >> For two, it seems that the ability to install bp_*.pl scripts was >> "lost" in the transition. > > What makes you say that? It certainly shouldn't be. What should happen > is you get asked what scripts you'd like to install (the same question > as before), but again its done in a much nicer way. > > (The major difference, I suppose, is that scripts_temp is no longer > generated; prior to "./Build install" you'll find the scripts in > blib/script/) > > >> For three, there's certainly a lot more that I can't remember right >> now. > > Please try and remember. I spent a lot of time trying to make sure that > Build.PL does everything Makefile.PL did, but much much better. > > > Thank you, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From aaron.j.mackey at gsk.com Wed Nov 15 13:29:30 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Wed, 15 Nov 2006 13:29:30 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" Message-ID: <OFE989A597.3219BF40-ON85257227.0064E293-85257227.00659451@gsk.com> What actual needs prompted the change from ExtUtils::MakeMaker to Module::Build? It seems that the switch was made without a complete understanding of all the bits and bobs in the existing Makefile.PL For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered by the main Makefile.PL) such that users can choose whether to test the install vs. a live database or not. This is an example of encapsulation: the specializied testing/install process for a module is kept with the module, and not in the monolithic main script. For two, it seems that the ability to install bp_*.pl scripts was "lost" in the transition. For three, there's certainly a lot more that I can't remember right now. I know Module::Build is shiny and new and preferred for startup development projects, but that cruddy old Makefile.PL still works, and does a number of clever things that do have reasons for existence, even if the collective wit of the mailing list can't remember all of them right away. -Aaron -- Aaron J. Mackey, Ph.D. Principal Scientist Bioinformatics Discovery & Analysis, Upper Providence GlaxoSmithKline 1250 South Collegeville Road, UP1345 P.O. Box 5089 Collegeville, PA 19426-0989 phone: 610-917-5761/8-282-5761 fax: 610-917-7901 email: Aaron.J.Mackey at gsk.com From bix at sendu.me.uk Wed Nov 15 16:28:30 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 21:28:30 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C180E8B3.B5B6%bosborne11@verizon.net> References: <C180E8B3.B5B6%bosborne11@verizon.net> Message-ID: <455B867E.8010001@sendu.me.uk> Brian Osborne wrote: > Sendu, > > One problem here, as I see it, is the fact that this change has been > introduced just days before the intended release. My intent is to go to RC4 instead, which pushes release a week or two away. God knows I wanted to release over a month ago, but I'm a perfectionist. > http://www.bioperl.org/wiki/Release_1.5.2 > > You won't find any mention of changing the build there, nor of Build.pl, or > Module::Build. This page is a nice example of "best practice", where > everything about the release is lined up and laid out, and making a big > change at the last minute is not best practice. Now, has Bioperl always made > a big deal out of best practice? No, but that's what's been nice about this > particular release so far, an emphasis on doing things correctly. This is assuredly all valid. But I feel this is a case of a necessary last minute addition. Necessary because I don't feel the old Makefile.PL is up to the job. Its merely unfortunate that I only discovered this so late into the RC cycle. Evidently I and all the other testers don't test the installation side of things, only the test scripts in t/. > Also, I understand that you think that your approach is better but such a > central change can't be adopted without discussion and some semblance of > consensus. So far I'm not getting any sense that anyone is agreeing with the > change but I am sensing discomfort with the idea, or resignation. I asked for comments and discussions 5 days ago. The only responses were positive or neutral (with reservations regarding putting it into 1.5.2, but not for the idea itself). If you don't press on and make things happen after positive feedback, nothing will ever get done at all. So to clarify, is anyone actually uncomfortable or 'resigned' to the idea? Does anyone feel strongly in favour of keeping Makefile.PL? > I have no strong opinion one way or another, Makefile or Build, but I do not > want to see significant changes at the last minute and I do not want > significant changes coming unilaterally. I agree. But again, I'm even less happy with the idea of releasing something that I know is inadequate simply because I discovered that too late. From cjfields at uiuc.edu Wed Nov 15 17:33:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 16:33:26 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <001901c70906$1441aa50$15327e82@pyrimidine> > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: .... > > For one, the Bio::DB::GFF Makefile.PL is independent (yet > triggered by > > the main Makefile.PL) such that users can choose whether to > test the > > install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves > no such functionality. Letting the user choose to do live > database tests was a function of the main Makefile.PL, which > I have carried over to the new Build.PL. (And made it better > in the process.) Scott Cain also indicated the Bio/DB Makefile.PL and MANIFEST files were not used anymore. ... > > For three, there's certainly a lot more that I can't remember right > > now. > > Please try and remember. I spent a lot of time trying to make > sure that Build.PL does everything Makefile.PL did, but much > much better. > > > Thank you, > Sendu. We can always reinstate the Makefile.PL if things blow up; I don't think they will, but that's what CVS is good for. I haven't had any problems on WinXP or Mac OS X yet beyond the pre-req error message Brian pointed out (and scripts seem to install fine on both OS's). Personally, I would have liked to wait until after the 1.5.2 final release to avoid any confusion and documentation changes, but that's not my call. We do need to let Scott and Lincoln in on these changes (they only know about the removal of the Bio/DB Makefile.PL). I think various install scripts look for a Makefile.PL, so if it isn't there things will tank on their end. We also need to post this everywhere possible in very big neon-colored letters (with fireworks and so on), since most users are used to 'perl Makefile.PL; make; make install'. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From pabignone at gmail.com Wed Nov 15 09:51:43 2006 From: pabignone at gmail.com (Paola Bignone) Date: Wed, 15 Nov 2006 14:51:43 +0000 Subject: [Bioperl-l] reverse complement - and features Message-ID: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Hi all, do you know of an easy way to reverse complement the sequence of an embl entry and the features associated with that sequence. I'm looking at genomic syntenic regions, and in some organisms the gene is in the plus strand while in others is in the minus. Thanks in advance, PAB From bix at sendu.me.uk Wed Nov 15 18:08:00 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:08:00 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c70906$1441aa50$15327e82@pyrimidine> References: <001901c70906$1441aa50$15327e82@pyrimidine> Message-ID: <455B9DD0.5000409@sendu.me.uk> Chris Fields wrote: > > We do need to let Scott and Lincoln in on these changes (they only know > about the removal of the Bio/DB Makefile.PL). I think various install > scripts look for a Makefile.PL, so if it isn't there things will tank on > their end. We also need to post this everywhere possible in very big > neon-colored letters (with fireworks and so on), since most users are used > to 'perl Makefile.PL; make; make install'. It doesn't need to be neon because most users will still be able to do exactly that; Makefile.PL will be part of the distributions (having been generated by Build.PL). For most people, there's not going to be any significant difference with this change. It'll be more like a behind-the-scenes thing. From lincoln.stein at gmail.com Wed Nov 15 17:43:21 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 15 Nov 2006 17:43:21 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B867E.8010001@sendu.me.uk> References: <C180E8B3.B5B6%bosborne11@verizon.net> <455B867E.8010001@sendu.me.uk> Message-ID: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> > > This is assuredly all valid. But I feel this is a case of a necessary > last minute addition. Necessary because I don't feel the old Makefile.PL > is up to the job. Its merely unfortunate that I only discovered this so > late into the RC cycle. Evidently I and all the other testers don't test > the installation side of things, only the test scripts in t/ > I tested script installation last week and it was all fine as far as I could tell. Are there any details about how installation was failing? Lincoln > Also, I understand that you think that your approach is better but such a > > central change can't be adopted without discussion and some semblance of > > consensus. So far I'm not getting any sense that anyone is agreeing with > the > > change but I am sensing discomfort with the idea, or resignation. > > I asked for comments and discussions 5 days ago. The only responses were > positive or neutral (with reservations regarding putting it into 1.5.2, > but not for the idea itself). If you don't press on and make things > happen after positive feedback, nothing will ever get done at all. Sorry, but I didn't see the discussion. So to clarify, is anyone actually uncomfortable or 'resigned' to the > idea? Does anyone feel strongly in favour of keeping Makefile.PL? I'm sorry we have to push the release back. I was unaware that Makefile.PLwas broken -- my preference would have been to fix it rather than to rewrite things from scratch. Lincoln > I have no strong opinion one way or another, Makefile or Build, but I do > not > > want to see significant changes at the last minute and I do not want > > significant changes coming unilaterally. > > I agree. But again, I'm even less happy with the idea of releasing > something that I know is inadequate simply because I discovered that too > late. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Wed Nov 15 17:31:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 16:31:56 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B8243.4080809@sendu.me.uk> Message-ID: <001801c70905$dbdd7a40$15327e82@pyrimidine> > Chris Fields wrote: > > All tests pass for WinXP. If anyone wants to install from > CVS using > > WinXP we'll need to get them to install Module::Build, as > it doesn't > > come standard with ActivePerl (although a PPM is available). I'm > > guessing make/nmake is still required, though not explicitly. > > I think one of the benefits of Module::Build is that it is > more cross-platform, and doesn't rely on a make-like thing. > > If you tried to install without Module::Build on WinXP, did > you get some kind of meaningful error message? Yes: C:\Perl\src\bioperl\core>perl Build.PL Base class package "Module::Build" is empty. (Perhaps you need to 'use' the module which defines that package first.) at ModuleBuildBioperl.pm line 12 BEGIN failed--compilation aborted at ModuleBuildBioperl.pm line 12. Compilation failed in require at Build.PL line 16. BEGIN failed--compilation aborted at Build.PL line 16. Which clued me in immediately. > > One oddity I noticed is if you use: > > > > perl Build.PL Build > > > > On Mac it manifies the POD; on WinXP it manify's and HTMLifies the > > POD. > > Nothing to do with me. I guess WinXP people like HTML docs :) > > > > I would suggest that we make this optional, though; not everybody > > wants the HTML/man pages. > > I disagree with making it optional, default off. I've never > been aware of having the option to not install man pages for > things that had man pages to install. It just happens and I'm > glad of it. > > Its telling that there doesn't seem to be command line arg to > turn doc installation off in Module::Build. Its a new > functionality I'd have to add, I think. Is there actually any > significant value in not installing docs? HTML docs are made by PPM upon module installation, so there is no need for making HTML at least on WinXP (and the conversion almost triples the time for the Build step). However, oddly, using 'Build test' only manifies the docs on WinXP (using 'Build' does both man and HTML). I have a feeling we will run into this very rarely (the average WinXP user will install using PPM), so it's not an immediate problem. I would like to hear what Mauricio finds on FreeBSD and see how other OS's fare. I see that there is a PPMMaker module with Module::Build, so we'll have to look into that for WinXP PPMs.. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 18:19:47 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:19:47 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> References: <C180E8B3.B5B6%bosborne11@verizon.net> <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> Message-ID: <455BA093.8040603@sendu.me.uk> Lincoln Stein wrote: > Sendu Bala wrote: > This is assuredly all valid. But I feel this is a case of a necessary > last minute addition. Necessary because I don't feel the old Makefile.PL > is up to the job. Its merely unfortunate that I only discovered this so > late into the RC cycle. Evidently I and all the other testers don't test > the installation side of things, only the test scripts in t/ > > I tested script installation last week and it was all fine as far as I > could tell. Are there any details about how installation was failing? Maybe this aspect got broken since after you tested (I don't think so though, judging by the fix), but scripts only got put in scripts_temp and nowhere else. The major prompt for the change was needing a complete META.yml for CPAN... > So to clarify, is anyone actually uncomfortable or 'resigned' to the > idea? Does anyone feel strongly in favour of keeping Makefile.PL? > > I'm sorry we have to push the release back. I was unaware that > Makefile.PL was broken -- my preference would have been to fix it rather > than to rewrite things from scratch. ... I'd have had to do far more rewriting things from scratch to get a complete META.yml out of Makefile.PL. I didn't want to reinvent the wheel, and Module::Build has lots of other benefits as well. I'd already done major adjustments to Makefile.PL previously; the move to Build.PL can be seen as just one more major behind-the-scenes adjustment, since Makefile.PL will still exist in distributions (having been generated by Build.PL) and people can still install the same way they have done in the past. The only real change for most users is that they now need Module::Build installed. From bix at sendu.me.uk Wed Nov 15 18:57:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:57:14 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810D8A.B5D0%bosborne11@verizon.net> References: <C1810D8A.B5D0%bosborne11@verizon.net> Message-ID: <455BA95A.5040404@sendu.me.uk> Brian Osborne wrote: > Sendu, > > This is not right. I just removed all the build stuff, Makefile* and Build*, > and did an update. There's no Makefile.PL, it's not part of the > distribution, there is Build.PL. As I mentioned in the other thread, Makefile.PL isn't in CVS, but it will be generated and included in distributions (ie. in .tar.gz file that you download from the website or via CPAN). As a CVS user you can generate one for yourself by: perl Build.PL ./Build manifest ./Build distmeta You should now have Makefile.PL on which you can do the usual stuff: perl Makefile.PL make make test make install From bosborne11 at verizon.net Wed Nov 15 15:54:27 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 15:54:27 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <C180E8B3.B5B6%bosborne11@verizon.net> Sendu, One problem here, as I see it, is the fact that this change has been introduced just days before the intended release. Take a look at the page that's supposed to describe 1.5.2 and associated work: http://www.bioperl.org/wiki/Release_1.5.2 You won't find any mention of changing the build there, nor of Build.pl, or Module::Build. This page is a nice example of "best practice", where everything about the release is lined up and laid out, and making a big change at the last minute is not best practice. Now, has Bioperl always made a big deal out of best practice? No, but that's what's been nice about this particular release so far, an emphasis on doing things correctly. That, and having enough people to do the work! Also, I understand that you think that your approach is better but such a central change can't be adopted without discussion and some semblance of consensus. So far I'm not getting any sense that anyone is agreeing with the change but I am sensing discomfort with the idea, or resignation. I have no strong opinion one way or another, Makefile or Build, but I do not want to see significant changes at the last minute and I do not want significant changes coming unilaterally. Brian O. On 11/15/06 2:33 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: >> What actual needs prompted the change from ExtUtils::MakeMaker to >> Module::Build? > > For the old Makefile.PL: > At the time I started, script installation was broken. Documentation > installation hasn't worked in a very long time. Handling of true > requirements and optional pre-requisites is completely inadequate. It > can't generate a suitable META.yml, and leaves the package non-ideal for > distribution on CPAN. > > It was also a nightmare keeping the Makefile.PL scripts in each cvs > module (live, run, db, network) in sync with each other. Now they can > have simple module-specific Build.PL scripts, with all the advanced > functionality in a rarely-updated and unchanged-between-modules > ModuleBuildBioperl.pm. > > >> It seems that the switch was made without a complete understanding of >> all the bits and bobs in the existing Makefile.PL > > I hope that's not the case; I tried to understand everything. Please let > me know if I've missed something. (To tidy up a question I asked about > the symlink script, I've resolved that and the symlink should also work > given the proviso outlined in the POD for maintenance/symlink_script.pl) > > >> For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered >> by the main Makefile.PL) such that users can choose whether to test >> the install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such > functionality. Letting the user choose to do live database tests was a > function of the main Makefile.PL, which I have carried over to the new > Build.PL. (And made it better in the process.) > > >> This is an example of encapsulation: the specializied testing/install >> process for a module is kept with the module, and not in the >> monolithic main script. > > From a maintenance point of view, it seems to me to be much easier if > all install-related things are in one place rather than scattered where > you might miss things. > > >> For two, it seems that the ability to install bp_*.pl scripts was >> "lost" in the transition. > > What makes you say that? It certainly shouldn't be. What should happen > is you get asked what scripts you'd like to install (the same question > as before), but again its done in a much nicer way. > > (The major difference, I suppose, is that scripts_temp is no longer > generated; prior to "./Build install" you'll find the scripts in > blib/script/) > > >> For three, there's certainly a lot more that I can't remember right >> now. > > Please try and remember. I spent a lot of time trying to make sure that > Build.PL does everything Makefile.PL did, but much much better. > > > Thank you, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Wed Nov 15 18:59:19 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:59:19 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810E20.B5D2%bosborne11@verizon.net> References: <C1810E20.B5D2%bosborne11@verizon.net> Message-ID: <455BA9D7.6020906@sendu.me.uk> Brian Osborne wrote: > Lincoln, > > All I know was the scripts weren't being installed, I fixed this by adding > "use IO::File" to Makefile.PL. Sendu mentioned a problem with documentation, > I don't know what he meant by this. 'man' docs weren't being generated/installed apparently due to some kind of issue with command line length. That's been a long-standing issue. From cjfields at uiuc.edu Wed Nov 15 19:01:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 18:01:57 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810D8A.B5D0%bosborne11@verizon.net> Message-ID: <001d01c70912$723c8a60$15327e82@pyrimidine> Brian, I think he means the actual releases or the 1.5.2 branch, not CVS. Sendu, I am seeing a general consensus towards not using Module::Build just now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar and I also had stated previously that this should probably wait until after 1.5.2 (which you seemed to agree with). I think we are all for the idea of moving forward, but it's a lot to impose just prior to a release (not to mention Thanksgiving here!). I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we should stick with that for now (i.e. not change over to Module::Build on the 1.5.2 branch). The install script fix that Brian committed to Makefile.PL in CVS HEAD prior to removal could be merged to branch-1.5.2. We could leave the Module::Build stuff in CVS for the next release to work out the bugs. I'm not sure whether we can have both Build.PL and Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl Build.PL' just overwrite the old Makefile.PL anyway? chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign > -----Original Message----- > From: Brian Osborne [mailto:bosborne11 at verizon.net] > Sent: Wednesday, November 15, 2006 5:32 PM > To: Sendu Bala; Chris Fields > Cc: aaron.j.mackey at gsk.com; bioperl-l > Subject: Re: [Bioperl-l] "progress": useful changes vs. > "shiny new thingie" > > Sendu, > > This is not right. I just removed all the build stuff, > Makefile* and Build*, and did an update. There's no > Makefile.PL, it's not part of the distribution, there is Build.PL. > > Brian O. > > > On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > > > exactly that; Makefile.PL will be part of the distributions (having > > been generated by Build.PL). > > From bix at sendu.me.uk Wed Nov 15 19:27:31 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 00:27:31 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001d01c70912$723c8a60$15327e82@pyrimidine> References: <001d01c70912$723c8a60$15327e82@pyrimidine> Message-ID: <455BB073.9040205@sendu.me.uk> Chris Fields wrote: > Brian, > > I think he means the actual releases or the 1.5.2 branch, not CVS. > > Sendu, I am seeing a general consensus towards not using Module::Build just > now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar and I also > had stated previously that this should probably wait until after 1.5.2 > (which you seemed to agree with). I think we are all for the idea of moving > forward, but it's a lot to impose just prior to a release (not to mention > Thanksgiving here!). > > I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we > should stick with that for now (i.e. not change over to Module::Build on the > 1.5.2 branch). The install script fix that Brian committed to Makefile.PL > in CVS HEAD prior to removal could be merged to branch-1.5.2. Its certainly possible to stay with Makefile.PL on the 1.5.2 branch. I /think/ that if I took a META.yml generated from HEAD's Build.PL and added it to the branch that should solve the CPAN issue at least. I would just want clarification that the consensus really is to stay with Makefile.PL for 1.5.2. The primary argument seems to be to not have anything too new and untested in the branch, but Makefile.PL itself has lots of new additions. My Makefile.PL improvements and the change to Build.PL have all been in the name of making 1.5.2 install well. The move to Build.PL was just the most appropriate way to fix some bugs and make needed changes. > We could leave the Module::Build stuff in CVS for the next release to work > out the bugs. I'm not sure whether we can have both Build.PL and > Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl Build.PL' > just overwrite the old Makefile.PL anyway? It would, but why would we want both in CVS? I'd strongly advise the cessation of development on the old Makefile.PL, and if it isn't going to be added to anymore, nor used by anyone, why keep it in CVS? It's just going to cause confusion and problems with people coming across issues in the old Makefile.PL. Wasted development time if someone tries to fix something in Makefile.PL that was already solved in Build.PL. Bizarre behaviour if you were doing something with old Makefile.PL but then managed to overwrite it with Build.PL's Makefile.PL and suddenly you're working with a whole different script. In short, not the most optimal of situations. From bosborne11 at verizon.net Wed Nov 15 18:31:38 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 18:31:38 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B9DD0.5000409@sendu.me.uk> Message-ID: <C1810D8A.B5D0%bosborne11@verizon.net> Sendu, This is not right. I just removed all the build stuff, Makefile* and Build*, and did an update. There's no Makefile.PL, it's not part of the distribution, there is Build.PL. Brian O. On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > exactly that; Makefile.PL will be part of the distributions (having been > generated by Build.PL). From bosborne11 at verizon.net Wed Nov 15 18:34:08 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 18:34:08 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> Message-ID: <C1810E20.B5D2%bosborne11@verizon.net> Lincoln, All I know was the scripts weren't being installed, I fixed this by adding "use IO::File" to Makefile.PL. Sendu mentioned a problem with documentation, I don't know what he meant by this. Brian O. On 11/15/06 5:43 PM, "Lincoln Stein" <lincoln.stein at gmail.com> wrote: > I tested script installation last week and it was all fine as far as I could > tell. Are there any details about how installation was failing? From bosborne11 at verizon.net Wed Nov 15 20:43:32 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 20:43:32 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BA95A.5040404@sendu.me.uk> Message-ID: <C1812C74.B5E3%bosborne11@verizon.net> Sendu, If I'm understanding you correctly you're saying that someone checking out bioperl-live, HEAD, would not see a Makefile.PL if we chose to use Build.PL, yes? And there would be a Makefile.PL in the distributions, yes? Brian O. On 11/15/06 6:57 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Brian Osborne wrote: >> Sendu, >> >> This is not right. I just removed all the build stuff, Makefile* and Build*, >> and did an update. There's no Makefile.PL, it's not part of the >> distribution, there is Build.PL. > > As I mentioned in the other thread, Makefile.PL isn't in CVS, but it > will be generated and included in distributions (ie. in .tar.gz file > that you download from the website or via CPAN). > > As a CVS user you can generate one for yourself by: > perl Build.PL > ./Build manifest > ./Build distmeta > > You should now have Makefile.PL on which you can do the usual stuff: > perl Makefile.PL > make > make test > make install From stefan.kirov at bms.com Wed Nov 15 19:34:02 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Wed, 15 Nov 2006 19:34:02 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" Message-ID: <db32bddda3.ddda3db32b@bms.com> Maybe I will just reiterate myself. I think the idea is good, but timing is bad. Sendu, from purely socialogical point of view Makefile.PL should be there. I bet that significant percent of the users would do cvs checkout, type perl Makefile.PL and start cursing. Perhaps you would not do this, but many of us do not read most of the docs, unless nothing else works. As a result you would have confusion and frustration. Many people would google 'bioperl install' and come up with old docs and wonder why it does not work. In a perfect world it would work. Just my thoughts. Stefan ----- Original Message ----- From: Chris Fields <cjfields at uiuc.edu> Date: Wednesday, November 15, 2006 7:01 pm Subject: Re: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" > Brian, > > I think he means the actual releases or the 1.5.2 branch, not CVS. > > Sendu, I am seeing a general consensus towards not using > Module::Build just > now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar > and I also > had stated previously that this should probably wait until after 1.5.2 > (which you seemed to agree with). I think we are all for the idea > of moving > forward, but it's a lot to impose just prior to a release (not to > mentionThanksgiving here!). > > I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we > should stick with that for now (i.e. not change over to > Module::Build on the > 1.5.2 branch). The install script fix that Brian committed to > Makefile.PLin CVS HEAD prior to removal could be merged to branch- > 1.5.2. > > We could leave the Module::Build stuff in CVS for the next release > to work > out the bugs. I'm not sure whether we can have both Build.PL and > Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl > Build.PL'just overwrite the old Makefile.PL anyway? > > chris > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > -----Original Message----- > > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > Sent: Wednesday, November 15, 2006 5:32 PM > > To: Sendu Bala; Chris Fields > > Cc: aaron.j.mackey at gsk.com; bioperl-l > > Subject: Re: [Bioperl-l] "progress": useful changes vs. > > "shiny new thingie" > > > > Sendu, > > > > This is not right. I just removed all the build stuff, > > Makefile* and Build*, and did an update. There's no > > Makefile.PL, it's not part of the distribution, there is Build.PL. > > > > Brian O. > > > > > > On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > > > > > exactly that; Makefile.PL will be part of the distributions > (having > > > been generated by Build.PL). > > > > > > _______________________________________________ > 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 Nov 15 20:48:43 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 20:48:43 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> Message-ID: <C1812DAB.B5E5%bosborne11@verizon.net> Sendu, That's right. Brian O. On 11/15/06 7:27 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. From joannec at bii.a-star.edu.sg Wed Nov 15 21:11:31 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 02:11:31 +0000 (UTC) Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations Message-ID: <loom.20061116T030106-109@post.gmane.org> Hi, I am a new user to BioPerl and am encountering some problems while parsing location statements. I have read the link http://www.bioperl.org/wiki/FAQ#How_do_I_parse_the_CDS_join_or_complement_statements_in_GenBank_or_EMBL_files_to_get_the_sub-locations.3F and tried to implement this. However I am encountering some problems. Given a testcase: CDS join(752472..752685,752752..753298,753335..754039) CDS complement(637431..639525) CDS 741745..741781 This means that my file has join, complement and simple location statements. Using Bio::Location::SplitLocationI object to get the coordinates, my output is: CDS 752472..752685,752752..753298,753335..754039 CDS CDS The complement and simple location statements were not parsed properly. Am I using the right BioPerl module to parse? Kindly assist on the appropriate steps to retrieve all 3 different location types. Thanks! Joanne From cjfields at uiuc.edu Wed Nov 15 21:33:25 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 20:33:25 -0600 Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations In-Reply-To: <loom.20061116T030106-109@post.gmane.org> References: <loom.20061116T030106-109@post.gmane.org> Message-ID: <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> On Nov 15, 2006, at 8:11 PM, Joanne Chen wrote: > Hi, > I am a new user to BioPerl and am encountering some problems while > parsing > location statements. > > I have read the link > http://www.bioperl.org/wiki/ > FAQ#How_do_I_parse_the_CDS_join_or_complement_statements_in_GenBank_or > _EMBL_files_to_get_the_sub-locations.3F > and tried to implement this. > > However I am encountering some problems. > > Given a testcase: > > CDS join(752472..752685,752752..753298,753335..754039) > > > CDS complement(637431..639525) > > > CDS 741745..741781 > > > This means that my file has join, complement and simple location > statements. > > Using Bio::Location::SplitLocationI object to get the coordinates, > my output is: > > CDS 752472..752685,752752..753298,753335..754039 > > CDS > > CDS > > > The complement and simple location statements were not parsed > properly. Am I > using the right BioPerl module to parse? Kindly assist on the > appropriate steps > to retrieve all 3 different location types. Thanks! > > > Joanne > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l If you are using the loop as shown in the FAQ: foreach my $feature ($seqobj->top_SeqFeatures){ if ( $feature->location->isa('Bio::Location::SplitLocationI') and $feature->primary_tag eq 'CDS' ) { foreach my $location ( $feature->location->sub_Location ) { print $location->start , ".." , $location->end, "\n"; } } } it will skip over simple locations, so the last two are passed over. You probably should use: foreach my $feature ($seqobj->top_SeqFeatures){ if ( $feature->primary_tag eq 'CDS' ) { foreach my $location ( $feature->location->each_Location ) { print $location->start , ".." , $location->end, "\n"; } } } Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 21:44:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 20:44:05 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> Message-ID: <DEAB987E-4700-4677-979B-E5708F6905D3@uiuc.edu> On Nov 15, 2006, at 6:27 PM, Sendu Bala wrote: >> I think the old Makefile.PL is still in the 1.5.2 branch. So >> maybe we >> should stick with that for now (i.e. not change over to >> Module::Build on the >> 1.5.2 branch). The install script fix that Brian committed to >> Makefile.PL >> in CVS HEAD prior to removal could be merged to branch-1.5.2. > > Its certainly possible to stay with Makefile.PL on the 1.5.2 branch. I > /think/ that if I took a META.yml generated from HEAD's Build.PL and > added it to the branch that should solve the CPAN issue at least. > > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. The primary argument seems to be to not > have > anything too new and untested in the branch, but Makefile.PL itself > has > lots of new additions. My Makefile.PL improvements and the change to > Build.PL have all been in the name of making 1.5.2 install well. The > move to Build.PL was just the most appropriate way to fix some bugs > and > make needed changes. Right, but those changes were made w/o much discussion; what discussion there was seemed to end with the agreement this would wait until after rel. 1.5.2. I think that's the main point. That and the timing seems to be a little off for implementing this (after three RC's and just prior to a final release). Everyone seems to think that switching to Module::Build would be a good idea, but the move was made rather arbitrarily and (borrowing Brian's well-chosen word) unilaterally. And, although the Makefile.PL was a bit clunky, it works for now. >> We could leave the Module::Build stuff in CVS for the next release >> to work >> out the bugs. I'm not sure whether we can have both Build.PL and >> Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl >> Build.PL' >> just overwrite the old Makefile.PL anyway? > > It would, but why would we want both in CVS? I'd strongly advise the > cessation of development on the old Makefile.PL, and if it isn't going > to be added to anymore, nor used by anyone, why keep it in CVS? It's > just going to cause confusion and problems with people coming across > issues in the old Makefile.PL. Wasted development time if someone > tries > to fix something in Makefile.PL that was already solved in Build.PL. > Bizarre behaviour if you were doing something with old Makefile.PL but > then managed to overwrite it with Build.PL's Makefile.PL and suddenly > you're working with a whole different script. > > In short, not the most optimal of situations. Stefan has hit upon the problem very succinctly; there is no Makefile.PL in CVS, so anyone checking out bioperl-live will immediately run into problems. Hence, there has to be a Makefile.PL in CVS HEAD, be it the old one or a new one, at least for the time being. And it seems many still want the old Makefile.PL for now (which is why I suggested it). If you left the old Makefile.PL in you could always add a deprecation message indicating the switch. It will at least give everybody some time to get used to using Module::Build and the new system (and hopefully dissuade them from working on it). Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From joannec at bii.a-star.edu.sg Wed Nov 15 22:17:27 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 03:17:27 +0000 (UTC) Subject: [Bioperl-l] =?utf-8?q?Parsing_the_CDS_join_or_complement_statemen?= =?utf-8?q?ts_to=09get_the_sub-locations?= References: <loom.20061116T030106-109@post.gmane.org> <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> Message-ID: <loom.20061116T041551-540@post.gmane.org> Thanks a lot for your help. It works. =) However I have a small problem. Now I would also like to determine its strand-ie. negative strand for complement and positive for all others. Is there a function to determine and print its strand OR a function to determine if it is a complement, join or simple? Joanne. From pmiguel at purdue.edu Wed Nov 15 22:53:02 2006 From: pmiguel at purdue.edu (Phillip SanMiguel) Date: Wed, 15 Nov 2006 22:53:02 -0500 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> Message-ID: <455BE09E.4020408@purdue.edu> Chris Fields wrote: >> I wish to fetch consensus sequence and the names of the trace >> (chromat) >> files used in the assembly from the .ace file >> >> For this purpose, I am using Bio::Assembly::IO. But I am unable to >> find the >> appropriate methods which would enable me to fetch this information. >> >> >> >> [..base segment documentation elided...] >> >> >> How do I retrieve this information contig wise? >> >> Kindly help. >> >> Regards, >> >> Sayali D Salodkar >> > > It looks like the relevant part of the Bio::Assembly::IO::ace parser > responsible for parsing this is commented out: > > # Loading base segments definitions (Base Segment field) > # /^BS (\d+) (\d+) (\S+)/ && do { > # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} > {'segments'})) { > # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . > " " . $2; > # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = > $1 . " " . $2 } > # }; > > I'm not sure why to be honest as I'm not very familiar with the > Bio::Assembly. Have you tried removing the comments to see what > happens? > > Chris, I'm pretty sure that the Base Segment tag (BS) is not the one Sayali wants. At least that is my reading of Sayali's wanting to get the consensus sequence and the traces names used in the assembly. I write this because of an email sent me by David Gordon in 2001 included here without his permission: > Phrap writes BS lines which > indicate, for each consensus position, which read phrap uses at that > position to become the consensus. These BS ("base segments") are > manipulated by Consed when there are changes to the assembly, such as > joins, tears, removing reads, or changing the consensus. Which is basically what Sayali quoted from the documentation from phrap. But it is not consistent with "trace names used in the assembly". -- Phillip From hlapp at gmx.net Thu Nov 16 00:52:23 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Nov 2006 00:52:23 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> Message-ID: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. The primary argument seems to be to not > have > anything too new and untested in the branch, but Makefile.PL itself > has > lots of new additions. My Makefile.PL improvements and the change to > Build.PL have all been in the name of making 1.5.2 install well. The > move to Build.PL was just the most appropriate way to fix some bugs > and > make needed changes. My take on this, aside from having said before that the move to Module::Build is certainly a good one except with not-so-great timing, is that the distribution if at all possible should have a working Makefile.PL. If Build.PL can coexist that'd be great. That would give you the opportunity to have Makefile.PL print out a message right at the beginning that if the installation process messes up one should try Build.PL. This would spare you from fixing any problems in Makefile.PL that are fixed in the Build.PL approach. As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub that just prints out a message telling you to use Build.PL and does nothing else. If you check out bioperl-live from CVS you need to be prepared to having checked out the live edge of the code. Edges can be rough. The key thing is that the build process works. Finally let's not forget that this is still a developer release. That means that a) perfection isn't needed, rather shorter release cycles, and b) development implies change. So the main reason why I find the timing less than optimal is because it prolongs the time until the next release. Implementing changes like this do require a lot of energy. I very much appreciate that Sendu invested the time and energy to make it work, even though unfortunately at the last hour. Who knows who would have had the energy after the release. If Sendu hadn't put in the work now, the next release master may have been stuck with an even messier Makefile.PL system. Instead of Monday morning quarterbacking after no-one stopped him when he asked about it, we should all help him make the release - and the build change - successful now that he has done most if not all of the migration work already. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Thu Nov 16 02:47:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 07:47:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1812C74.B5E3%bosborne11@verizon.net> References: <C1812C74.B5E3%bosborne11@verizon.net> Message-ID: <455C1790.3080408@sendu.me.uk> Brian Osborne wrote: > Sendu, > > If I'm understanding you correctly you're saying that someone checking out > bioperl-live, HEAD, would not see a Makefile.PL if we chose to use Build.PL, > yes? And there would be a Makefile.PL in the distributions, yes? Yes, that is what I had meant. Though now following Hilmar's suggestion, I might create a stub in CVS for Makefile.PL that tells you to use Build.PL. I don't think it appropriate to have a working Makefile.PL in CVS though; not the old one for reasons outlined previously, and not one generated by Build.PL, because generated files don't need version control and only confuse matters when they become controlled. Ok, so the current plan is: # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml # CVS core gets a Makefile.PL stub telling you to use Build.PL # CVS db, run, network stay with Makefile.PL until after final release of 1.5.2, then move to Build.PL with Makefile.PL stub (because they don't have a 1.5.2 branch) Is everyone happy with that, or are there further suggestions for something better? From joannec at bii.a-star.edu.sg Thu Nov 16 02:55:22 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 07:55:22 +0000 (UTC) Subject: [Bioperl-l] =?utf-8?q?Parsing_the_CDS_join_or_complement_statemen?= =?utf-8?q?ts_to=09get_the_sub-locations?= References: <loom.20061116T030106-109@post.gmane.org> <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> <loom.20061116T041551-540@post.gmane.org> Message-ID: <loom.20061116T085446-347@post.gmane.org> Got the strand problem fixed. Thanks. =) From bix at sendu.me.uk Thu Nov 16 02:55:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 07:55:41 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C1790.3080408@sendu.me.uk> References: <C1812C74.B5E3%bosborne11@verizon.net> <455C1790.3080408@sendu.me.uk> Message-ID: <455C197D.6000107@sendu.me.uk> Sendu Bala wrote: > Brian Osborne wrote: >> Sendu, >> >> If I'm understanding you correctly you're saying that someone checking >> out >> bioperl-live, HEAD, would not see a Makefile.PL if we chose to use >> Build.PL, >> yes? And there would be a Makefile.PL in the distributions, yes? > > Yes, that is what I had meant. Though now following Hilmar's suggestion, > I might create a stub in CVS for Makefile.PL that tells you to use > Build.PL. I don't think it appropriate to have a working Makefile.PL in > CVS though; not the old one for reasons outlined previously, and not one > generated by Build.PL, because generated files don't need version > control and only confuse matters when they become controlled. > > Ok, so the current plan is: > # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml Also, # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who read the docs on the website/elsewhere (which will be updated to explain the new Build.PL system) don't get confused when that doesn't work, for wide testing, and to get people used to it for the next release. The old Makefile.PL will have 2 changes: Brians bug-fix and a little message pointing out that Build.PL is now the preferred installation system, but Makefile.PL still works. > # CVS core gets a Makefile.PL stub telling you to use Build.PL > # CVS db, run, network stay with Makefile.PL until after final release > of 1.5.2, then move to Build.PL with Makefile.PL stub (because they > don't have a 1.5.2 branch) > > Is everyone happy with that, or are there further suggestions for > something better? From rvosa at sfu.ca Thu Nov 16 02:19:43 2006 From: rvosa at sfu.ca (Rutger Vos) Date: Wed, 15 Nov 2006 23:19:43 -0800 Subject: [Bioperl-l] indexing with several processors In-Reply-To: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> References: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> Message-ID: <455C110F.4000600@sfu.ca> I notice nobody has responded yet. Without looking at the code I'm guessing here, but I would be very surprised if any part of bioperl is smart enough to be able to switch to some kind of mpi architecture, or any other clever way of parallelizing tasks on multi-processor architectures. If you can split the job up by hand and start scripts on the chunks, that might work. Good luck, Rutger guillermo wrote: > Hello, > > While using the Bio::Index::GenBank module for indexing Genbank, is > there any option to run the process with more than one processor. > > Thanks > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los > ficheros adjuntos, pueden contener informaci?n protegida para el uso > exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n > o cualquier otro tipo de transmisi?n por parte de otra persona que no > sea el destinatario. Si usted recibe por error este correo, se ruega > comunicarlo al remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any > attachments may contain confidential and privileged information for > the sole use of the designated recipient named above. Distribution, > reproduction or any other use of this transmission by any party other > than the intended recipient is prohibited. If you are not the intended > recipient please contact the sender and delete all copies. > > ------------------------------------------------------------------------ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > ------------------------------------------------------------------------ > > No virus found in this incoming message. > Checked by AVG Free Edition. > Version: 7.1.409 / Virus Database: 268.14.5/534 - Release Date: 11/14/2006 > -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Rutger A. Vos Postdoctoral research fellow University of British Columbia Personal site: http://www.sfu.ca/~rvosa CIPRES: http://www.phylo.org Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From n.haigh at sheffield.ac.uk Thu Nov 16 04:14:52 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 09:14:52 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> Message-ID: <455C2C0C.1080403@sheffield.ac.uk> Hilmar Lapp wrote: > On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > > >> I would just want clarification that the consensus really is to stay >> with Makefile.PL for 1.5.2. The primary argument seems to be to not >> have >> anything too new and untested in the branch, but Makefile.PL itself >> has >> lots of new additions. My Makefile.PL improvements and the change to >> Build.PL have all been in the name of making 1.5.2 install well. The >> move to Build.PL was just the most appropriate way to fix some bugs >> and >> make needed changes. >> > > My take on this, aside from having said before that the move to > Module::Build is certainly a good one except with not-so-great > timing, is that the distribution if at all possible should have a > working Makefile.PL. > I was in the process of writing a rather long e-mail to try to stem the tide of Sendu-bashing :-P But, this response serves as a better platform for my comments. I don't see the change to Build.PL as an issue - especially if we have another RC. I think it would be worse to introduce Build.PL in the "stable" 1.6 release than in the 1.5.x developer series. I think one good reason for using Build.PL when Sendu brought the issue up, is that it is more important as far as building a package for CPAN rather than an end user - and since Sendu is the release pumpkin he is the one with the strongest opinion for changing it now, rather than later - it would make his job much easier! I believe Sendu mentioned that a Makefile.PL would be included in the CPAN package but is not in CVS as it would be generated from Build.PL for backward compatibility - is that right Sendu? How does installing via CPAN affect this? Does it give higher priority to Build.PL over Makefile.PL and thus use Build.PL for the install? > If Build.PL can coexist that'd be great. That would give you the > opportunity to have Makefile.PL print out a message right at the > beginning that if the installation process messes up one should try > Build.PL. This would spare you from fixing any problems in > Makefile.PL that are fixed in the Build.PL approach. > Good idea, for anyone downloading the .tar.gz from CPAN if they issue "perl Makefile.PL" without knowing Build.PL was there it should hopefully work, but if not, issue a comment at the end to say try "perl Build.PL" if anything seemed to go wrong. > As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub > that just prints out a message telling you to use Build.PL and does > nothing else. If you check out bioperl-live from CVS you need to be > prepared to having checked out the live edge of the code. Edges can > be rough. The key thing is that the build process works. > I was going to suggest something like this with regard to a Makefile.PL in CVS. This would then be overwritten by the Makefile.PL produced from Build.PL by the release pumpkin when making the CPAN package. > Finally let's not forget that this is still a developer release. That > means that a) perfection isn't needed, rather shorter release cycles, > and b) development implies change. So the main reason why I find the > timing less than optimal is because it prolongs the time until the > next release. > If we go for short release cycles, and regular bug fix release, we will no longer have to say to users: "This is a known bug/issue in release x.y.z, it has been fixed in CVS HEAD so get it from there" we can roll out fixes in regular releases. This way CVS is then used solely by developers and those really wanting to live on the bleeding edge code. Therefore, it is important to get Build.PL in place to let the release cycle and CPAN packages built quickly, easily and without hassle - which I believe is the problem with Makefile.PL as it currently is. > Implementing changes like this do require a lot of energy. I very > much appreciate that Sendu invested the time and energy to make it > work, even though unfortunately at the last hour. Who knows who would > have had the energy after the release. If Sendu hadn't put in the > work now, the next release master may have been stuck with an even > messier Makefile.PL system. Instead of Monday morning quarterbacking > after no-one stopped him when he asked about it, we should all help > him make the release - and the build change - successful now that he > has done most if not all of the migration work already. > > -hilmar > Hear, hear - well done Sendu on all your hard work! Personally, I think the move to Build.PL is a good one - it may be a little late in this particular release, but I think that the problem is not that it is a late change, but that it wasn't picked up sooner. It fits well with the goal of making releases and big fix releases more regular, and if these are made available via CPAN, then the use of CVS is for developers and those wanting to live on the edge. Build.PL helps all this by making is easier and quicker to make CPAN packages. It also means we have a while before the "stable" 1.6 release to ensure it is working effectively - better than dropping it in on the 1.6 release isn't it? I think it's work the delay and an extra RC! Anyway, my 2 pence worth! Nath From n.haigh at sheffield.ac.uk Thu Nov 16 04:04:00 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 09:04:00 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> Message-ID: <455C2980.4000609@sheffield.ac.uk> Hilmar Lapp wrote: > On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > > >> I would just want clarification that the consensus really is to stay >> with Makefile.PL for 1.5.2. The primary argument seems to be to not >> have >> anything too new and untested in the branch, but Makefile.PL itself >> has >> lots of new additions. My Makefile.PL improvements and the change to >> Build.PL have all been in the name of making 1.5.2 install well. The >> move to Build.PL was just the most appropriate way to fix some bugs >> and >> make needed changes. >> > > My take on this, aside from having said before that the move to > Module::Build is certainly a good one except with not-so-great > timing, is that the distribution if at all possible should have a > working Makefile.PL. > I was in the process of writing a rather long e-mail to try to stem the tide of Sendu-bashing :-P But, this response serves as a better platform for my comments. I don't see the change to Build.PL as an issue - especially if we have another RC. I think it would be worse to introduce Build.PL in the "stable" 1.6 release than in the 1.5.x developer series. I think one good reason for using Build.PL when Sendu brought the issue up, is that it is more important as far as building a package for CPAN rather than an end user - and since Sendu is the release pumpkin he is the one with the strongest opinion for changing it now, rather than later - it would make his job much easier! I believe Sendu mentioned that a Makefile.PL would be included in the CPAN package but is not in CVS as it would be generated from Build.PL for backward compatibility - is that right Sendu? How does installing via CPAN affect this? Does it give higher priority to Build.PL over Makefile.PL and thus use Build.PL for the install? > If Build.PL can coexist that'd be great. That would give you the > opportunity to have Makefile.PL print out a message right at the > beginning that if the installation process messes up one should try > Build.PL. This would spare you from fixing any problems in > Makefile.PL that are fixed in the Build.PL approach. > Good idea, for anyone downloading the .tar.gz from CPAN if they issue "perl Makefile.PL" without knowing Build.PL was there it should hopefully work, but if not, issue a comment at the end to say try "perl Build.PL" if anything seemed to go wrong. > As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub > that just prints out a message telling you to use Build.PL and does > nothing else. If you check out bioperl-live from CVS you need to be > prepared to having checked out the live edge of the code. Edges can > be rough. The key thing is that the build process works. > I was going to suggest something like this with regard to a Makefile.PL in CVS. This would then be overwritten by the Makefile.PL produced from Build.PL by the release pumpkin when making the CPAN package. > Finally let's not forget that this is still a developer release. That > means that a) perfection isn't needed, rather shorter release cycles, > and b) development implies change. So the main reason why I find the > timing less than optimal is because it prolongs the time until the > next release. > If we go for short release cycles, and regular bug fix release, we will no longer have to say to users: "This is a known bug/issue in release x.y.z, it has been fixed in CVS HEAD so get it from there" we can roll out fixes in regular releases. This way CVS is then used solely by developers and those really wanting to live on the bleeding edge code. Therefore, it is important to get Build.PL in place to let the release cycle and CPAN packages built quickly, easily and without hassle - which I believe is the problem with Makefile.PL as it currently is. > Implementing changes like this do require a lot of energy. I very > much appreciate that Sendu invested the time and energy to make it > work, even though unfortunately at the last hour. Who knows who would > have had the energy after the release. If Sendu hadn't put in the > work now, the next release master may have been stuck with an even > messier Makefile.PL system. Instead of Monday morning quarterbacking > after no-one stopped him when he asked about it, we should all help > him make the release - and the build change - successful now that he > has done most if not all of the migration work already. > > -hilmar > Here, here - well done Sendu on all your hard work! Personally, I think the move to Build.PL is a good one - it may be a little late in this particular release, but I think that the problem is not that it is a late change, but that it wasn't picked up sooner. It fits well with the goal of making releases and big fix releases more regular, and if these are made available via CPAN, then the use of CVS is for developers and those wanting to live on the edge. Build.PL helps all this by making is easier and quicker to make CPAN packages. It also means we have a while before the "stable" 1.6 release to ensure it is working effectively - better than dropping it in on the 1.6 release isn't it? I think it's work the delay and an extra RC! Anyway, my 2 pence worth! Nath -- > A: Yes. >> Q: Are you sure? >> >>> A: Because it reverses the logical flow of conversation. >>> >>>> Q: Why is top posting frowned upon? >>>> Get Thunderbird <http://www.mozilla.org/products/thunderbird/> From bix at sendu.me.uk Thu Nov 16 04:26:45 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 09:26:45 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2C0C.1080403@sheffield.ac.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> <455C2C0C.1080403@sheffield.ac.uk> Message-ID: <455C2ED5.4060602@sendu.me.uk> Nathan S. Haigh wrote: > I believe Sendu mentioned that a Makefile.PL would be included in the > CPAN package but is not in CVS as it would be generated from > Build.PL for backward compatibility - is that right Sendu? Yes. > How does installing via CPAN affect this? Does it give higher > priority to Build.PL over Makefile.PL and thus use Build.PL for the > install? I don't know about priorities (but assume it would prefer Build.PL), but in any case, the generated Makefile.PL basically just calls Build.PL, so it makes no difference. > Build.PL helps all this by making is easier and quicker to make CPAN > packages. It also means we have a while before the "stable" 1.6 > release to ensure it is working effectively - better than dropping it > in on the 1.6 release isn't it? I think it's work the delay and an > extra RC! Yes, it surely needs to happen before 1.6. As suggested here and originally in the other thread, 1.5.2 can be the transition release with old Makefile.PL and Build.PL as well (set up to not overwrite Makefile.PL). From bix at sendu.me.uk Thu Nov 16 06:35:25 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 11:35:25 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <001801c70905$dbdd7a40$15327e82@pyrimidine> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> Message-ID: <455C4CFD.5080005@sendu.me.uk> Chris Fields wrote: > I see that there is a PPMMaker module with Module::Build, so we'll have to > look into that for WinXP PPMs.. Nathan, does: perl Build.PL ./Build ppmdist create anything useful? For me it generates a tar.gz containing blib, and a ppd file (the contents of which can be adjusted by supplying "an optional argument codebase which is used in the generated ppd file to specify the (usually relative) URL of the distribution. By default, this value is the distribution name without any path information", eg. ./Build ppmdist --codebase "MSWin32-x86-multi-thread/Bioperl....tar.gz"). Is this PPM4 format? What else needs to be done to it to make it suitable? I can easily extend the ppmdist action to do whatever you want, so let me know. From bix at sendu.me.uk Thu Nov 16 06:45:03 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 11:45:03 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <45531968.6080607@sendu.me.uk> References: <45531968.6080607@sendu.me.uk> Message-ID: <455C4F3F.1090901@sendu.me.uk> Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Developers: > Once again I'm hopeful that this is the last RC. If all goes well > expect final release in about a weeks time. Please check and update > documentation. Sadly all didn't go well. Some remaining bugs are present in the Run package which are now being worked on (there was also a WinXP core bug already fixed by Chris). Expect RC4 sometime this week, which will also include a transitional Build.PL as an alternative to installing with Makefile.PL. From bikash_lohia2000 at yahoo.com Thu Nov 16 07:30:04 2006 From: bikash_lohia2000 at yahoo.com (bikash lohia) Date: Thu, 16 Nov 2006 04:30:04 -0800 (PST) Subject: [Bioperl-l] i am new to group, require a help Message-ID: <20061116123004.87840.qmail@web54213.mail.yahoo.com> hello group, I am new to this group and want a help.i have list of accesion id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to manually search gene database of NCBI for converting this accession no. of cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i want to do it through perl programming where the program directly takes the list of id ( such as AK105331,Ak070197) from notepad file and searches in gene database of ncbi. to give results in accession id starting with OS****** .i want only the accession id of corresponding Ak***** id. for example - AK070197 of nucleotide databse = Os02g0669100 of gene database. i want to convert all this AK***** ids to OS***** ids through programming in perl/bioperl as manually not possible for long list. please help. i have no idea how can the code be. with thanks in advance from Bikash --------------------------------- Sponsored Link Degrees for working adults in as fast as 1 year. Bachelors, Masters, Associates. Top schools From n.haigh at sheffield.ac.uk Thu Nov 16 07:45:14 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 12:45:14 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C4CFD.5080005@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> Message-ID: <455C5D5A.5020205@sheffield.ac.uk> Sendu Bala wrote: > Chris Fields wrote: >> I see that there is a PPMMaker module with Module::Build, so we'll >> have to >> look into that for WinXP PPMs.. > > Nathan, does: > > perl Build.PL > ./Build ppmdist > > create anything useful? For me it generates a tar.gz containing blib, > and a ppd file (the contents of which can be adjusted by supplying "an > optional argument codebase which is used in the generated ppd file to > specify the (usually relative) URL of the distribution. By default, > this value is the distribution name without any path information", eg. > ./Build ppmdist --codebase "MSWin32-x86-multi-thread/Bioperl....tar.gz"). > > Is this PPM4 format? What else needs to be done to it to make it > suitable? I can easily extend the ppmdist action to do whatever you > want, so let me know. Sorry, but i've been busy this last week etc so haven't be able to test RC3 on WinXP yet - hopefully Chris' tests have been sufficient. Essentially a PPM dist comprises of the .tar.gz file you described (of the blib dir) and then the XML file (.ppd) which describes the package and it's dependencies. The syntax of the XML has changed for PPM4 (which required me to do these changes by hand on the ppd that was previously output by "make ppd". For PPM4 the XML in the ppd file can be copied over to packages.xml file in our PPM repository. the codebase URL can be relative/absolute and it's exact value depends on the relative position of the XML (whether in the .ppd or package.xml file) and the .tar.gz file. Thus, by default, they would have to reside in the same dir on our server. Without looking at the XML I couldn't say if it was PPM3 or PPM4 compatible. Could you e-mail me the ppd file and I'll take a look. Cheers Nath From cjfields at uiuc.edu Thu Nov 16 07:45:13 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 06:45:13 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C197D.6000107@sendu.me.uk> References: <C1812C74.B5E3%bosborne11@verizon.net> <455C1790.3080408@sendu.me.uk> <455C197D.6000107@sendu.me.uk> Message-ID: <F9D837E4-4614-4905-A171-9738ED1D01D8@uiuc.edu> On Nov 16, 2006, at 1:55 AM, Sendu Bala wrote: ... > Also, > # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who > read the docs on the website/elsewhere (which will be updated to > explain > the new Build.PL system) don't get confused when that doesn't work, > for wide testing, and to get people used to it for the next > release. The > old Makefile.PL will have 2 changes: Brians bug-fix and a little > message > pointing out that Build.PL is now the preferred installation > system, but > Makefile.PL still works. Sounds fine to me. The old Makefile.PL is in the branch along with the new system, we leave a stub in place for Makefile.PL in CVS HEAD, and everybody's happy (hopefully). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 08:08:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 07:08:57 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2980.4000609@sheffield.ac.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> <455C2980.4000609@sheffield.ac.uk> Message-ID: <4723715A-551A-4402-A98C-14B64EEDD80E@uiuc.edu> On Nov 16, 2006, at 3:04 AM, Nathan S. Haigh wrote: > ... >> If Build.PL can coexist that'd be great. That would give you the >> opportunity to have Makefile.PL print out a message right at the >> beginning that if the installation process messes up one should try >> Build.PL. This would spare you from fixing any problems in >> Makefile.PL that are fixed in the Build.PL approach. > > Good idea, for anyone downloading the .tar.gz from CPAN if they issue > "perl Makefile.PL" without knowing Build.PL was there it should > hopefully work, but if not, issue a comment at the end to say try > "perl > Build.PL" if anything seemed to go wrong. That's amazingly similar to the suggestion I made ;> Seriously, when we make any changes in Bioperl they should be made with the community in mind. If I were to download RC3 directly from the website, it uses the old Makefile.PL. Therefore I would expect the new RC and the final release to have a similar installation procedure. Same with CVS. And I'll note that the CVS docs and wiki still state that Makefile.PL is the one to use. If we can redirect them to the current way, all the better. But sudden dramatic changes, even in a developer release, are probably not the way to go. > If we go for short release cycles, and regular bug fix release, we > will > no longer have to say to users: > "This is a known bug/issue in release x.y.z, it has been fixed in CVS > HEAD so get it from there" > we can roll out fixes in regular releases. This way CVS is then used > solely by developers and those really wanting to live on the bleeding > edge code. Therefore, it is important to get Build.PL in place to let > the release cycle and CPAN packages built quickly, easily and without > hassle - which I believe is the problem with Makefile.PL as it > currently is. Shorter developer cycles are definitely better. Like Hilmar suggests, they don't have to be perfect (though relatively bug- free). If you look back through the old releases I don't think you'll find many with all tests passing on all OS's. I would like to get a 1.5.3 out by spring, then start towards cleaning up for a summer-fall rel. 1.6. Maybe that's wishful thinking. >> Implementing changes like this do require a lot of energy. I very >> much appreciate that Sendu invested the time and energy to make it >> work, even though unfortunately at the last hour. Who knows who would >> have had the energy after the release. If Sendu hadn't put in the >> work now, the next release master may have been stuck with an even >> messier Makefile.PL system. Instead of Monday morning quarterbacking >> after no-one stopped him when he asked about it, we should all help >> him make the release - and the build change - successful now that he >> has done most if not all of the migration work already. >> >> -hilmar >> > > Here, here - well done Sendu on all your hard work! > Personally, I think the move to Build.PL is a good one - it may be a > little late in this particular release, but I think that the > problem is > not that it is a late change, but that it wasn't picked up sooner. It > fits well with the goal of making releases and big fix releases more > regular, and if these are made available via CPAN, then the use of CVS > is for developers and those wanting to live on the edge. Build.PL > helps > all this by making is easier and quicker to make CPAN packages. It > also > means we have a while before the "stable" 1.6 release to ensure it is > working effectively - better than dropping it in on the 1.6 release > isn't it? I think it's work the delay and an extra RC! > > Anyway, my 2 pence worth! > Nath I don't think anyone is knocking Sendu for his effort here. I will remind everybody that this was discussed in a previous thread and a decision was made (and agreed to by Sendu) to wait until after this release to implement Build, hence the backlash. Brian summed it up quite well. We all support this; the timimg was just bad. That's all. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 08:21:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 13:21:27 +0000 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? Message-ID: <455C65D7.5060704@sendu.me.uk> Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if the intent was that it not be included in any distribution. I've had a very quick look at it and the docs seem a little out of date. More importantly, I couldn't get it to return any results. I can't find any tests for it in the t/ directory either. Is there any interest in developing this module to get it into a working and tested state, or should I exclude it from the up-coming release of Bioperl? If no one wants to maintain it, should it be deprecated? Thank you, Sendu. From roy at colibase.bham.ac.uk Thu Nov 16 08:18:55 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Thu, 16 Nov 2006 13:18:55 +0000 Subject: [Bioperl-l] reverse complement - and features In-Reply-To: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> References: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Message-ID: <455C653F.7010907@colibase.bham.ac.uk> > do you know of an easy way to reverse complement the sequence of an > embl entry and the features associated with that sequence. > I'm looking at genomic syntenic regions, and in some organisms the > gene is in the plus strand while in others is in the minus. Try the revcom_with_features method from Bio::SeqUtils: $revcom=Bio::SeqUtils->revcom_with_features($seq); (Apparently the documentation isn't correct for this. I have submitted a patch to Bugzilla.) Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From n.haigh at sheffield.ac.uk Thu Nov 16 08:37:33 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 13:37:33 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C6028.3060402@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455C6028.3060402@sendu.me.uk> Message-ID: <455C699D.1040407@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sorry, but i've been busy this last week etc so haven't be able to test >> RC3 on WinXP yet - hopefully Chris' tests have been sufficient. > > No problem, thanks for all your testing effort! > > >> Essentially a PPM dist comprises of the .tar.gz file you described (of >> the blib dir) and then the XML file (.ppd) which describes the package >> and it's dependencies. > > Is the .ppd ever included in the .tar.gz, or is it always separate? > > Nope - always separate. >> The syntax of the XML has changed for PPM4 (which >> required me to do these changes by hand on the ppd that was previously >> output by "make ppd". > > Is there a reference for the format anywhere? > Erm not really - that I know of. There is this thread which I use for reference: http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 > >> For PPM4 the XML in the ppd file can be copied >> over to packages.xml file in our PPM repository. the codebase URL can be >> relative/absolute and it's exact value depends on the relative position >> of the XML (whether in the .ppd or package.xml file) and the .tar.gz >> file. Thus, by default, they would have to reside in the same dir on our >> server. >> >> Without looking at the XML I couldn't say if it was PPM3 or PPM4 >> compatible. Could you e-mail me the ppd file and I'll take a look. > > It's pretty basic: > > <SOFTPKG NAME="bioperl" VERSION="1,005002003,0,0"> > <TITLE>bioperl > Bioinformatics Toolkit > Bioperl Team <bioperl-l at bioperl.org> > > > > > > If I made it output the sort of information in the current > http://bioperl.org/DIST/RC/package.xml, would that be fine? Did you > have any kind of automation for creating that package.xml, or do you > see a good potential way of automating it? This PPD doesn't contain any info about what modules it provides (ideally, it should have a provide tags for all modules in bioperl) or the dependencies via the require tag. I didn't have an automated way of making it. Previously, the output of "make ppd" used PREREQ_PM from makefile.pl to create PPM3 dependency tags for all modules in PREREQ_PM. I just modified the tags to REQUIRE and added '::' to the end of modules that didn't natively have one. This should all be detailed in the above in - here again for convenience: http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 There must be an automated way to generate the PPM4 compatible PPDs - I think there is a way to generate one from the CPAN distribution. I think this might be the way ActiveState does it? Nath From bix at sendu.me.uk Thu Nov 16 08:47:05 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 13:47:05 +0000 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> References: <455C65D7.5060704@sendu.me.uk> <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> Message-ID: <455C6BD9.6090100@sendu.me.uk> Allen Day wrote: > Hi Sendu, > > Several years ago I was asked by Jim Kent to stop maintaining it. He > was concerned it would overload the UCSC servers. It's not in the > distribution for the same reason. Thanks, I'll deprecate it then. From gcarbajosa at cnio.es Thu Nov 16 08:12:58 2006 From: gcarbajosa at cnio.es (guillermo) Date: Thu, 16 Nov 2006 14:12:58 +0100 Subject: [Bioperl-l] indexing whole genbank Message-ID: Hello, I wrote to this list before because I wasn?t able to index the whole of genebank. I?ve tried to do it spliting the work by creating small indexes and it has worked perfectly so that seems the way to do it. Thanks for your comments, Guillermo **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From cjfields at uiuc.edu Thu Nov 16 10:08:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:08:08 -0600 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <455C65D7.5060704@sendu.me.uk> Message-ID: <001501c70991$06b14fe0$15327e82@pyrimidine> > Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if > the intent was that it not be included in any distribution. > I've had a very quick look at it and the docs seem a little > out of date. More importantly, I couldn't get it to return > any results. > > I can't find any tests for it in the t/ directory either. Is > there any interest in developing this module to get it into a > working and tested state, or should I exclude it from the > up-coming release of Bioperl? > > If no one wants to maintain it, should it be deprecated? > > > Thank you, > Sendu. I would definitely exclude it if it doesn't work or have tests. Have you contacted the author (Allen Day)? I wonder if he has updated the code but hasn't committed it. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Thu Nov 16 10:17:23 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Nov 2006 10:17:23 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C197D.6000107@sendu.me.uk> References: <455C1790.3080408@sendu.me.uk> <455C197D.6000107@sendu.me.uk> Message-ID: <75FDB3A6-BFB6-4120-92B1-04D54D708E4C@gmx.net> Sounds great to me. -hilmar On Nov 16, 2006, at 2:55 AM, Sendu Bala wrote: >> Ok, so the current plan is: >> # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml > Also, > # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who > read the docs on the website/elsewhere (which will be updated to > explain > the new Build.PL system) don't get confused when that doesn't work, > for wide testing, and to get people used to it for the next > release. The > old Makefile.PL will have 2 changes: Brians bug-fix and a little > message > pointing out that Build.PL is now the preferred installation > system, but > Makefile.PL still works. > > >> # CVS core gets a Makefile.PL stub telling you to use Build.PL >> # CVS db, run, network stay with Makefile.PL until after final >> release >> of 1.5.2, then move to Build.PL with Makefile.PL stub (because they >> don't have a 1.5.2 branch) >> >> Is everyone happy with that, or are there further suggestions for >> something better? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Thu Nov 16 10:29:31 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:29:31 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C699D.1040407@sheffield.ac.uk> Message-ID: <001601c70994$02da28d0$15327e82@pyrimidine> ... > > > > Is there a reference for the format anywhere? > > > > Erm not really - that I know of. There is this thread which I use for > reference: > http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 Looks like kobes is using PPM::Make (he should; it's his distribution). We'll need to make sure that Module::Build uses that as well, since it seems there are some significant changes. ... > There must be an automated way to generate the PPM4 > compatible PPDs - I think there is a way to generate one from > the CPAN distribution. I think this might be the way > ActiveState does it? > > Nath I think ActiveState has it's own automated build process. For PPM3 they used the PPD section from the regular makefile (from Makefile.PL and ExtUtils::MakeMaker). Notably they still indicate using 'nmake ppd' when generating Makefile.PL, so maybe they use an updated or modified ExtUtils::MakeMaker? Or they add tags for the Makefile.PL: use ExtUtils::MakeMaker; # See lib/ExtUtils/MakeMaker.pm for details of how to influence # the contents of the Makefile that is written. WriteMakefile( 'NAME' => 'Term::Control', 'VERSION_FROM' => 'Control.pm', # finds $VERSION ($] ge '5.005') ? ( 'AUTHOR' => 'Johnny Doel (johnny at doel.org)', 'ABSTRACT' => 'Control the IO for terminals', # extra tags here? ) : (), ); The reason you may not see a certain distribution built into a PPM is b/c a particular dependency is not available for one reason or another, tests fail during the make process, etc. They will try to build specific ones upon request. Many of the ones in Kobes are generated by users who want up-to-date distros or ones not built automatically by ActiveState, though Randy Kobes himself sets up most of them. Significantly, he has already switched over to PPM4; maybe we should contact him about this? Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 10:31:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:31:08 -0600 Subject: [Bioperl-l] indexing whole genbank In-Reply-To: Message-ID: <001701c70994$3d332400$15327e82@pyrimidine> > Hello, > > I wrote to this list before because I wasn?t able to index > the whole of genebank. I?ve tried to do it spliting the work > by creating small indexes and it has worked perfectly so that > seems the way to do it. > > Thanks for your comments, > Guillermo Thanks for the update. I think that the problem was a full GenBank file is way too large for flatfile indexing (I think it's around 800 GB unpacked now). Nice to know doing it by divisions works. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 11:29:33 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 16:29:33 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <17756.36534.549232.263868@satchel.alerce.com> References: <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> <455BA093.8040603@sendu.me.uk> <17756.36534.549232.263868@satchel.alerce.com> Message-ID: <455C91ED.2030008@sendu.me.uk> George Hartzell wrote: > Sendu Bala writes: > > [...] > > The only real change for most users is that they now need Module::Build > > installed. > > Module::Build can be a real pain-in-the_%$* if you're used to > installing perl modules in a specialized place using something like > this: > > perl Makefile.PL PREFIX=~/perl-stuff > > Granted, MakeMaker's handling of that has been inconsistent across > platforms over the years, but on a single system at least it's > manageable. > > If/when bioperl swaps over to a Module::Build based system, PLEASE > make a big&loud reference to the "Installing in the same location as > ExtUtils::MakeMaker" section of the Module::Build::Cookbook so that > folks have a fighting chance of avoiding unpleasant surprises. Thanks, I've added a clarification to the INSTALL file. From hartzell at alerce.com Thu Nov 16 11:15:50 2006 From: hartzell at alerce.com (George Hartzell) Date: Thu, 16 Nov 2006 08:15:50 -0800 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BA093.8040603@sendu.me.uk> References: <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> <455BA093.8040603@sendu.me.uk> Message-ID: <17756.36534.549232.263868@satchel.alerce.com> Sendu Bala writes: > [...] > The only real change for most users is that they now need Module::Build > installed. Module::Build can be a real pain-in-the_%$* if you're used to installing perl modules in a specialized place using something like this: perl Makefile.PL PREFIX=~/perl-stuff Granted, MakeMaker's handling of that has been inconsistent across platforms over the years, but on a single system at least it's manageable. If/when bioperl swaps over to a Module::Build based system, PLEASE make a big&loud reference to the "Installing in the same location as ExtUtils::MakeMaker" section of the Module::Build::Cookbook so that folks have a fighting chance of avoiding unpleasant surprises. That section says, in part: With the introduction of "--prefix" in Module::Build 0.28 and "INSTALL_BASE" in ExtUtils::MakeMaker 6.31 its [sic] easy to get them both to install in the same locations. First, ensure you have at least version 0.28 of Module::Build installed and 6.31 of ExtUtils::MakeMaker. Prior versions have differeing installation behaviours. People may need to upgrade their installations [at least the ExtUtils::MakeMaker and Module::Build bits], but at least they'll see the train barreling down at them. g. From roy at colibase.bham.ac.uk Thu Nov 16 11:49:49 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Thu, 16 Nov 2006 16:49:49 +0000 Subject: [Bioperl-l] reverse complement - and features In-Reply-To: <40d6e6580611160828m5f7047e0gadec36f958a69990@mail.gmail.com> References: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> <455C653F.7010907@colibase.bham.ac.uk> <40d6e6580611160828m5f7047e0gadec36f958a69990@mail.gmail.com> Message-ID: <455C96AD.8030804@colibase.bham.ac.uk> > that method sounds promising, although the documentation seems to be > copy-and-paste from the trunc_with_features() method. Yes, I was a bit lazy with that. It has been fixed in CVS (thanks Chris) and will be included in the new 1.5.2 release. > I included in my script, although it doesn't complaint but no being > there, it doesn't do anything with the file. > I looked at the version of bioperl in the server where I'm running, > and it is 1.5.0 and the SeqUtils.pm does not include the > revcom_with_features(). > Do you know if I can install the SeqUtils.pm module in my directory, > and call it with use lib "/home/xxxx/xxxx/lib/perl"; ? Yes, that should work. You can download the most recent version from: http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioperl-live/Bio/SeqUtils.pm?rev=HEAD&content-type=text/plain You can put that file in the directory /home/xxxx/xxxx/lib/perl/Bio/ and it should then be recognised as the preferred Bio::SeqUtils module if you use lib as you say. Good luck with it. Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From cjfields at uiuc.edu Thu Nov 16 11:55:39 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 10:55:39 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2ED5.4060602@sendu.me.uk> Message-ID: <001901c709a0$0b6a6d50$15327e82@pyrimidine> > Nathan S. Haigh wrote: > > I believe Sendu mentioned that a Makefile.PL would be > included in the > > CPAN package but is not in CVS as it would be generated > from Build.PL > > for backward compatibility - is that right Sendu? > > Yes. > > > > How does installing via CPAN affect this? Does it give > higher priority > > to Build.PL over Makefile.PL and thus use Build.PL for the install? > > I don't know about priorities (but assume it would prefer > Build.PL), but in any case, the generated Makefile.PL > basically just calls Build.PL, so it makes no difference. > > > > Build.PL helps all this by making is easier and quicker to > make CPAN > > packages. It also means we have a while before the "stable" 1.6 > > release to ensure it is working effectively - better than > dropping it > > in on the 1.6 release isn't it? I think it's work the delay and an > > extra RC! > > Yes, it surely needs to happen before 1.6. As suggested here > and originally in the other thread, 1.5.2 can be the > transition release with old Makefile.PL and Build.PL as well > (set up to not overwrite Makefile.PL). So far, we have these modes of installation: 1) Direct installation using CPAN -> INSTALL 2) Regular distribution (either from the Bioperl website or CPAN) using 'make/nmake' ->INSTALL, INSTALL.WIN 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN 4) PPM (Windows-only) -> INSTALL.WIN Anything using make/nmake will need to be changed in docs. Do you want to switch everything over to using 'perl Build.PL'? Also, since the 'manifying' problem is now fixed we can remove the blurb about it from INSTALL and the wiki. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 11:59:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 16:59:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> References: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: <455C98F0.9050909@sendu.me.uk> Chris Fields wrote: > So far, we have these modes of installation: > > 1) Direct installation using CPAN -> INSTALL > 2) Regular distribution (either from the Bioperl website or CPAN) using > 'make/nmake' ->INSTALL, INSTALL.WIN > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > 4) PPM (Windows-only) -> INSTALL.WIN > > Anything using make/nmake will need to be changed in docs. Do you want to > switch everything over to using 'perl Build.PL'? > > Also, since the 'manifying' problem is now fixed we can remove the blurb > about it from INSTALL and the wiki. I've already updated docs in CVS. The emails are just very slow to get through to guts. Do an update and let me know if I missed anything. I'll add the changes to the wiki when I get a chance. From n.haigh at sheffield.ac.uk Thu Nov 16 12:44:28 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 17:44:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> References: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: <455CA37C.3070704@sheffield.ac.uk> --snip-- >> Yes, it surely needs to happen before 1.6. As suggested here >> and originally in the other thread, 1.5.2 can be the >> transition release with old Makefile.PL and Build.PL as well >> (set up to not overwrite Makefile.PL). >> > > So far, we have these modes of installation: > > 1) Direct installation using CPAN -> INSTALL > 2) Regular distribution (either from the Bioperl website or CPAN) using > 'make/nmake' ->INSTALL, INSTALL.WIN > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > Chris, Do you ever have a problem with nmake when doing an install from a regular distribution or CVS? I'm sure I used to get an nmake problem which wouldn't let you proceed further - might have been "nmake test" and it might be a while back now. Nath From cjfields at uiuc.edu Thu Nov 16 12:58:14 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 11:58:14 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455CA37C.3070704@sheffield.ac.uk> Message-ID: <000001c709a8$c9c1b760$15327e82@pyrimidine> > --snip-- > >> Yes, it surely needs to happen before 1.6. As suggested here and > >> originally in the other thread, 1.5.2 can be the > transition release > >> with old Makefile.PL and Build.PL as well (set up to not overwrite > >> Makefile.PL). > >> > > > > So far, we have these modes of installation: > > > > 1) Direct installation using CPAN -> INSTALL > > 2) Regular distribution (either from the Bioperl website or CPAN) > > using 'make/nmake' ->INSTALL, INSTALL.WIN > > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > > > > Chris, > > Do you ever have a problem with nmake when doing an install > from a regular distribution or CVS? I'm sure I used to get an > nmake problem which wouldn't let you proceed further - might > have been "nmake test" > and it might be a while back now. > > Nath I haven't had problems beyond the '-w' paranoia and 'Subroutine x redefined at' warnings, which is an ActivePerl issue. 'nmake test' works for me (that's what I have been using on all the RC's and using bioperl-live). I think 'Build test' also uses nmake, so if that works nmake should also work. I have used both an old version (1.5) and the recent VC++ nmake version (8.00.50727.42) w/o problems. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From pcantalupo at gmail.com Thu Nov 16 11:26:31 2006 From: pcantalupo at gmail.com (Paul Cantalupo) Date: Thu, 16 Nov 2006 11:26:31 -0500 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID Message-ID: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Hello, Is there a way with Bioperl (or some other tool - NCBI EUtils?) to convert a Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's that I need to convert to Mouse GeneIDs so that I can compare them to my Mouse microarray data. Thank you, Paul -- Paul Cantalupo Research Specialist/Systems Programmer 559 Crawford Hall Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Work: 412-624-4687 Fax: 412-624-4759 Ask me about Toastmasters: www.toastmasters.org Midday Club Treasurer From bosborne11 at verizon.net Thu Nov 16 13:09:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 16 Nov 2006 13:09:01 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: Chris, So a package like bioperl-ext, normally requiring a C compiler and make/nmake, now no longer needs make/nmake? I don't recall this coming up in our discussions... Brian O. On 11/16/06 11:55 AM, "Chris Fields" wrote: > Anything using make/nmake will need to be changed in docs. From bix at sendu.me.uk Thu Nov 16 13:14:12 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 18:14:12 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: References: Message-ID: <455CAA74.60500@sendu.me.uk> Brian Osborne wrote: > Chris, > > So a package like bioperl-ext, normally requiring a C compiler and > make/nmake, now no longer needs make/nmake? I don't recall this coming up in > our discussions... I'm sure you'd still need compiler tools to do compilation. I wasn't sure what to say about bioperl-ext in the docs, so I didn't change anything. bioperl-ext isn't my concern (see the thread where I was deciding which packages needed a unified release), so I'll not be trying to change it over to Build.PL From bix at sendu.me.uk Thu Nov 16 13:16:48 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 18:16:48 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: References: Message-ID: <455CAB10.1090703@sendu.me.uk> Brian Osborne wrote: > George, > > But the most recent versions of Module::Build do the installations > correctly? And it's as simple as specifying PREFIX or LIB? In Build.PL's case, it's --prefix or --lib, but yes. For both Module::Build and MakeMaker in recent versions, --install_base is recommended. From cjfields at uiuc.edu Thu Nov 16 13:41:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 12:41:56 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: Message-ID: <000101c709ae$e475bfb0$15327e82@pyrimidine> > Chris, > > So a package like bioperl-ext, normally requiring a C > compiler and make/nmake, now no longer needs make/nmake? I > don't recall this coming up in our discussions... > > Brian O. The makefile setup for bioperl-ext is much more complex than for the others, so I don't know how that would be handled using Module::Build. I tried it earlier on before the RCs on Mac OS X and it installed fine, but Inline complained when running other tests so I tossed it. I don't think it ever worked under Windows using nmake, unless you're using CygWin/GNU make. I believe the Build file must use make/nmake somehow, so there must be a way to compile C code included with the distribution. I just haven't had time to invesitgate yet. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Thu Nov 16 14:05:27 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 19:05:27 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <000101c709ae$e475bfb0$15327e82@pyrimidine> References: <000101c709ae$e475bfb0$15327e82@pyrimidine> Message-ID: <455CB677.6080608@sheffield.ac.uk> Chris Fields wrote: >> Chris, >> >> So a package like bioperl-ext, normally requiring a C >> compiler and make/nmake, now no longer needs make/nmake? I >> don't recall this coming up in our discussions... >> >> Brian O. >> > > The makefile setup for bioperl-ext is much more complex than for the others, > so I don't know how that would be handled using Module::Build. I tried it > earlier on before the RCs on Mac OS X and it installed fine, but Inline > complained when running other tests so I tossed it. I don't think it ever > worked under Windows using nmake, unless you're using CygWin/GNU make. > > I believe the Build file must use make/nmake somehow, so there must be a way > to compile C code included with the distribution. I just haven't had time > to invesitgate yet. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > I was under the impression that Module::Build is pure Perl and thus wouldn't use make/nmake. This page might help, look under "code" in this section: http://search.cpan.org/~kwilliams/Module-Build-0.2805/lib/Module/Build.pm#ACTIONS According to change logs they use ExtUtils::CBuilder to do all compiling of C code (since version 0.27_01) see: http://search.cpan.org/src/KWILLIAMS/Module-Build-0.27_03/Changes HTH Nathan From bosborne11 at verizon.net Thu Nov 16 13:05:15 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 16 Nov 2006 13:05:15 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <17756.36534.549232.263868@satchel.alerce.com> Message-ID: George, But the most recent versions of Module::Build do the installations correctly? And it's as simple as specifying PREFIX or LIB? Brian O. On 11/16/06 11:15 AM, "George Hartzell" wrote: > Module::Build can be a real pain-in-the_%$* if you're used to > installing perl modules in a specialized place using something like > this: > > perl Makefile.PL PREFIX=~/perl-stuff From er at xs4all.nl Thu Nov 16 16:01:12 2006 From: er at xs4all.nl (Erik) Date: Thu, 16 Nov 2006 22:01:12 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch Message-ID: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> Hi all, Using bioperl-live, I noticed a problem with the parsing in Bio/SeqIO/genbank.pm. It occurs in the DBSOURCE section, where the 'dblink' annotation gets its values. I got several values that had a double colon, like InterPro::IPR011000 etc. Not all 'dblink' values were affected. Here is a patch which seems to fix it / it works for me: ======= --- Bio/SeqIO/genbank.pm.orig 2006-11-16 18:33:30.060417520 +0100 +++ Bio/SeqIO/genbank.pm 2006-11-16 20:29:59.014934936 +0100 @@ -504,7 +504,7 @@ my $db; # this is because GenBank dropped the spaces!!! # I'm sure we're not going to get this right - if( $id =~ s/^(EchoBASE|IntAct|SWISS-2DPAGE|ECO2DBASE|ECOGENE|TIGRFAMs|TIGR|GO|InterPro|Pfam|PROSITE|SGD|GermOnline|HSSP|PhosSite)//i ) { + if( $id =~ s/^(EchoBASE|IntAct|SWISS-2DPAGE|ECO2DBASE|ECOGENE|TIGRFAMs|TIGR|GO|InterPro|Pfam|PROSITE|SGD|GermOnline|HSSP|PhosSite)://i ) { $db = $1; } $annotation->add_Annotation======= I also wrote a few tests for the problem, which also needed an extra file in t/data. I will attach the lot hth, Erik -------------- next part -------------- A non-text attachment was scrubbed... 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Name: genbank.pm.diff Type: application/octet-stream Size: 608 bytes Desc: not available URL: From jason at bioperl.org Thu Nov 16 14:45:24 2006 From: jason at bioperl.org (Jason Stajich) Date: Thu, 16 Nov 2006 11:45:24 -0800 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> References: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Message-ID: have you tried ensembl's biomart? http://www.ensembl.org/Multi/martview you will want the ortholog table. -jason On Nov 16, 2006, at 8:26 AM, Paul Cantalupo wrote: > Hello, > > Is there a way with Bioperl (or some other tool - NCBI EUtils?) to > convert a > Human NCBI GeneID to a Mouse GeneID. I have a list of Human > GeneID's that I > need to convert to Mouse GeneIDs so that I can compare them to my > Mouse > microarray data. > > Thank you, > > Paul > > -- > Paul Cantalupo > Research Specialist/Systems Programmer > 559 Crawford Hall > Department of Biological Sciences > University of Pittsburgh > Pittsburgh, PA 15260 > Work: 412-624-4687 > Fax: 412-624-4759 > > Ask me about Toastmasters: www.toastmasters.org > Midday Club Treasurer > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From allenday at ucla.edu Thu Nov 16 08:43:35 2006 From: allenday at ucla.edu (Allen Day) Date: Thu, 16 Nov 2006 05:43:35 -0800 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <455C65D7.5060704@sendu.me.uk> References: <455C65D7.5060704@sendu.me.uk> Message-ID: <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> Hi Sendu, Several years ago I was asked by Jim Kent to stop maintaining it. He was concerned it would overload the UCSC servers. It's not in the distribution for the same reason. -Allen On 11/16/06, Sendu Bala wrote: > Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if the intent > was that it not be included in any distribution. I've had a very quick > look at it and the docs seem a little out of date. More importantly, I > couldn't get it to return any results. > > I can't find any tests for it in the t/ directory either. Is there any > interest in developing this module to get it into a working and tested > state, or should I exclude it from the up-coming release of Bioperl? > > If no one wants to maintain it, should it be deprecated? > > > Thank you, > Sendu. > From torsten.seemann at infotech.monash.edu.au Thu Nov 16 19:42:41 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 17 Nov 2006 11:42:41 +1100 Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch In-Reply-To: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> References: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> Message-ID: <455D0581.4010805@infotech.monash.edu.au> Erik, > Using bioperl-live, I noticed a problem with the parsing in > Bio/SeqIO/genbank.pm. > It occurs in the DBSOURCE section, where the 'dblink' annotation gets its > values. I got several values that had a double colon, like > InterPro::IPR011000 etc. Not all 'dblink' values were affected. > Here is a patch which seems to fix it / it works for me: Thank you very much for your contribution of bug fix and patch and new tests, you have been very thorough. However, these contributions are best done via the Bugzilla tracking system: http://bugzilla.open-bio.org/ For more information see: http://www.bioperl.org/wiki/Bugs -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From cjfields at uiuc.edu Thu Nov 16 08:47:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 07:47:26 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C5D5A.5020205@sheffield.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> Message-ID: On Nov 16, 2006, at 6:45 AM, Nathan S. Haigh wrote: > Sendu Bala wrote: >> Chris Fields wrote: >>> I see that there is a PPMMaker module with Module::Build, so we'll >>> have to >>> look into that for WinXP PPMs.. >> >> Nathan, does: >> >> perl Build.PL >> ./Build ppmdist >> >> create anything useful? For me it generates a tar.gz containing blib, >> and a ppd file (the contents of which can be adjusted by supplying >> "an >> optional argument codebase which is used in the generated ppd file to >> specify the (usually relative) URL of the distribution. By default, >> this value is the distribution name without any path information", >> eg. >> ./Build ppmdist --codebase "MSWin32-x86-multi-thread/ >> Bioperl....tar.gz"). >> >> Is this PPM4 format? What else needs to be done to it to make it >> suitable? I can easily extend the ppmdist action to do whatever you >> want, so let me know. > > Sorry, but i've been busy this last week etc so haven't be able to > test > RC3 on WinXP yet - hopefully Chris' tests have been sufficient. > > Essentially a PPM dist comprises of the .tar.gz file you described (of > the blib dir) and then the XML file (.ppd) which describes the package > and it's dependencies. The syntax of the XML has changed for PPM4 > (which > required me to do these changes by hand on the ppd that was previously > output by "make ppd". For PPM4 the XML in the ppd file can be copied > over to packages.xml file in our PPM repository. the codebase URL > can be > relative/absolute and it's exact value depends on the relative > position > of the XML (whether in the .ppd or package.xml file) and the .tar.gz > file. Thus, by default, they would have to reside in the same dir > on our > server. > > Without looking at the XML I couldn't say if it was PPM3 or PPM4 > compatible. Could you e-mail me the ppd file and I'll take a look. > > Cheers > Nath I'll also try making a PPM here. I noticed that Module::Build has a developer release; I may check with the developers about PPM compatibility. I hate to say it, but we might need to get a PPM3 rolled for this release if people ask for it. There has been some backlash about PPM4 so a lot of people are actually downgrading to an older ActivePerl installations for PPM3. We'll just make a barebones version if this pops up (and no Bundle). One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a developer release, but as the latest release (which implies it is stable): http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Not sure what's going on there, but I don't think that was intended, correct? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 21:51:49 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 20:51:49 -0600 Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations In-Reply-To: References: Message-ID: <277B1C9B-1719-47C5-9A34-9B4E179A78A0@uiuc.edu> On Nov 16, 2006, at 1:55 AM, Joanne Chen wrote: > Got the strand problem fixed. Thanks. =) No problem. Just as a heads up, we plan on making some changes to SplitLocations but nothing too dramatic (hopefully). chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From dmessina at wustl.edu Thu Nov 16 22:54:50 2006 From: dmessina at wustl.edu (David Messina) Date: Thu, 16 Nov 2006 21:54:50 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B3F11.6070102@campus.iztacala.unam.mx> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> <455B3F11.6070102@campus.iztacala.unam.mx> Message-ID: <450674EB-F9CA-4BBF-8EB9-D08423FD16FD@wustl.edu> Sorry, just seeing this now. > ignored, only run manually by people who want to install Deobfuscator? Thanks for asking. As Mauricio said, manual installation only is what I would suggest. Dave From torsten.seemann at infotech.monash.edu.au Thu Nov 16 19:19:42 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 17 Nov 2006 11:19:42 +1100 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast In-Reply-To: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> References: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> Message-ID: <455D001E.4000409@infotech.monash.edu.au> Andrew, >> Anyone have any opinions as to how easy/difficult it would be >> to incorporate mpiblast into >> Bio::Tools::Run::StandAloneBlast? It runs essentially the >> same way as blastall, and its output is nearly identical. > I think plans were to rewrite StandAloneBlast and RemoteBlast to make them > more 'generic' (i.e. capable of running other BLAST-related programs), > though I'm not sure at what stage everything is. Chris is correct is saying there were plans to rewrite the Blast modules - at the time myself, Roger Hall, Chris? and Jason were involved, but unfortunately Roger fell ill in Feb 2006 and had to have urgent heart surgery. (And my wife had a baby :-) Here's some of the early discussion: http://portal.open-bio.org/pipermail/bioperl-l/2006-February/020745.html ANYWAY, I think it might be possible to incorporate mpiblast easily, even without changing Bioperl if we are lucky, via the ->executable() setter method. If not, I added rpsblast support last year which is similar to blastall, so it'd probably be achievable. How does the the output of mpiblast differ to NCBI blastall ? What command line options does mpiblast take? -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From bix at sendu.me.uk Fri Nov 17 02:38:30 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 07:38:30 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> Message-ID: <455D66F6.4070804@sendu.me.uk> Chris Fields wrote: > One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a > developer release, but as the latest release (which implies it is stable): > > http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ > > Not sure what's going on there, but I don't think that was intended, > correct? It wasn't intended. I've deleted the file and if you refresh you should find that page doesn't exist anymore? From bix at sendu.me.uk Fri Nov 17 05:20:11 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 10:20:11 +0000 Subject: [Bioperl-l] Testing with Build.PL Message-ID: <455D8CDB.1070100@sendu.me.uk> Developers, For those not familiar with Module::Build and Build.PL I thought I'd point out some useful testing-related things. To run the whole test suite (the same thing that happens during an install process), say: perl Build.PL (answer 'n' to the script installation question to reduce the amount of output you see later on) ./Build test To run a single test script you can of course continue to do: perl -I. -w t/script.t However to see what would really happen during the full "./Build test" you can say: ./Build test --test_files t/script.t To do the same but see the full test output say: ./Build test --test_files t/script.t --verbose If anyone else has tips, please post them. Cheers, Sendu. From sanges at biogem.it Fri Nov 17 05:14:03 2006 From: sanges at biogem.it (Remo Sanges) Date: Fri, 17 Nov 2006 10:14:03 +0000 Subject: [Bioperl-l] Fellowships for Junior Scientists Message-ID: <455D8B6B.1050108@biogem.it> Apologies for the off topic post... AREA Science Park (http://www.area.trieste.it/opencms/opencms/area/en/) and CBM (http://www.cbm.fvg.it/?lang=en_US) are launching a mobility initiative aimed at attracting international scientists to work with the biomedical research community of Trieste. Research areas: * Biostatistics * Systems Biology * Algorithm Development The fellowships are funded by AREA Science Park and the CBM - Consortium for Molecular Biomedicine as part of an international mobility programme run by AREA Science Park and the CBM. The programme aims at attracting young scientists to the Friuli Venezia Giulia Region and adding them to the community of researchers operating in Trieste in the field of biomedicine. CBM and AREA Science Park are two research institutes recognised by the Ministry of Education, Universities and Research. Here there are laboratories integrating dry and wet lab research and developing a wide research program encompassing functional and comparative genomics, bioinformatics database, software development and algorithm development. The laboratories are already integrated in international collaborative projects tackling non-coding RNA genes, regulatory elements, and bioinformatics workflow management systems. For further information: http://www.cbm.fvg.it/?page=mobility&lang=en_US&id=2 Regards Remo Sanges From er at xs4all.nl Fri Nov 17 05:57:43 2006 From: er at xs4all.nl (Erik) Date: Fri, 17 Nov 2006 11:57:43 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch In-Reply-To: <455D0581.4010805@infotech.monash.edu.au> References: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> <455D0581.4010805@infotech.monash.edu.au> Message-ID: <16667.156.83.0.21.1163761063.squirrel@webmail.xs4all.nl> > However, these contributions are best done via the Bugzilla tracking > system: http://bugzilla.open-bio.org/ ok, I'll do that, but a little later today. Maybe just as well as I later thought of some, err.., imperfections in the tests anyway :) Erik From cjfields at uiuc.edu Fri Nov 17 08:43:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 07:43:38 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455D66F6.4070804@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> Message-ID: <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> On Nov 17, 2006, at 1:38 AM, Sendu Bala wrote: > Chris Fields wrote: >> One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a >> developer release, but as the latest release (which implies it is >> stable): >> >> http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ >> >> Not sure what's going on there, but I don't think that was intended, >> correct? > > It wasn't intended. I've deleted the file and if you refresh you > should > find that page doesn't exist anymore? The page is still there, but the distribution is gone (i.e. the 'Download' link is now dead). http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Fri Nov 17 08:51:03 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 13:51:03 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> Message-ID: <455DBE47.90501@sendu.me.uk> Chris Fields wrote: > > On Nov 17, 2006, at 1:38 AM, Sendu Bala wrote: > >> Chris Fields wrote: >>> One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a >>> developer release, but as the latest release (which implies it is >>> stable): >>> >>> http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ >>> >>> Not sure what's going on there, but I don't think that was intended, >>> correct? >> >> It wasn't intended. I've deleted the file and if you refresh you should >> find that page doesn't exist anymore? > > The page is still there, but the distribution is gone (i.e. the > 'Download' link is now dead). > > http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Hmm, I see just a big 'Not found' message for a non-existing page. I think the old page is still stuck in a cache somewhere for you. In any case, don't whatever you do look in the super-sekrit http://search.cpan.org/~sendu/ because I'm testing out CPAN stuff and getting it horribly wrong. Multiple times. I'll make a post when CPAN stuff is ready to test. From cuiw at ncbi.nlm.nih.gov Fri Nov 17 09:59:15 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Fri, 17 Nov 2006 09:59:15 -0500 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Message-ID: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> You can query HomoloGene DB using NCBI EUtils: ESearch like this: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=homologene& term=BRCA1[gene%20name]&retmode=text Once get HomoloGene id then Then Efetch: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=homologene&i d=5276 Just SOAP it to get the gi and acc via taxid. Good luck. Wenwu Cui -----Original Message----- From: Paul Cantalupo [mailto:pcantalupo at gmail.com] Sent: Thursday, November 16, 2006 11:27 AM To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID Hello, Is there a way with Bioperl (or some other tool - NCBI EUtils?) to convert a Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's that I need to convert to Mouse GeneIDs so that I can compare them to my Mouse microarray data. Thank you, Paul -- Paul Cantalupo Research Specialist/Systems Programmer 559 Crawford Hall Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Work: 412-624-4687 Fax: 412-624-4759 Ask me about Toastmasters: www.toastmasters.org Midday Club Treasurer _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Fri Nov 17 12:43:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 17:43:55 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455DF2BC.9010601@sheffield.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> Message-ID: <455DF4DB.5000808@sendu.me.uk> Nathan S. Haigh wrote: > Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked up as > a developer release? I didn't try that variation, but have decided to go with bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a developer release. I've outlined the numbering scheme here: http://www.bioperl.org/wiki/Making_a_BioPerl_release#Making_the_distribution_directory From cjfields at uiuc.edu Fri Nov 17 13:30:20 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 12:30:20 -0600 Subject: [Bioperl-l] CPAN Versioning, was [something else] In-Reply-To: <455DF4DB.5000808@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> Message-ID: <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> On Nov 17, 2006, at 11:43 AM, Sendu Bala wrote: > Nathan S. Haigh wrote: >> Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked >> up as >> a developer release? > > I didn't try that variation, but have decided to go with > bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a > developer > release. > > I've outlined the numbering scheme here: > http://www.bioperl.org/wiki/ > Making_a_BioPerl_release#Making_the_distribution_directory I noticed that Module::Build now has a developer release that uses this: Module-Build-0.2805_01.tar.gz So the '_###' seems to be key. If so I see a versioning dilemma that depends on what we want to call rel 1.5.2. If we used 'bioperl-1.5.2_004' for the RCs, then logically the final dev release would be 'bioperl-1.5.2', which would not be designated a dev release on CPAN (if the underscore rule holds up, that is). If we plan on having CPAN designate it a developer release (which I think is the consensus among the developers, since 1.6 would be the stable release), then the final 1.5.2 version would be something like 'bioperl-1.5_02' or 'bioperl-1.5_002'. RCs would be '1.5_02-RC#'. Or maybe even '1.5_02_##', which a few modules seem to use. However, even that is tricky; what do we call rel 1.6.1, a point release in the stable series? 'bioperl-1.6_2' would then be a developer release! Argghhh! Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Nov 17 13:51:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 12:51:27 -0600 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> References: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> Message-ID: <55142E31-33F7-442C-B358-E81FA57E9F9E@uiuc.edu> On Nov 17, 2006, at 8:59 AM, Cui, Wenwu ((NIH/NLM/NCBI)) [C] wrote: > You can query HomoloGene DB using NCBI EUtils: > > ESearch like this: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? > db=homologene& > term=BRCA1[gene%20name]&retmode=text > > Once get HomoloGene id then > Then Efetch: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? > db=homologene&i > d=5276 > > Just SOAP it to get the gi and acc via taxid. > > Good luck. > > Wenwu Cui > > > -----Original Message----- > From: Paul Cantalupo [mailto:pcantalupo at gmail.com] > Sent: Thursday, November 16, 2006 11:27 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID > > Hello, > > Is there a way with Bioperl (or some other tool - NCBI EUtils?) to > convert a > Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's > that I > need to convert to Mouse GeneIDs so that I can compare them to my > Mouse > microarray data. > > Thank you, > > Paul > ... You could also use esearch(homologene, using history)->elink (homologene_gene, using history)->esummary(elink 'cookie'). I have set up a (very) experimental BioPerl interface to NCBI eutils (Bio::DB::EUtilities). If you update from CVS (this won't be in the 1.5.2 release), you could do something like this: ------------------------------------------------------ use Bio::DB::EUtilities; my $term = 'BRCA1[gene name]'; # grab BRCA1 homologene UID my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => $term, -usehistory => 'y'); $esearch->get_response; my @h_genes = $esearch->get_ids; # what Gene UIDs are linked to the Homologene UID? my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', -db => 'gene', -cookie => $esearch->next_cookie, -cmd => 'neighbor_history'); $elink->get_response; # what taxids go with which GeneID? my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', -cookie => $elink->next_cookie); $esum->get_response; while (my $docsum = $esum->next_docsum) { print $docsum->esummary_id,"\n"; print "\t\tTaxID: ",$docsum->get_Content_by_name('TaxID'),"\n"; print "\t\tOrganism: ",$docsum->get_Content_by_name ('Orgname'),"\n"; } ------------------------------------------------------ A future bioperl SOAP interface for eutils is also not out of the question either, just haven't had time to play around with it. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Fri Nov 17 14:35:11 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 19:35:11 +0000 Subject: [Bioperl-l] CPAN Versioning, was [something else] In-Reply-To: <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> Message-ID: <455E0EEF.4080806@sendu.me.uk> Chris Fields wrote: > > On Nov 17, 2006, at 11:43 AM, Sendu Bala wrote: > >> Nathan S. Haigh wrote: >>> Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked up as >>> a developer release? >> >> I didn't try that variation, but have decided to go with >> bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a developer >> release. >> >> I've outlined the numbering scheme here: >> http://www.bioperl.org/wiki/Making_a_BioPerl_release#Making_the_distribution_directory >> > > I noticed that Module::Build now has a developer release that uses this: > > Module-Build-0.2805_01.tar.gz > > So the '_###' seems to be key. If so I see a versioning dilemma that > depends on what we want to call rel 1.5.2. [snip] See the page I linked above. It shows what the filenames will be for RCs , releases and point releases for developer and non-developer releases. From gwu at molbio.mgh.harvard.edu Sat Nov 18 01:39:46 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 01:39:46 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455E0EEF.4080806@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> Message-ID: <455EAAB2.4010004@molbio.mgh.harvard.edu> Hi everyone, I saw some problems when installing BioPerl 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could not solve all the dependency issues with one shot of 'install Bundle::BioPerl'. Some packages such as GD-2.35 just could not be installed. And it turned out that CPAN refused to install BioPerl with some test return value 255. Then I went to /root/.cpan/build to configure, test, rebuild those problematic packages. After several more runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl successfully. Below attached is the output of CPAN, which stills complains three packages have issues: Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel. I think the first two are typos somewhere in the Bundle::BioPerl. And the third module is not on the server and could be found on the CPAN site. So my question is : Is this the right way to install BioPerl? It took me two days to figure it out but still not 100% sure all packages are installed properly. Any feedback is appreciated. Gang ================================================= cpan> install Bundle::BioPerl Ace is up to date. Bio::ASN1::EntrezGene is up to date. Class::AutoClass is up to date. Clone is up to date. Convert::Binary::C is up to date. Running install for module Data::Stag::writer The module Data::Stag::writer isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i Data::Stag::writer'. DBD::mysql is up to date. GD::SVG is up to date. GD is up to date. Graph::Directed is up to date. HTML::Parser is up to date. Running install for module HTTP::Request::Common- The module HTTP::Request::Common- isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i HTTP::Request::Common-'. LWP::UserAgent is up to date. Set::Scalar is up to date. SOAP::Lite is up to date. Running install for module Spreadhseet::ParseExcel The module Spreadhseet::ParseExcel isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i Spreadhseet::ParseExcel'. Storable is up to date. SVG is up to date. SVG::Graph is up to date. Text::Shellwords is up to date. XML::DOM::XPath is up to date. XML::Parser::PerlSAX is up to date. XML::SAX is up to date. XML::SAX::Base is up to date. XML::SAX::Writer is up to date. XML::Simple is up to date. XML::Twig is up to date. XML::Writer is up to date. Bundle summary: The following items in bundle Bundle::BioPerl had installation problems: Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel ==================================================== From bix at sendu.me.uk Sat Nov 18 03:04:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 18 Nov 2006 08:04:14 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <455EBE7E.4060105@sendu.me.uk> gang wu wrote: > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. What problems did you run into specifically with GD? > And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. Do you remember what the other problematic packages were, and what you had to do to get them working? > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. All three are typos. We'll get those fixed. > So my question is : Is this the right way to install BioPerl? At the present moment, yes. For 1.5.2 I'll probably be recommending not using Bundle::BioPerl once I fix some other things. > It took me two days to figure it out but still not 100% sure all packages are > installed properly. I'm sorry for the troubles you ran into. We'll try and do better for the final release of 1.5.2. From gwu at molbio.mgh.harvard.edu Sat Nov 18 03:07:47 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:07:47 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <455EBF53.4010701@molbio.mgh.harvard.edu> It turned out that most of the modules of BioPerl were not installed at all. And none of the scripts were installed. I had to download and install bioperl-1.5.2-RC3.tar.gz again. A similar problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually copied all stuff under Bio folder to the corresponding Perl library folder. Is it Ok to do it in this way? Gang gang wu wrote: > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. > > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. > > So my question is : Is this the right way to install BioPerl? It took me > two days to figure it out but still not 100% sure all packages are > installed properly. > > Any feedback is appreciated. > > Gang > > ================================================= > cpan> install Bundle::BioPerl > Ace is up to date. > Bio::ASN1::EntrezGene is up to date. > Class::AutoClass is up to date. > Clone is up to date. > Convert::Binary::C is up to date. > Running install for module Data::Stag::writer > > The module Data::Stag::writer isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Data::Stag::writer'. > DBD::mysql is up to date. > GD::SVG is up to date. > GD is up to date. > Graph::Directed is up to date. > HTML::Parser is up to date. > Running install for module HTTP::Request::Common- > > The module HTTP::Request::Common- isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i HTTP::Request::Common-'. > LWP::UserAgent is up to date. > Set::Scalar is up to date. > SOAP::Lite is up to date. > Running install for module Spreadhseet::ParseExcel > > The module Spreadhseet::ParseExcel isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Spreadhseet::ParseExcel'. > Storable is up to date. > SVG is up to date. > SVG::Graph is up to date. > Text::Shellwords is up to date. > XML::DOM::XPath is up to date. > XML::Parser::PerlSAX is up to date. > XML::SAX is up to date. > XML::SAX::Base is up to date. > XML::SAX::Writer is up to date. > XML::Simple is up to date. > XML::Twig is up to date. > XML::Writer is up to date. > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > ==================================================== > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From N.Haigh at sheffield.ac.uk Sat Nov 18 03:22:00 2006 From: N.Haigh at sheffield.ac.uk (Nathan Haigh) Date: Sat, 18 Nov 2006 08:22:00 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Hi Gang, At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - we are in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things wrong with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such that it may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 and CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as dependencies will fail to install. I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - these will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install process much easier to the users. Thanks Nathan Quoting gang wu : > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. > > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. > > So my question is : Is this the right way to install BioPerl? It took me > two days to figure it out but still not 100% sure all packages are > installed properly. > > Any feedback is appreciated. > > Gang > > ================================================= > cpan> install Bundle::BioPerl > Ace is up to date. > Bio::ASN1::EntrezGene is up to date. > Class::AutoClass is up to date. > Clone is up to date. > Convert::Binary::C is up to date. > Running install for module Data::Stag::writer > > The module Data::Stag::writer isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Data::Stag::writer'. > DBD::mysql is up to date. > GD::SVG is up to date. > GD is up to date. > Graph::Directed is up to date. > HTML::Parser is up to date. > Running install for module HTTP::Request::Common- > > The module HTTP::Request::Common- isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i HTTP::Request::Common-'. > LWP::UserAgent is up to date. > Set::Scalar is up to date. > SOAP::Lite is up to date. > Running install for module Spreadhseet::ParseExcel > > The module Spreadhseet::ParseExcel isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Spreadhseet::ParseExcel'. > Storable is up to date. > SVG is up to date. > SVG::Graph is up to date. > Text::Shellwords is up to date. > XML::DOM::XPath is up to date. > XML::Parser::PerlSAX is up to date. > XML::SAX is up to date. > XML::SAX::Base is up to date. > XML::SAX::Writer is up to date. > XML::Simple is up to date. > XML::Twig is up to date. > XML::Writer is up to date. > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > ==================================================== > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From gwu at molbio.mgh.harvard.edu Sat Nov 18 03:30:30 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:30:30 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EBE7E.4060105@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> Message-ID: <455EC4A6.4040103@molbio.mgh.harvard.edu> Sendu Bala wrote: > gang wu wrote: >> Hi everyone, >> >> I saw some problems when installing BioPerl >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could >> not solve all the dependency issues with one shot of 'install >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >> installed. > > What problems did you run into specifically with GD? If I enable JPEG, GIFS and XPM, none of the test could pass. Since I usually use only PNG for output, I can live without them. I am not sure if it's system related problem. All of them work fine with my 32 bit Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with newer libgd runnig Redhat AS4 AMD/EM64T does not work. > >> And it turned out that CPAN refused to install BioPerl with >> some test return value 255. Then I went to /root/.cpan/build to >> configure, test, rebuild those problematic packages. After several more >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >> successfully. > > Do you remember what the other problematic packages were, and what you > had to do to get them working? > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I guess it should be XML::DOM::XPath.pm. I could not recall what other packages had issues, but basically it's special package configuration issue. >> Below attached is the output of CPAN, which stills complains three >> packages have issues: Data::Stag::writer HTTP::Request::Common- >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in >> the Bundle::BioPerl. And the third module is not on the server and could >> be found on the CPAN site. > > All three are typos. We'll get those fixed. > > >> So my question is : Is this the right way to install BioPerl? > > At the present moment, yes. For 1.5.2 I'll probably be recommending > not using Bundle::BioPerl once I fix some other things. > See my another message for other issues. > >> It took me two days to figure it out but still not 100% sure all >> packages are >> installed properly. > > I'm sorry for the troubles you ran into. We'll try and do better for > the final release of 1.5.2. Actually your hard work is benifiting the whole community and we all owe you a Thank You. From gwu at molbio.mgh.harvard.edu Sat Nov 18 03:44:45 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:44:45 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Message-ID: <455EC7FD.5010707@molbio.mgh.harvard.edu> Hi Nathan, Thanks for your message. I saw the C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you use 'install Bundle::BioPerl', which will definitely frustrate a bunch of users. Can this release be held for a while before most of the bugs are cleared? Thanks again. Gang Gang Nathan Haigh wrote: > Hi Gang, > > At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - we are > in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things wrong > with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). > > I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such that it > may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 and > CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as > dependencies will fail to install. > > I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - these > will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. > > If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install process > much easier to the users. > > Thanks > Nathan > > > Quoting gang wu : > > >> Hi everyone, >> >> I saw some problems when installing BioPerl >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could >> not solve all the dependency issues with one shot of 'install >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >> installed. And it turned out that CPAN refused to install BioPerl with >> some test return value 255. Then I went to /root/.cpan/build to >> configure, test, rebuild those problematic packages. After several more >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >> successfully. >> >> Below attached is the output of CPAN, which stills complains three >> packages have issues: Data::Stag::writer HTTP::Request::Common- >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in >> the Bundle::BioPerl. And the third module is not on the server and could >> be found on the CPAN site. >> >> So my question is : Is this the right way to install BioPerl? It took me >> two days to figure it out but still not 100% sure all packages are >> installed properly. >> >> Any feedback is appreciated. >> >> Gang >> >> ================================================= >> cpan> install Bundle::BioPerl >> Ace is up to date. >> Bio::ASN1::EntrezGene is up to date. >> Class::AutoClass is up to date. >> Clone is up to date. >> Convert::Binary::C is up to date. >> Running install for module Data::Stag::writer >> >> The module Data::Stag::writer isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i Data::Stag::writer'. >> DBD::mysql is up to date. >> GD::SVG is up to date. >> GD is up to date. >> Graph::Directed is up to date. >> HTML::Parser is up to date. >> Running install for module HTTP::Request::Common- >> >> The module HTTP::Request::Common- isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i HTTP::Request::Common-'. >> LWP::UserAgent is up to date. >> Set::Scalar is up to date. >> SOAP::Lite is up to date. >> Running install for module Spreadhseet::ParseExcel >> >> The module Spreadhseet::ParseExcel isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i Spreadhseet::ParseExcel'. >> Storable is up to date. >> SVG is up to date. >> SVG::Graph is up to date. >> Text::Shellwords is up to date. >> XML::DOM::XPath is up to date. >> XML::Parser::PerlSAX is up to date. >> XML::SAX is up to date. >> XML::SAX::Base is up to date. >> XML::SAX::Writer is up to date. >> XML::Simple is up to date. >> XML::Twig is up to date. >> XML::Writer is up to date. >> Bundle summary: The following items in bundle Bundle::BioPerl had >> installation problems: >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >> ==================================================== >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 gwu at molbio.mgh.harvard.edu Sat Nov 18 03:57:49 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:57:49 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <455EC4A6.4040103@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> Message-ID: <455ECB0D.5090606@molbio.mgh.harvard.edu> Hi everyone, I used to use MySQL to host the BioSQL schema and load Genbank into it with the 'load_seqdatabase.pl' without problem(except extremely slow. It took about 12 hours to load Arabidopsis thaliana). I just loaded the BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database without problem. When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with MySQL while always saw an error with Oracle: Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. , where the code is $sth->bind_param(); Any idea what the problem is? Gang From N.Haigh at sheffield.ac.uk Sat Nov 18 04:56:57 2006 From: N.Haigh at sheffield.ac.uk (Nathan Haigh) Date: Sat, 18 Nov 2006 09:56:57 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EC7FD.5010707@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> Message-ID: <1163843817.455ed8e970075@webmail.shef.ac.uk> Hi Chris, Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it contains some errors. I think Sendu *may* have some further instructions regarding this package a bit closer to the 1.5.2 release. Cheers Nathan Quoting gang wu : > Hi Nathan, > > Thanks for your message. I saw the > C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you > use 'install Bundle::BioPerl', which will definitely frustrate a bunch > of users. Can this release be held for a while before most of the bugs > are cleared? > > Thanks again. > Gang > > > Gang > > Nathan Haigh wrote: > > Hi Gang, > > > > At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - > we are > > in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things > wrong > > with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). > > > > I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such > that it > > may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 > and > > CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as > > dependencies will fail to install. > > > > I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - > these > > will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. > > > > If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install > process > > much easier to the users. > > > > Thanks > > Nathan > > > > > > Quoting gang wu : > > > > > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > >> > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in > >> the Bundle::BioPerl. And the third module is not on the server and could > >> be found on the CPAN site. > >> > >> So my question is : Is this the right way to install BioPerl? It took me > >> two days to figure it out but still not 100% sure all packages are > >> installed properly. > >> > >> Any feedback is appreciated. > >> > >> Gang > >> > >> ================================================= > >> cpan> install Bundle::BioPerl > >> Ace is up to date. > >> Bio::ASN1::EntrezGene is up to date. > >> Class::AutoClass is up to date. > >> Clone is up to date. > >> Convert::Binary::C is up to date. > >> Running install for module Data::Stag::writer > >> > >> The module Data::Stag::writer isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i Data::Stag::writer'. > >> DBD::mysql is up to date. > >> GD::SVG is up to date. > >> GD is up to date. > >> Graph::Directed is up to date. > >> HTML::Parser is up to date. > >> Running install for module HTTP::Request::Common- > >> > >> The module HTTP::Request::Common- isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i HTTP::Request::Common-'. > >> LWP::UserAgent is up to date. > >> Set::Scalar is up to date. > >> SOAP::Lite is up to date. > >> Running install for module Spreadhseet::ParseExcel > >> > >> The module Spreadhseet::ParseExcel isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i Spreadhseet::ParseExcel'. > >> Storable is up to date. > >> SVG is up to date. > >> SVG::Graph is up to date. > >> Text::Shellwords is up to date. > >> XML::DOM::XPath is up to date. > >> XML::Parser::PerlSAX is up to date. > >> XML::SAX is up to date. > >> XML::SAX::Base is up to date. > >> XML::SAX::Writer is up to date. > >> XML::Simple is up to date. > >> XML::Twig is up to date. > >> XML::Writer is up to date. > >> Bundle summary: The following items in bundle Bundle::BioPerl had > >> installation problems: > >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > >> ==================================================== > >> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/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 uiuc.edu Sat Nov 18 09:35:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 18 Nov 2006 08:35:38 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163843817.455ed8e970075@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> Message-ID: It probably doesn't need to be pulled, just updated to fix errors, spelling, etc. The problems reported with GD are common and normally are due to libgd issues or C code compilation problems during the test run (the DEPENDENCIES doc and wiki page indicate this). DBI/ DBD::mysql is another one that sometimes requires finessing (I remember it giving problems on CygWin and Mac OS X). Chris D. probably just needs a list of issues that need fixing. You also have to realize we're heading into Thanksgiving so some people may be incommunicado for the time being. Spelling is the main problem. Beyond that there really isn't anything we can do about those requirements beside not requiring them (i.e. removing them then explaining that particular components won't work), but then it wouldn't be a proper Bundle package. It's a catch-22. If there isn't a place in the install docs yet some of these issues could use a bit more detail or explanation, or at least redirect to some proper installation instructions based on the platform. I think, now that this is on CPAN, you'll likely see many more questions popping up. Chris (F.) On Nov 18, 2006, at 3:56 AM, Nathan Haigh wrote: > Hi Chris, > > Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it > contains some errors. I think Sendu *may* have some further > instructions regarding > this package a bit closer to the 1.5.2 release. > > Cheers > Nathan > > > > Quoting gang wu : > >> Hi Nathan, >> >> Thanks for your message. I saw the >> C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you >> use 'install Bundle::BioPerl', which will definitely frustrate a >> bunch >> of users. Can this release be held for a while before most of the >> bugs >> are cleared? >> >> Thanks again. >> Gang >> >> >> Gang >> >> Nathan Haigh wrote: >>> Hi Gang, >>> >>> At the moment we are having a few teathing problems with CPAN >>> packages. I notice that you are trying to install the 1.5.2 >>> release candidate 3 - >> we are >>> in the final stages of getting out the official 1.5.2 developer >>> release (hopefully in the next couple of weeks). There are indeed >>> a few things >> wrong >>> with the latest Bundle::BioPerl package but we thought we'd hold >>> off updating it until the 1.5.2 release (or shortly before). >>> >>> I think that the problem with CPAN installing dependencies is >>> that it has no way to correctly ordering the installation of >>> dependencies, such >> that it >>> may be neccessary to run the install several time in order to get >>> everything installed. For example, if prerequisite 2 depends on >>> prerequisite 1 >> and >>> CPAN installs prerequisite 2 first, then it's test suite will >>> probably fail and thus the installation of the package siting >>> both these as >>> dependencies will fail to install. >>> >>> I believe you are correct in the way you are installing bioperl, >>> but we still have a few issues to sort out with regards to the >>> CPAN packages - >> these >>> will definately be sorted out by the time of the 1.5.2 release in >>> a matter of weeks. >>> >>> If anyone is aware of a way to force CPAN to install modules in a >>> specific order, please let Sendu know - we may be able to make >>> the install >> process >>> much easier to the users. >>> >>> Thanks >>> Nathan >>> >>> >>> Quoting gang wu : >>> >>> >>>> Hi everyone, >>>> >>>> I saw some problems when installing BioPerl >>>> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>>> CPAN could >>>> not solve all the dependency issues with one shot of 'install >>>> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>>> installed. And it turned out that CPAN refused to install >>>> BioPerl with >>>> some test return value 255. Then I went to /root/.cpan/build to >>>> configure, test, rebuild those problematic packages. After >>>> several more >>>> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>>> successfully. >>>> >>>> Below attached is the output of CPAN, which stills complains three >>>> packages have issues: Data::Stag::writer HTTP::Request::Common- >>>> Spreadhseet::ParseExcel. I think the first two are typos >>>> somewhere in >>>> the Bundle::BioPerl. And the third module is not on the server >>>> and could >>>> be found on the CPAN site. >>>> >>>> So my question is : Is this the right way to install BioPerl? It >>>> took me >>>> two days to figure it out but still not 100% sure all packages are >>>> installed properly. >>>> >>>> Any feedback is appreciated. >>>> >>>> Gang >>>> >>>> ================================================= >>>> cpan> install Bundle::BioPerl >>>> Ace is up to date. >>>> Bio::ASN1::EntrezGene is up to date. >>>> Class::AutoClass is up to date. >>>> Clone is up to date. >>>> Convert::Binary::C is up to date. >>>> Running install for module Data::Stag::writer >>>> >>>> The module Data::Stag::writer isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i Data::Stag::writer'. >>>> DBD::mysql is up to date. >>>> GD::SVG is up to date. >>>> GD is up to date. >>>> Graph::Directed is up to date. >>>> HTML::Parser is up to date. >>>> Running install for module HTTP::Request::Common- >>>> >>>> The module HTTP::Request::Common- isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i HTTP::Request::Common-'. >>>> LWP::UserAgent is up to date. >>>> Set::Scalar is up to date. >>>> SOAP::Lite is up to date. >>>> Running install for module Spreadhseet::ParseExcel >>>> >>>> The module Spreadhseet::ParseExcel isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i Spreadhseet::ParseExcel'. >>>> Storable is up to date. >>>> SVG is up to date. >>>> SVG::Graph is up to date. >>>> Text::Shellwords is up to date. >>>> XML::DOM::XPath is up to date. >>>> XML::Parser::PerlSAX is up to date. >>>> XML::SAX is up to date. >>>> XML::SAX::Base is up to date. >>>> XML::SAX::Writer is up to date. >>>> XML::Simple is up to date. >>>> XML::Twig is up to date. >>>> XML::Writer is up to date. >>>> Bundle summary: The following items in bundle Bundle::BioPerl had >>>> installation problems: >>>> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >>>> ==================================================== >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Sat Nov 18 12:13:10 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sat, 18 Nov 2006 12:13:10 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EC4A6.4040103@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> Message-ID: <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> What version of libgd do you have installed? With recent versions of libgd (more recent than two years old) you will not be given the chance to select whether to compile JPEG, GIF and XPM support, since these options are selected automatically by running libgd-config. Lincoln On 11/18/06, gang wu wrote: > > > Sendu Bala wrote: > > gang wu wrote: > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN > could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. > > > > What problems did you run into specifically with GD? > If I enable JPEG, GIFS and XPM, none of the test could pass. Since I > usually use only PNG for output, I can live without them. I am not sure > if it's system related problem. All of them work fine with my 32 bit > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with newer > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > >> And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > > > > Do you remember what the other problematic packages were, and what you > > had to do to get them working? > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > guess it should be XML::DOM::XPath.pm. I could not recall what other > packages had issues, but basically it's special package configuration > issue. > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in > >> the Bundle::BioPerl. And the third module is not on the server and > could > >> be found on the CPAN site. > > > > All three are typos. We'll get those fixed. > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > At the present moment, yes. For 1.5.2 I'll probably be recommending > > not using Bundle::BioPerl once I fix some other things. > > > See my another message for other issues. > > > >> It took me two days to figure it out but still not 100% sure all > >> packages are > >> installed properly. > > > > I'm sorry for the troubles you ran into. We'll try and do better for > > the final release of 1.5.2. > Actually your hard work is benifiting the whole community and we all owe > you a Thank You. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From dag at sonsorol.org Sat Nov 18 12:47:07 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Sat, 18 Nov 2006 12:47:07 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> Message-ID: <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> Hi folks, On November 17th, Victor de Jager filed a bug report with CPAN (thanks Victor!) covering the following issues with the 2.1.6 bundle: > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > > This should be Spreadsheet::ParseExcel of course. > Data::Stag::writer does not exist in CPAN, should be > Data::Stag::Writer > > Hope it helps, meanwhile I got around using the CVS version. > Best regards I immediately fixed the errors and uploaded version 2.1.7 on the same day, by now it has probably propagated through the CPAN mirror system but you can find it directly here: http://search.cpan.org/~craffi/ Please let me know directly (email: dag at sonsorol.org) if there are *other* things that need to be added or updated. Sorry for the problems with 2.1.6 -- the contents of that Bundle were given to me by someone else on Oct 17th :) and I think I was sitting on a plane at the time and did not have time to do a local CPAN test with it. My apologies. Regards, Chris On Nov 18, 2006, at 9:35 AM, Chris Fields wrote: > It probably doesn't need to be pulled, just updated to fix errors, > spelling, etc. The problems reported with GD are common and > normally are due to libgd issues or C code compilation problems > during the test run (the DEPENDENCIES doc and wiki page indicate > this). DBI/DBD::mysql is another one that sometimes requires > finessing (I remember it giving problems on CygWin and Mac OS X). > Chris D. probably just needs a list of issues that need fixing. > You also have to realize we're heading into Thanksgiving so some > people may be incommunicado for the time being. > > Spelling is the main problem. Beyond that there really isn't > anything we can do about those requirements beside not requiring > them (i.e. removing them then explaining that particular components > won't work), but then it wouldn't be a proper Bundle package. It's > a catch-22. If there isn't a place in the install docs yet some of > these issues could use a bit more detail or explanation, or at > least redirect to some proper installation instructions based on > the platform. > > I think, now that this is on CPAN, you'll likely see many more > questions popping up. > > Chris (F.) > > On Nov 18, 2006, at 3:56 AM, Nathan Haigh wrote: > >> Hi Chris, >> >> Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it >> contains some errors. I think Sendu *may* have some further >> instructions regarding >> this package a bit closer to the 1.5.2 release. >> >> Cheers >> Nathan >> >> >> >> Quoting gang wu : >> >>> Hi Nathan, >>> >>> Thanks for your message. I saw the >>> C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if >>> you >>> use 'install Bundle::BioPerl', which will definitely frustrate a >>> bunch >>> of users. Can this release be held for a while before most of the >>> bugs >>> are cleared? >>> >>> Thanks again. >>> Gang >>> >>> >>> Gang >>> >>> Nathan Haigh wrote: >>>> Hi Gang, >>>> >>>> At the moment we are having a few teathing problems with CPAN >>>> packages. I notice that you are trying to install the 1.5.2 >>>> release candidate 3 - >>> we are >>>> in the final stages of getting out the official 1.5.2 developer >>>> release (hopefully in the next couple of weeks). There are >>>> indeed a few things >>> wrong >>>> with the latest Bundle::BioPerl package but we thought we'd hold >>>> off updating it until the 1.5.2 release (or shortly before). >>>> >>>> I think that the problem with CPAN installing dependencies is >>>> that it has no way to correctly ordering the installation of >>>> dependencies, such >>> that it >>>> may be neccessary to run the install several time in order to >>>> get everything installed. For example, if prerequisite 2 depends >>>> on prerequisite 1 >>> and >>>> CPAN installs prerequisite 2 first, then it's test suite will >>>> probably fail and thus the installation of the package siting >>>> both these as >>>> dependencies will fail to install. >>>> >>>> I believe you are correct in the way you are installing bioperl, >>>> but we still have a few issues to sort out with regards to the >>>> CPAN packages - >>> these >>>> will definately be sorted out by the time of the 1.5.2 release >>>> in a matter of weeks. >>>> >>>> If anyone is aware of a way to force CPAN to install modules in >>>> a specific order, please let Sendu know - we may be able to make >>>> the install >>> process >>>> much easier to the users. >>>> >>>> Thanks >>>> Nathan >>>> >>>> >>>> Quoting gang wu : >>>> >>>> >>>>> Hi everyone, >>>>> >>>>> I saw some problems when installing BioPerl >>>>> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>>>> CPAN could >>>>> not solve all the dependency issues with one shot of 'install >>>>> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>>>> installed. And it turned out that CPAN refused to install >>>>> BioPerl with >>>>> some test return value 255. Then I went to /root/.cpan/build to >>>>> configure, test, rebuild those problematic packages. After >>>>> several more >>>>> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>>>> successfully. >>>>> >>>>> Below attached is the output of CPAN, which stills complains three >>>>> packages have issues: Data::Stag::writer HTTP::Request::Common- >>>>> Spreadhseet::ParseExcel. I think the first two are typos >>>>> somewhere in >>>>> the Bundle::BioPerl. And the third module is not on the server >>>>> and could >>>>> be found on the CPAN site. >>>>> >>>>> So my question is : Is this the right way to install BioPerl? >>>>> It took me >>>>> two days to figure it out but still not 100% sure all packages are >>>>> installed properly. >>>>> >>>>> Any feedback is appreciated. >>>>> >>>>> Gang >>>>> >>>>> ================================================= >>>>> cpan> install Bundle::BioPerl >>>>> Ace is up to date. >>>>> Bio::ASN1::EntrezGene is up to date. >>>>> Class::AutoClass is up to date. >>>>> Clone is up to date. >>>>> Convert::Binary::C is up to date. >>>>> Running install for module Data::Stag::writer >>>>> >>>>> The module Data::Stag::writer isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i Data::Stag::writer'. >>>>> DBD::mysql is up to date. >>>>> GD::SVG is up to date. >>>>> GD is up to date. >>>>> Graph::Directed is up to date. >>>>> HTML::Parser is up to date. >>>>> Running install for module HTTP::Request::Common- >>>>> >>>>> The module HTTP::Request::Common- isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i HTTP::Request::Common-'. >>>>> LWP::UserAgent is up to date. >>>>> Set::Scalar is up to date. >>>>> SOAP::Lite is up to date. >>>>> Running install for module Spreadhseet::ParseExcel >>>>> >>>>> The module Spreadhseet::ParseExcel isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i Spreadhseet::ParseExcel'. >>>>> Storable is up to date. >>>>> SVG is up to date. >>>>> SVG::Graph is up to date. >>>>> Text::Shellwords is up to date. >>>>> XML::DOM::XPath is up to date. >>>>> XML::Parser::PerlSAX is up to date. >>>>> XML::SAX is up to date. >>>>> XML::SAX::Base is up to date. >>>>> XML::SAX::Writer is up to date. >>>>> XML::Simple is up to date. >>>>> XML::Twig is up to date. >>>>> XML::Writer is up to date. >>>>> Bundle summary: The following items in bundle Bundle::BioPerl had >>>>> installation problems: >>>>> Data::Stag::writer HTTP::Request::Common- >>>>> Spreadhseet::ParseExcel >>>>> ==================================================== >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/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 > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > From n.haigh at sheffield.ac.uk Sat Nov 18 13:32:17 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Sat, 18 Nov 2006 18:32:17 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> Message-ID: <455F51B1.6000301@sheffield.ac.uk> Chris Dagdigian wrote: > > Hi folks, > > On November 17th, Victor de Jager filed a bug report with CPAN (thanks > Victor!) covering the following issues with the 2.1.6 bundle: > >> Bundle summary: The following items in bundle Bundle::BioPerl had >> installation problems: >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >> >> This should be Spreadsheet::ParseExcel of course. >> Data::Stag::writer does not exist in CPAN, should be Data::Stag::Writer >> >> Hope it helps, meanwhile I got around using the CVS version. >> Best regards > > I immediately fixed the errors and uploaded version 2.1.7 on the same > day, by now it has probably propagated through the CPAN mirror system > but you can find it directly here: > > http://search.cpan.org/~craffi/ > > Please let me know directly (email: dag at sonsorol.org) if there are > *other* things that need to be added or updated. > > Sorry for the problems with 2.1.6 -- the contents of that Bundle were > given to me by someone else on Oct 17th :) and I think I was sitting > on a plane at the time and did not have time to do a local CPAN test > with it. My apologies. > > Regards, > Chris > > That was me - my bad! :-[ Nath From hlapp at gmx.net Sat Nov 18 22:08:00 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 18 Nov 2006 22:08:00 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <455ECB0D.5090606@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> Message-ID: <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> This is very odd. I would mean that preparing the statement failed, i.e., that the generated SQL was not accepted by the server (or the Oracle client library). Which test does this happen with? Could you run the test alone in which it happens with TEST_VERBOSE turned on? E.g., $ make test_03simpleseq TEST_VERBOSE=1 if it's the simpleseq test that's causing the failure. Capture the output in a file and send it to me. -hilmar On Nov 18, 2006, at 3:57 AM, gang wu wrote: > Hi everyone, > > I used to use MySQL to host the BioSQL schema and load Genbank into it > with the 'load_seqdatabase.pl' without problem(except extremely > slow. It > took about 12 hours to load Arabidopsis thaliana). I just loaded the > BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database > without > problem. > > When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with > MySQL while always saw an error with Oracle: > Can't call method "bind_param" on an undefined value at > /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm > line 939. > > , where the code is $sth->bind_param(); > > Any idea what the problem is? > > Gang > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From gwu at molbio.mgh.harvard.edu Sat Nov 18 22:09:08 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 22:09:08 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> Message-ID: <455FCAD4.7050709@molbio.mgh.harvard.edu> Lincoln, Thanks for your message. I have gd-2.0.28-4.4E.1 and gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. Attached is the output. Gang ================================================== [root at elegans GD-2.35]# perl Makefile.PL NOTICE: This module requires libgd 2.0.28 or higher. If you are using Math::Trig 1.01 or lower, it has a bug that causes a "prerequisite not found" warning to be issued. You may safely ignore this warning. Type perl Makefile.PL -h for command-line option summary Where is libgd installed? [/usr/lib] Please choose the features that match how libgd was built: Build JPEG support? [y] Build PNG support? [y] Build FreeType support? [y] Build GIF support? [y] Build support for animated GIFs? [y] Build XPM support? [y] If you experience compile problems, please check the @INC, @LIBPATH and @LIBS arrays defined in Makefile.PL and manually adjust, if necessary. Checking if your kit is complete... Looks good Writing Makefile for GD [root at elegans GD-2.35]# make cp GD/Polyline.pm blib/lib/GD/Polyline.pm cp qd.pl blib/lib/qd.pl cp GD/Image.pm blib/lib/GD/Image.pm cp GD.pm blib/lib/GD.pm AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) cp GD/Simple.pm blib/lib/GD/Simple.pm cp GD/Polygon.pm blib/lib/GD/Polygon.pm /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc && mv GD.xsc GD.c gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c GD.xs: In function `XS_GD__Image_STORABLE_thaw': GD.xs:923: warning: cast from pointer to integer of different size GD.xs: In function `XS_GD__Image_gifanimbegin': GD.xs:990: warning: cast to pointer from integer of different size GD.xs: In function `XS_GD__Image_gifanimadd': GD.xs:1015: warning: cast to pointer from integer of different size GD.xs: In function `XS_GD__Image_gifanimend': GD.xs:1034: warning: cast to pointer from integer of different size Running Mkbootstrap for GD () chmod 644 GD.bs rm -f blib/arch/auto/GD/GD.so gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11 /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11 /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when searching for -lXpm /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when searching for -lXpm /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc chmod 755 blib/arch/auto/GD/GD.so cp GD.bs blib/arch/auto/GD/GD.bs chmod 644 blib/arch/auto/GD/GD.bs cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bdf2gdfont.pl Manifying blib/man1/bdf2gdfont.pl.1 Manifying blib/man3/GD::Polyline.3pm Manifying blib/man3/GD::Image.3pm Manifying blib/man3/GD::Simple.3pm Manifying blib/man3/GD.3pm Manifying blib/man3/GD::Polygon.3pm [root at elegans GD-2.35]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. at t/GD.t line 14 Compilation failed in require at t/GD.t line 14. BEGIN failed--compilation aborted at t/GD.t line 14. t/GD..........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-12 Failed 12/12 tests, 0.00% okay t/Polyline....Can't load '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 Compilation failed in require at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. BEGIN failed--compilation aborted at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. Compilation failed in require at t/Polyline.t line 10. BEGIN failed--compilation aborted at t/Polyline.t line 10. t/Polyline....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED test 1 Failed 1/1 tests, 0.00% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/GD.t 255 65280 12 23 191.67% 1-12 t/Polyline.t 255 65280 1 2 200.00% 1 Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. make: *** [test_dynamic] Error 255 [root at elegans GD-2.35]# =========================================================== Lincoln Stein wrote: > What version of libgd do you have installed? With recent versions of > libgd (more recent than two years old) you will not be given the > chance to select whether to compile JPEG, GIF and XPM support, since > these options are selected automatically by running libgd-config. > > Lincoln > > On 11/18/06, *gang wu* > wrote: > > > Sendu Bala wrote: > > gang wu wrote: > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously > CPAN could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. > > > > What problems did you run into specifically with GD? > If I enable JPEG, GIFS and XPM, none of the test could pass. Since I > usually use only PNG for output, I can live without them. I am not > sure > if it's system related problem. All of them work fine with my 32 bit > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with > newer > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > >> And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After > several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > > > > Do you remember what the other problematic packages were, and > what you > > had to do to get them working? > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > guess it should be XML::DOM::XPath.pm. I could not recall what other > packages had issues, but basically it's special package > configuration issue. > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos > somewhere in > >> the Bundle::BioPerl. And the third module is not on the server > and could > >> be found on the CPAN site. > > > > All three are typos. We'll get those fixed. > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > At the present moment, yes. For 1.5.2 I'll probably be recommending > > not using Bundle::BioPerl once I fix some other things. > > > See my another message for other issues. > > > >> It took me two days to figure it out but still not 100% sure all > >> packages are > >> installed properly. > > > > I'm sorry for the troubles you ran into. We'll try and do better for > > the final release of 1.5.2. > Actually your hard work is benifiting the whole community and we > all owe > you a Thank You. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu From bix at sendu.me.uk Sun Nov 19 10:51:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 19 Nov 2006 15:51:55 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EBF53.4010701@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> Message-ID: <45607D9B.4010703@sendu.me.uk> gang wu wrote: > It turned out that most of the modules of BioPerl were not installed at > all. And none of the scripts were installed. I had to download and > install bioperl-1.5.2-RC3.tar.gz > again. A similar > problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually > copied all stuff under Bio folder to the corresponding Perl library > folder. Is it Ok to do it in this way? It will work, but is hardly good enough from our point of view (you shouldn't have to do that). Can you tell me exactly what you mean by 'were not installed'? What did you do to try and install? How did you determine that installation had failed? With CPAN, if you were still getting errors during testing, what were those remaining errors, and did you do a forced install to ignore the errors? If a forced install didn't actually install anything, what message did CPAN give you about that, if any? With the manual download, after doing "perl Makefile.PL", what is your output of "make install"? Thank you, Sendu. From lincoln.stein at gmail.com Sun Nov 19 10:54:11 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sun, 19 Nov 2006 10:54:11 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455FCAD4.7050709@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> <455FCAD4.7050709@molbio.mgh.harvard.edu> Message-ID: <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> That's very odd. gd.0.28 should install gdlib-config, and the existence of this executable should inhibit the interactive questions. Could you see if there's a gdlib-config executable installed on your system? Lincoln On 11/18/06, gang wu wrote: > > Lincoln, > Thanks for your message. I have gd-2.0.28-4.4E.1 and > gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. > Attached is the output. > > Gang > > ================================================== > [root at elegans GD-2.35]# perl Makefile.PL > NOTICE: This module requires libgd 2.0.28 or higher. > > If you are using Math::Trig 1.01 or lower, it has a bug that > causes a "prerequisite not found" warning to be issued. You may > safely ignore this warning. > > Type perl Makefile.PL -h for command-line option summary > > > Where is libgd installed? [/usr/lib] > > Please choose the features that match how libgd was built: > Build JPEG support? [y] > Build PNG support? [y] > Build FreeType support? [y] > Build GIF support? [y] > Build support for animated GIFs? [y] > Build XPM support? [y] > > If you experience compile problems, please check the @INC, @LIBPATH and > @LIBS > arrays defined in Makefile.PL and manually adjust, if necessary. > > Checking if your kit is complete... > Looks good > Writing Makefile for GD > [root at elegans GD-2.35]# make > cp GD/Polyline.pm blib/lib/GD/Polyline.pm > cp qd.pl blib/lib/qd.pl > cp GD/Image.pm blib/lib/GD/Image.pm > cp GD.pm blib/lib/GD.pm > AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) > cp GD/Simple.pm blib/lib/GD/Simple.pm > cp GD/Polygon.pm blib/lib/GD/Polygon.pm > /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap > /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc > && mv GD.xsc GD.c > gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE > -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g > -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC > "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG > -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c > GD.xs: In function `XS_GD__Image_STORABLE_thaw': > GD.xs:923: warning: cast from pointer to integer of different size > GD.xs: In function `XS_GD__Image_gifanimbegin': > GD.xs:990: warning: cast to pointer from integer of different size > GD.xs: In function `XS_GD__Image_gifanimadd': > GD.xs:1015: warning: cast to pointer from integer of different size > GD.xs: In function `XS_GD__Image_gifanimend': > GD.xs:1034: warning: cast to pointer from integer of different size > Running Mkbootstrap for GD () > chmod 644 GD.bs > rm -f blib/arch/auto/GD/GD.so > gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 > -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 > -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm > /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz > /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz > /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm > /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when > searching for -lX11 > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when > searching for -lX11 > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when > searching for -lXpm > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when > searching for -lXpm > /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc > /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc > chmod 755 blib/arch/auto/GD/GD.so > cp GD.bs blib/arch/auto/GD/GD.bs > chmod 644 blib/arch/auto/GD/GD.bs > cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" > blib/script/bdf2gdfont.pl > Manifying blib/man1/bdf2gdfont.pl.1 > Manifying blib/man3/GD::Polyline.3pm > Manifying blib/man3/GD::Image.3pm > Manifying blib/man3/GD::Simple.3pm > Manifying blib/man3/GD.3pm > Manifying blib/man3/GD::Polygon.3pm > [root at elegans GD-2.35]# make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: > ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at > /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. > at t/GD.t line 14 > Compilation failed in require at t/GD.t line 14. > BEGIN failed--compilation aborted at t/GD.t line 14. > t/GD..........dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-12 > Failed 12/12 tests, 0.00% okay > t/Polyline....Can't load > '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: > /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: > gdImageGifAnimAddPtr at > /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. > at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 > Compilation failed in require at > /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. > BEGIN failed--compilation aborted at > /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. > Compilation failed in require at t/Polyline.t line 10. > BEGIN failed--compilation aborted at t/Polyline.t line 10. > t/Polyline....dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED test 1 > Failed 1/1 tests, 0.00% okay > Failed Test Stat Wstat Total Fail Failed List of Failed > > ------------------------------------------------------------------------------- > t/GD.t 255 65280 12 23 191.67% 1-12 > t/Polyline.t 255 65280 1 2 200.00% 1 > Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. > make: *** [test_dynamic] Error 255 > [root at elegans GD-2.35]# > =========================================================== > > Lincoln Stein wrote: > > What version of libgd do you have installed? With recent versions of > > libgd (more recent than two years old) you will not be given the > > chance to select whether to compile JPEG, GIF and XPM support, since > > these options are selected automatically by running libgd-config. > > > > Lincoln > > > > On 11/18/06, *gang wu* > > wrote: > > > > > > Sendu Bala wrote: > > > gang wu wrote: > > >> Hi everyone, > > >> > > >> I saw some problems when installing BioPerl > > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously > > CPAN could > > >> not solve all the dependency issues with one shot of 'install > > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > > >> installed. > > > > > > What problems did you run into specifically with GD? > > If I enable JPEG, GIFS and XPM, none of the test could pass. Since > I > > usually use only PNG for output, I can live without them. I am not > > sure > > if it's system related problem. All of them work fine with my 32 bit > > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with > > newer > > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > > > >> And it turned out that CPAN refused to install BioPerl with > > >> some test return value 255. Then I went to /root/.cpan/build to > > >> configure, test, rebuild those problematic packages. After > > several more > > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > > >> successfully. > > > > > > Do you remember what the other problematic packages were, and > > what you > > > had to do to get them working? > > > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > > guess it should be XML::DOM::XPath.pm. I could not recall what other > > packages had issues, but basically it's special package > > configuration issue. > > >> Below attached is the output of CPAN, which stills complains > three > > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > > >> Spreadhseet::ParseExcel. I think the first two are typos > > somewhere in > > >> the Bundle::BioPerl. And the third module is not on the server > > and could > > >> be found on the CPAN site. > > > > > > All three are typos. We'll get those fixed. > > > > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > > > At the present moment, yes. For 1.5.2 I'll probably be > recommending > > > not using Bundle::BioPerl once I fix some other things. > > > > > See my another message for other issues. > > > > > >> It took me two days to figure it out but still not 100% sure all > > >> packages are > > >> installed properly. > > > > > > I'm sorry for the troubles you ran into. We'll try and do better > for > > > the final release of 1.5.2. > > Actually your hard work is benifiting the whole community and we > > all owe > > you a Thank You. > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From lincoln.stein at gmail.com Sun Nov 19 12:22:25 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sun, 19 Nov 2006 12:22:25 -0500 Subject: [Bioperl-l] [Gmod-gbrowse] aggregators issue? In-Reply-To: <455CE3CE.4060305@mail.med.upenn.edu> References: <455CE3CE.4060305@mail.med.upenn.edu> Message-ID: <6dce9a0b0611190922h7eb79928y46104c17266eccce@mail.gmail.com> Hi, What you want to do is what the heterogeneous_segments glyph does. The redgreen_box glyph originally only operated on the top level feature and not with aggregated features. However, since what you want to do is reasonable I've added a new color_subparts option, so that you will get the right effect with this modified stanza: [Linkage2] feature = qtl color_subparts = 1 glyph = redgreen_box key = Linkage2 You'll need to update bioperl to get this fix. The xyplot issue that you reported was a real bug in bioperl. This has now been fixed in both the release candidate and HEAD CVS repositories. Lincoln On 11/16/06, mmorley wrote: > > Hello All, > > Not sure where the problem lies but I'm trying to display results from a > Linkage analysis (many really).. > Perhaps my logic on the data structure is wrong but I have a peak > (locus,QTL,etc) that exceeds some defined significance that I have > predefined. > Within each peak there are markers (SNPs in this case) each with a level > of significance(score). Instead of displaying each SNP value as say in > XY plot... I have a score for the SNP to SNP interval.. The idea being > is I'd like to display the data using the redgreen_box glyph. > > To make it easier I created a little small test set which can be placed > on the Volvox tutorial ctgA > > Here is the gff data: > ---------------------------------------- > ctgA test peak 0 40000 . . . peak 3 ; Note > "EIF4G2" > ctgA test signal 0 1 0.4 . . peak 3 ; > ctgA test signal 2 25000 0.7 . . peak 3 ; > ctgA test signal 25000 35000 0.6 . . peak 3 ; > ctgA test signal 35000 40000 0.5 . . peak 3 ; > ctgA test peak 0 40000 . . . peak 10 ; Note "LRAP" > ctgA test signal 0 1 0.3 . . peak 10 ; > ctgA test signal 2 25000 0.4 . . peak 10 ; > ctgA test signal 25000 35000 0.7 . . peak 10 ; > ctgA test signal 35000 40000 0.5 . . peak 10 ; > --------------------------------------------------- > > here is my aggregator: > -------------------------------------- > qtl{signal/peak} > ----------------------------------------- > and my track: > --------------------------------------------- > [Linkage2] > feature = qtl > glyph = redgreen_box > key = Linkage2 > ------------------------------------------- > > right now very basic... the problem is well nothing is displayed using > that track... I do however get the label for each printed.. but no > graphic. If I change the feature to "signal" I do get data plotted but > each signal is on a different line,which is expected but not what I want. > > Also as a side note if I decide to plot the data as an xy_plot using the > following track stanza: > [Linkage] > feature = qtl > glyph = xyplot > graph_type = line > height = 50 > min_score = 0 > max_score = 1 > scale = right > key = Linkage > > I get both peaks plotted but within the same plot... However a second > plot is created it is just empty. > > Hopefully I'm convening this well... and if not hopefully fairly easy to > test... > > > -Mike > > > -- > Michael Morley > Bioinformatics Specialist > University of Pennsylvania > Department of Pediatrics > 3516 Civic Center Blvd., > 510B Abramson Pediatric Research Center, > Philadelphia, PA 19104-4318. > Phone: (215) 590-7673 > FAX: (215) 590-3709 > > > > > > > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From pmiguel at purdue.edu Sun Nov 19 19:58:42 2006 From: pmiguel at purdue.edu (Phillip SanMiguel) Date: Sun, 19 Nov 2006 19:58:42 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <45607D9B.4010703@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> Message-ID: <4560FDC2.4000309@purdue.edu> Sendu Bala wrote: > gang wu wrote: > >> It turned out that most of the modules of BioPerl were not installed at >> all. And none of the scripts were installed. I had to download and >> install bioperl-1.5.2-RC3.tar.gz >> again. A similar >> problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually >> copied all stuff under Bio folder to the corresponding Perl library >> folder. Is it Ok to do it in this way? >> > > It will work, but is hardly good enough from our point of view (you > shouldn't have to do that). > > Can you tell me exactly what you mean by 'were not installed'? What did > you do to try and install? How did you determine that installation had > failed? > > [...] My guess is that he thought that bioperl bundle installed the dependencies *and* bioperl itself. That was my presumption the first time I saw it on CPAN. -- Phillip From bikash_lohia2000 at yahoo.com Mon Nov 20 07:45:38 2006 From: bikash_lohia2000 at yahoo.com (bikash lohia) Date: Mon, 20 Nov 2006 04:45:38 -0800 (PST) Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi Message-ID: <20061120124538.40740.qmail@web54205.mail.yahoo.com> hello group, I am new to this group and want a help.i have list of accesion id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to manually search gene database of NCBI for converting this accession no. of cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i want to do it through perl programming where the program directly takes the list of id ( such as AK105331,Ak070197) from notepad file and searches in gene database of ncbi. to give results in accession id starting with OS****** .i want only the accession id of corresponding Ak***** id. for example - AK070197 of nucleotide databse = Os02g0669100 of gene database. i want to convert all this AK***** ids to OS***** ids through programming in perl/bioperl as manually not possible for long list. please help. i have no idea how can the code be. with thanks in advance from Bikash --------------------------------- Everyone is raving about the all-new Yahoo! Mail beta. From sdavis2 at mail.nih.gov Mon Nov 20 08:31:48 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 08:31:48 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi In-Reply-To: <20061120124538.40740.qmail@web54205.mail.yahoo.com> References: <20061120124538.40740.qmail@web54205.mail.yahoo.com> Message-ID: <200611200831.49098.sdavis2@mail.nih.gov> On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean From sdavis2 at mail.nih.gov Mon Nov 20 08:31:48 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 08:31:48 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi In-Reply-To: <20061120124538.40740.qmail@web54205.mail.yahoo.com> References: <20061120124538.40740.qmail@web54205.mail.yahoo.com> Message-ID: <200611200831.49098.sdavis2@mail.nih.gov> On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean From avilella at gmail.com Mon Nov 20 09:53:08 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 20 Nov 2006 14:53:08 +0000 Subject: [Bioperl-l] mmap perl Message-ID: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> Hi all, A bit of an off-topic: Has anyone ever investigated with libcache-mmap-perl or libcache-fastmmap-perl? Cheers, Albert. From cuiw at ncbi.nlm.nih.gov Mon Nov 20 10:45:13 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 10:45:13 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812330@NIHCESMLBX8.nih.gov> This script only works for 1 ACC to 1 Gene ID. perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 10:45:13 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 10:45:13 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812330@NIHCESMLBX8.nih.gov> This script only works for 1 ACC to 1 Gene ID. perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 11:03:44 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 11:03:44 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812332@NIHCESMLBX8.nih.gov> Correction: perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id")' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 11:03:44 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 11:03:44 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812332@NIHCESMLBX8.nih.gov> Correction: perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id")' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From gwu at molbio.mgh.harvard.edu Mon Nov 20 10:57:48 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 10:57:48 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> Message-ID: <4561D07C.4060800@molbio.mgh.harvard.edu> Hi Hilmar, Thanks for your message. Below are several tests for Oracle and MySQL. MySQL actually also has two tests with failed items which may be related to data in BioSQL database. Could it be my Oracle installation/configuration has some issues? Thanks. Gang Output of 'make test' for Oracle ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....ok 14/19Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. t/01dbadaptor.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-19 Failed 5/19 tests, 73.68% okay t/02species.......ok 5/65Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. t/02species.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-65 Failed 60/65 tests, 7.69% okay t/03simpleseq.....ok 5/59Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/03simpleseq.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-59 Failed 54/59 tests, 8.47% okay t/04swiss.........ok 5/52Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 78. t/04swiss.........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-52 Failed 47/52 tests, 9.62% okay t/05seqfeature....ok 3/48Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/05seqfeature....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 4-48 Failed 45/48 tests, 6.25% okay t/06comment.......ok 2/11Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/06comment.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-11 Failed 9/11 tests, 18.18% okay t/07dblink........ok 2/18Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/07dblink........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/08genbank.......ok 2/18Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/08genbank.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/09fuzzy2........ok 2/21Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 64. t/09fuzzy2........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-21 Failed 19/21 tests, 9.52% okay t/10ensembl.......ok 2/15Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1420. t/10ensembl.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-15 Failed 13/15 tests, 13.33% okay t/11locuslink.....ok 4/110Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/11locuslink.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-110 Failed 106/110 tests, 3.64% okay t/12ontology......ok 4/738Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 98. t/12ontology......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-738 Failed 734/738 tests, 0.54% okay t/13remove........ok 1/59Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. t/13remove........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-59 Failed 58/59 tests, 1.69% okay t/14query.........ok t/15cluster.......ok 5/160Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/15cluster.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-160 Failed 155/160 tests, 3.12% okay t/16obda..........ok 2/12Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/16obda..........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-12 Failed 10/12 tests, 16.67% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 t/02species.t 255 65280 65 120 184.62% 6-65 t/03simpleseq.t 255 65280 59 108 183.05% 6-59 t/04swiss.t 255 65280 52 94 180.77% 6-52 t/05seqfeature.t 255 65280 48 90 187.50% 4-48 t/06comment.t 255 65280 11 18 163.64% 3-11 t/07dblink.t 255 65280 18 32 177.78% 3-18 t/08genbank.t 255 65280 18 32 177.78% 3-18 t/09fuzzy2.t 255 65280 21 38 180.95% 3-21 t/10ensembl.t 255 65280 15 26 173.33% 3-15 t/11locuslink.t 255 65280 110 212 192.73% 5-110 t/12ontology.t 255 65280 738 1468 198.92% 5-738 t/13remove.t 255 65280 59 116 196.61% 2-59 t/15cluster.t 255 65280 160 310 193.75% 6-160 t/16obda.t 255 65280 12 20 166.67% 3-12 Failed 15/16 test scripts, 6.25% okay. 1347/1423 subtests failed, 5.34% okay. make: *** [test_dynamic] Error 255 ======================================================= Output of 'make test TEST_VERBOSE=1' for Oracle ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....1..19 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-19 Failed 5/19 tests, 73.68% okay t/02species.......1..65 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-65 Failed 60/65 tests, 7.69% okay t/03simpleseq.....1..59 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-59 Failed 54/59 tests, 8.47% okay t/04swiss.........1..52 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 78. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-52 Failed 47/52 tests, 9.62% okay t/05seqfeature....1..48 ok 1 ok 2 ok 3 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 4-48 Failed 45/48 tests, 6.25% okay t/06comment.......1..11 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-11 Failed 9/11 tests, 18.18% okay t/07dblink........1..18 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/08genbank.......1..18 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/09fuzzy2........1..21 todo 17; ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 64. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-21 Failed 19/21 tests, 9.52% okay t/10ensembl.......1..15 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1420. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-15 Failed 13/15 tests, 13.33% okay t/11locuslink.....1..110 ok 1 ok 2 ok 3 ok 4 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-110 Failed 106/110 tests, 3.64% okay t/12ontology......1..738 ok 1 ok 2 ok 3 ok 4 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 98. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-738 Failed 734/738 tests, 0.54% okay t/13remove........1..59 ok 1 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-59 Failed 58/59 tests, 1.69% okay t/14query.........1..18 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok t/15cluster.......1..160 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-160 Failed 155/160 tests, 3.12% okay t/16obda..........1..12 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-12 Failed 10/12 tests, 16.67% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 t/02species.t 255 65280 65 120 184.62% 6-65 t/03simpleseq.t 255 65280 59 108 183.05% 6-59 t/04swiss.t 255 65280 52 94 180.77% 6-52 t/05seqfeature.t 255 65280 48 90 187.50% 4-48 t/06comment.t 255 65280 11 18 163.64% 3-11 t/07dblink.t 255 65280 18 32 177.78% 3-18 t/08genbank.t 255 65280 18 32 177.78% 3-18 t/09fuzzy2.t 255 65280 21 38 180.95% 3-21 t/10ensembl.t 255 65280 15 26 173.33% 3-15 t/11locuslink.t 255 65280 110 212 192.73% 5-110 t/12ontology.t 255 65280 738 1468 198.92% 5-738 t/13remove.t 255 65280 59 116 196.61% 2-59 t/15cluster.t 255 65280 160 310 193.75% 6-160 t/16obda.t 255 65280 12 20 166.67% 3-12 Failed 15/16 test scripts, 6.25% okay. 1347/1423 subtests failed, 5.34% okay. make: *** [test_dynamic] Error 255 ======================================================= Output of 'make test' for MySQL =================================================== [root at elegans bioperl-db-1.5.2-RC3]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....ok t/02species.......FAILED tests 11, 14-40, 49-119 Failed 99/65 tests, -52.31% okay t/03simpleseq.....ok t/04swiss.........ok t/05seqfeature....ok t/06comment.......ok t/07dblink........ok t/08genbank.......ok t/09fuzzy2........ok t/10ensembl.......ok t/11locuslink.....ok t/12ontology......ok t/13remove........ok t/14query.........ok t/15cluster.......ok 155/160 -------------------- WARNING --------------------- MSG: failed to store one or more child objects for an instance of class Bio::Cluster::UniGene (PK=168) --------------------------------------------------- t/15cluster.......ok t/16obda..........ok Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/02species.t 65 136 209.23% 11 14-40 49-119 Failed 1/16 test scripts, 93.75% okay. 28/1423 subtests failed, 98.03% okay. make: *** [test_dynamic] Error 255 ====================================================== Output of 'make test_02species TEST_VERBOSE=1' for MySQL ====================================================== [root at elegans bioperl-db-1.5.2-RC3]# make test_02species TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests @ARGV;' t/02species.t t/02species....1..65 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 not ok 11 # Test 11 got: '29' (t/02species.t at line 45) # Expected: '11' ok 12 ok 13 not ok 14 # Test 14 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 49 fail #3) # Expected: 'Hominidae' not ok 15 # Test 15 got: 'Hominidae' (t/02species.t at line 49 fail #4) # Expected: 'Catarrhini' not ok 16 # Test 16 got: 'Hominoidea' (t/02species.t at line 49 fail #5) # Expected: 'Primates' not ok 17 # Test 17 got: 'Catarrhini' (t/02species.t at line 49 fail #6) # Expected: 'Eutheria' not ok 18 # Test 18 got: 'Simiiformes' (t/02species.t at line 49 fail #7) # Expected: 'Mammalia' not ok 19 # Test 19 got: 'Haplorrhini' (t/02species.t at line 49 fail #8) # Expected: 'Vertebrata' not ok 20 # Test 20 got: 'Primates' (t/02species.t at line 49 fail #9) # Expected: 'Chordata' not ok 21 # Test 21 got: 'Euarchontoglires' (t/02species.t at line 49 fail #10) # Expected: 'Metazoa' not ok 22 # Test 22 got: 'Eutheria' (t/02species.t at line 49 fail #11) # Expected: 'Eukaryota' not ok 23 # Failed test 23 in t/02species.t at line 49 fail #12 not ok 24 # Failed test 24 in t/02species.t at line 49 fail #13 not ok 25 # Failed test 25 in t/02species.t at line 49 fail #14 not ok 26 # Failed test 26 in t/02species.t at line 49 fail #15 not ok 27 # Failed test 27 in t/02species.t at line 49 fail #16 not ok 28 # Failed test 28 in t/02species.t at line 49 fail #17 not ok 29 # Failed test 29 in t/02species.t at line 49 fail #18 not ok 30 # Failed test 30 in t/02species.t at line 49 fail #19 not ok 31 # Failed test 31 in t/02species.t at line 49 fail #20 not ok 32 # Failed test 32 in t/02species.t at line 49 fail #21 not ok 33 # Failed test 33 in t/02species.t at line 49 fail #22 not ok 34 # Failed test 34 in t/02species.t at line 49 fail #23 not ok 35 # Failed test 35 in t/02species.t at line 49 fail #24 not ok 36 # Failed test 36 in t/02species.t at line 49 fail #25 not ok 37 # Failed test 37 in t/02species.t at line 49 fail #26 not ok 38 # Failed test 38 in t/02species.t at line 49 fail #27 not ok 39 # Failed test 39 in t/02species.t at line 49 fail #28 not ok 40 # Failed test 40 in t/02species.t at line 49 fail #29 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 not ok 49 # Test 49 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 63 fail #3) # Expected: 'Hominidae' not ok 50 # Test 50 got: 'Hominidae' (t/02species.t at line 63 fail #4) # Expected: 'Catarrhini' not ok 51 # Test 51 got: 'Hominoidea' (t/02species.t at line 63 fail #5) # Expected: 'Primates' not ok 52 # Test 52 got: 'Catarrhini' (t/02species.t at line 63 fail #6) # Expected: 'Eutheria' not ok 53 # Test 53 got: 'Simiiformes' (t/02species.t at line 63 fail #7) # Expected: 'Mammalia' not ok 54 # Test 54 got: 'Haplorrhini' (t/02species.t at line 63 fail #8) # Expected: 'Vertebrata' not ok 55 # Test 55 got: 'Primates' (t/02species.t at line 63 fail #9) # Expected: 'Chordata' not ok 56 # Test 56 got: 'Euarchontoglires' (t/02species.t at line 63 fail #10) # Expected: 'Metazoa' not ok 57 # Test 57 got: 'Eutheria' (t/02species.t at line 63 fail #11) # Expected: 'Eukaryota' not ok 58 # Failed test 58 in t/02species.t at line 63 fail #12 not ok 59 # Failed test 59 in t/02species.t at line 63 fail #13 not ok 60 # Failed test 60 in t/02species.t at line 63 fail #14 not ok 61 # Failed test 61 in t/02species.t at line 63 fail #15 not ok 62 # Failed test 62 in t/02species.t at line 63 fail #16 not ok 63 # Failed test 63 in t/02species.t at line 63 fail #17 not ok 64 # Failed test 64 in t/02species.t at line 63 fail #18 not ok 65 # Failed test 65 in t/02species.t at line 63 fail #19 not ok 66 # Failed test 66 in t/02species.t at line 63 fail #20 not ok 67 # Failed test 67 in t/02species.t at line 63 fail #21 not ok 68 # Failed test 68 in t/02species.t at line 63 fail #22 not ok 69 # Failed test 69 in t/02species.t at line 63 fail #23 not ok 70 # Failed test 70 in t/02species.t at line 63 fail #24 not ok 71 # Failed test 71 in t/02species.t at line 63 fail #25 not ok 72 # Failed test 72 in t/02species.t at line 63 fail #26 not ok 73 # Failed test 73 in t/02species.t at line 63 fail #27 not ok 74 # Failed test 74 in t/02species.t at line 63 fail #28 not ok 75 # Failed test 75 in t/02species.t at line 63 fail #29 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 not ok 90 # Test 90 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 91 fail #3) # Expected: 'Hominidae' not ok 91 # Test 91 got: 'Hominidae' (t/02species.t at line 91 fail #4) # Expected: 'Catarrhini' not ok 92 # Test 92 got: 'Hominoidea' (t/02species.t at line 91 fail #5) # Expected: 'Primates' not ok 93 # Test 93 got: 'Catarrhini' (t/02species.t at line 91 fail #6) # Expected: 'Eutheria' not ok 94 # Test 94 got: 'Simiiformes' (t/02species.t at line 91 fail #7) # Expected: 'Mammalia' not ok 95 # Test 95 got: 'Haplorrhini' (t/02species.t at line 91 fail #8) # Expected: 'Vertebrata' not ok 96 # Test 96 got: 'Primates' (t/02species.t at line 91 fail #9) # Expected: 'Chordata' not ok 97 # Test 97 got: 'Euarchontoglires' (t/02species.t at line 91 fail #10) # Expected: 'Metazoa' not ok 98 # Test 98 got: 'Eutheria' (t/02species.t at line 91 fail #11) # Expected: 'Eukaryota' not ok 99 # Failed test 99 in t/02species.t at line 91 fail #12 not ok 100 # Failed test 100 in t/02species.t at line 91 fail #13 not ok 101 # Failed test 101 in t/02species.t at line 91 fail #14 not ok 102 # Failed test 102 in t/02species.t at line 91 fail #15 not ok 103 # Failed test 103 in t/02species.t at line 91 fail #16 not ok 104 # Failed test 104 in t/02species.t at line 91 fail #17 not ok 105 # Failed test 105 in t/02species.t at line 91 fail #18 not ok 106 # Failed test 106 in t/02species.t at line 91 fail #19 not ok 107 # Failed test 107 in t/02species.t at line 91 fail #20 not ok 108 # Failed test 108 in t/02species.t at line 91 fail #21 not ok 109 # Failed test 109 in t/02species.t at line 91 fail #22 not ok 110 # Failed test 110 in t/02species.t at line 91 fail #23 not ok 111 # Failed test 111 in t/02species.t at line 91 fail #24 not ok 112 # Failed test 112 in t/02species.t at line 91 fail #25 not ok 113 # Failed test 113 in t/02species.t at line 91 fail #26 not ok 114 # Failed test 114 in t/02species.t at line 91 fail #27 not ok 115 # Failed test 115 in t/02species.t at line 91 fail #28 not ok 116 # Failed test 116 in t/02species.t at line 91 fail #29 ok 117 ok 118 ok 119 FAILED tests 11, 14-40, 49-119 Failed 99/65 tests, -52.31% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/02species.t 65 136 209.23% 11 14-40 49-119 Failed 1/1 test scripts, 0.00% okay. 28/65 subtests failed, 56.92% okay. make: *** [test_02species] Error 255 ======================================================= Output of 'make test_15cluster TEST_VERBOSE=1' for MySQL ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test_15cluster TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests @ARGV;' t/15cluster.t t/15cluster....1..160 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 -------------------- WARNING --------------------- MSG: failed to store one or more child objects for an instance of class Bio::Cluster::UniGene (PK=201) --------------------------------------------------- ok 156 ok 157 ok 158 ok 159 ok 160 ok All tests successful. Files=1, Tests=160, 18 wallclock secs ( 4.39 cusr + 0.37 csys = 4.76 CPU) ======================================================= Hilmar Lapp wrote: > This is very odd. I would mean that preparing the statement failed, > i.e., that the generated SQL was not accepted by the server (or the > Oracle client library). > > Which test does this happen with? > > Could you run the test alone in which it happens with TEST_VERBOSE > turned on? E.g., > > $ make test_03simpleseq TEST_VERBOSE=1 > > if it's the simpleseq test that's causing the failure. Capture the > output in a file and send it to me. > > -hilmar > > On Nov 18, 2006, at 3:57 AM, gang wu wrote: > >> Hi everyone, >> >> I used to use MySQL to host the BioSQL schema and load Genbank into it >> with the 'load_seqdatabase.pl' without problem(except extremely slow. It >> took about 12 hours to load Arabidopsis thaliana). I just loaded the >> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database without >> problem. >> >> When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with >> MySQL while always saw an error with Oracle: >> Can't call method "bind_param" on an undefined value at >> /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm >> >> line 939. >> >> , where the code is $sth->bind_param(); >> >> Any idea what the problem is? >> >> Gang >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > --=========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > > From dmessina at wustl.edu Mon Nov 20 11:31:55 2006 From: dmessina at wustl.edu (David Messina) Date: Mon, 20 Nov 2006 10:31:55 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4560FDC2.4000309@purdue.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> Message-ID: On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: > [...] > My guess is that he thought that bioperl bundle installed the > dependencies *and* bioperl itself. That was my presumption the first > time I saw it on CPAN. Me too, actually. Perhaps there could be a big, bold warning displayed when using CPAN to install Bundle::BioPerl, saying something like "you will still need to install BioPerl separately by doing ..." ? Likewise, I think the INSTALL document that comes with the BioPerl distribution (and on the wiki) implies the difference between BioPerl and Bundle::BioPerl but doesn't say so explicitly. I'd be happy to add this to INSTALL if there are no objections... Dave From sdavis2 at mail.nih.gov Mon Nov 20 12:23:33 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 12:23:33 -0500 Subject: [Bioperl-l] mmap perl In-Reply-To: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> References: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> Message-ID: <200611201223.33703.sdavis2@mail.nih.gov> On Monday 20 November 2006 09:53, Albert Vilella wrote: > Hi all, > > A bit of an off-topic: > > Has anyone ever investigated with libcache-mmap-perl or > libcache-fastmmap-perl? Hi, Albert. You will probably need to be more specific here. Yes, there are perl implementations of MANY caching schemes. Sean From cjfields at uiuc.edu Mon Nov 20 12:36:41 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 11:36:41 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: Message-ID: <000301c70cca$70f8d030$15327e82@pyrimidine> > On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: > > [...] > > My guess is that he thought that bioperl bundle installed the > > dependencies *and* bioperl itself. That was my presumption > the first > > time I saw it on CPAN. > > Me too, actually. > > Perhaps there could be a big, bold warning displayed when > using CPAN to install Bundle::BioPerl, saying something like > "you will still need to install BioPerl separately by doing ..." ? > > Likewise, I think the INSTALL document that comes with the > BioPerl distribution (and on the wiki) implies the difference > between BioPerl and Bundle::BioPerl but doesn't say so explicitly. > > I'd be happy to add this to INSTALL if there are no objections... > > Dave Dave, Go ahead. We need to also make the change on the wiki in the relevant pages. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 20 12:46:02 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 20 Nov 2006 17:46:02 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> Message-ID: <4561E9DA.3020002@sendu.me.uk> David Messina wrote: > On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: >> [...] >> My guess is that he thought that bioperl bundle installed the >> dependencies *and* bioperl itself. That was my presumption the first >> time I saw it on CPAN. > > Me too, actually. > > Perhaps there could be a big, bold warning displayed when using CPAN > to install Bundle::BioPerl, saying something like "you will still > need to install BioPerl separately by doing ..." ? > > Likewise, I think the INSTALL document that comes with the BioPerl > distribution (and on the wiki) implies the difference between BioPerl > and Bundle::BioPerl but doesn't say so explicitly. The description for Bundle::BioPerl (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) says: "NOTE: This Bundle does not install BioPerl" > I'd be happy to add this to INSTALL if there are no objections... I'll be changing the INSTALL docs to say not to use Bundle::BioPerl when installing with CPAN (you don't need it). Bundle::BioPerl is only for convenience when installing manually from archives or CVS. From cjfields at uiuc.edu Mon Nov 20 12:52:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 11:52:12 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4561D07C.4060800@molbio.mgh.harvard.edu> Message-ID: <000701c70ccc$9b9c9360$15327e82@pyrimidine> > Hi Hilmar, > > Thanks for your message. Below are several tests for Oracle > and MySQL. > MySQL actually also has two tests with failed items which may > be related to data in BioSQL database. > > Could it be my Oracle installation/configuration has some issues? > > Thanks. > > Gang ... You stated in a previous post that you had preloaded taxonomy; the various species test fails may be from that. Hilmar pointed out in a previous thread that tests require a BioSQL database without NCBI taxonomy loaded (i.e. just the schema). The INSTALL doc should now state that. As for the rest, could it be the DBharness.biosql.conf file setup, which assumes MySQL by default? If you switch to Oracle you have to indicate the proper DBD driver in the conf file: ... # DBD driver to use - mandatory 'driver' => 'oracle', ... Chris > Hilmar Lapp wrote: > > This is very odd. I would mean that preparing the statement failed, > > i.e., that the generated SQL was not accepted by the server (or the > > Oracle client library). > > > > Which test does this happen with? > > > > Could you run the test alone in which it happens with TEST_VERBOSE > > turned on? E.g., > > > > $ make test_03simpleseq TEST_VERBOSE=1 > > > > if it's the simpleseq test that's causing the failure. Capture the > > output in a file and send it to me. > > > > -hilmar > > > > On Nov 18, 2006, at 3:57 AM, gang wu wrote: > > > >> Hi everyone, > >> > >> I used to use MySQL to host the BioSQL schema and load > Genbank into it > >> with the 'load_seqdatabase.pl' without problem(except > extremely slow. It > >> took about 12 hours to load Arabidopsis thaliana). I just > loaded the > >> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy > database without > >> problem. > >> > >> When I 'make test' with bioperl-db-1.5.2.R3, all tests can > pass with > >> MySQL while always saw an error with Oracle: > >> Can't call method "bind_param" on an undefined value at > >> > /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ BasePersistenceAdaptor.pm > >> > >> line 939. > >> > >> , where the code is $sth->bind_param(); > >> > >> Any idea what the problem is? > >> > >> Gang > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > --=========================================================== > > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > > =========================================================== > > > > > > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From dmessina at wustl.edu Mon Nov 20 13:34:27 2006 From: dmessina at wustl.edu (David Messina) Date: Mon, 20 Nov 2006 12:34:27 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4561E9DA.3020002@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> <4561E9DA.3020002@sendu.me.uk> Message-ID: <911B53D4-1E95-4B52-A604-DA3C776EB71A@wustl.edu> On Nov 20, 2006, at 11:46 AM, Sendu Bala wrote: > The description for Bundle::BioPerl > (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) > > says: > "NOTE: This Bundle does not install BioPerl" Right, but if you are in the CPAN shell, you won't see that: cpan[2]> b Bundle::BioPerl CPAN_USERID CRAFFI (Chris Dagdigian ) CPAN_VERSION 2.001008 CPAN_FILE C/CR/CRAFFI/Bundle-BioPerl-2.1.8.tar.gz UPLOAD_DATE 2006-11-18 MANPAGE Bundle::BioPerl - A bundle to install external CPAN modules used by BioPerl 1.5.2 CONTAINS Ace Bio::ASN1::EntrezGene Class::AutoClass Clone Convert::Binary::C Data::Stag::Writer DBD::mysql GD::SVG GD Graph::Directed HTML::Parser HTTP::Request::Common LWP::UserAgent Set::Scalar SOAP::Lite Spreadsheet::ParseExcel Storable SVG SVG::Graph Text::Shellwords XML::DOM::XPath XML::Parser::PerlSAX XML::SAX XML::SAX::Base XML::SAX::Writer XML::Simple XML::Twig XML::Writer INST_FILE /Users/davemessina/.cpan/Bundle/BioPerl.pm INST_VERSION 2.1.8 Nor if you type: cpan[6]> readme Bundle::BioPerl Not to make too much of this (some will miss it no matter how many warnings there are), but I am suggesting that it could be a little more noticeable, that's all. > I'll be changing the INSTALL docs to say not to use Bundle::BioPerl > when installing with CPAN (you don't need it). Bundle::BioPerl is > only for convenience when installing manually from archives or CVS. Ah, okay, great, Sendu. I didn't know that. ;) I'll leave it to you, then. Dave From gwu at molbio.mgh.harvard.edu Mon Nov 20 13:31:34 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:31:34 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <45607D9B.4010703@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> Message-ID: <4561F486.9050601@molbio.mgh.harvard.edu> Hi Sendu, I think the package was not installed at all. The only thing I saw in the Bio folder is ANS1 which was another package(I mistakenly thought it's the only package installed by Bundle-BioPerl 2.1.16). I did not force install with CPAN. So is it possible that the three typos forbid bioperl be installed? Thanks. Gang Sendu Bala wrote: > gang wu wrote: >> It turned out that most of the modules of BioPerl were not installed >> at all. And none of the scripts were installed. I had to download and >> install bioperl-1.5.2-RC3.tar.gz >> again. A similar >> problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually >> copied all stuff under Bio folder to the corresponding Perl library >> folder. Is it Ok to do it in this way? > > It will work, but is hardly good enough from our point of view (you > shouldn't have to do that). > > Can you tell me exactly what you mean by 'were not installed'? What > did you do to try and install? How did you determine that installation > had failed? > > With CPAN, if you were still getting errors during testing, what were > those remaining errors, and did you do a forced install to ignore the > errors? If a forced install didn't actually install anything, what > message did CPAN give you about that, if any? > > With the manual download, after doing "perl Makefile.PL", what is your > output of "make install"? > > > Thank you, > Sendu. From gwu at molbio.mgh.harvard.edu Mon Nov 20 13:39:55 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:39:55 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> <455FCAD4.7050709@molbio.mgh.harvard.edu> <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> Message-ID: <4561F67B.7070401@molbio.mgh.harvard.edu> No gdlib-config was found on my system. The rpm is the newest version from Redhat AS 4 channel for AMD/EM64T. Do you think I need to update the package myself? Thanks Gang Lincoln Stein wrote: > That's very odd. gd.0.28 should install gdlib-config, and the existence of > this executable should inhibit the interactive questions. Could you see if > there's a gdlib-config executable installed on your system? > > Lincoln > > On 11/18/06, gang wu wrote: > >> Lincoln, >> Thanks for your message. I have gd-2.0.28-4.4E.1 and >> gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. >> Attached is the output. >> >> Gang >> >> ================================================== >> [root at elegans GD-2.35]# perl Makefile.PL >> NOTICE: This module requires libgd 2.0.28 or higher. >> >> If you are using Math::Trig 1.01 or lower, it has a bug that >> causes a "prerequisite not found" warning to be issued. You may >> safely ignore this warning. >> >> Type perl Makefile.PL -h for command-line option summary >> >> >> Where is libgd installed? [/usr/lib] >> >> Please choose the features that match how libgd was built: >> Build JPEG support? [y] >> Build PNG support? [y] >> Build FreeType support? [y] >> Build GIF support? [y] >> Build support for animated GIFs? [y] >> Build XPM support? [y] >> >> If you experience compile problems, please check the @INC, @LIBPATH and >> @LIBS >> arrays defined in Makefile.PL and manually adjust, if necessary. >> >> Checking if your kit is complete... >> Looks good >> Writing Makefile for GD >> [root at elegans GD-2.35]# make >> cp GD/Polyline.pm blib/lib/GD/Polyline.pm >> cp qd.pl blib/lib/qd.pl >> cp GD/Image.pm blib/lib/GD/Image.pm >> cp GD.pm blib/lib/GD.pm >> AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) >> cp GD/Simple.pm blib/lib/GD/Simple.pm >> cp GD/Polygon.pm blib/lib/GD/Polygon.pm >> /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap >> /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc >> && mv GD.xsc GD.c >> gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE >> -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include >> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g >> -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC >> "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG >> -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c >> GD.xs: In function `XS_GD__Image_STORABLE_thaw': >> GD.xs:923: warning: cast from pointer to integer of different size >> GD.xs: In function `XS_GD__Image_gifanimbegin': >> GD.xs:990: warning: cast to pointer from integer of different size >> GD.xs: In function `XS_GD__Image_gifanimadd': >> GD.xs:1015: warning: cast to pointer from integer of different size >> GD.xs: In function `XS_GD__Image_gifanimend': >> GD.xs:1034: warning: cast to pointer from integer of different size >> Running Mkbootstrap for GD () >> chmod 644 GD.bs >> rm -f blib/arch/auto/GD/GD.so >> gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 >> -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 >> -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm >> /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz >> /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz >> /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm >> /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when >> searching for -lX11 >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when >> searching for -lX11 >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when >> searching for -lXpm >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when >> searching for -lXpm >> /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc >> /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc >> chmod 755 blib/arch/auto/GD/GD.so >> cp GD.bs blib/arch/auto/GD/GD.bs >> chmod 644 blib/arch/auto/GD/GD.bs >> cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" >> blib/script/bdf2gdfont.pl >> Manifying blib/man1/bdf2gdfont.pl.1 >> Manifying blib/man3/GD::Polyline.3pm >> Manifying blib/man3/GD::Image.3pm >> Manifying blib/man3/GD::Simple.3pm >> Manifying blib/man3/GD.3pm >> Manifying blib/man3/GD::Polygon.3pm >> [root at elegans GD-2.35]# make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: >> ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at >> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. >> at t/GD.t line 14 >> Compilation failed in require at t/GD.t line 14. >> BEGIN failed--compilation aborted at t/GD.t line 14. >> t/GD..........dubious >> >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-12 >> Failed 12/12 tests, 0.00% okay >> t/Polyline....Can't load >> '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: >> /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: >> gdImageGifAnimAddPtr at >> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. >> at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 >> Compilation failed in require at >> /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. >> BEGIN failed--compilation aborted at >> /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. >> Compilation failed in require at t/Polyline.t line 10. >> BEGIN failed--compilation aborted at t/Polyline.t line 10. >> t/Polyline....dubious >> >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED test 1 >> Failed 1/1 tests, 0.00% okay >> Failed Test Stat Wstat Total Fail Failed List of Failed >> >> ------------------------------------------------------------------------------- >> t/GD.t 255 65280 12 23 191.67% 1-12 >> t/Polyline.t 255 65280 1 2 200.00% 1 >> Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. >> make: *** [test_dynamic] Error 255 >> [root at elegans GD-2.35]# >> =========================================================== >> >> Lincoln Stein wrote: >> >>> What version of libgd do you have installed? With recent versions of >>> libgd (more recent than two years old) you will not be given the >>> chance to select whether to compile JPEG, GIF and XPM support, since >>> these options are selected automatically by running libgd-config. >>> >>> Lincoln >>> >>> On 11/18/06, *gang wu* >> > wrote: >>> >>> >>> Sendu Bala wrote: >>> > gang wu wrote: >>> >> Hi everyone, >>> >> >>> >> I saw some problems when installing BioPerl >>> >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>> CPAN could >>> >> not solve all the dependency issues with one shot of 'install >>> >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>> >> installed. >>> > >>> > What problems did you run into specifically with GD? >>> If I enable JPEG, GIFS and XPM, none of the test could pass. Since >>> >> I >> >>> usually use only PNG for output, I can live without them. I am not >>> sure >>> if it's system related problem. All of them work fine with my 32 bit >>> Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with >>> newer >>> libgd runnig Redhat AS4 AMD/EM64T does not work. >>> > >>> >> And it turned out that CPAN refused to install BioPerl with >>> >> some test return value 255. Then I went to /root/.cpan/build to >>> >> configure, test, rebuild those problematic packages. After >>> several more >>> >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>> >> successfully. >>> > >>> > Do you remember what the other problematic packages were, and >>> what you >>> > had to do to get them working? >>> > >>> XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I >>> guess it should be XML::DOM::XPath.pm. I could not recall what other >>> packages had issues, but basically it's special package >>> configuration issue. >>> >> Below attached is the output of CPAN, which stills complains >>> >> three >> >>> >> packages have issues: Data::Stag::writer HTTP::Request::Common- >>> >> Spreadhseet::ParseExcel. I think the first two are typos >>> somewhere in >>> >> the Bundle::BioPerl. And the third module is not on the server >>> and could >>> >> be found on the CPAN site. >>> > >>> > All three are typos. We'll get those fixed. >>> > >>> > >>> >> So my question is : Is this the right way to install BioPerl? >>> > >>> > At the present moment, yes. For 1.5.2 I'll probably be >>> >> recommending >> >>> > not using Bundle::BioPerl once I fix some other things. >>> > >>> See my another message for other issues. >>> > >>> >> It took me two days to figure it out but still not 100% sure all >>> >> packages are >>> >> installed properly. >>> > >>> > I'm sorry for the troubles you ran into. We'll try and do better >>> >> for >> >>> > the final release of 1.5.2. >>> Actually your hard work is benifiting the whole community and we >>> all owe >>> you a Thank You. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 >>> (516) 367-8380 (voice) >>> (516) 367-8389 (fax) >>> FOR URGENT MESSAGES & SCHEDULING, >>> PLEASE CONTACT MY ASSISTANT, >>> SANDRA MICHELSEN, AT michelse at cshl.edu >>> >> > > > From gwu at molbio.mgh.harvard.edu Mon Nov 20 13:54:46 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:54:46 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4561E9DA.3020002@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> <4561E9DA.3020002@sendu.me.uk> Message-ID: <4561F9F6.5020700@molbio.mgh.harvard.edu> Sendu Bala wrote: > David Messina wrote: > >> On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: >> >>> [...] >>> My guess is that he thought that bioperl bundle installed the >>> dependencies *and* bioperl itself. That was my presumption the first >>> time I saw it on CPAN. >>> >> Me too, actually. >> >> Perhaps there could be a big, bold warning displayed when using CPAN >> to install Bundle::BioPerl, saying something like "you will still >> need to install BioPerl separately by doing ..." ? >> >> Likewise, I think the INSTALL document that comes with the BioPerl >> distribution (and on the wiki) implies the difference between BioPerl >> and Bundle::BioPerl but doesn't say so explicitly. >> > > The description for Bundle::BioPerl > (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) > > says: > "NOTE: This Bundle does not install BioPerl" > > > >> I'd be happy to add this to INSTALL if there are no objections... >> > > I'll be changing the INSTALL docs to say not to use Bundle::BioPerl when > installing with CPAN (you don't need it). Bundle::BioPerl is only for > convenience when installing manually from archives or CVS. > This can save a lot of time and confusion. But why can't BioPerl be installed with Bundle::BioPerl when using CPAN? It sounds convenient. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From gwu at molbio.mgh.harvard.edu Mon Nov 20 14:40:56 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 14:40:56 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000701c70ccc$9b9c9360$15327e82@pyrimidine> References: <000701c70ccc$9b9c9360$15327e82@pyrimidine> Message-ID: <456204C8.8000404@molbio.mgh.harvard.edu> Chris Fields wrote: >> Hi Hilmar, >> >> Thanks for your message. Below are several tests for Oracle >> and MySQL. >> MySQL actually also has two tests with failed items which may >> be related to data in BioSQL database. >> >> Could it be my Oracle installation/configuration has some issues? >> >> Thanks. >> >> Gang >> > > ... > > You stated in a previous post that you had preloaded taxonomy; the various > species test fails may be from that. Hilmar pointed out in a previous > thread that tests require a BioSQL database without NCBI taxonomy loaded > (i.e. just the schema). The INSTALL doc should now state that. > You are right, all tests can pass for MySQL after unloading NCBI Taxonomy data. But output for Oracle tests were not affected. Thanks. > As for the rest, could it be the DBharness.biosql.conf file setup, which > assumes MySQL by default? If you switch to Oracle you have to indicate the > proper DBD driver in the conf file: > > ... > > # DBD driver to use - mandatory > 'driver' => 'oracle', > > ... > > I did change the configuration, or it can not pass the DBI connection tests. Below is part of my parameters: 'driver' => 'Oracle', 'host' => 'elegans', 'user' => 'biosqldb_sgowner', 'port' => '1521', 'password' => 'pass', 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], 'dbname' => 'oracle_sid', 'database' => 'biosql', > Chris > > > >> Hilmar Lapp wrote: >> >>> This is very odd. I would mean that preparing the statement failed, >>> i.e., that the generated SQL was not accepted by the server (or the >>> Oracle client library). >>> >>> Which test does this happen with? >>> >>> Could you run the test alone in which it happens with TEST_VERBOSE >>> turned on? E.g., >>> >>> $ make test_03simpleseq TEST_VERBOSE=1 >>> >>> if it's the simpleseq test that's causing the failure. Capture the >>> output in a file and send it to me. >>> >>> -hilmar >>> >>> On Nov 18, 2006, at 3:57 AM, gang wu wrote: >>> >>> >>>> Hi everyone, >>>> >>>> I used to use MySQL to host the BioSQL schema and load >>>> >> Genbank into it >> >>>> with the 'load_seqdatabase.pl' without problem(except >>>> >> extremely slow. It >> >>>> took about 12 hours to load Arabidopsis thaliana). I just >>>> >> loaded the >> >>>> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy >>>> >> database without >> >>>> problem. >>>> >>>> When I 'make test' with bioperl-db-1.5.2.R3, all tests can >>>> >> pass with >> >>>> MySQL while always saw an error with Oracle: >>>> Can't call method "bind_param" on an undefined value at >>>> >>>> >> /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ >> > BasePersistenceAdaptor.pm > >>>> line 939. >>>> >>>> , where the code is $sth->bind_param(); >>>> >>>> Any idea what the problem is? >>>> >>>> Gang >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> --=========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >>> >>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > From cjfields at uiuc.edu Mon Nov 20 15:19:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 14:19:56 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <456204C8.8000404@molbio.mgh.harvard.edu> Message-ID: <000301c70ce1$3ee70190$15327e82@pyrimidine> ... > You are right, all tests can pass for MySQL after unloading > NCBI Taxonomy data. But output for Oracle tests were not > affected. Thanks. Yes, the oracle tests were by far the worst, which suggests something in the driver/configuration. > > As for the rest, could it be the DBharness.biosql.conf file setup, > > which assumes MySQL by default? If you switch to Oracle > you have to > > indicate the proper DBD driver in the conf file: > > > > ... > > > > # DBD driver to use - mandatory > > 'driver' => 'oracle', > > > > ... > > > > > I did change the configuration, or it can not pass the DBI > connection tests. Below is part of my parameters: > 'driver' => 'Oracle', > 'host' => 'elegans', > 'user' => 'biosqldb_sgowner', > 'port' => '1521', > 'password' => 'pass', > 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], > 'dbname' => 'oracle_sid', > 'database' => 'biosql', Try changing the driver to all lower case (i.e. from 'Oracle' to 'oracle'). Also, the schema_sql is still set to the mysql schema (not oracle). That shouldn't make a difference, but you never know. Hopefully that isn't your real password! Chris From gwu at molbio.mgh.harvard.edu Mon Nov 20 15:34:07 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 15:34:07 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000301c70ce1$3ee70190$15327e82@pyrimidine> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> Message-ID: <4562113F.6040306@molbio.mgh.harvard.edu> Chris Fields wrote: > ... > >> You are right, all tests can pass for MySQL after unloading >> NCBI Taxonomy data. But output for Oracle tests were not >> affected. Thanks. >> > > Yes, the oracle tests were by far the worst, which suggests something in the > driver/configuration. > > >>> As for the rest, could it be the DBharness.biosql.conf file setup, >>> which assumes MySQL by default? If you switch to Oracle >>> >> you have to >> >>> indicate the proper DBD driver in the conf file: >>> >>> ... >>> >>> # DBD driver to use - mandatory >>> 'driver' => 'oracle', >>> >>> ... >>> >>> >>> >> I did change the configuration, or it can not pass the DBI >> connection tests. Below is part of my parameters: >> 'driver' => 'Oracle', >> 'host' => 'elegans', >> 'user' => 'biosqldb_sgowner', >> 'port' => '1521', >> 'password' => 'pass', >> 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], >> 'dbname' => 'oracle_sid', >> 'database' => 'biosql', >> > > Try changing the driver to all lower case (i.e. from 'Oracle' to 'oracle'). > Also, the schema_sql is still set to the mysql schema (not oracle). That > shouldn't make a difference, but you never know. > Can not change 'Oracle' to 'oracle', the DBD driver name is DBD::Oracle. It's an odd naming inconsistence. MySQL DBD driver name is DBD::mysql. How about PostgreSQL DBD driver naming? > Hopefully that isn't your real password! > > Chris > > From ryanx07 at hotmail.com Mon Nov 20 15:42:47 2006 From: ryanx07 at hotmail.com (L Xu) Date: Mon, 20 Nov 2006 15:42:47 -0500 Subject: [Bioperl-l] Error message for installation Message-ID: I got an error message when I installed Bioperl through ActivePerl following the online instruction about window installation: ERROR: Installing File-Spec-0.82 would downgrade File::Spec from version 3.12 to 0.82 and File::Spec::Functions from version 1.3 to 1.1 and File::Spec::Mac from version 1.4 to 1.2 and File::Spec::OS2 from version 1.2 to 1.1 and File::Spec::Unix from version 1.5 to 1.2 and File::Spec::VMS from version 1.4 to 1.1 and File::Spec::Win32 from version 1.6 to 1.2 It looks like the Bioperl 1.4 using some old version files compared to ActivePerl. I wonder if these old version files can cause some problems and how to fix them. Thanks and happy thanksgiving. L _________________________________________________________________ Get FREE company branded e-mail accounts and business Web site from Microsoft Office Live http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ From hlapp at gmx.net Mon Nov 20 16:28:29 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:28:29 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4561F0F4.3060106@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> Message-ID: <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> It looks like you are using the MySQL schema under Oracle. There are different DDL scripts for each supported RDBMS. The ones for Oracle are in the sql/biosql-ora subdirectory. Note the INSTALL document in that directory. -hilmar On Nov 20, 2006, at 1:16 PM, gang wu wrote: > Hi Hilmar, > > Below is the output. Thanks. > > Gang > ========================================================== > [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 > [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor > TEST_VERBOSE=1 > PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ > perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e > 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests > @ARGV;' t/01dbadaptor.t > t/01dbadaptor....1..19 > ok 1 > ok 2 > ok 3 > ok 4 > ok 5 > ok 6 > ok 7 > ok 8 > ok 9 > ok 10 > ok 11 > attempting to load adaptor class for BioNamespace > ok 12 > attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor > instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor > ok 13 > ok 14 > attempting to load driver for adaptor class > Bio::DB::BioSQL::BioNamespaceAdaptor > attempting to load driver for adaptor class > Bio::DB::BioSQL::BasePersistenceAdaptor > Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as > driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor > preparing UK select statement: SELECT biodatabase.oid, > biodatabase.name, biodatabase.authority FROM biodatabase WHERE name > = ? > DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": > invalid identifier (DBD ERROR: error possibly near <*> indicator at > char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = :p1') [for > Statement "SELECT biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ > Bio/DB/BioSQL/BaseDriver.pm line 1800. > BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) > Can't call method "bind_param" on an undefined value at blib/lib/ > Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. > dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-19 > Failed 5/19 tests, 73.68% okay > Failed Test Stat Wstat Total Fail Failed List of Failed > ---------------------------------------------------------------------- > --------- > t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 > Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% > okay. > make: *** [test_01dbadaptor] Error 2 > ========================================================= > > > Hilmar Lapp wrote: >> Hi Gang, >> >> what I wanted to get at was the error message from the driver when >> it fails to generate the prepared statement, but this is not in >> the output. >> >> I believe you need set the HARNESS_VERBOSE environment variable to >> 1 before testing to get what I need: >> >> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >> csh/tcsh >> $ make test_01dbadaptor TEST_VERBOSE=1 >> >> This will lead to _a lot_ of debugging output. Do not run this for >> the entire test suite. >> >> The errors for mysql I believe are related to the fact that have >> loaded the NCBI taxonomy before testing? Run the tests on a fresh >> (completely empty) instance of BioSQL. >> >> Let me know what you get for the Oracle test above. >> >> -hilmar >> >> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >> >>> Hi Hilmar, >>> >>> Thanks for your message. Below are several tests for Oracle and >>> MySQL. MySQL actually also has two tests with failed items which >>> may be related to data in BioSQL database. >>> >>> Could it be my Oracle installation/configuration has some issues? >>> >>> Thanks. >>> >>> Gang >> >> --=========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> >> -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Nov 20 16:33:50 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:33:50 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000301c70ce1$3ee70190$15327e82@pyrimidine> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> Message-ID: <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> On Nov 20, 2006, at 3:19 PM, Chris Fields wrote: > Try changing the driver to all lower case (i.e. from 'Oracle' to > 'oracle'). This can in fact be harmful. The driver-specific code is loaded from files or directories named after the driver. On case-sensitive file systems, changing the case will render those files inaccessible. > Also, the schema_sql is still set to the mysql schema (not > oracle). That > shouldn't make a difference, but you never know. It doesn't make a difference if the schema instance exists already (and I wouldn't recommend anything else). -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Nov 20 16:34:30 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:34:30 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4562113F.6040306@molbio.mgh.harvard.edu> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> <4562113F.6040306@molbio.mgh.harvard.edu> Message-ID: <24789A58-9A86-4B83-9CBB-CE2597B1DA60@gmx.net> On Nov 20, 2006, at 3:34 PM, gang wu wrote: > How about PostgreSQL DBD driver naming? DBD::Pg -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From Kevin.M.Brown at asu.edu Mon Nov 20 16:44:22 2006 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Mon, 20 Nov 2006 14:44:22 -0700 Subject: [Bioperl-l] Budle::BioPerl dependency issues Message-ID: <1A4207F8295607498283FE9E93B775B4024C58D3@EX02.asurite.ad.asu.edu> Redhat tends to have two different packages. GD and GD-devel. The first is for runtime applications to use, the other is needed to be able to build code against GD. They do this for almost all the libraries (e.g. glibc & glibc-devel, x11 and x11-devel, etc...). > No gdlib-config was found on my system. The rpm is the newest version > from Redhat AS 4 channel for AMD/EM64T. Do you think I need to update > the package myself? Thanks From n.haigh at sheffield.ac.uk Mon Nov 20 17:45:24 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 20 Nov 2006 22:45:24 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <45623004.1010807@sheffield.ac.uk> Could you answer the following questions, so that we know your setup and are better able to respond: 1) Can you confirm what version of ActivePerl you are running. 2) Can you confirm what PPM repositories you have enabled. 3) Can you confirm what version of Bioperl you tried to install. This issue has cropped up before, but I can't remember off hand exactly what the problem was, or how it was solved. I think it might be a problem with using the new PPM4 GUI to install bioperl 1.4 from the old style PPD. I'll await your response before making further comments. Thanks Nath L Xu wrote: > I got an error message when I installed Bioperl through ActivePerl following > the online instruction about window installation: > > ERROR: Installing File-Spec-0.82 would downgrade File::Spec from version > 3.12 to 0.82 and File::Spec::Functions from version 1.3 to 1.1 and > File::Spec::Mac from version 1.4 to 1.2 and File::Spec::OS2 from version 1.2 > to 1.1 and File::Spec::Unix from version 1.5 to 1.2 and File::Spec::VMS from > version 1.4 to 1.1 and File::Spec::Win32 from version 1.6 to 1.2 > > It looks like the Bioperl 1.4 using some old version files compared to > ActivePerl. I wonder if these old version files can cause some problems and > how to fix them. > > Thanks and happy thanksgiving. > > > L > > _________________________________________________________________ > Get FREE company branded e-mail accounts and business Web site from > Microsoft Office Live > http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From n.haigh at sheffield.ac.uk Mon Nov 20 17:49:51 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 20 Nov 2006 22:49:51 +0000 Subject: [Bioperl-l] Bioperl 1.4 on Windows Message-ID: <4562310F.8080403@sheffield.ac.uk> There have been at least a coupl eof posts recently about users having problems installing bioperl 1.4 using the PPM GUI shipped with ActivePerl 5.8.8.819. I think this is because the Bioperl 1.4 ppd is built for PPM3 and not PPM4. Would it make sense to update the Bioperl 1.4 PPD since it is the official "stable" release? Nath From cjfields at uiuc.edu Mon Nov 20 18:07:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 17:07:12 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> Message-ID: On Nov 20, 2006, at 3:33 PM, Hilmar Lapp wrote: > > On Nov 20, 2006, at 3:19 PM, Chris Fields wrote: > >> Try changing the driver to all lower case (i.e. from 'Oracle' to >> 'oracle'). > > This can in fact be harmful. The driver-specific code is loaded > from files or directories named after the driver. On case-sensitive > file systems, changing the case will render those files inaccessible. Yeah, just noticed that the driver is DBD::Oracle. I thought it might be lowercase, like DBD::mysql. >> Also, the schema_sql is still set to the mysql schema (not >> oracle). That >> shouldn't make a difference, but you never know. > > It doesn't make a difference if the schema instance exists already > (and I wouldn't recommend anything else). > > -hilmar The conf file indicates that as well. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Mon Nov 20 18:33:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 17:33:48 -0600 Subject: [Bioperl-l] Bioperl 1.4 on Windows In-Reply-To: <4562310F.8080403@sheffield.ac.uk> References: <4562310F.8080403@sheffield.ac.uk> Message-ID: On Nov 20, 2006, at 4:49 PM, Nathan S. Haigh wrote: > There have been at least a coupl eof posts recently about users having > problems installing bioperl 1.4 using the PPM GUI shipped with > ActivePerl 5.8.8.819. I think this is because the Bioperl 1.4 ppd is > built for PPM3 and not PPM4. Would it make sense to update the Bioperl > 1.4 PPD since it is the official "stable" release? > > Nath We could change the PPD to remove any versioning requirements. It's possible that PPM4 treats them as explicit version requirements, so instead of installing rel. X or greater, it only tries to install rel. X, which then has version requirements of it's own that PPM4 misreads. Not sure if this is a common problem with PPM4 but it's definitely bad. The best course of action for Windows users will be to update to 1.5.2 when the final version is released. The vast majority will be using it for parsing BLAST reports and retrieving sequences, both of which have undergone major revisions since 1.4 (in fact, I don't think BLAST report parsing will work if they run a BLAST version before 2.2.13). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jcv128 at psu.edu Mon Nov 20 19:52:47 2006 From: jcv128 at psu.edu (Juan Cristobal Vera) Date: Mon, 20 Nov 2006 19:52:47 -0500 Subject: [Bioperl-l] GO terms not present in Swiss annotation object Message-ID: <1164070364l.1106082l.0l@psu.edu> Hi, I'm writing a simple application to extract various fields from swissprot objects and I can't access the GO terms found in "dblink" part of the swiss format flat files. I'm not a professional programmer and I can't figure out why this is occuring. All the other "dblink" keys are being generated as far as I can tell (e.g. embl, pfam, etc). The GO terms are just skipped over and it's driving me crazy. Not sure if this is a bug or a deliberate strategy I'm unfamiliar with. I apologize if this is not the correct forum to ask for this sort of help and would ask to be directed to the proper one. Juan Cristobal Vera Graduate Student Department of Biology Penn State University 208 Mueller Laboratory University Park, PA 16802 (814)863-2957 From cjfields at uiuc.edu Tue Nov 21 01:19:59 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 00:19:59 -0600 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164070364l.1106082l.0l@psu.edu> References: <1164070364l.1106082l.0l@psu.edu> Message-ID: Juan, The DBLink objects should be generated. You'll need to give us a bit more information to go on, though. We need an example sequence, your local version of Bioperl, maybe a test script, etc. This is the right forum for this, yes, if you are using BioPerl. Chris On Nov 20, 2006, at 6:52 PM, Juan Cristobal Vera wrote: > > > Hi, > I'm writing a simple application to extract various fields from > swissprot objects and I can't access the GO terms found in > "dblink" part of the swiss format flat files. I'm not a > professional programmer and I can't figure out why this is > occuring. All the other "dblink" keys are being > generated as far as I can tell (e.g. embl, pfam, etc). The GO > terms are just skipped over and it's driving me crazy. Not sure if > this is a bug or a deliberate strategy I'm unfamiliar with. I > apologize if this is not the correct forum to ask for this sort of > help and would ask to be directed to the proper one. > > > > Juan Cristobal Vera > > Graduate Student > > Department of Biology > > Penn State University > > 208 Mueller Laboratory > > University Park, PA 16802 > > (814)863-2957 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From gwu at molbio.mgh.harvard.edu Tue Nov 21 03:11:03 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 03:11:03 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> Message-ID: <4562B497.6080805@molbio.mgh.harvard.edu> Can you show me where it indicates I am actually using the MySQL schema. I am pretty sure that I used the sql script files from sql/biosql-ora(Has anyone actually tried to install MySQL schema on Oracle?). I can reinstall the schema if you think that's the way to solve the problem. Thanks very much. Gang Hilmar Lapp wrote: > It looks like you are using the MySQL schema under Oracle. There are > different DDL scripts for each supported RDBMS. The ones for Oracle > are in the sql/biosql-ora subdirectory. Note the INSTALL document in > that directory. > > -hilmar > > > On Nov 20, 2006, at 1:16 PM, gang wu wrote: > > >> Hi Hilmar, >> >> Below is the output. Thanks. >> >> Gang >> ========================================================== >> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >> TEST_VERBOSE=1 >> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >> @ARGV;' t/01dbadaptor.t >> t/01dbadaptor....1..19 >> ok 1 >> ok 2 >> ok 3 >> ok 4 >> ok 5 >> ok 6 >> ok 7 >> ok 8 >> ok 9 >> ok 10 >> ok 11 >> attempting to load adaptor class for BioNamespace >> ok 12 >> attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor >> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >> ok 13 >> ok 14 >> attempting to load driver for adaptor class >> Bio::DB::BioSQL::BioNamespaceAdaptor >> attempting to load driver for adaptor class >> Bio::DB::BioSQL::BasePersistenceAdaptor >> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >> preparing UK select statement: SELECT biodatabase.oid, >> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >> = ? >> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >> invalid identifier (DBD ERROR: error possibly near <*> indicator at >> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >> Statement "SELECT biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >> Bio/DB/BioSQL/BaseDriver.pm line 1800. >> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >> Can't call method "bind_param" on an undefined value at blib/lib/ >> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >> dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 15-19 >> Failed 5/19 tests, 73.68% okay >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ---------------------------------------------------------------------- >> --------- >> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >> okay. >> make: *** [test_01dbadaptor] Error 2 >> ========================================================= >> >> >> Hilmar Lapp wrote: >> >>> Hi Gang, >>> >>> what I wanted to get at was the error message from the driver when >>> it fails to generate the prepared statement, but this is not in >>> the output. >>> >>> I believe you need set the HARNESS_VERBOSE environment variable to >>> 1 before testing to get what I need: >>> >>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>> csh/tcsh >>> $ make test_01dbadaptor TEST_VERBOSE=1 >>> >>> This will lead to _a lot_ of debugging output. Do not run this for >>> the entire test suite. >>> >>> The errors for mysql I believe are related to the fact that have >>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>> (completely empty) instance of BioSQL. >>> >>> Let me know what you get for the Oracle test above. >>> >>> -hilmar >>> >>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>> >>> >>>> Hi Hilmar, >>>> >>>> Thanks for your message. Below are several tests for Oracle and >>>> MySQL. MySQL actually also has two tests with failed items which >>>> may be related to data in BioSQL database. >>>> >>>> Could it be my Oracle installation/configuration has some issues? >>>> >>>> Thanks. >>>> >>>> Gang >>>> >>> --=========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >>> >>> >>> > > From n.haigh at sheffield.ac.uk Tue Nov 21 03:47:40 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 21 Nov 2006 08:47:40 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <4562BD2C.4000906@sheffield.ac.uk> L Xu wrote: > Thank you for the prompt response. Here is the information you needed: > (1)ActivePerl version 5.8.8.819 and PPM version 4.00 > (2)http://ppm4.activestate.com/MsWin32-x86/5.8/819/package.xml > http://bioperl.org/DIST/RC > http://bioperl.org/DIST > http://theoryx5.uwinnipeg.ca/ppms > http://www.Bribes.org/perl/ppm > (3)bioperl-1.4 > > Once again, thank you very much. > > L When you do a search for Bioperl, do you also get listing for Bioperl 1.5.2 RC2. If you do, try to install that and let us know how you get on. If you don't see a 1.5.2 RC2 let me know and I'll try to find out what the problem is. The PPM package is a little behind since there is an RC4 - I'll try to get the RC4 packaged today if I have time. We are hoping that RC4 is the last release candidate before the official 1.5.2 release, so if you do install the RC2 remember to upgrade the package in a week or two. Cheers Nath From er at xs4all.nl Tue Nov 21 07:16:53 2006 From: er at xs4all.nl (Erik) Date: Tue, 21 Nov 2006 13:16:53 +0100 (CET) Subject: [Bioperl-l] double-colon bug Message-ID: <6661.156.83.1.251.1164111413.squirrel@webmail.xs4all.nl> Hi all, Could one of the committers apply the fix as proposed for bug 2146 ? It's a small change: added a ':' to the regex at line 507. I did add a 'show the bug' snippet, albeit somewhat belatedly. It passes all 135 genbank tests with that change. Also, it fixes my application :) Thanks, Erik http://bugzilla.open-bio.org/show_bug.cgi?id=2146 From cjfields at uiuc.edu Tue Nov 21 08:21:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 07:21:35 -0600 Subject: [Bioperl-l] Error message for installation In-Reply-To: <4562BD2C.4000906@sheffield.ac.uk> References: <4562BD2C.4000906@sheffield.ac.uk> Message-ID: <67BD6F52-A994-4FC7-8E4F-375F21D1E1F9@uiuc.edu> All of the RCs are in their own directory; http://www.bioperl.org/DIST/RC I couldn't install 1.5.2 myself unless I set the repository to that directory. I think that's fine as long as we set the final release to the regular installation directory (http://www.bioperl.org/DIST) and use package.xml to point to the other required packages in the RC directory. Chris On Nov 21, 2006, at 2:47 AM, Nathan S. Haigh wrote: > L Xu wrote: >> Thank you for the prompt response. Here is the information you >> needed: >> (1)ActivePerl version 5.8.8.819 and PPM version 4.00 >> (2)http://ppm4.activestate.com/MsWin32-x86/5.8/819/package.xml >> http://bioperl.org/DIST/RC >> http://bioperl.org/DIST >> http://theoryx5.uwinnipeg.ca/ppms >> http://www.Bribes.org/perl/ppm >> (3)bioperl-1.4 >> >> Once again, thank you very much. >> >> L > > When you do a search for Bioperl, do you also get listing for Bioperl > 1.5.2 RC2. If you do, try to install that and let us know how you get > on. If you don't see a 1.5.2 RC2 let me know and I'll try to find out > what the problem is. > > The PPM package is a little behind since there is an RC4 - I'll try to > get the RC4 packaged today if I have time. We are hoping that RC4 > is the > last release candidate before the official 1.5.2 release, so if you do > install the RC2 remember to upgrade the package in a week or two. > > Cheers > Nath > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Tue Nov 21 09:56:29 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 21 Nov 2006 14:56:29 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <4563139D.2040108@sheffield.ac.uk> L Xu wrote: > I tried to install 1,5,2RC2, but got the following error message: > ################### > ...... > Generating HTML for Heap-0.71 ... DONE > Generating HTML for Error-0.17008 ... DONE > Generating HTML for XML-RegExp-0.03 ... DONE > Installing to site area ... failed > > ERROR: File conflict; package Bioperl-1.4 already provide > C:/Perl/html/bin/bp_aacomp.html > ########################## > Should I first uninstall Bioperl-1.4, if so how to do it? Thanks. > > > L > I'll have a look at this a bit later this afternoon. If you are using the PPM4 GUI, you should be able to right click an installed package and click remove (or something to that effect) and you will then have to apply the changes (like when you install a package). Once it's uninstalled, try installing 1.5.2 RC2 and let me know how you go. Cheers Nath From akarger at CGR.Harvard.edu Tue Nov 21 10:21:18 2006 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 21 Nov 2006 10:21:18 -0500 Subject: [Bioperl-l] Translating alternate start codons Message-ID: I think this is more a Bio question than a Bioperl question. I did this: ######### #!/usr/local/bin/perl use strict; use warnings; use Bio::Seq; use Bio::Tools::CodonTable; my $seqobj = Bio::PrimarySeq->new ( -seq => 'ATATGATAA', -id => 'GeneFragment-12', -accession_number => 'X78121', -alphabet => 'dna', ); $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; print "ATA $is a valid start codon\n"; print "Table 4: ", $seqobj->translate("-codontable_id" => 4)->seq,"\n"; print "Table 1: ", $seqobj->translate("-codontable_id" => 1)->seq,"\n"; ########### I got this: ATA is a valid start codon Table 4: IW* Table 1: I** But EMBL tells me that EMBLCDS:AAT64955 starts with an M: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[EMBLCDS:'A AT64955']+-qnum+1+-enum+3 So, does Bioperl purposely not translate start codons to M, while EMBL does? Am I supposed to just change the I to M explicitly in my code? I didn't see an obvious option to translate() to do it. Thanks, - Amir Karger Research Computing Life Sciences Division Harvard University 617-496-0626 From bix at sendu.me.uk Tue Nov 21 10:21:34 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 15:21:34 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Message-ID: <4563197E.7010909@sendu.me.uk> Nathan Haigh wrote: > > If anyone is aware of a way to force CPAN to install modules in a > specific order, please let Sendu know - we may be able to make the > install process much easier to the users. As regards the Bundle, you just have to specify the modules in the desired order. The question is, what order of installation, if any, results in no first-time failures? From akarger at CGR.Harvard.edu Tue Nov 21 11:16:01 2006 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 21 Nov 2006 11:16:01 -0500 Subject: [Bioperl-l] Translating alternate start codons Message-ID: > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > Amir, > > The best documentation for translate() is in the online > Bioperl Tutorial, > have you checked that? > > Brian O. Thanks for the quick response. The tutorial is quite informative. It seems to me that the POD needs to document -complete more thoroughly, though: Or if you expect a complete coding sequence (CDS) translation, with inititator at the beginning and terminator at the end: $protein_seq_obj = $cds_seq_obj->translate(-complete => 1); This doesn't really explain what it does. I guess -complete was chosen as a compromise between having too many options and having lots of functionality. In my case, I want to keep the *, and I don't want warnings about terminators in the middle, because I've got a bunch of pseudogenes. So I'll just translate the M myself. I'm sure you've had many "the documentation is spread out in too many places" discussions before, and I know keeping docs up to date is Hard. Oh well. -Amir > > > On 11/21/06 10:21 AM, "Amir Karger" wrote: > > > I think this is more a Bio question than a Bioperl question. > > > > I did this: > > > > ######### > > #!/usr/local/bin/perl > > > > use strict; > > use warnings; > > > > use Bio::Seq; > > use Bio::Tools::CodonTable; > > > > my $seqobj = Bio::PrimarySeq->new ( > > -seq => 'ATATGATAA', > > -id => 'GeneFragment-12', > > -accession_number => 'X78121', > > -alphabet => 'dna', > > ); > > > > $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); > > my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; > > print "ATA $is a valid start codon\n"; > > print "Table 4: ", $seqobj->translate("-codontable_id" => > 4)->seq,"\n"; > > print "Table 1: ", $seqobj->translate("-codontable_id" => > 1)->seq,"\n"; > > ########### > > > > I got this: > > ATA is a valid start codon > > Table 4: IW* > > Table 1: I** > > > > But EMBL tells me that EMBLCDS:AAT64955 starts with an M: > > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ > EMBLCDS:'A > > AT64955']+-qnum+1+-enum+3 > > > > So, does Bioperl purposely not translate start codons to M, > while EMBL > > does? Am I supposed to just change the I to M explicitly in > my code? I > > didn't see an obvious option to translate() to do it. > > > > Thanks, > > > > - Amir Karger > > Research Computing > > Life Sciences Division > > Harvard University > > 617-496-0626 > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From gwu at molbio.mgh.harvard.edu Tue Nov 21 12:00:55 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 12:00:55 -0500 Subject: [Bioperl-l] Two BioPerl-1.5.2-RC3 installation issues Message-ID: <456330C7.1020801@molbio.mgh.harvard.edu> When installing bioperl-1.5.2RC3, I chose to run the BioDBGFF tests with MySQL database. Below is the warning message. =============================================== Checking if your kit is complete... Warning: the following files are missing in your kit: t/BioDBSeqFeature_mysql.t Please inform the author. Writing Makefile for Bio =============================================== Another thins is the installation of Bio-ASN1-EntrezGene-1.09, the 'make test' requires bioperl be preinstalled(Bio::Index::...) while bioperl requires it be preinstalled. Is this a circle reference issue? Gang Gang From bix at sendu.me.uk Tue Nov 21 12:31:37 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:31:37 +0000 Subject: [Bioperl-l] Two BioPerl-1.5.2-RC3 installation issues In-Reply-To: <456330C7.1020801@molbio.mgh.harvard.edu> References: <456330C7.1020801@molbio.mgh.harvard.edu> Message-ID: <456337F9.6090001@sendu.me.uk> gang wu wrote: > When installing bioperl-1.5.2RC3, I chose to run the BioDBGFF tests with > MySQL database. Below is the warning message. > =============================================== > Checking if your kit is complete... > Warning: the following files are missing in your kit: > t/BioDBSeqFeature_mysql.t > Please inform the author. > Writing Makefile for Bio > =============================================== That should get resolved in RC4. > Another thins is the installation of Bio-ASN1-EntrezGene-1.09, the 'make > test' requires bioperl be preinstalled(Bio::Index::...) while bioperl > requires it be preinstalled. Is this a circle reference issue? Yes it is. You'll have to force install one of them. Again, it should get resolved in RC4 (Bio::ASN1::EntrezGene won't be a requirement). Thank you for your feedback, Sendu. From bix at sendu.me.uk Tue Nov 21 12:41:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:41:04 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read Message-ID: <45633A30.7060009@sendu.me.uk> With the new Build.PL, when it does its check to see if optional external modules are installed or not, for each module that isn't installed I can print out details of what Bioperl modules need it and why and then ask if you'd like to install that module before proceeding. This is obviously very useful for people doing one-off installations from CPAN, giving them informed choices and letting them avoid any problems with particular external modules (vs. having all or nothing by installing Bundle::BioPerl). But for developers, if you choose not to install a module, you'll keep getting asked if you want to install it every time you run Build.PL. So the question is, would this be too annoying? How often do you run Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I run it all the time because I'm developing the thing and trying to sort out installation issues, but would it bother anyone else? Cheers, Sendu. From bix at sendu.me.uk Tue Nov 21 12:45:46 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:45:46 +0000 Subject: [Bioperl-l] Changing default reply-to on this list Message-ID: <45633B4A.6060804@sendu.me.uk> Hi, I'd like to propose changing the default reply-to for posts on this list from the current 'reply to the poster' to 'reply to the mailing list'. That way people can just hit 'reply' instead of 'reply to all' in order to get a reply back to the list. If people then changed the current habit of 'reply to all' to just 'reply' it would avoid people being replied to getting multiple copies of the reply - one direct, a second from the mailing list. Cheers, Sendu. From stefan.kirov at bms.com Tue Nov 21 13:08:02 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 13:08:02 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: <45634082.6040001@bms.com> Sendu, This is not a problem - see prerequisites_policy ask/follow options for CPAN config. Hope this helps. Stefan Sendu Bala wrote: > With the new Build.PL, when it does its check to see if optional > external modules are installed or not, for each module that isn't > installed I can print out details of what Bioperl modules need it and > why and then ask if you'd like to install that module before proceeding. > > This is obviously very useful for people doing one-off installations > from CPAN, giving them informed choices and letting them avoid any > problems with particular external modules (vs. having all or nothing by > installing Bundle::BioPerl). > > But for developers, if you choose not to install a module, you'll keep > getting asked if you want to install it every time you run Build.PL. > > So the question is, would this be too annoying? How often do you run > Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I > run it all the time because I'm developing the thing and trying to sort > out installation issues, but would it bother anyone else? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bix at sendu.me.uk Tue Nov 21 13:17:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 18:17:10 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45634082.6040001@bms.com> References: <45633A30.7060009@sendu.me.uk> <45634082.6040001@bms.com> Message-ID: <456342A6.4060000@sendu.me.uk> Stefan Kirov wrote: > Sendu, > This is not a problem - see > prerequisites_policy ask/follow > options for CPAN config. That does not apply to the situation I describe. The follow policy applies to required modules when installing with CPAN. I am talking about installing modules that are /not/ required when using CPAN and even when /not/ using CPAN to do an installation. From n.haigh at sheffield.ac.uk Tue Nov 21 13:20:15 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 21 Nov 2006 18:20:15 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <4563435F.5010400@sheffield.ac.uk> Sendu Bala wrote: > Hi, > > I'd like to propose changing the default reply-to for posts on this list > from the current 'reply to the poster' to 'reply to the mailing list'. > That way people can just hit 'reply' instead of 'reply to all' in order > to get a reply back to the list. > > If people then changed the current habit of 'reply to all' to just > 'reply' it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > I don't seem to get multiple copies! However, the first reason (to just hit replay) is reason enough to change the default behaviour! :-) Nath From stefan.kirov at bms.com Tue Nov 21 13:24:39 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 13:24:39 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <456342A6.4060000@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> <45634082.6040001@bms.com> <456342A6.4060000@sendu.me.uk> Message-ID: <45634467.5010300@bms.com> Sendu Bala wrote: > Stefan Kirov wrote: >> Sendu, >> This is not a problem - see >> prerequisites_policy ask/follow >> options for CPAN config. > > That does not apply to the situation I describe. The follow policy > applies to required modules when installing with CPAN. I am talking > about installing modules that are /not/ required when using CPAN and > even when /not/ using CPAN to do an installation. > Sorry, I did not get that.... I personally do not run make often and would guess this to be case for most people as well. Stefan From stefan.kirov at bms.com Tue Nov 21 12:20:34 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 12:20:34 -0500 Subject: [Bioperl-l] Performance of Bio::Species Message-ID: <45633562.2030107@bms.com> New Bio::Species implementation seems to degrade significantly performance. It seems this happens when the Bio::Tree::Tree is constructed. See the stats bellow (based on simple Bio::Species object construction, script and test sequence file attached): 10000 iterrations new implementation: Constructor: 115 wallclock secs (113.50 usr + 0.67 sys = 114.17 CPU) Accessor: 0 wallclock secs ( 0.17 usr + 0.00 sys = 0.17 CPU) old implementation (bioperl-1.4 Constructor: 1 wallclock secs ( 0.84 usr + 0.10 sys = 0.94 CPU) Accessor: 0 wallclock secs ( 0.13 usr + 0.01 sys = 0.14 CPU) You can see that when reading a genbank file you would double the time necessary to construct the Bio::Seq object (100 iterations): old implementation (bioperl-1.4 Constructor: 0 wallclock secs ( 0.01 usr + 0.00 sys = 0.01 CPU) Accessor: 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU) Constructor(seqio)/reading seq: 3 wallclock secs ( 2.51 usr + 0.31 sys = 2.83 CPU) new implementation: Constructor: 2 wallclock secs ( 1.14 usr + 0.01 sys = 1.15 CPU) Accessor: 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU) Constructor(seqio)/reading seq: 5 wallclock secs ( 5.10 usr + 0.20 sys = 5.30 CPU) This may not pose a problem to people who read few sequences or files with no lineage data, but it could be a significant headache otherwise. I saw from CVS that Sendu knows there are memory leaks (I find cycles). If the classification is supplied incorrectly (includes a reference to an array in the classification array) things get really messy (~17 GB of RAM for a Bio::Species object), though weird enough the cycle is not indefinite. If I have more time I will try to debug this further and submit a formal bug report/patch, but I am not sure if I will anytime soon. I am sure there are people who understand Bio::Taxon/Bio::Tree::Tree better than me and might have better idea how to fix this. Stefan /// use Bio::Species; use Benchmark; use Bio::SeqIO; my @classification=qw( sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota ); my $species; my $t1 = new Benchmark; for my $i (1..100) { $species = Bio::Species->new(-classification => [@classification]); } my $t2 = new Benchmark; for my $i (1..100) { my $bin = $species->binomial; } my $t3 = new Benchmark; print "Constructor: ", timestr(timediff($t2, $t1)),"\n"; print "Accessor: ", timestr(timediff($t3, $t2)),"\n"; my $f=shift; my $t4= new Benchmark; for my $i (1..100) { my $sio=new Bio::SeqIO(-file=>$f,-format=>'genbank'); my $seq=$sio->next_seq; } my $t5= new Benchmark; print "Constructor(seqio)/reading seq: ", timestr(timediff($t5, $t4)),"\n"; -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: NM_000161.genbank URL: From dmessina at wustl.edu Tue Nov 21 14:06:38 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:06:38 -0600 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> > it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. This behavior can be changed by going to http://lists.open-bio.org/mailman/listinfo/bioperl-l entering your subscribed email address in the last field on the page, clicking the "unsubscribe or edit options" button to the right of that field. On the next page, enter your password in the password field and click "Log in". On the options page that you see next, the last option, called "Avoid duplicate copies of messages?", should be set to "Yes" if you don't want multiple copies. Dave From dmessina at wustl.edu Tue Nov 21 14:11:06 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:11:06 -0600 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> Would it be possible to set it up such that when the user is asked whether to install an unrequired module, the possible answers are "yes", "no", "skip all"? The latter being to skip all subsequent questions about unrequired modules. Dave From bix at sendu.me.uk Tue Nov 21 14:30:52 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:30:52 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> References: <45633A30.7060009@sendu.me.uk> <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> Message-ID: <456353EC.9030304@sendu.me.uk> David Messina wrote: > Would it be possible to set it up such that when the user is asked > whether to install an unrequired module, the possible answers are "yes", > "no", "skip all"? The latter being to skip all subsequent questions > about unrequired modules. Yes, thanks, that's a good idea. I currently (in my private copy) have the default as 'no', but if changed as above, should the default be to 'skip all'? Or, perhaps have an initial question 'do you want to be asked to install optional modules you don't have' would be better? From hlapp at gmx.net Tue Nov 21 14:33:11 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:33:11 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4562B497.6080805@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> Message-ID: The Oracle error is ORA-00904: "BIODATABASE"."OID": invalid identifier and if you look at the accompanying statement, it's the UK select statement: SELECT <*>biodatabase.oid, biodatabase.name, biodatabase.authority FROM biodatabase WHERE name = :p1 The column OID must exist in the Biodatabase table (which actually is a synonym to the SG_BIODATABASE table), if it is the Oracle schema. This actually prompts another suggestion, sorry for not asking that first: did you actually install the BioSQL-API on top of the schema by running the script BS-create-Biosql-API.sql? (It seems that the statement it chokes on is also the first statement being prepared, so this may well be the reason) -hilmar On Nov 21, 2006, at 3:11 AM, gang wu wrote: > Can you show me where it indicates I am actually using the MySQL > schema. > I am pretty sure that I used the sql script files from > sql/biosql-ora(Has anyone actually tried to install MySQL schema on > Oracle?). I can reinstall the schema if you think that's the way to > solve the problem. Thanks very much. > > Gang > > Hilmar Lapp wrote: >> It looks like you are using the MySQL schema under Oracle. There are >> different DDL scripts for each supported RDBMS. The ones for Oracle >> are in the sql/biosql-ora subdirectory. Note the INSTALL document in >> that directory. >> >> -hilmar >> >> >> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >> >> >>> Hi Hilmar, >>> >>> Below is the output. Thanks. >>> >>> Gang >>> ========================================================== >>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>> TEST_VERBOSE=1 >>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>> @ARGV;' t/01dbadaptor.t >>> t/01dbadaptor....1..19 >>> ok 1 >>> ok 2 >>> ok 3 >>> ok 4 >>> ok 5 >>> ok 6 >>> ok 7 >>> ok 8 >>> ok 9 >>> ok 10 >>> ok 11 >>> attempting to load adaptor class for BioNamespace >>> ok 12 >>> attempting to load module >>> Bio::DB::BioSQL::BioNamespaceAdaptor >>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>> ok 13 >>> ok 14 >>> attempting to load driver for adaptor class >>> Bio::DB::BioSQL::BioNamespaceAdaptor >>> attempting to load driver for adaptor class >>> Bio::DB::BioSQL::BasePersistenceAdaptor >>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>> preparing UK select statement: SELECT biodatabase.oid, >>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >>> = ? >>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>> invalid identifier (DBD ERROR: error possibly near <*> indicator at >>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>> Statement "SELECT biodatabase.oid, biodatabase.name, >>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >>> Can't call method "bind_param" on an undefined value at blib/lib/ >>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>> dubious >>> Test returned status 255 (wstat 65280, 0xff00) >>> DIED. FAILED tests 15-19 >>> Failed 5/19 tests, 73.68% okay >>> Failed Test Stat Wstat Total Fail Failed List of Failed >>> -------------------------------------------------------------------- >>> -- >>> --------- >>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>> okay. >>> make: *** [test_01dbadaptor] Error 2 >>> ========================================================= >>> >>> >>> Hilmar Lapp wrote: >>> >>>> Hi Gang, >>>> >>>> what I wanted to get at was the error message from the driver when >>>> it fails to generate the prepared statement, but this is not in >>>> the output. >>>> >>>> I believe you need set the HARNESS_VERBOSE environment variable to >>>> 1 before testing to get what I need: >>>> >>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>> csh/tcsh >>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>> >>>> This will lead to _a lot_ of debugging output. Do not run this for >>>> the entire test suite. >>>> >>>> The errors for mysql I believe are related to the fact that have >>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>> (completely empty) instance of BioSQL. >>>> >>>> Let me know what you get for the Oracle test above. >>>> >>>> -hilmar >>>> >>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>> >>>> >>>>> Hi Hilmar, >>>>> >>>>> Thanks for your message. Below are several tests for Oracle and >>>>> MySQL. MySQL actually also has two tests with failed items which >>>>> may be related to data in BioSQL database. >>>>> >>>>> Could it be my Oracle installation/configuration has some issues? >>>>> >>>>> Thanks. >>>>> >>>>> Gang >>>>> >>>> --=========================================================== >>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>> =========================================================== >>>> >>>> >>>> >>>> >>>> >>>> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From dmessina at wustl.edu Tue Nov 21 14:36:10 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:36:10 -0600 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <456353EC.9030304@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> <456353EC.9030304@sendu.me.uk> Message-ID: <5DF4D1D9-754F-443F-ADDE-4127C579BF82@wustl.edu> On Nov 21, 2006, at 1:30 PM, Sendu Bala wrote: > Yes, thanks, that's a good idea. I currently (in my private copy) > have the default as 'no', but if changed as above, should the > default be to 'skip all'? Yeah, that makes sense to me. > Or, perhaps have an initial question 'do you want to be asked to > install optional modules you don't have' would be better? I think that would work fine, too -- whichever is easiest for you... Dave From bix at sendu.me.uk Tue Nov 21 14:37:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:37:14 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45633562.2030107@bms.com> References: <45633562.2030107@bms.com> Message-ID: <4563556A.1050101@sendu.me.uk> Stefan Kirov wrote: > New Bio::Species implementation seems to degrade significantly > performance. It seems this happens when the Bio::Tree::Tree is constructed. > See the stats bellow (based on simple Bio::Species object construction, > script and test sequence file attached): [snip] Thanks. If you come up with anything, please file that bug report. I certainly regard this as an important thing that must be fixed, though I don't know if I should hold up release of 1.5.2 for it. Now that you've reported on it I'm leaning toward yes, since the new Bio::Species implementation is one of the major new features of 1.5.2 and it ought to work well. Anyway, for the memory leak I have some ideas I haven't tried yet; I don't know if my efforts will solve the speed issue though. If anyone can spare the time to look at the problem, please do. Cheers, Sendu. From hlapp at gmx.net Tue Nov 21 14:46:45 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:46:45 -0500 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <93D5ABA0-290A-4087-8999-4FFBA6CFD918@gmx.net> I don't think that's a good idea. First, it is really hard to reply to someone off-list that way. Second, it is especially annoying given that reply-to-poster is generally considered best-practice and so therefore almost all lists reply off-list if you just hit reply. In fact I had this set to reply-to-list on one of our (NESCent's) own listserves to help the less computer-savvy but it was so annoying that I set it back to reply-to-sender within days. Compared to that, hitting the delete key on the duplicate takes about 0.2 seconds for me and hasn't bothered me much ever. Bottom line is, if you suggest people to change their habits then it is close impossible if it is only a single place that likes to do it the other way. -hilmar On Nov 21, 2006, at 12:45 PM, Sendu Bala wrote: > Hi, > > I'd like to propose changing the default reply-to for posts on this > list >> from the current 'reply to the poster' to 'reply to the mailing >> list'. > That way people can just hit 'reply' instead of 'reply to all' in > order > to get a reply back to the list. > > If people then changed the current habit of 'reply to all' to just > 'reply' it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Nov 21 14:41:25 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:41:25 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: I typically run (ran) perl Makefile.PL when I'm forced to, i.e., if someone changed Makefile.PL in the repository and I cvs update. Or if something is just going weird, as a last resort before rebooting ;) On Nov 21, 2006, at 12:41 PM, Sendu Bala wrote: > With the new Build.PL, when it does its check to see if optional > external modules are installed or not, for each module that isn't > installed I can print out details of what Bioperl modules need it and > why and then ask if you'd like to install that module before > proceeding. > > This is obviously very useful for people doing one-off installations >> from CPAN, giving them informed choices and letting them avoid any > problems with particular external modules (vs. having all or > nothing by > installing Bundle::BioPerl). > > But for developers, if you choose not to install a module, you'll keep > getting asked if you want to install it every time you run Build.PL. > > So the question is, would this be too annoying? How often do you run > Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I > run it all the time because I'm developing the thing and trying to > sort > out installation issues, but would it bother anyone else? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Nov 21 14:56:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:56:18 -0500 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4563556A.1050101@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > I don't know if I should hold up release of 1.5.2 for it. Now that > you've > reported on it I'm leaning toward yes, since the new Bio::Species > implementation is one of the major new features of 1.5.2 and it > ought to > work well. I disagree to some extent. This is a developer release, so not everything is expected to work perfectly. What's not desirable is if fixing this required another entire redesign of the API, so that every dev release introduces different API. The thing is, you'll really only get trouble reports once you put it out and people start using it in anger. Don't expect to make it perfect before. > > Anyway, for the memory leak I have some ideas I haven't tried yet; I > don't know if my efforts will solve the speed issue though. The memory leak sounds more concerning to me. Under which circumstances would it crash a script or blow throuhg all of say 1-2GB when it should have taken only a tenth of that. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Tue Nov 21 14:58:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:58:58 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> References: <45633B4A.6060804@sendu.me.uk> <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> Message-ID: <45635A82.6070209@sendu.me.uk> David Messina wrote: >> it would avoid people being replied to getting multiple copies >> of the reply - one direct, a second from the mailing list. > > This behavior can be changed by going to > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > entering your subscribed email address in the last field on the page, > clicking the "unsubscribe or edit options" button to the right of > that field. > > On the next page, enter your password in the password field and click > "Log in". On the options page that you see next, the last option, > called "Avoid duplicate copies of messages?", should be set to "Yes" > if you don't want multiple copies. Ah, thanks for that. Given Hilmar's reply, forget the proposal. I'll just live in misery :( From bosborne11 at verizon.net Tue Nov 21 14:58:00 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 21 Nov 2006 14:58:00 -0500 Subject: [Bioperl-l] Translating alternate start codons In-Reply-To: Message-ID: Amir, I think I understand your question, perhaps not, and I think the recommended solution is to create your own "custom" codon table. See t/CodonTable.t for an example. Brian O. On 11/21/06 11:16 AM, "Amir Karger" wrote: >> From: Brian Osborne [mailto:bosborne11 at verizon.net] >> >> Amir, >> >> The best documentation for translate() is in the online >> Bioperl Tutorial, >> have you checked that? >> >> Brian O. > > Thanks for the quick response. The tutorial is quite informative. > It seems to me that the POD needs to document -complete more thoroughly, > though: > > Or if you expect a complete coding sequence (CDS) > translation, > with inititator at the beginning and terminator at the > end: > > $protein_seq_obj = $cds_seq_obj->translate(-complete > => 1); > > This doesn't really explain what it does. > > I guess -complete was chosen as a compromise between having too many > options and having lots of functionality. In my case, I want to keep the > *, and I don't want warnings about terminators in the middle, because > I've got a bunch of pseudogenes. So I'll just translate the M myself. > > I'm sure you've had many "the documentation is spread out in too many > places" discussions before, and I know keeping docs up to date is Hard. > Oh well. > > -Amir > >> >> >> On 11/21/06 10:21 AM, "Amir Karger" wrote: >> >>> I think this is more a Bio question than a Bioperl question. >>> >>> I did this: >>> >>> ######### >>> #!/usr/local/bin/perl >>> >>> use strict; >>> use warnings; >>> >>> use Bio::Seq; >>> use Bio::Tools::CodonTable; >>> >>> my $seqobj = Bio::PrimarySeq->new ( >>> -seq => 'ATATGATAA', >>> -id => 'GeneFragment-12', >>> -accession_number => 'X78121', >>> -alphabet => 'dna', >>> ); >>> >>> $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); >>> my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; >>> print "ATA $is a valid start codon\n"; >>> print "Table 4: ", $seqobj->translate("-codontable_id" => >> 4)->seq,"\n"; >>> print "Table 1: ", $seqobj->translate("-codontable_id" => >> 1)->seq,"\n"; >>> ########### >>> >>> I got this: >>> ATA is a valid start codon >>> Table 4: IW* >>> Table 1: I** >>> >>> But EMBL tells me that EMBLCDS:AAT64955 starts with an M: >>> >> http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ >> EMBLCDS:'A >>> AT64955']+-qnum+1+-enum+3 >>> >>> So, does Bioperl purposely not translate start codons to M, >> while EMBL >>> does? Am I supposed to just change the I to M explicitly in >> my code? I >>> didn't see an obvious option to translate() to do it. >>> >>> Thanks, >>> >>> - Amir Karger >>> Research Computing >>> Life Sciences Division >>> Harvard University >>> 617-496-0626 >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Tue Nov 21 15:16:18 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 20:16:18 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: <45635E92.7080000@sendu.me.uk> Hilmar Lapp wrote: > > On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > >> Anyway, for the memory leak I have some ideas I haven't tried yet; I >> don't know if my efforts will solve the speed issue though. > > The memory leak sounds more concerning to me. Under which circumstances > would it crash a script or blow throuhg all of say 1-2GB when it should > have taken only a tenth of that. Its been reported as causing problems if you do something like parse a large embl file with many (10s of thousands) sequences in it. So basically any situation that you make lots of Bio::Species objects. IIRC the reporter ran out of memory on a ~40000 sequence embl file. Neither the memory leak fix or speed fix ought to require any API change. I'm fairly certain that the memory leak, at least, is confined to a problem with (as suggested) Bio::Tree* stuff failing to clean up on destruction. There was in fact already an unnoticed problem with Bio::Tree::Node not getting cleaned up (see my #*** comment in the code), but my Bio::Species-related changes exacerbated the problem and also made them noticeable, since you're more likely to create thousands of Bio::Species than you were Bio::Tree::Node. From jason at bioperl.org Tue Nov 21 00:57:54 2006 From: jason at bioperl.org (Jason Stajich) Date: Mon, 20 Nov 2006 21:57:54 -0800 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164070364l.1106082l.0l@psu.edu> References: <1164070364l.1106082l.0l@psu.edu> Message-ID: a specific accession and example code will make it easier for someone to reproduce (and debug) your problem. On Nov 20, 2006, at 4:52 PM, Juan Cristobal Vera wrote: > > > Hi, > I'm writing a simple application to extract various fields from > swissprot objects and I can't access the GO terms found in > "dblink" part of the swiss format flat files. I'm not a > professional programmer and I can't figure out why this is > occuring. All the other "dblink" keys are being > generated as far as I can tell (e.g. embl, pfam, etc). The GO > terms are just skipped over and it's driving me crazy. Not sure if > this is a bug or a deliberate strategy I'm unfamiliar with. I > apologize if this is not the correct forum to ask for this sort of > help and would ask to be directed to the proper one. > > > > Juan Cristobal Vera > > Graduate Student > > Department of Biology > > Penn State University > > 208 Mueller Laboratory > > University Park, PA 16802 > > (814)863-2957 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason at bioperl.org http://jason.open-bio.org/ From stefan.kirov at bms.com Tue Nov 21 15:20:40 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 15:20:40 -0500 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: <45635F98.8030901@bms.com> Hilmar Lapp wrote: > On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > > >> I don't know if I should hold up release of 1.5.2 for it. Now that >> you've >> reported on it I'm leaning toward yes, since the new Bio::Species >> implementation is one of the major new features of 1.5.2 and it >> ought to >> work well. >> > > I disagree to some extent. This is a developer release, so not > everything is expected to work perfectly. > > What's not desirable is if fixing this required another entire > redesign of the API, so that every dev release introduces different API. > > The thing is, you'll really only get trouble reports once you put it > out and people start using it in anger. Don't expect to make it > perfect before. > > >> Anyway, for the memory leak I have some ideas I haven't tried yet; I >> don't know if my efforts will solve the speed issue though. >> > > The memory leak sounds more concerning to me. Under which > circumstances would it crash a script or blow throuhg all of say > 1-2GB when it should have taken only a tenth of that. > > As I was saying, I did pass ref to an array in the classification (wrong parsing): push @classification,'sapiens', 'Homo', 'Hominidae', $arrayref; and my script took 17-18 GB. I am really surprised it stopped getting more RAM and finished successfully. I did not explore further. Stefan > -hilmar > > From gwu at molbio.mgh.harvard.edu Tue Nov 21 15:33:10 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 15:33:10 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> Message-ID: <45636286.6040504@molbio.mgh.harvard.edu> Hi Hilmar, I just rebuilt the Oracle BioSQL database by strictly following the INSTALL doc. You are right that BS-create-Biosql-API.sql must be run to make bioperl-db work with it(the oid columns). But my installation problem was caused by running BS-create-Biosql-API2.sql after it, which rendered the database not compatible with bioperl-db. If I ran only BS-create-Biosql-API.sql, ll bioperl-db tests could pass. Does this mean that the Oracle version is not interoperable between the Bio- projects at this point? Did I miss anything in the INSTALL or README? I only saw a line "-- all others (Biojava, etc)" but did not realize I could not run both BS-create-Biosql-API.sql and BS-create-Biosql-API2.sql. I this is the case, can you please add it to the docs? Thanks very much for your help. Gang Hilmar Lapp wrote: > The Oracle error is > > ORA-00904: "BIODATABASE"."OID": invalid identifier > > and if you look at the accompanying statement, it's the UK select > statement: > > SELECT <*>biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = :p1 > > The column OID must exist in the Biodatabase table (which actually is > a synonym to the SG_BIODATABASE table), if it is the Oracle schema. > > This actually prompts another suggestion, sorry for not asking that > first: did you actually install the BioSQL-API on top of the schema by > running the script BS-create-Biosql-API.sql? (It seems that the > statement it chokes on is also the first statement being prepared, so > this may well be the reason) > > -hilmar > > On Nov 21, 2006, at 3:11 AM, gang wu wrote: > >> Can you show me where it indicates I am actually using the MySQL schema. >> I am pretty sure that I used the sql script files from >> sql/biosql-ora(Has anyone actually tried to install MySQL schema on >> Oracle?). I can reinstall the schema if you think that's the way to >> solve the problem. Thanks very much. >> >> Gang >> >> Hilmar Lapp wrote: >>> It looks like you are using the MySQL schema under Oracle. There are >>> different DDL scripts for each supported RDBMS. The ones for Oracle >>> are in the sql/biosql-ora subdirectory. Note the INSTALL document in >>> that directory. >>> >>> -hilmar >>> >>> >>> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >>> >>> >>>> Hi Hilmar, >>>> >>>> Below is the output. Thanks. >>>> >>>> Gang >>>> ========================================================== >>>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>>> TEST_VERBOSE=1 >>>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >>>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>>> @ARGV;' t/01dbadaptor.t >>>> t/01dbadaptor....1..19 >>>> ok 1 >>>> ok 2 >>>> ok 3 >>>> ok 4 >>>> ok 5 >>>> ok 6 >>>> ok 7 >>>> ok 8 >>>> ok 9 >>>> ok 10 >>>> ok 11 >>>> attempting to load adaptor class for BioNamespace >>>> ok 12 >>>> attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor >>>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>>> ok 13 >>>> ok 14 >>>> attempting to load driver for adaptor class >>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>> attempting to load driver for adaptor class >>>> Bio::DB::BioSQL::BasePersistenceAdaptor >>>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>>> preparing UK select statement: SELECT biodatabase.oid, >>>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >>>> = ? >>>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>>> invalid identifier (DBD ERROR: error possibly near <*> indicator at >>>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>>> Statement "SELECT biodatabase.oid, biodatabase.name, >>>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >>>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>>> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >>>> Can't call method "bind_param" on an undefined value at blib/lib/ >>>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>>> dubious >>>> Test returned status 255 (wstat 65280, 0xff00) >>>> DIED. FAILED tests 15-19 >>>> Failed 5/19 tests, 73.68% okay >>>> Failed Test Stat Wstat Total Fail Failed List of Failed >>>> ---------------------------------------------------------------------- >>>> --------- >>>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>>> okay. >>>> make: *** [test_01dbadaptor] Error 2 >>>> ========================================================= >>>> >>>> >>>> Hilmar Lapp wrote: >>>> >>>>> Hi Gang, >>>>> >>>>> what I wanted to get at was the error message from the driver when >>>>> it fails to generate the prepared statement, but this is not in >>>>> the output. >>>>> >>>>> I believe you need set the HARNESS_VERBOSE environment variable to >>>>> 1 before testing to get what I need: >>>>> >>>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>>> csh/tcsh >>>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>>> >>>>> This will lead to _a lot_ of debugging output. Do not run this for >>>>> the entire test suite. >>>>> >>>>> The errors for mysql I believe are related to the fact that have >>>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>>> (completely empty) instance of BioSQL. >>>>> >>>>> Let me know what you get for the Oracle test above. >>>>> >>>>> -hilmar >>>>> >>>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>>> >>>>> >>>>>> Hi Hilmar, >>>>>> >>>>>> Thanks for your message. Below are several tests for Oracle and >>>>>> MySQL. MySQL actually also has two tests with failed items which >>>>>> may be related to data in BioSQL database. >>>>>> >>>>>> Could it be my Oracle installation/configuration has some issues? >>>>>> >>>>>> Thanks. >>>>>> >>>>>> Gang >>>>>> >>>>> --=========================================================== >>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>>> =========================================================== >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > --=========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > > From jason at bioperl.org Tue Nov 21 11:47:37 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 21 Nov 2006 08:47:37 -0800 Subject: [Bioperl-l] Translating alternate start codons In-Reply-To: References: Message-ID: <8273f6c20611210847q7178025bm8e5367a5ae2138d4@mail.gmail.com> It seem then you don't want to use 'complete' since you don't always expect complete CDSes. Shouldn't you just translate to generate the peptide and then operate on the initial and terminal residues to achieve what you want. substr($peptide,0,1,'M'); chop($peptide) if substr($peptide,-1,1) eq $TERMINATOR; This is a community project so any help in improving apparent deficiencies in documentation are gladly welcomed - the wiki is designed to let everyone contribute. I think that clarifications and better descriptions for modules should reside there so please add your input on the webpages. A dev with write access can migrate updated documentation to the module's POD where appropriate. -jason On 11/21/06, Amir Karger wrote: > > > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > > > Amir, > > > > The best documentation for translate() is in the online > > Bioperl Tutorial, > > have you checked that? > > > > Brian O. > > Thanks for the quick response. The tutorial is quite informative. > It seems to me that the POD needs to document -complete more thoroughly, > though: > > Or if you expect a complete coding sequence (CDS) > translation, > with inititator at the beginning and terminator at the > end: > > $protein_seq_obj = $cds_seq_obj->translate(-complete > => 1); > > This doesn't really explain what it does. > > I guess -complete was chosen as a compromise between having too many > options and having lots of functionality. In my case, I want to keep the > *, and I don't want warnings about terminators in the middle, because > I've got a bunch of pseudogenes. So I'll just translate the M myself. > > I'm sure you've had many "the documentation is spread out in too many > places" discussions before, and I know keeping docs up to date is Hard. > Oh well. > > -Amir > > > > > > > On 11/21/06 10:21 AM, "Amir Karger" wrote: > > > > > I think this is more a Bio question than a Bioperl question. > > > > > > I did this: > > > > > > ######### > > > #!/usr/local/bin/perl > > > > > > use strict; > > > use warnings; > > > > > > use Bio::Seq; > > > use Bio::Tools::CodonTable; > > > > > > my $seqobj = Bio::PrimarySeq->new ( > > > -seq => 'ATATGATAA', > > > -id => 'GeneFragment-12', > > > -accession_number => 'X78121', > > > -alphabet => 'dna', > > > ); > > > > > > $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); > > > my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; > > > print "ATA $is a valid start codon\n"; > > > print "Table 4: ", $seqobj->translate("-codontable_id" => > > 4)->seq,"\n"; > > > print "Table 1: ", $seqobj->translate("-codontable_id" => > > 1)->seq,"\n"; > > > ########### > > > > > > I got this: > > > ATA is a valid start codon > > > Table 4: IW* > > > Table 1: I** > > > > > > But EMBL tells me that EMBLCDS:AAT64955 starts with an M: > > > > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ > > EMBLCDS:'A > > > AT64955']+-qnum+1+-enum+3 > > > > > > So, does Bioperl purposely not translate start codons to M, > > while EMBL > > > does? Am I supposed to just change the I to M explicitly in > > my code? I > > > didn't see an obvious option to translate() to do it. > > > > > > Thanks, > > > > > > - Amir Karger > > > Research Computing > > > Life Sciences Division > > > Harvard University > > > 617-496-0626 > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich jason at bioperl.org http://www.duke.edu/~jes12/ From bosborne11 at verizon.net Tue Nov 21 15:53:39 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 21 Nov 2006 15:53:39 -0500 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: <200611211032.kALAWahR014137@dev.open-bio.org> Message-ID: Bioperl-l, INSTALL has changed in CVS but the Wiki's version has not - you always have to change both versions of the INSTALL instructions, this is how Chris has elected to do it. Brian O. Date: Tue, 21 Nov 2006 10:32:36 +0000 To: Subject: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 Update of /home/repository/bioperl/bioperl-live In directory dev.open-bio.org:/tmp/cvs-serv14112 Modified Files: DEPENDENCIES INSTALL INSTALL.WIN Log Message: clarification for Bundle::BioPerl, updates for Build.PL Index: DEPENDENCIES =================================================================== RCS file: /home/repository/bioperl/bioperl-live/DEPENDENCIES,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** DEPENDENCIES 14 Nov 2006 15:13:24 -0000 1.1 --- DEPENDENCIES 21 Nov 2006 10:32:34 -0000 1.2 *************** *** 5,10 **** The following packages are used by Bioperl. Not all are required for Bioperl to operate properly, however some functionality will be missing ! without them. You can easily install all of these, except srsperl.pm, ! using the Bundle::BioPerl CPAN bundle. The DBD::mysql, DB_File and XML::Parser modules require other applications --- 5,11 ---- The following packages are used by Bioperl. Not all are required for Bioperl to operate properly, however some functionality will be missing ! without them. You can easily install all of these by using CPAN to install ! Bioperl, or if you have installed Bioperl manually (from archive or CVS), ! by using the Bundle::BioPerl CPAN bundle. The DBD::mysql, DB_File and XML::Parser modules require other applications Index: INSTALL =================================================================== RCS file: /home/repository/bioperl/bioperl-live/INSTALL,v retrieving revision 1.57 retrieving revision 1.58 diff -C2 -d -r1.57 -r1.58 *** INSTALL 16 Nov 2006 16:27:49 -0000 1.57 --- INSTALL 21 Nov 2006 10:32:34 -0000 1.58 *************** *** 1,24 **** # $Id$ ! Installing Bioperl for Unix ! * BIOPERL INSTALLATION ! * SYSTEM REQUIREMENTS ! * OPTIONAL ! * ADDITIONAL INSTALLATION INFORMATION ! * THE BIOPERL BUNDLE ! * INSTALLING BIOPERL THE EASY WAY USING CPAN ! * INSTALLING BIOPERL THE EASY WAY USING GNU 'make' ! * WHERE ARE THE MAN PAGES? ! * EXTERNAL PROGRAMS ! * Environment Variables ! * INSTALLING BIOPERL SCRIPTS ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA ! * INSTALLING BIOPERL MODULES THE HARD WAY ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION ! * THE TEST SYSTEM ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE ! * CONFIGURING for BSD and Solaris boxes ! * INSTALLATION BIOPERL INSTALLATION --- 1,24 ---- # $Id$ ! Installing Bioperl for Unix ! * BIOPERL INSTALLATION ! * SYSTEM REQUIREMENTS ! * OPTIONAL ! * ADDITIONAL INSTALLATION INFORMATION ! * THE BIOPERL BUNDLE ! * INSTALLING BIOPERL THE EASY WAY USING CPAN ! * INSTALLING BIOPERL THE EASY WAY USING Build.PL ! * WHERE ARE THE MAN PAGES? ! * EXTERNAL PROGRAMS ! * Environment Variables ! * INSTALLING BIOPERL SCRIPTS ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA ! * INSTALLING BIOPERL MODULES THE HARD WAY ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION ! * THE TEST SYSTEM ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE ! * CONFIGURING for BSD and Solaris boxes ! * INSTALLATION BIOPERL INSTALLATION *************** *** 41,48 **** modules is included in the DEPENDENCIES file. ! The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation of these ! external modules easy. Simply install the bundle using your CPAN shell and ! all necessary modules will be installed. See THE BIOPERL BUNDLE, ! below. OPTIONAL --- 41,49 ---- modules is included in the DEPENDENCIES file. ! When not using CPAN to install Bioperl itself, the CPAN Bioperl Bundle ! (Bundle::BioPerl) makes installation of these external modules easy. Simply ! install the bundle using your CPAN shell and many optional modules will be ! installed. See THE BIOPERL BUNDLE, below. However, it is recommended you use ! CPAN to install Bioperl and not use Bundle::BioPerl. OPTIONAL *************** *** 61,64 **** --- 62,72 ---- THE BIOPERL BUNDLE + You do not need to install Bundle::BioPerl if you will install Bioperl + using CPAN. This is for users manually installing Bioperl from archives + or CVS, who also want an easy way to install the optional external + modules that Bioperl makes use of. + + Bundle::BioPerl does *not* install Bioperl. + You typically need root privileges to install using CPAN. If you don't have these privileges please see INSTALLING BIOPERL IN A PERSONAL *************** *** 86,96 **** CPAN: Storable loaded ok Going to read /home/bosborne/.cpan/Metadata ! Database was generated on Tue, 24 Feb 2004 23:55:23 GMT ! DistributionB/BI/BIRNEY/bioperl-1.2.tar.gz ! DistributionB/BI/BIRNEY/bioperl-1.4.tar.gz Now install: ! cpan>install B/BI/BIRNEY/bioperl-1.4.tar.gz If you've installed everything perfectly and all the network connections --- 94,105 ---- CPAN: Storable loaded ok Going to read /home/bosborne/.cpan/Metadata ! Database was generated on Mon, 20 Nov 2006 05:24:36 GMT ! Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz ! Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz ! Distribution S/SE/SENDU/bioperl-1.5.2_100.tar.gz Now install: ! cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz If you've installed everything perfectly and all the network connections *************** *** 100,105 **** undetected bug in Bioperl, flawed test script, problems with CGI script used for sequence retrieval at public database, and so on. Remember ! that there are over 700 modules in Bioperl and the test suite is running ! more than 9000 individual tests, a few failed tests may not affect your usage of Bioperl. --- 109,114 ---- undetected bug in Bioperl, flawed test script, problems with CGI script used for sequence retrieval at public database, and so on. Remember ! that there are over 800 modules in Bioperl and the test suite is running ! more than 12000 individual tests, a few failed tests may not affect your usage of Bioperl. *************** *** 107,111 **** Bioperl and you'd like to install anyway do: ! cpan>force install B/BI/BIRNEY/bioperl-1.4.tar.gz This is what most experienced Bioperl users would do. However, if you're --- 116,120 ---- Bioperl and you'd like to install anyway do: ! cpan>force install S/SE/SENDU/bioperl-1.5.2_100.tar.gz This is what most experienced Bioperl users would do. However, if you're *************** *** 113,117 **** bioperl-l at bioperl.org. ! INSTALLING BIOPERL THE EASY WAY USING GNU 'make' The advantage of this approach is it's stepwise, so it's easy to stop and --- 122,126 ---- bioperl-l at bioperl.org. ! INSTALLING BIOPERL THE EASY WAY USING Build.PL The advantage of this approach is it's stepwise, so it's easy to stop and *************** *** 120,126 **** Download, then unpack the tar file. For example: ! >gunzip bioperl-1.5.2.tar.gz ! >tar xvf bioperl-1.5.2.tar ! >cd bioperl-1.5.2 Now issue the make commands: --- 129,135 ---- Download, then unpack the tar file. For example: ! >gunzip bioperl-1.5.2_100.tar.gz ! >tar xvf bioperl-1.5.2_100.tar ! >cd bioperl-1.5.2_100 Now issue the make commands: *************** *** 135,141 **** undetected bug in Bioperl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that ! there are over 700 modules in Bioperl and the test suite is running almost ! 9000 individual tests, a few failed tests may not affect your usage of ! Bioperl. If you decide that the failed tests will not affect how you intend to use --- 144,150 ---- undetected bug in Bioperl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that ! there are over 800 modules in Bioperl and the test suite is running more ! than 12000 individual tests, a few failed tests may not affect your usage ! of Bioperl. If you decide that the failed tests will not affect how you intend to use *************** *** 148,154 **** bioperl-l at bioperl.org. ! To 'make install' you need write permission in the perl5/site_perl/source ! area. Usually this will require you becoming root, so you will want to ! talk to your systems manager if you don't have the necessary privileges. It is also straightforward to install the package outside of the this --- 157,164 ---- bioperl-l at bioperl.org. ! To './Build install' you need write permission in the perl5/site_perl/source ! area (or similar, depending on your environment). Usually this will require ! you becoming root, so you will want to talk to your systems manager if you ! don't have the necessary privileges. It is also straightforward to install the package outside of the this *************** *** 158,165 **** WHERE ARE THE MAN PAGES? ! When using Makefile.PL, we had to disable the automatic creation of man ! pages because this step was triggering a "line too long" error on some ! OSs due to shell constraints. If you want man pages installed use the ! Build.PL installation process. EXTERNAL PROGRAMS --- 168,176 ---- WHERE ARE THE MAN PAGES? ! When using Makefile.PL (no longer covered in this documentation), we had ! to disable the automatic creation of man pages because this step was ! triggering a "line too long" error on some OSs due to shell constraints. ! If you want man pages installed use the Build.PL installation process ! discussed above. EXTERNAL PROGRAMS *************** *** 229,234 **** like, simply answer the questions on 'perl Build.PL'. The installation directory can be specified by ! perl Build.PL ! ./Build install --install_path script=/foo/scripts By default they install to /usr/bin or similar, depending on platform. --- 240,245 ---- like, simply answer the questions on 'perl Build.PL'. The installation directory can be specified by ! perl Build.PL ! ./Build install --install_path script=/foo/scripts By default they install to /usr/bin or similar, depending on platform. *************** *** 297,301 **** execute the make commands from the Compile/SW directory. ! If all else fails or are unable to access the perl distribution directories, ask your system administrator to place the files there for you. You can always execute perl scripts in the same directory as the --- 308,312 ---- execute the make commands from the Compile/SW directory. ! If all else fails and you are unable to access the perl distribution directories, ask your system administrator to place the files there for you. You can always execute perl scripts in the same directory as the *************** *** 312,316 **** #!/usr/bin/perl use lib "/home/users/dag/lib/perl5/"; ! use Bio::Seq; #<...insert whizzy perl code here...> --- 323,327 ---- #!/usr/bin/perl use lib "/home/users/dag/lib/perl5/"; ! use Bio::Perl; #<...insert whizzy perl code here...> *************** *** 319,341 **** csh or tcsh: ! setenv PERL5LIB /home/users/dag/lib/perl5// bash or sh: ! export PERL5LIB=/home/users/dag/lib/perl5// THE TEST SYSTEM The Bioperl test system is located in the t/ directory and is ! automatically run whenever you execute the 'make test' command. Alternatively if you want to investigate the behavior of a specific test ! such as the SeqIO test you would type: ! >perl -I. -w t/SeqIO.t ! The -I. tells Perl to use the current directory as the include path - this ! makes sure you are testing the modules in this directory not ones ! installed elsewhere in your PERL5LIB path. The -w tells Perl to print all ! warnings. If you are trying to learn how to use a module, often the test suite is a --- 330,357 ---- csh or tcsh: ! setenv PERL5LIB /home/users/dag/lib/perl5/ bash or sh: ! export PERL5LIB=/home/users/dag/lib/perl5/ THE TEST SYSTEM The Bioperl test system is located in the t/ directory and is ! automatically run whenever you execute the './Build test' command ! (having previously run 'Perl Build.PL'; if you have already installed ! Bioperl answer 'no' to script installation to get nicer test output ! later). Alternatively if you want to investigate the behavior of a specific test ! such as the Seq test you would type: ! >./Build test --test_files t/Seq.t --verbose ! The ./ ensures you are using the Build script in the current directory to ! make sure you are testing the modules in this directory not ones ! installed elsewhere. The --test_files arguement can be used multiple times ! to try a set of test scripts in one go. The --verbose arguement outputs ! the detailed test results, instead of just the summary you see during ! './Build test'. If you are trying to learn how to use a module, often the test suite is a *************** *** 385,388 **** This should install the compiled extension. The Bio::Tools::pSW module will work cleanly now. - - \ No newline at end of file --- 401,402 ---- Index: INSTALL.WIN =================================================================== RCS file: /home/repository/bioperl/bioperl-live/INSTALL.WIN,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -d -r1.23 -r1.24 *** INSTALL.WIN 14 Nov 2006 15:13:24 -0000 1.23 --- INSTALL.WIN 21 Nov 2006 10:32:34 -0000 1.24 *************** *** 80,89 **** 7) Right click the latest version of Bioperl available and choose ! install. ! ! 7a) This package will be sufficient for the main ! functionality of Bioperl. However, if you require ! full functionality, you should also install the ! latest Bundle-BioPerl package. 8) Click the green arrow (Run marked actions) to complete the --- 80,85 ---- 7) Right click the latest version of Bioperl available and choose ! install. (Note for users of previous Bioperl releases: you should ! not have to use the Bundle-BioPerl package anymore.) 8) Click the green arrow (Run marked actions) to complete the _______________________________________________ Bioperl-guts-l mailing list Bioperl-guts-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l ------ End of Forwarded Message From bix at sendu.me.uk Tue Nov 21 16:32:02 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 21:32:02 +0000 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: References: Message-ID: <45637052.4040003@sendu.me.uk> Brian Osborne wrote: > Bioperl-l, > > INSTALL has changed in CVS but the Wiki's version has not - you always have > to change both versions of the INSTALL instructions, this is how Chris has > elected to do it. Yes, I will edit the wiki when I've finished with the INSTALL docs. (I may be changing them further, please don't consider the current information gospel.) From hlapp at gmx.net Tue Nov 21 16:44:50 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 16:44:50 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <45636286.6040504@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> <45636286.6040504@molbio.mgh.harvard.edu> Message-ID: <064D0938-C753-40BD-8A0D-C900985193B8@gmx.net> Yes this needs to be better documented. Note that you can use both APIs if you install them under different users (= schema in Oracle). I'm not 100% sure whether both variants are fully prepared for this; you may have to create synonyms for the schema-owner tables first, i.e., SQL> CREATE SYNONYM sg_biodatabase FOR biosqlowner.sg_biodatabase; etc, assuming that are logged on as the user under which you want to create the API, and biosqlowner is the schema-owner of the BioSQL instance. Did you want to use BioSQL with both bioperl and biojava? -hilmar On Nov 21, 2006, at 3:33 PM, gang wu wrote: > Hi Hilmar, > > I just rebuilt the Oracle BioSQL database by strictly following the > INSTALL doc. You are right that BS-create-Biosql-API.sql must be > run to make bioperl-db work with it(the oid columns). But my > installation problem was caused by running BS-create-Biosql- > API2.sql after it, which rendered the database not compatible with > bioperl-db. If I ran only BS-create-Biosql-API.sql, ll bioperl-db > tests could pass. Does this mean that the Oracle version is not > interoperable between the Bio- projects at this point? > > Did I miss anything in the INSTALL or README? I only saw a line "-- > all others (Biojava, etc)" but did not realize I could not run both > BS-create-Biosql-API.sql and BS-create-Biosql-API2.sql. I this is > the case, can you please add it to the docs? > > Thanks very much for your help. > > Gang > > Hilmar Lapp wrote: >> The Oracle error is >> >> ORA-00904: "BIODATABASE"."OID": invalid identifier >> >> and if you look at the accompanying statement, it's the UK select >> statement: >> >> SELECT <*>biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = :p1 >> >> The column OID must exist in the Biodatabase table (which actually >> is a synonym to the SG_BIODATABASE table), if it is the Oracle >> schema. >> >> This actually prompts another suggestion, sorry for not asking >> that first: did you actually install the BioSQL-API on top of the >> schema by running the script BS-create-Biosql-API.sql? (It seems >> that the statement it chokes on is also the first statement being >> prepared, so this may well be the reason) >> >> -hilmar >> >> On Nov 21, 2006, at 3:11 AM, gang wu wrote: >> >>> Can you show me where it indicates I am actually using the MySQL >>> schema. >>> I am pretty sure that I used the sql script files from >>> sql/biosql-ora(Has anyone actually tried to install MySQL schema on >>> Oracle?). I can reinstall the schema if you think that's the way to >>> solve the problem. Thanks very much. >>> >>> Gang >>> >>> Hilmar Lapp wrote: >>>> It looks like you are using the MySQL schema under Oracle. There >>>> are >>>> different DDL scripts for each supported RDBMS. The ones for Oracle >>>> are in the sql/biosql-ora subdirectory. Note the INSTALL >>>> document in >>>> that directory. >>>> >>>> -hilmar >>>> >>>> >>>> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >>>> >>>> >>>>> Hi Hilmar, >>>>> >>>>> Below is the output. Thanks. >>>>> >>>>> Gang >>>>> ========================================================== >>>>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>>>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>>>> TEST_VERBOSE=1 >>>>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/ >>>>> lib64/ >>>>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>>>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>>>> @ARGV;' t/01dbadaptor.t >>>>> t/01dbadaptor....1..19 >>>>> ok 1 >>>>> ok 2 >>>>> ok 3 >>>>> ok 4 >>>>> ok 5 >>>>> ok 6 >>>>> ok 7 >>>>> ok 8 >>>>> ok 9 >>>>> ok 10 >>>>> ok 11 >>>>> attempting to load adaptor class for BioNamespace >>>>> ok 12 >>>>> attempting to load module >>>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> ok 13 >>>>> ok 14 >>>>> attempting to load driver for adaptor class >>>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> attempting to load driver for adaptor class >>>>> Bio::DB::BioSQL::BasePersistenceAdaptor >>>>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>>>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> preparing UK select statement: SELECT biodatabase.oid, >>>>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE >>>>> name >>>>> = ? >>>>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>>>> invalid identifier (DBD ERROR: error possibly near <*> >>>>> indicator at >>>>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>>>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>>>> Statement "SELECT biodatabase.oid, biodatabase.name, >>>>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/ >>>>> lib/ >>>>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>>>> BioNamespaceAdaptor: binding UK column 1 to >>>>> "__dummy__" (namespace) >>>>> Can't call method "bind_param" on an undefined value at blib/lib/ >>>>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>>>> dubious >>>>> Test returned status 255 (wstat 65280, 0xff00) >>>>> DIED. FAILED tests 15-19 >>>>> Failed 5/19 tests, 73.68% okay >>>>> Failed Test Stat Wstat Total Fail Failed List of Failed >>>>> ------------------------------------------------------------------ >>>>> ---- >>>>> --------- >>>>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>>>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>>>> okay. >>>>> make: *** [test_01dbadaptor] Error 2 >>>>> ========================================================= >>>>> >>>>> >>>>> Hilmar Lapp wrote: >>>>> >>>>>> Hi Gang, >>>>>> >>>>>> what I wanted to get at was the error message from the driver >>>>>> when >>>>>> it fails to generate the prepared statement, but this is not in >>>>>> the output. >>>>>> >>>>>> I believe you need set the HARNESS_VERBOSE environment >>>>>> variable to >>>>>> 1 before testing to get what I need: >>>>>> >>>>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>>>> csh/tcsh >>>>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>>>> >>>>>> This will lead to _a lot_ of debugging output. Do not run this >>>>>> for >>>>>> the entire test suite. >>>>>> >>>>>> The errors for mysql I believe are related to the fact that have >>>>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>>>> (completely empty) instance of BioSQL. >>>>>> >>>>>> Let me know what you get for the Oracle test above. >>>>>> >>>>>> -hilmar >>>>>> >>>>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>>>> >>>>>> >>>>>>> Hi Hilmar, >>>>>>> >>>>>>> Thanks for your message. Below are several tests for Oracle and >>>>>>> MySQL. MySQL actually also has two tests with failed items which >>>>>>> may be related to data in BioSQL database. >>>>>>> >>>>>>> Could it be my Oracle installation/configuration has some >>>>>>> issues? >>>>>>> >>>>>>> Thanks. >>>>>>> >>>>>>> Gang >>>>>>> >>>>>> --=========================================================== >>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>>>> =========================================================== >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> --=========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> >> -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Tue Nov 21 18:54:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 17:54:32 -0600 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164141156l.712786l.0l@psu.edu> References: <1164141156l.712786l.0l@psu.edu> Message-ID: <101BBBA4-391D-4F87-8181-F754A2357DA8@uiuc.edu> You'll want to always reply to the list as well. I would say update to a newer version; many changes have been made to parsing GenBank/ SwissProt/EMBL since rel 1.4, including dblinks. If you're using windows you'll need to follow the instructions on the website for the latest release candidate: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Note that the release candidates are located in a different repository, so you'll need to set that up to find them. chris On Nov 21, 2006, at 2:32 PM, Juan Cristobal Vera wrote: > ok, thanks for responding! > I'm using ActivePerl 5.8.8 build 819 on a windows machine (sorry) > and the bioperl 1.4 PPM3 package. Perhaps this is too old? > Here's part of my code (mostly derived from bioperl docs): > ......................... > #cut > > $seqInObj = $indexObj->get_Seq_by_id($line); #get sequence and > create seq object > > #cut > > if (defined $seqInObj->annotation){ > $annotObj = $seqInObj->annotation; #create annotation object > foreach $key ($annotObj->get_all_annotation_keys){ > @values = $annotObj->get_Annotations($key); > foreach $value (@values){ > if (lc($key) eq "dblink"){ > print $outfh "Annotation: $key\n"; > print $outfh $value->as_text,"\n"; > $dbhash_ref = $value->hash_tree; > for $dbKey (keys %{$dbhash_ref}) { > print $outfh $dbKey,": ",$dbhash_ref-> > {$dbKey},"\n"; #none of these prints produce GO terms > } > } > } > } > } > ......................... > My program searches an indexed database on my machine, creates the > objects, and prints out relevant annotations. > Here are some of the accessions I used for testing: > P19351 TNNT_DROME > P36188 TNNI_DROME > P11147 HSP7D_DROME > .......................................... > the relevant output looks something like this (for debugging) for > P19351: > ...................................................................... > Direct database link to X58188 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: X58188 > optional_id: CAA41171.1 > Annotation: dblink > Direct database link to X59376 in database EMBL > database: EMBL > comment: -; mRNA. > primary_id: X59376 > optional_id: CAA42020.1 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48802.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48803.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48804.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48805.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAN09458.1 > Annotation: dblink > Direct database link to AY122145 in database EMBL > database: EMBL > comment: -; mRNA. > primary_id: AY122145 > optional_id: AAM52657.1 > Annotation: dblink > Direct database link to A40547 in database PIR > database: PIR > primary_id: A40547 > optional_id: A40547 > Annotation: dblink > Direct database link to B38594 in database PIR > database: PIR > primary_id: B38594 > optional_id: B38594 > Annotation: dblink > Direct database link to Dm.1717 in database UniGene > database: UniGene > primary_id: Dm.1717 > optional_id: - > Annotation: dblink > Direct database link to P45379 in database HSSP > database: HSSP > primary_id: P45379 > optional_id: 1J1E > Annotation: dblink > Direct database link to P36188 in database IntAct > database: IntAct > primary_id: P36188 > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PA in database KEGG > database: KEGG > primary_id: dme:CG7178-PA > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PB in database KEGG > database: KEGG > primary_id: dme:CG7178-PB > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PC in database KEGG > database: KEGG > primary_id: dme:CG7178-PC > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PD in database KEGG > database: KEGG > primary_id: dme:CG7178-PD > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PG in database KEGG > database: KEGG > primary_id: dme:CG7178-PG > optional_id: - > Annotation: dblink > Direct database link to FBgn0004028 in database FlyBase > database: FlyBase > primary_id: FBgn0004028 > optional_id: wupA > Annotation: dblink > Direct database link to IPR001978 in database InterPro > database: InterPro > primary_id: IPR001978 > optional_id: Troponin > Annotation: dblink > Direct database link to PF00992 in database Pfam > database: Pfam > comment: 1 > primary_id: PF00992 > optional_id: Troponin > .............................................. > as you can see, no GO terms above > ...................................................... > Vs. the actual content of the flat file from for the dblinks from > P19351: > DR EMBL; X54504; CAA38366.1; -; mRNA. > DR EMBL; AY439172; AAR24583.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24584.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24585.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24586.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24587.1; -; Genomic_DNA. > DR EMBL; AY665838; AAU09446.1; -; mRNA. > DR EMBL; AE014298; AAF48288.2; -; Genomic_DNA. > DR EMBL; AE014298; AAF48289.2; -; Genomic_DNA. > DR EMBL; AE014298; AAF48290.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52491.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52492.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52493.1; -; Genomic_DNA. > DR EMBL; AY051989; AAK93413.1; -; mRNA. > DR EMBL; AY070875; AAL48497.1; ALT_SEQ; mRNA. > DR PIR; S13251; S13251. > DR UniGene; Dm.20472; -. > DR HSSP; P45379; 1J1E. > DR Ensembl; CG7107; Drosophila melanogaster. > DR KEGG; dme:CG7107-PE; -. > DR KEGG; dme:CG7107-PF; -. > DR KEGG; dme:CG7107-PG; -. > DR FlyBase; FBgn0004169; up. > DR GO; GO:0007498; P:mesoderm development; IEP:FlyBase. ...... > where the GO term is last entry in dblink section above. > Any help you could provide would be most welcome. Let me know if > this is insufficient information or if you need a working script. > > > On Tue, 21 Nov 2006 00:19:59 -0600 Chris Fields wrote: > Juan, The DBLink objects should be generated. You'll need to give > us a bit more information to go on, though. We need an example > sequence, your local version of Bioperl, maybe a test script, etc. > This is the right forum for this, yes, if you are using BioPerl. > Chris On Nov 20, 2006, at 6:52 PM, Juan Cristobal Vera wrote: > > > > Hi, > I'm writing a simple application to extract various fields > from > swissprot objects and I can't access the GO terms found in > > "dblink" part of the swiss format flat files. I'm not a > > professional programmer and I can't figure out why this is > > occuring. All the other "dblink" keys are being > > generated as far as I can tell (e.g. embl, pfam, etc). The GO > > terms are just skipped over and it's driving me crazy. Not sure if > > this is a bug or a deliberate strategy I'm unfamiliar with. I > > apologize if this is not the correct forum to ask for this sort of > > help and would ask to be directed to the proper one. > > > > Juan > Cristobal Vera > > Graduate Student > > Department of Biology > > > Penn State University > > 208 Mueller Laboratory > > University > Park, PA 16802 > > (814)863-2957 > > > _______________________________________________ > Bioperl-l mailing > list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/ > mailman/listinfo/bioperl-l Christopher Fields Postdoctoral > Researcher Lab of Dr. Robert Switzer Dept of Biochemistry > University of Illinois Urbana-Champaign > > Juan Cristobal Vera > Graduate Student > Department of Biology > Penn State University > 208 Mueller Laboratory > University Park, PA 16802 > (814)863-2957 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Nov 21 18:56:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 17:56:48 -0600 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: References: Message-ID: On Nov 21, 2006, at 2:53 PM, Brian Osborne wrote: > Bioperl-l, > > INSTALL has changed in CVS but the Wiki's version has not - you > always have > to change both versions of the INSTALL instructions, this is how > Chris has > elected to do it. > > Brian O. Agreed (thanks Brian for pointing that out). I have to update these by hand until I can find a more automated way (which will be hard considering the meta content in the wiki). Chris > > > > Date: Tue, 21 Nov 2006 10:32:36 +0000 > To: > Subject: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 > INSTALL, 1.57, > 1.58 INSTALL.WIN, 1.23, 1.24 > > Update of /home/repository/bioperl/bioperl-live > In directory dev.open-bio.org:/tmp/cvs-serv14112 > > Modified Files: > DEPENDENCIES INSTALL INSTALL.WIN > Log Message: > clarification for Bundle::BioPerl, updates for Build.PL > > Index: DEPENDENCIES > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/DEPENDENCIES,v > retrieving revision 1.1 > retrieving revision 1.2 > diff -C2 -d -r1.1 -r1.2 > *** DEPENDENCIES 14 Nov 2006 15:13:24 -0000 1.1 > --- DEPENDENCIES 21 Nov 2006 10:32:34 -0000 1.2 > *************** > *** 5,10 **** > The following packages are used by Bioperl. Not all are required for > Bioperl to operate properly, however some functionality will be > missing > ! without them. You can easily install all of these, except > srsperl.pm, > ! using the Bundle::BioPerl CPAN bundle. > > The DBD::mysql, DB_File and XML::Parser modules require other > applications > --- 5,11 ---- > The following packages are used by Bioperl. Not all are required for > Bioperl to operate properly, however some functionality will be > missing > ! without them. You can easily install all of these by using CPAN > to install > ! Bioperl, or if you have installed Bioperl manually (from archive > or CVS), > ! by using the Bundle::BioPerl CPAN bundle. > > The DBD::mysql, DB_File and XML::Parser modules require other > applications > > Index: INSTALL > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/INSTALL,v > retrieving revision 1.57 > retrieving revision 1.58 > diff -C2 -d -r1.57 -r1.58 > *** INSTALL 16 Nov 2006 16:27:49 -0000 1.57 > --- INSTALL 21 Nov 2006 10:32:34 -0000 1.58 > *************** > *** 1,24 **** > # $Id$ > > ! Installing Bioperl for Unix > > ! * BIOPERL INSTALLATION > ! * SYSTEM REQUIREMENTS > ! * OPTIONAL > ! * ADDITIONAL INSTALLATION INFORMATION > ! * THE BIOPERL BUNDLE > ! * INSTALLING BIOPERL THE EASY WAY USING CPAN > ! * INSTALLING BIOPERL THE EASY WAY USING GNU 'make' > ! * WHERE ARE THE MAN PAGES? > ! * EXTERNAL PROGRAMS > ! * Environment Variables > ! * INSTALLING BIOPERL SCRIPTS > ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA > ! * INSTALLING BIOPERL MODULES THE HARD WAY > ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION > ! * THE TEST SYSTEM > ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE > ! * CONFIGURING for BSD and Solaris boxes > ! * INSTALLATION > > BIOPERL INSTALLATION > --- 1,24 ---- > # $Id$ > > ! Installing Bioperl for Unix > > ! * BIOPERL INSTALLATION > ! * SYSTEM REQUIREMENTS > ! * OPTIONAL > ! * ADDITIONAL INSTALLATION INFORMATION > ! * THE BIOPERL BUNDLE > ! * INSTALLING BIOPERL THE EASY WAY USING CPAN > ! * INSTALLING BIOPERL THE EASY WAY USING Build.PL > ! * WHERE ARE THE MAN PAGES? > ! * EXTERNAL PROGRAMS > ! * Environment Variables > ! * INSTALLING BIOPERL SCRIPTS > ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA > ! * INSTALLING BIOPERL MODULES THE HARD WAY > ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION > ! * THE TEST SYSTEM > ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE > ! * CONFIGURING for BSD and Solaris boxes > ! * INSTALLATION > > BIOPERL INSTALLATION > *************** > *** 41,48 **** > modules is included in the DEPENDENCIES file. > > ! The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation of > these > ! external modules easy. Simply install the bundle using your CPAN > shell and > ! all necessary modules will be installed. See THE BIOPERL BUNDLE, > ! below. > > OPTIONAL > --- 41,49 ---- > modules is included in the DEPENDENCIES file. > > ! When not using CPAN to install Bioperl itself, the CPAN Bioperl > Bundle > ! (Bundle::BioPerl) makes installation of these external modules easy. > Simply > ! install the bundle using your CPAN shell and many optional > modules will be > ! installed. See THE BIOPERL BUNDLE, below. However, it is > recommended you > use > ! CPAN to install Bioperl and not use Bundle::BioPerl. > > OPTIONAL > *************** > *** 61,64 **** > --- 62,72 ---- > THE BIOPERL BUNDLE > > + You do not need to install Bundle::BioPerl if you will install > Bioperl > + using CPAN. This is for users manually installing Bioperl from > archives > + or CVS, who also want an easy way to install the optional external > + modules that Bioperl makes use of. > + > + Bundle::BioPerl does *not* install Bioperl. > + > You typically need root privileges to install using CPAN. If you > don't > have these privileges please see INSTALLING BIOPERL IN A PERSONAL > *************** > *** 86,96 **** > CPAN: Storable loaded ok > Going to read /home/bosborne/.cpan/Metadata > ! Database was generated on Tue, 24 Feb 2004 23:55:23 GMT > ! DistributionB/BI/BIRNEY/bioperl-1.2.tar.gz > ! DistributionB/BI/BIRNEY/bioperl-1.4.tar.gz > > Now install: > > ! cpan>install B/BI/BIRNEY/bioperl-1.4.tar.gz > > If you've installed everything perfectly and all the network > connections > --- 94,105 ---- > CPAN: Storable loaded ok > Going to read /home/bosborne/.cpan/Metadata > ! Database was generated on Mon, 20 Nov 2006 05:24:36 GMT > ! Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz > ! Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz > ! Distribution S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > Now install: > > ! cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > If you've installed everything perfectly and all the network > connections > *************** > *** 100,105 **** > undetected bug in Bioperl, flawed test script, problems with CGI > script used for sequence retrieval at public database, and so on. > Remember > ! that there are over 700 modules in Bioperl and the test suite is > running > ! more than 9000 individual tests, a few failed tests may not > affect your > usage of Bioperl. > > --- 109,114 ---- > undetected bug in Bioperl, flawed test script, problems with CGI > script used for sequence retrieval at public database, and so on. > Remember > ! that there are over 800 modules in Bioperl and the test suite is > running > ! more than 12000 individual tests, a few failed tests may not > affect your > usage of Bioperl. > > *************** > *** 107,111 **** > Bioperl and you'd like to install anyway do: > > ! cpan>force install B/BI/BIRNEY/bioperl-1.4.tar.gz > > This is what most experienced Bioperl users would do. However, if > you're > --- 116,120 ---- > Bioperl and you'd like to install anyway do: > > ! cpan>force install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > This is what most experienced Bioperl users would do. However, if > you're > *************** > *** 113,117 **** > bioperl-l at bioperl.org. > > ! INSTALLING BIOPERL THE EASY WAY USING GNU 'make' > > The advantage of this approach is it's stepwise, so it's easy to > stop and > --- 122,126 ---- > bioperl-l at bioperl.org. > > ! INSTALLING BIOPERL THE EASY WAY USING Build.PL > > The advantage of this approach is it's stepwise, so it's easy to > stop and > *************** > *** 120,126 **** > Download, then unpack the tar file. For example: > > ! >gunzip bioperl-1.5.2.tar.gz > ! >tar xvf bioperl-1.5.2.tar > ! >cd bioperl-1.5.2 > > Now issue the make commands: > --- 129,135 ---- > Download, then unpack the tar file. For example: > > ! >gunzip bioperl-1.5.2_100.tar.gz > ! >tar xvf bioperl-1.5.2_100.tar > ! >cd bioperl-1.5.2_100 > > Now issue the make commands: > *************** > *** 135,141 **** > undetected bug in Bioperl, flawed test script, problems with CGI > script > using for sequence retrieval at public database, and so on. > Remember that > ! there are over 700 modules in Bioperl and the test suite is > running almost > ! 9000 individual tests, a few failed tests may not affect your > usage of > ! Bioperl. > > If you decide that the failed tests will not affect how you > intend to use > --- 144,150 ---- > undetected bug in Bioperl, flawed test script, problems with CGI > script > using for sequence retrieval at public database, and so on. > Remember that > ! there are over 800 modules in Bioperl and the test suite is > running more > ! than 12000 individual tests, a few failed tests may not affect > your usage > ! of Bioperl. > > If you decide that the failed tests will not affect how you > intend to use > *************** > *** 148,154 **** > bioperl-l at bioperl.org. > > ! To 'make install' you need write permission in the perl5/ > site_perl/source > ! area. Usually this will require you becoming root, so you will > want to > ! talk to your systems manager if you don't have the necessary > privileges. > > It is also straightforward to install the package outside of the > this > --- 157,164 ---- > bioperl-l at bioperl.org. > > ! To './Build install' you need write permission in the > perl5/site_perl/source > ! area (or similar, depending on your environment). Usually this will > require > ! you becoming root, so you will want to talk to your systems > manager if you > ! don't have the necessary privileges. > > It is also straightforward to install the package outside of the > this > *************** > *** 158,165 **** > WHERE ARE THE MAN PAGES? > > ! When using Makefile.PL, we had to disable the automatic creation > of man > ! pages because this step was triggering a "line too long" error on > some > ! OSs due to shell constraints. If you want man pages installed use > the > ! Build.PL installation process. > > EXTERNAL PROGRAMS > --- 168,176 ---- > WHERE ARE THE MAN PAGES? > > ! When using Makefile.PL (no longer covered in this documentation), > we had > ! to disable the automatic creation of man pages because this step was > ! triggering a "line too long" error on some OSs due to shell > constraints. > ! If you want man pages installed use the Build.PL installation > process > ! discussed above. > > EXTERNAL PROGRAMS > *************** > *** 229,234 **** > like, simply answer the questions on 'perl Build.PL'. > The installation directory can be specified by > ! perl Build.PL > ! ./Build install --install_path script=/foo/scripts > By default they install to /usr/bin or similar, depending on > platform. > > --- 240,245 ---- > like, simply answer the questions on 'perl Build.PL'. > The installation directory can be specified by > ! perl Build.PL > ! ./Build install --install_path script=/foo/scripts > By default they install to /usr/bin or similar, depending on > platform. > > *************** > *** 297,301 **** > execute the make commands from the Compile/SW directory. > > ! If all else fails or are unable to access the perl distribution > directories, ask your system administrator to place the files > there for > you. You can always execute perl scripts in the same directory as > the > --- 308,312 ---- > execute the make commands from the Compile/SW directory. > > ! If all else fails and you are unable to access the perl distribution > directories, ask your system administrator to place the files > there for > you. You can always execute perl scripts in the same directory as > the > *************** > *** 312,316 **** > #!/usr/bin/perl > use lib "/home/users/dag/lib/perl5/"; > ! use Bio::Seq; > #<...insert whizzy perl code here...> > > --- 323,327 ---- > #!/usr/bin/perl > use lib "/home/users/dag/lib/perl5/"; > ! use Bio::Perl; > #<...insert whizzy perl code here...> > > *************** > *** 319,341 **** > csh or tcsh: > > ! setenv PERL5LIB /home/users/dag/lib/perl5// > > bash or sh: > > ! export PERL5LIB=/home/users/dag/lib/perl5// > > THE TEST SYSTEM > > The Bioperl test system is located in the t/ directory and is > ! automatically run whenever you execute the 'make test' command. > Alternatively if you want to investigate the behavior of a > specific test > ! such as the SeqIO test you would type: > > ! >perl -I. -w t/SeqIO.t > > ! The -I. tells Perl to use the current directory as the include > path - this > ! makes sure you are testing the modules in this directory not ones > ! installed elsewhere in your PERL5LIB path. The -w tells Perl to > print all > ! warnings. > > If you are trying to learn how to use a module, often the test > suite is a > --- 330,357 ---- > csh or tcsh: > > ! setenv PERL5LIB /home/users/dag/lib/perl5/ > > bash or sh: > > ! export PERL5LIB=/home/users/dag/lib/perl5/ > > THE TEST SYSTEM > > The Bioperl test system is located in the t/ directory and is > ! automatically run whenever you execute the './Build test' command > ! (having previously run 'Perl Build.PL'; if you have already > installed > ! Bioperl answer 'no' to script installation to get nicer test output > ! later). > Alternatively if you want to investigate the behavior of a > specific test > ! such as the Seq test you would type: > > ! >./Build test --test_files t/Seq.t --verbose > > ! The ./ ensures you are using the Build script in the current > directory to > ! make sure you are testing the modules in this directory not ones > ! installed elsewhere. The --test_files arguement can be used > multiple times > ! to try a set of test scripts in one go. The --verbose arguement > outputs > ! the detailed test results, instead of just the summary you see > during > ! './Build test'. > > If you are trying to learn how to use a module, often the test > suite is a > *************** > *** 385,388 **** > This should install the compiled extension. The Bio::Tools::pSW > module will work cleanly now. > - > - > \ No newline at end of file > --- 401,402 ---- > > Index: INSTALL.WIN > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/INSTALL.WIN,v > retrieving revision 1.23 > retrieving revision 1.24 > diff -C2 -d -r1.23 -r1.24 > *** INSTALL.WIN 14 Nov 2006 15:13:24 -0000 1.23 > --- INSTALL.WIN 21 Nov 2006 10:32:34 -0000 1.24 > *************** > *** 80,89 **** > > 7) Right click the latest version of Bioperl available > and > choose > ! install. > ! > ! 7a) This package will be sufficient for > the main > ! functionality of Bioperl. However, if you > require > ! full functionality, you should also > install the > ! latest Bundle-BioPerl package. > > 8) Click the green arrow (Run marked actions) to > complete the > --- 80,85 ---- > > 7) Right click the latest version of Bioperl available > and > choose > ! install. (Note for users of previous Bioperl releases: > you > should > ! not have to use the Bundle-BioPerl package anymore.) > > 8) Click the green arrow (Run marked actions) to > complete the > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l > > ------ End of Forwarded Message > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jcv128 at psu.edu Tue Nov 21 15:53:07 2006 From: jcv128 at psu.edu (Juan Cristobal Vera) Date: Tue, 21 Nov 2006 15:53:07 -0500 Subject: [Bioperl-l] GO terms not present in Swiss annotation object-more details Message-ID: <1164142374l.1118292l.0l@psu.edu> Hi, I'm writing a simple application to extract various fields from swissprot objects and I can't access the GO terms found in dblink part of the swiss format flat files. I'm not a professional programmer and I can't figure out why this is occuring. All the other dblink keys are being generated as far as I can tell (e.g. embl, pfam, etc). The GO terms are just skipped over and it's driving me crazy. Not sure if this is a bug or a deliberate strategy I'm unfamiliar with. I'm using ActivePerl 5.8.8 build 819 on a windows machine (sorry) and the bioperl 1.4 PPM3 package. Perhaps this is too old? Here's part of my code (mostly derived from bioperl docs): ......................... #cut $seqInObj = $indexObj->get_Seq_by_id($line); #get sequence and create seq object #cut if (defined $seqInObj->annotation){ $annotObj = $seqInObj->annotation; #create annotation object foreach $key ($annotObj->get_all_annotation_keys){ @values =$annotObj->get_Annotations($key); foreach $value (@values){ if (lc($key) eq "dblink"){ print $outfh "Annotation: $key\n"; print $outfh $value->as_text,"\n"; $dbhash_ref = $value->hash_tree; for $dbKey (keys %{$dbhash_ref}) { print $outfh $dbKey,":",$dbhash_ref->{$dbKey},"\n"; #none of these prints produce GO terms } } } } } ......................... My program searches an indexed database on my machine, creates the objects, and prints out relevant annotations. Here are some of the accessions I used for testing: P19351 TNNT_DROME P36188 TNNI_DROME P11147 HSP7D_DROME .......................................... the relevant output looks something like this (for debugging) for P19351: ...................................................................... Direct database link to X58188 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: X58188 optional_id: CAA41171.1 Annotation: dblink Direct database link to X59376 in database EMBL database: EMBL comment: -; mRNA. primary_id: X59376 optional_id: CAA42020.1 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48802.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48803.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48804.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48805.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAN09458.1 Annotation: dblink Direct database link to AY122145 in database EMBL database: EMBL comment: -; mRNA. primary_id: AY122145 optional_id: AAM52657.1 Annotation: dblink Direct database link to A40547 in database PIR database: PIR primary_id: A40547 optional_id: A40547 Annotation: dblink Direct database link to B38594 in database PIR database: PIR primary_id: B38594 optional_id: B38594 Annotation: dblink Direct database link to Dm.1717 in database UniGene database: UniGene primary_id: Dm.1717 optional_id: - Annotation: dblink Direct database link to P45379 in database HSSP database: HSSP primary_id: P45379 optional_id: 1J1E Annotation: dblink Direct database link to P36188 in database IntAct database: IntAct primary_id: P36188 optional_id: - Annotation: dblink Direct database link to dme:CG7178-PA in database KEGG database: KEGG primary_id: dme:CG7178-PA optional_id: - Annotation: dblink Direct database link to dme:CG7178-PB in database KEGG database: KEGG primary_id: dme:CG7178-PB optional_id: - Annotation: dblink Direct database link to dme:CG7178-PC in database KEGG database: KEGG primary_id: dme:CG7178-PC optional_id: - Annotation: dblink Direct database link to dme:CG7178-PD in database KEGG database: KEGG primary_id: dme:CG7178-PD optional_id: - Annotation: dblink Direct database link to dme:CG7178-PG in database KEGG database: KEGG primary_id: dme:CG7178-PG optional_id: - Annotation: dblink Direct database link to FBgn0004028 in database FlyBase database: FlyBase primary_id: FBgn0004028 optional_id: wupA Annotation: dblink Direct database link to IPR001978 in database InterPro database: InterPro primary_id: IPR001978 optional_id: Troponin Annotation: dblink Direct database link to PF00992 in database Pfam database: Pfam comment: 1 primary_id: PF00992 optional_id: Troponin .............................................. as you can see, no GO terms above ...................................................... Vs. the actual content of the flat file from for the dblinks from P19351: DR EMBL; X54504; CAA38366.1; -; mRNA. DR EMBL; AY439172; AAR24583.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24584.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24585.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24586.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24587.1; -; Genomic_DNA. DR EMBL; AY665838; AAU09446.1; -; mRNA. DR EMBL; AE014298; AAF48288.2; -; Genomic_DNA. DR EMBL; AE014298; AAF48289.2; -; Genomic_DNA. DR EMBL; AE014298; AAF48290.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52491.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52492.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52493.1; -; Genomic_DNA. DR EMBL; AY051989; AAK93413.1; -; mRNA. DR EMBL; AY070875; AAL48497.1; ALT_SEQ; mRNA. DR PIR; S13251; S13251. DR UniGene; Dm.20472; -. DR HSSP; P45379; 1J1E. DR Ensembl; CG7107; Drosophila melanogaster. DR KEGG; dme:CG7107-PE; -. DR KEGG; dme:CG7107-PF; -. DR KEGG; dme:CG7107-PG; -. DR FlyBase; FBgn0004169; up. DR GO; GO:0007498; P:mesoderm development; IEP:FlyBase. ...... where the GO term is last entry in dblink section above. Any help you could provide would be most welcome. Let me know if this is insufficient information or if you need a working script. Juan Cristobal Vera Graduate Student Department of Biology Penn State University 208 Mueller Laboratory University Park, PA 16802 (814)863-2957 From s.bulashevska at dkfz-heidelberg.de Wed Nov 22 06:20:32 2006 From: s.bulashevska at dkfz-heidelberg.de (Svetlana Bulashevska) Date: Wed, 22 Nov 2006 12:20:32 +0100 Subject: [Bioperl-l] a question on gene retrieval Message-ID: <45643280.3000001@dkfz.de> Dear Sirs, I am very new to bioperl and I would highly appreciate if you could advise me on the following. I have the locations of the sequences (like chr5|-1|102826728|102828399) in the human genome and I would like to retrieve what known genes lay in the close proximity to the sequences (they can also overlap with the sequence). What bioperl modules and classes should I use? Thank you very much, Svetlana Bulashevska. From bosborne11 at verizon.net Wed Nov 22 09:04:35 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 22 Nov 2006 09:04:35 -0500 Subject: [Bioperl-l] a question on gene retrieval In-Reply-To: <45643280.3000001@dkfz.de> Message-ID: Svetlana, There's a page discussing these sorts of questions at the Bioperl Wiki: http://www.bioperl.org/wiki/Getting_Genomic_Sequences It sounds like you just want to compare pairs of coordinates initially, not retrieve sequence, yes? Brian O. On 11/22/06 6:20 AM, "Svetlana Bulashevska" wrote: > Dear Sirs, > I am very new to bioperl and I would highly appreciate if you could > advise me on the following. > I have the locations of the sequences (like chr5|-1|102826728|102828399) > in the human genome > and I would like to retrieve what known genes lay in the close proximity > to the sequences (they can also overlap with the sequence). What bioperl > modules and classes should I use? > Thank you very much, > Svetlana Bulashevska. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Wed Nov 22 11:50:07 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Wed, 22 Nov 2006 11:50:07 -0500 Subject: [Bioperl-l] a question on gene retrieval In-Reply-To: <45643280.3000001@dkfz.de> Message-ID: <18C407FD4FFB424292D769FBD68C1987018123A1@NIHCESMLBX8.nih.gov> You can use LWP to retrieve the following URL http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=5&maps=genes [102826728:104828399]-r&cmd=txt and then parse the HTML. Good luck! Wenwu Cui -----Original Message----- From: Svetlana Bulashevska [mailto:s.bulashevska at dkfz-heidelberg.de] Sent: Wednesday, November 22, 2006 6:21 AM To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] a question on gene retrieval Dear Sirs, I am very new to bioperl and I would highly appreciate if you could advise me on the following. I have the locations of the sequences (like chr5|-1|102826728|102828399) in the human genome and I would like to retrieve what known genes lay in the close proximity to the sequences (they can also overlap with the sequence). What bioperl modules and classes should I use? Thank you very much, Svetlana Bulashevska. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cain at cshl.edu Wed Nov 22 14:09:13 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 14:09:13 -0500 (EST) Subject: [Bioperl-l] Unable to build Module::Build on CentOS Message-ID: Hello, I don't want to throw too much fuel on the Module::Build fire, but I have just discovered that I can't get Module::Build to install on CentOS 4.4. It appears that the developers of MB are aware of the problem, but the currently release ---------------------------------------------------------------------- Scott Cain, Ph. D. cain at cshl.org GMOD Coordinator, http://www.gmod.org/ (216)392-3087 ---------------------------------------------------------------------- From cain at cshl.edu Wed Nov 22 14:59:53 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 14:59:53 -0500 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: References: Message-ID: <1164225594.2639.2.camel@localhost.localdomain> Whoops! That was a half composed message that I thought I canceled. \me blushes Oh well, I was going to write a short note to indicate that in fact, I could not get Module::Build to pass tests on CentOS 4.4 and the authors appear to be aware of the problem, but I have no idea if it is likely to be fixed any time soon. So, if anyone wants to install BioPerl 1.5.2 on any CentOS boxes, they have to force install Module::Build. :-/ Scott On Wed, 2006-11-22 at 14:09 -0500, Scott Cain wrote: > Hello, > > I don't want to throw too much fuel on the Module::Build fire, but I have > just discovered that I can't get Module::Build to install on CentOS 4.4. > It appears that the developers of MB are aware of the problem, but the > currently release > > ---------------------------------------------------------------------- > Scott Cain, Ph. D. cain at cshl.org > GMOD Coordinator, http://www.gmod.org/ (216)392-3087 > ---------------------------------------------------------------------- > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From cain at cshl.edu Wed Nov 22 15:04:25 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 15:04:25 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows Message-ID: <1164225865.2639.8.camel@localhost.localdomain> Hello, I just wanted to mention that I made a few minor changes to Build.PL so that I could get `perl Build.PL` to complete successfully. I am using ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't present either. The main thing I did was to have the BioDBGFF test subroutine quit without asking any questions if Build.PL detected that it was running on Windows. There may be a more elegant way of fixing the problem, but I just wanted it to work (as I am also working a release candidate of GBrowse that depends on the release candidate of bioperl). Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From bix at sendu.me.uk Wed Nov 22 18:16:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 22 Nov 2006 23:16:10 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <1164225594.2639.2.camel@localhost.localdomain> References: <1164225594.2639.2.camel@localhost.localdomain> Message-ID: <4564DA3A.1000601@sendu.me.uk> Scott Cain wrote: > Whoops! That was a half composed message that I thought I canceled. > > \me blushes > > Oh well, I was going to write a short note to indicate that in fact, I > could not get Module::Build to pass tests on CentOS 4.4 and the authors > appear to be aware of the problem, but I have no idea if it is likely to > be fixed any time soon. So, if anyone wants to install BioPerl 1.5.2 on > any CentOS boxes, they have to force install Module::Build. :-/ Thanks for the info. 1.5.2 will come with the old ExtUtils::MakeMaker-based Makefile.PL so it should still be possible to install without a force. From bix at sendu.me.uk Wed Nov 22 18:30:07 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 22 Nov 2006 23:30:07 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164225865.2639.8.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> Message-ID: <4564DD7F.8090301@sendu.me.uk> Scott Cain wrote: > Hello, > > I just wanted to mention that I made a few minor changes to Build.PL so > that I could get `perl Build.PL` to complete successfully. I am using > ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > present either. The main thing I did was to have the BioDBGFF test > subroutine quit without asking any questions if Build.PL detected that > it was running on Windows. Is it completely impossible for it to pass under Windows? I find that quite a shame! I'm surprised it was necessary to make your changes, because it already had to return true from: DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0}) Can Windows pass that test without DBD::mysql installed, and having passed it why does it then fail the actual BioDBSeqFeature_mysql.t script? The cleanest way to do your change would be to make some change to the test_db() sub, eg: sub test_db { eval {require DBI;}; if ($^O =~ /mswin/i) { return "Windows isn't supported"; } unless (DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0})) { return "Could not connect to test database"; } return; } From cjfields at uiuc.edu Wed Nov 22 22:32:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 22 Nov 2006 21:32:34 -0600 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <4564DD7F.8090301@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> Message-ID: On Nov 22, 2006, at 5:30 PM, Sendu Bala wrote: > Scott Cain wrote: >> Hello, >> >> I just wanted to mention that I made a few minor changes to >> Build.PL so >> that I could get `perl Build.PL` to complete successfully. I am >> using >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't >> present either. The main thing I did was to have the BioDBGFF test >> subroutine quit without asking any questions if Build.PL detected >> that >> it was running on Windows. > > Is it completely impossible for it to pass under Windows? I find that > quite a shame! > > I'm surprised it was necessary to make your changes, because it > already > had to return true from: > > DBI->connect('dbi:mysql:test',undef,undef, > {RaiseError=>0,PrintError=>0}) > > Can Windows pass that test without DBD::mysql installed, and having > passed it why does it then fail the actual BioDBSeqFeature_mysql.t > script? I think he means the BioDBGFF.t tests, not BioDBSeqFeature_mysql.t. Myself, I can't get the Build script to detect my local MySQL on WinXP, though the BioDBGFF.t tests passed. I haven't been back to work since last Friday so I can't run updated WinXP tests myself. ... chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From roy at colibase.bham.ac.uk Tue Nov 21 13:51:30 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Tue, 21 Nov 2006 18:51:30 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <45634AB2.1020701@colibase.bham.ac.uk> > I'd like to propose changing the default reply-to for posts on this list > from the current 'reply to the poster' to 'reply to the mailing list'. > That way people can just hit 'reply' instead of 'reply to all' in order > to get a reply back to the list. We did this on our mailing list, and found it to be problematic if the messages still appear to come from an individual rather than the list- people may not realise they are replying to the whole list. This can lead to all sorts of issues- my boss and a collaborator once had a discussion (fortunately nothing too sensitive) that was accidentally copied to everyone in their field. The alternative is to overwrite the from: field as well as reply-to:, but then you rely on people having suitably informative signatures should anyone want to contact them off-list, and it makes the archives less useful. See also this: http://www.unicom.com/pw/reply-to-harmful.html Maybe you could tag a reminder to reply-all on every list message? Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From torsten.seemann at infotech.monash.edu.au Wed Nov 22 21:09:42 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Thu, 23 Nov 2006 13:09:42 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: References: Message-ID: <456502E6.8030409@infotech.monash.edu.au> > I don't want to throw too much fuel on the Module::Build fire, but I have > just discovered that I can't get Module::Build to install on CentOS 4.4. I concur with this problem :-( Most of the errors seem to be due to the large number of environmental variables I have set: "Couldn't run Build.PL: Argument list too long at /root/.cpan/build/Module-Build-0.2805/blib/lib/Module/Build/Compat.pm line 200." I had to "force install" the latest Module::Build to get bioperl-live tested and installed via Build.PL. -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From bix at sendu.me.uk Thu Nov 23 02:44:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 07:44:16 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <456502E6.8030409@infotech.monash.edu.au> References: <456502E6.8030409@infotech.monash.edu.au> Message-ID: <45655150.7090300@sendu.me.uk> Torsten Seemann wrote: >> I don't want to throw too much fuel on the Module::Build fire, but I have >> just discovered that I can't get Module::Build to install on CentOS 4.4. > > I concur with this problem :-( > > Most of the errors seem to be due to the large number of environmental > variables I have set: > > "Couldn't run Build.PL: Argument list too long at > /root/.cpan/build/Module-Build-0.2805/blib/lib/Module/Build/Compat.pm > line 200." > > I had to "force install" the latest Module::Build to get bioperl-live > tested and installed via Build.PL. Did everything with the Bioperl Build.PL script work fine after that? From bix at sendu.me.uk Thu Nov 23 05:48:05 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 10:48:05 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <4564DD7F.8090301@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> Message-ID: <45657C65.50200@sendu.me.uk> Sendu Bala wrote: > Scott Cain wrote: >> Hello, >> >> I just wanted to mention that I made a few minor changes to Build.PL so >> that I could get `perl Build.PL` to complete successfully. I am using >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't >> present either. The main thing I did was to have the BioDBGFF test >> subroutine quit without asking any questions if Build.PL detected that >> it was running on Windows. > > Is it completely impossible for it to pass under Windows? I find that > quite a shame! > > I'm surprised it was necessary to make your changes, because it already > had to return true from: [snip] Sorry, that all made no sense because I didn't pay attention to what changes you actually made. Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if being on mswin still causes a problem, or can the excludes_os restriction on line 78 of Build.PL be lifted now? Cheers, Sendu. From Squig at web.de Thu Nov 23 05:46:30 2006 From: Squig at web.de (Squig at web.de) Date: Thu, 23 Nov 2006 11:46:30 +0100 Subject: [Bioperl-l] Bioperl-ext and Staden Package Message-ID: <914558313@web.de> Hello, I have a short question concerning bioperl-ext and the io_lib from the staden package. Are there plans to fix bioperl-ext so it could be used with the actual version of io_lib (at the moment 1.10.1)? Myself has no experience in evoking externally written c - code from perl. But I think the changes to the io_lib - api are very well documented so a fix shouldn't be to hard for somebody with experience in this field. Please correct me if I'm totally wrong. Here you find the changes, you have to scroll a little bit down to "Changes". https://sourceforge.net/project/shownotes.php?release_id=340318&group_id=100316 If you think I could give a helping hand, please let me know. With kind regards, Stefan _______________________________________________________________________ Viren-Scan f?r Ihren PC! Jetzt f?r jeden. Sofort, online und kostenlos. Gleich testen! http://www.pc-sicherheit.web.de/freescan/?mc=022222 From cjfields at uiuc.edu Thu Nov 23 09:12:20 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 08:12:20 -0600 Subject: [Bioperl-l] Bioperl-ext and Staden Package In-Reply-To: <914558313@web.de> References: <914558313@web.de> Message-ID: On Nov 23, 2006, at 4:46 AM, Squig at web.de wrote: > Hello, > > I have a short question concerning bioperl-ext and the io_lib from > the staden package. > > Are there plans to fix bioperl-ext so it could be used with the > actual version of io_lib (at the moment 1.10.1)? This is one of the things tentatively planned but there have been no volunteers for it. > Myself has no experience in evoking externally written c - code > from perl. But I think the changes to the io_lib - api are very > well documented so a fix shouldn't be to hard for somebody with > experience in this field. Please correct me if I'm totally wrong. > > Here you find the changes, you have to scroll a little bit down to > "Changes". > https://sourceforge.net/project/shownotes.php? > release_id=340318&group_id=100316 > > If you think I could give a helping hand, please let me know. > > > With kind regards, > > Stefan > Any help would be greatly appreciated! There are tests included with bioperl-ext which you can add to or modify if needed. You can post patches for any changed code to bugzilla. Here's a HOWTO: http://www.bioperl.org/wiki/HOWTO:SubmitPatch Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sdavis2 at mail.nih.gov Thu Nov 23 10:43:37 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu, 23 Nov 2006 10:43:37 -0500 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45634AB2.1020701@colibase.bham.ac.uk> References: <45633B4A.6060804@sendu.me.uk> <45634AB2.1020701@colibase.bham.ac.uk> Message-ID: <4565C1A9.4080605@mail.nih.gov> Roy Chaudhuri wrote: >> I'd like to propose changing the default reply-to for posts on this list >> from the current 'reply to the poster' to 'reply to the mailing list'. >> That way people can just hit 'reply' instead of 'reply to all' in order >> to get a reply back to the list. >> > > We did this on our mailing list, and found it to be problematic if the > messages still appear to come from an individual rather than the list- > people may not realise they are replying to the whole list. This can > lead to all sorts of issues- my boss and a collaborator once had a > discussion (fortunately nothing too sensitive) that was accidentally > copied to everyone in their field. The alternative is to overwrite the > from: field as well as reply-to:, but then you rely on people having > suitably informative signatures should anyone want to contact them > off-list, and it makes the archives less useful. > > See also this: > http://www.unicom.com/pw/reply-to-harmful.html > I tend to agree here. I have seen some pretty significant accidents due to this feature. I think less harm is done by simply putting the thread back on list, if appropriate, if the sender happens to send to the original sender and not the entire list. Sean From bix at sendu.me.uk Thu Nov 23 16:18:01 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 21:18:01 +0000 Subject: [Bioperl-l] Please do not commit without testing Message-ID: <45661009.8040303@sendu.me.uk> Developers, Please do not commit changes without testing the test suite first, especially to branches! Note that: perl -I. -w t/test.t is NOT a good enough test, especially for test scripts that still use Test and not Test::More. (The above doesn't capture an incorrect number of tests in the plan.) Always initially do: ./Build test --test_files t/test.t --verbose Then run the entire test suite: ./Build test Thank you, Sendu. From The_Polymorph at rocketmail.com Thu Nov 23 16:30:42 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 23 Nov 2006 13:30:42 -0800 (PST) Subject: [Bioperl-l] Bioperl install question. Message-ID: <541373.13923.qm@web50815.mail.yahoo.com> Hi all. My set-up: WinXP (SP2) ActiveState Perl 5.8.8 I used the perl package manager to download BioPerl 1.2.3 but since that is rather old, I downloaded BioPerl-1.4.zip. Can anyone help me from this point? Where should I unzip the file to? Thanks, ~Katie ____________________________________________________________________________________ Want to start your own business? Learn how on Yahoo! Small Business. http://smallbusiness.yahoo.com/r-index From cjfields at uiuc.edu Thu Nov 23 16:43:30 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 15:43:30 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661009.8040303@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> Message-ID: On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: > Developers, > > Please do not commit changes without testing the test suite first, > especially to branches! > > Note that: > > perl -I. -w t/test.t > > is NOT a good enough test, especially for test scripts that still use > Test and not Test::More. (The above doesn't capture an incorrect > number > of tests in the plan.) > > Always initially do: > > ./Build test --test_files t/test.t --verbose > > Then run the entire test suite: > > ./Build test My bad. As a lousy excuse I have been extremely busy with family this holiday. However, the various changes using Module::Build need to be well-documented both in CVS docs and on the wiki. Your latter example ('./Build test --test_files t/test.t --verbose') is nowhere to be found. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 23 17:07:06 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 22:07:06 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> Message-ID: <45661B8A.9060405@sendu.me.uk> Chris Fields wrote: > > On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: > >> Developers, >> >> Please do not commit changes without testing the test suite first, >> especially to branches! >> >> Note that: >> >> perl -I. -w t/test.t >> >> is NOT a good enough test, especially for test scripts that still use >> Test and not Test::More. (The above doesn't capture an incorrect number >> of tests in the plan.) >> >> Always initially do: >> >> ./Build test --test_files t/test.t --verbose >> >> Then run the entire test suite: >> >> ./Build test [snip] > However, the various changes using Module::Build need to be > well-documented both in CVS docs and on the wiki. Your latter example > ('./Build test --test_files t/test.t --verbose') is nowhere to be found. I posted to the list about it on the 17th in thread 'Testing with Build.PL'. Where would you suggest a good place on the wiki would be to mention something like that? From cjfields at uiuc.edu Thu Nov 23 17:23:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 16:23:12 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> On Nov 23, 2006, at 4:07 PM, Sendu Bala wrote: > Chris Fields wrote: >> ... > [snip] >> However, the various changes using Module::Build need to be well- >> documented both in CVS docs and on the wiki. Your latter example >> ('./Build test --test_files t/test.t --verbose') is nowhere to be >> found. > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would > be to mention something like that? The mail list isn't the best place to document this; very few people (including developers) will take the time to go back digging through old posts except as a last resort. Hence these need to be well- documented AND easily accessible. Relevant changes need to be made everywhere that testing or using make/nmake is mentioned in CVS or the wiki. For the testing case I raised, maybe adding something to the various INSTALL docs and the FAQ would be a good start. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 23 17:36:47 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 22:36:47 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> Message-ID: <4566227F.4060102@sendu.me.uk> Chris Fields wrote: > On Nov 23, 2006, at 4:07 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> ... >> [snip] >>> However, the various changes using Module::Build need to be >>> well-documented both in CVS docs and on the wiki. Your latter >>> example ('./Build test --test_files t/test.t --verbose') is nowhere >>> to be found. >> >> I posted to the list about it on the 17th in thread 'Testing with >> Build.PL'. Where would you suggest a good place on the wiki would be >> to mention something like that? > > The mail list isn't the best place to document this; very few people > (including developers) will take the time to go back digging through old > posts except as a last resort. Hence these need to be well-documented > AND easily accessible. Relevant changes need to be made everywhere that > testing or using make/nmake is mentioned in CVS or the wiki. For the > testing case I raised, maybe adding something to the various INSTALL > docs and the FAQ would be a good start. It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's also on the wiki version of same.) I'm not sure that a developer would think to look in the installation documentation for that kind of information, so I've added the info to http://www.bioperl.org/wiki/Bioperl_Best_Practices#Testing as well. From n.haigh at sheffield.ac.uk Thu Nov 23 17:39:17 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 23 Nov 2006 22:39:17 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <45662315.5090600@sheffield.ac.uk> Sendu Bala wrote: > Chris Fields wrote: > >> On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: >> >> >>> Developers, >>> >>> Please do not commit changes without testing the test suite first, >>> especially to branches! >>> >>> Note that: >>> >>> perl -I. -w t/test.t >>> >>> is NOT a good enough test, especially for test scripts that still use >>> Test and not Test::More. (The above doesn't capture an incorrect number >>> of tests in the plan.) >>> >>> Always initially do: >>> >>> ./Build test --test_files t/test.t --verbose >>> >>> Then run the entire test suite: >>> >>> ./Build test >>> > [snip] > >> However, the various changes using Module::Build need to be >> well-documented both in CVS docs and on the wiki. Your latter example >> ('./Build test --test_files t/test.t --verbose') is nowhere to be found. >> > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would be to > mention something like that? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > I'd possibly put it somewhere like: http://www.bioperl.org/wiki/Developer_Information If there's enough stuff to create a new page? If so, how about a page called "testing" or "test suite" or "running tests"?? Just ensure it's given the "Developer resources" Category to make it that bit easier to locate. Nath From n.haigh at sheffield.ac.uk Thu Nov 23 17:31:58 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 23 Nov 2006 22:31:58 +0000 Subject: [Bioperl-l] Bioperl install question. In-Reply-To: <541373.13923.qm@web50815.mail.yahoo.com> References: <541373.13923.qm@web50815.mail.yahoo.com> Message-ID: <4566215E.9090409@sheffield.ac.uk> Caitlin wrote: > Hi all. > > My set-up: > > WinXP (SP2) > ActiveState Perl 5.8.8 > > > I used the perl package manager to download BioPerl 1.2.3 but since > that is rather old, I downloaded BioPerl-1.4.zip. Can anyone help me > from this point? Where should I unzip the file to? > > Thanks, > > ~Katie > > > Hi Katie, First of all try installing Bioperl 1.5.2 RC2 by following the installation instructions for windows at: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows#Installation_Guide See how you get on with that and let us know if you have troubles, or indeed if you manage to install successfully! Thanks Nathan From bix at sendu.me.uk Thu Nov 23 18:31:59 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 23:31:59 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45662909.3010101@infotech.monash.edu.au> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> <45662909.3010101@infotech.monash.edu.au> Message-ID: <45662F6F.2090700@sendu.me.uk> Torsten Seemann wrote: >>> I had to "force install" the latest Module::Build to get bioperl-live >>> tested and installed via Build.PL. >> >> Did everything with the Bioperl Build.PL script work fine after that? > > Yes. > > However it was much "slower" to install, it initially pauses for a long > time, then eventually does the install. I'm guessing you're describing the period of time that it manifies the documentation? Don't you see lots of output detailing what is going on at each moment in time? From torsten.seemann at infotech.monash.edu.au Thu Nov 23 18:50:30 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 24 Nov 2006 10:50:30 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45662F6F.2090700@sendu.me.uk> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> <45662909.3010101@infotech.monash.edu.au> <45662F6F.2090700@sendu.me.uk> Message-ID: <456633C6.5080109@infotech.monash.edu.au> >>>> I had to "force install" the latest Module::Build to get >>>> bioperl-live tested and installed via Build.PL. >>> >>> Did everything with the Bioperl Build.PL script work fine after that? >> >> Yes. >> >> However it was much "slower" to install, it initially pauses for a >> long time, then eventually does the install. > > I'm guessing you're describing the period of time that it manifies the > documentation? Don't you see lots of output detailing what is going on > at each moment in time? Yes I see all the usual output. The pause is between the following two events:. ... ... Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 . # (no output for 15+ seconds on unloaded server) . Installing /usr/share/man/man1/bp_chaos_plot.pl.1" ... ... -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From torsten.seemann at infotech.monash.edu.au Thu Nov 23 18:04:41 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 24 Nov 2006 10:04:41 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45655150.7090300@sendu.me.uk> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> Message-ID: <45662909.3010101@infotech.monash.edu.au> >> I had to "force install" the latest Module::Build to get bioperl-live >> tested and installed via Build.PL. > > Did everything with the Bioperl Build.PL script work fine after that? Yes. However it was much "slower" to install, it initially pauses for a long time, then eventually does the install. -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From cjfields at uiuc.edu Thu Nov 23 23:04:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 22:04:58 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <4566227F.4060102@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> Message-ID: On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: ... > It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's > also on the wiki version of same.) Okay, but I find the Windows page hasn't been updated (still shows nmake). Everything needs to be changed, not just the UNIX pages > I'm not sure that a developer would think to look in the installation > documentation for that kind of information, so I've added the info to > http://www.bioperl.org/wiki/Bioperl_Best_Practices#Testing as well. Sounds good. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 23 23:09:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 22:09:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45662315.5090600@sheffield.ac.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45662315.5090600@sheffield.ac.uk> Message-ID: On Nov 23, 2006, at 4:39 PM, Nathan S. Haigh wrote: > Sendu Bala wrote: >> >> I posted to the list about it on the 17th in thread 'Testing with >> Build.PL'. Where would you suggest a good place on the wiki would >> be to >> mention something like that? >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > I'd possibly put it somewhere like: > http://www.bioperl.org/wiki/Developer_Information > > If there's enough stuff to create a new page? If so, how about a page > called "testing" or "test suite" or "running tests"?? > > Just ensure it's given the "Developer resources" Category to make it > that bit easier to locate. > > Nath ... I think we need to gear some docs not just towards users but also towards potential developers, so maybe a HOWTO for writing and running tests might be the best way to go. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From The_Polymorph at rocketmail.com Thu Nov 23 23:29:18 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 23 Nov 2006 20:29:18 -0800 (PST) Subject: [Bioperl-l] BioPerl install question (update). Message-ID: <20061124042918.5392.qmail@web50801.mail.yahoo.com> Hi all. Ok. I upgraded my ActiveState perl install from build 817 to build 819 and followed the directions located at the site below to install BioPerl 1.5.2 RC2: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Thanks for the help Nathan! ~Katie ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited From bix at sendu.me.uk Fri Nov 24 02:54:19 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 07:54:19 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> Message-ID: <4566A52B.80304@sendu.me.uk> Chris Fields wrote: > On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: > ... > >> It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's >> also on the wiki version of same.) > > Okay, but I find the Windows page hasn't been updated (still shows > nmake). Everything needs to be changed, not just the UNIX pages I don't know what to say for the windows docs. I can't even get perl -V to work on my Windows machine: &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. The Build.PL scripts fails similarly: &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. Can't locate the perl binary used to run this script in (C:\Perl\bin C:\Perl\bin C:\Perl\bin . C:\Program Files\ActiveState Komodo 3.5 C:\Perl\bin C:\WINDOWS\sy stem32 C:\WINDOWS C:\WINDOWS\System32\Wbem C:\Program Files\ATI Technologies\ATI .ACE) I took it that you had no problems? Should I just make the Windows docs similar to the Unix ones? (Or can you do the appropriate update?) From bix at sendu.me.uk Fri Nov 24 03:56:15 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 08:56:15 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 Message-ID: <4566B3AF.2050305@sendu.me.uk> Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. See http://www.bioperl.org/wiki/Release_1.5.2 for instructions on getting and testing this RC. Everyone: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into. Please try the new Build.PL installation script and report back how you get on. Also try installing using CPAN. Your CPAN mirrors may not be current enough, so you may have delete all entries in your urllist first. Developers: Please experiment with installation, especially via CPAN. If you already have all/most prerequisite external modules installed, try uninstalling some and report how effective the system is at reinstalling them for you. RC5 may form the final release for some of the packages (probably all except for bioperl-run), so any further commits made, even to branch-1-5-2, may not make final release. If you think you've committed an important bug fix that should be part of final release, let me know. Thank you, Sendu. PS. What happened to RC4? I didn't announce it, but it was available on CPAN where I did some testing on it. From n.haigh at sheffield.ac.uk Fri Nov 24 04:35:01 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Fri, 24 Nov 2006 09:35:01 +0000 Subject: [Bioperl-l] Bioperl install question. In-Reply-To: <20061124012953.66815.qmail@web50812.mail.yahoo.com> References: <20061124012953.66815.qmail@web50812.mail.yahoo.com> Message-ID: <4566BCC5.7050003@sheffield.ac.uk> Caitlin wrote: > Hi Nathan, > > Thanks for the quick reply. I wasn't able to locate a Perl Package > Manager GUI from the Start menu. The only options displayed are: > > Documentation > OLE Browser > Perl Package Manager > > Clicking on 'Perl Package Manager' loads ppm in a console window (i.e. > non-GUI environment). Should I re-install ActivePerl? If so, that would > eliminate my installed modules wouldn't it? > > Thanks, > > ~Katie > > It sounds like you probably have a version of ActivePerl < 5.8.8.819. If this is the case, download and install the latest ActivePerl version >= 5.8.8.819. If you do a reinstall into the same location as your current ActivePerl installation you will probably maintain all the currently installed modules - but I can't say for definate. Once you have ActivePerl >= 5.8.8.819 installed, you should be able to follow the instructions in the link I provided previously. Nath From n.haigh at sheffield.ac.uk Fri Nov 24 04:38:54 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Fri, 24 Nov 2006 09:38:54 +0000 Subject: [Bioperl-l] BioPerl install question (update). In-Reply-To: <20061124042918.5392.qmail@web50801.mail.yahoo.com> References: <20061124042918.5392.qmail@web50801.mail.yahoo.com> Message-ID: <4566BDAE.50105@sheffield.ac.uk> Caitlin wrote: > Hi all. > > Ok. I upgraded my ActiveState perl install from build 817 to build 819 > and followed the directions located at the site below to install > BioPerl 1.5.2 RC2: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Thanks for the help Nathan! > > ~Katie > > Ah - have just sent an e-mail to say update to build 819! We should be releasing the proper 1.5.2 release quite soon (hopefully in a week or two) At that stage, you should update the bioperl package. It nice to hear it when things work! Nath From cjfields at uiuc.edu Fri Nov 24 07:15:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 24 Nov 2006 06:15:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <4566A52B.80304@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> <4566A52B.80304@sendu.me.uk> Message-ID: On Nov 24, 2006, at 1:54 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: >> ... >>> It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. >>> (It's >>> also on the wiki version of same.) >> Okay, but I find the Windows page hasn't been updated (still shows >> nmake). Everything needs to be changed, not just the UNIX pages > > I don't know what to say for the windows docs. I can't even get > > perl -V > > to work on my Windows machine: > > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > > The Build.PL scripts fails similarly: > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > Can't locate the perl binary used to run this script in (C:\Perl > \bin C:\Perl\bin > C:\Perl\bin . C:\Program Files\ActiveState Komodo 3.5 C:\Perl\bin > C:\WINDOWS\sy > stem32 C:\WINDOWS C:\WINDOWS\System32\Wbem C:\Program Files\ATI > Technologies\ATI > .ACE) > > I took it that you had no problems? Should I just make the Windows > docs similar to the Unix ones? (Or can you do the appropriate update?) No, everything worked on my machine. I'll try making the necessary changes as soon as I can, but it won't be today. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Fri Nov 24 16:38:07 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 16:38:07 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: Is it possible to add a file to the repository (at least temporarily) called README.Build or something that would contain those examples? I find myself saving your emails which I don't think is the most efficient way for me to have those bits handy when I'll need them. -hilmar On Nov 23, 2006, at 5:07 PM, Sendu Bala wrote: > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would > be to > mention something like that? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Fri Nov 24 17:08:37 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 22:08:37 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <45676D65.6000409@sendu.me.uk> Hilmar Lapp wrote: > Is it possible to add a file to the repository (at least temporarily) > called README.Build or something that would contain those examples? > > I find myself saving your emails which I don't think is the most > efficient way for me to have those bits handy when I'll need them. Given that Makefile.PL is just a stub that prints a message about Build.PL, I can just extend the message to include more tips? From hlapp at gmx.net Fri Nov 24 17:27:43 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 17:27:43 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45676D65.6000409@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> Message-ID: On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: > Hilmar Lapp wrote: >> Is it possible to add a file to the repository (at least temporarily) >> called README.Build or something that would contain those examples? >> >> I find myself saving your emails which I don't think is the most >> efficient way for me to have those bits handy when I'll need them. > > Given that Makefile.PL is just a stub that prints a message about > Build.PL, I can just extend the message to include more tips? You could but that wouldn't substitute. Typing ./Build instead of make is not too hard of a change to make; however, you don't want me to go back and run perl Makefile.PL to get a quick refresher every time I want to use a more advanced feature of the generated Build file, do you? -hilmar > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Fri Nov 24 17:46:49 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 22:46:49 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> Message-ID: <45677659.404@sendu.me.uk> Hilmar Lapp wrote: > > On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: > >> Hilmar Lapp wrote: >>> Is it possible to add a file to the repository (at least temporarily) >>> called README.Build or something that would contain those examples? >>> >>> I find myself saving your emails which I don't think is the most >>> efficient way for me to have those bits handy when I'll need them. >> >> Given that Makefile.PL is just a stub that prints a message about >> Build.PL, I can just extend the message to include more tips? > > You could but that wouldn't substitute. Typing ./Build instead of make > is not too hard of a change to make; however, you don't want me to go > back and run perl Makefile.PL to get a quick refresher every time I want > to use a more advanced feature of the generated Build file, do you? If you can remember at least that it is ./Build you need to do something with, it has lovely in-built help. It's entirely standard stuff so nothing to learn - just remember its there! > ./Build -h No action '-h' defined, try running the 'help' action. ./Build help ./Build help test From hlapp at gmx.net Fri Nov 24 19:08:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 19:08:18 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45677659.404@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> <45677659.404@sendu.me.uk> Message-ID: <965EC1D8-AC7D-491A-BCFE-82776D724161@gmx.net> On Nov 24, 2006, at 5:46 PM, Sendu Bala wrote: > If you can remember at least that it is ./Build you need to do > something > with, it has lovely in-built help. It's entirely standard stuff so > nothing to learn - just remember its there! > >> ./Build -h > No action '-h' defined, try running the 'help' action. > > > > ./Build help > > > > ./Build help test > > Sounds nice & will surely be helpful. I guess what I was trying to say is that you could make the value of the examples you typed up in emails already (including the above) much more lasting by copy&pasting them into a document that's within easy reach of a developer who is losing his/her nerves because somebody from the extended family spilled cranberry sauce across his/her new laptop over Thanksgiving. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Fri Nov 24 19:13:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 24 Nov 2006 18:13:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45677659.404@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> <45677659.404@sendu.me.uk> Message-ID: <9AF9038D-71FD-46AD-A486-5B9472BC29AA@uiuc.edu> On Nov 24, 2006, at 4:46 PM, Sendu Bala wrote: > Hilmar Lapp wrote: >> >> On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: >> >>> Hilmar Lapp wrote: >>>> Is it possible to add a file to the repository (at least >>>> temporarily) >>>> called README.Build or something that would contain those examples? >>>> >>>> I find myself saving your emails which I don't think is the most >>>> efficient way for me to have those bits handy when I'll need them. >>> >>> Given that Makefile.PL is just a stub that prints a message about >>> Build.PL, I can just extend the message to include more tips? >> >> You could but that wouldn't substitute. Typing ./Build instead of >> make >> is not too hard of a change to make; however, you don't want me to go >> back and run perl Makefile.PL to get a quick refresher every time >> I want >> to use a more advanced feature of the generated Build file, do you? > > If you can remember at least that it is ./Build you need to do > something > with, it has lovely in-built help. It's entirely standard stuff so > nothing to learn - just remember its there! > >> ./Build -h > No action '-h' defined, try running the 'help' action. > > > > ./Build help > > > > ./Build help test > > Hilmar's suggestion of collecting these snippets of Build-related commands in a single place seems like a good start, since it doesn't really pertain to installation but is of use for developers and future release pumpkins. As for the help example above, as helpful as it is, I don't think most would know it was even there unless it was pointed out. A few blurbs in the FAQ, maybe in the 'BioPerl in General' or a new developer section, might also help. 'How do I run tests using Module::Build?' or 'Where can I find out more about Module::Build?', for instance. It's also much easier (at least to me) to point out to new users or developers that any relevant information is found in 'document x' vs. 'this post on the mail list, found in the mail archives at this link, just follow the thread...'. chris (still recovering after being dragged out on Black Friday). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Fri Nov 24 18:16:47 2006 From: jason at bioperl.org (Jason Stajich) Date: Fri, 24 Nov 2006 15:16:47 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45635F98.8030901@bms.com> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> Message-ID: <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> Can we just weaken the references with Scalar::Util? This should solve the problem for circular refs. Is Scalar::Util part of the core distro in the min perl we are supporting? I can add this in Bio::Tree::Node and look around to see where else it is a problem. We just need a simple script to verify it is having an effect (i.e. a bug report with this). -jason On Nov 21, 2006, at 12:20 PM, Stefan Kirov wrote: > Hilmar Lapp wrote: >> On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: >> >> >>> I don't know if I should hold up release of 1.5.2 for it. Now that >>> you've >>> reported on it I'm leaning toward yes, since the new Bio::Species >>> implementation is one of the major new features of 1.5.2 and it >>> ought to >>> work well. >>> >> >> I disagree to some extent. This is a developer release, so not >> everything is expected to work perfectly. >> >> What's not desirable is if fixing this required another entire >> redesign of the API, so that every dev release introduces >> different API. >> >> The thing is, you'll really only get trouble reports once you put it >> out and people start using it in anger. Don't expect to make it >> perfect before. >> >> >>> Anyway, for the memory leak I have some ideas I haven't tried yet; I >>> don't know if my efforts will solve the speed issue though. >>> >> >> The memory leak sounds more concerning to me. Under which >> circumstances would it crash a script or blow throuhg all of say >> 1-2GB when it should have taken only a tenth of that. >> >> > As I was saying, I did pass ref to an array in the classification > (wrong > parsing): > push @classification,'sapiens', 'Homo', 'Hominidae', $arrayref; > and my script took 17-18 GB. I am really surprised it stopped getting > more RAM and finished successfully. I did not explore further. > Stefan >> -hilmar >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Sat Nov 25 07:47:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 12:47:28 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> Message-ID: <45683B60.9090402@sendu.me.uk> Jason Stajich wrote: > Can we just weaken the references with Scalar::Util? This should solve > the problem for circular refs. I don't know about Stefan's problem, but I tried weakening refs - it fixed the memory leak I was seeing, but caused other problems. > Is Scalar::Util part of the core distro in the min perl we are supporting? Yes. > I can add this in Bio::Tree::Node and look around to see where else it > is a problem. We just need a simple script to verify it is having an > effect (i.e. a bug report with this). perl -w -MBio::SeqIO -e '$si = new Bio::SeqIO(-file => "5UTR.Pln_nr.dat", -format => "embl"); while ($seq = $si->next_seq) { $seq->id; }' Where 5UTR.Pln_nr.dat is a large embl file with ~50000 sequences. For me this takes ~11mins to parse and ~2GB memory. Once I weakened refs in all the places I could find in Bio::Tree::Node and Bio::Tree::Tree it used a constant 0.3% of memory but still took around 11mins. However lots of the tests in the test suite then fail, because Nodes are often made purely to add into a Tree, with the requirement that the Tree keeps hard refs to them all (else the Tree would fall apart). I think the Tree actually only keeps a ref to its root Node, which means Nodes in general must keep hard refs to their Descendants. With that constraint, I haven't been able to break the deadlock and get these things to clean up. Hopefully I'm missing something obvious; please look into it. From cjfields at uiuc.edu Sat Nov 25 08:32:43 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 25 Nov 2006 07:32:43 -0600 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45683B60.9090402@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> Message-ID: <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: ... > I think the Tree actually only keeps a ref to its root Node, which > means > Nodes in general must keep hard refs to their Descendants. With that > constraint, I haven't been able to break the deadlock and get these > things to clean up. > > Hopefully I'm missing something obvious; please look into it. I'm curious to see if this affects sequence parsing (i.e. SwissProt DB parsing). Does anyone know? It sounds pretty serious. Sendu, could you commit a bug report for this? I don't think this should hold up rel 1.5.2 (it's a dev release) but it would be nice to get it fixed. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Sat Nov 25 08:57:53 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 13:57:53 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> Message-ID: <45684BE1.8010902@sendu.me.uk> Chris Fields wrote: > > On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: > ... > >> I think the Tree actually only keeps a ref to its root Node, which means >> Nodes in general must keep hard refs to their Descendants. With that >> constraint, I haven't been able to break the deadlock and get these >> things to clean up. >> >> Hopefully I'm missing something obvious; please look into it. > > I'm curious to see if this affects sequence parsing (i.e. SwissProt DB > parsing). Does anyone know? It sounds pretty serious. Any time you create lots of Bio::Species objects the memory leak ought to arise. > Sendu, could you commit a bug report for this? I don't think this > should hold up rel 1.5.2 (it's a dev release) but it would be nice to > get it fixed. http://bugzilla.open-bio.org/show_bug.cgi?id=2149 From bix at sendu.me.uk Sat Nov 25 17:08:59 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 22:08:59 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> Message-ID: <4568BEFB.4070201@sendu.me.uk> Jason Stajich wrote: > > The circular ref is from Bio::Species when you have > $self->{tree} = Bio::Tree::Tree->new(-root => $self); > > I added a weaken call in Bio::Species code explicitly -- we can't > generally weaken the ref to the root node in Bio::Tree::Tree as that > breaks some other things as you saw. Thanks. Though there's still the issue with Bio::Tree::Node::node_cleanup not doing anything. > I'm not sure I am digging what you've done with Bio::Tree::Tree. Why > didn't you make a specialized Tree object for Taxonomy stuff so that you > can add methods like lineage_node, etc? http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because it's a Tree function. It goes hand in hand with get_lca(), which was already there. I suppose you're saying it would have been more appropriate to have a new Tree-based object that only differed in its new() instead of adding an option to Tree's new()? My thinking was that both the -node option and get_lineage_nodes() are useful for trees in general, not just Bio::Taxon. From jason at bioperl.org Sat Nov 25 16:20:41 2006 From: jason at bioperl.org (Jason Stajich) Date: Sat, 25 Nov 2006 13:20:41 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45684BE1.8010902@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> Message-ID: The circular ref is from Bio::Species when you have $self->{tree} = Bio::Tree::Tree->new(-root => $self); I added a weaken call in Bio::Species code explicitly -- we can't generally weaken the ref to the root node in Bio::Tree::Tree as that breaks some other things as you saw. I'm not sure I am digging what you've done with Bio::Tree::Tree. Why didn't you make a specialized Tree object for Taxonomy stuff so that you can add methods like lineage_node, etc? We'll talk about it in more detail in Dec I guess to see if we can clean up some of the things here. -jason On Nov 25, 2006, at 5:57 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: >> ... >>> I think the Tree actually only keeps a ref to its root Node, >>> which means >>> Nodes in general must keep hard refs to their Descendants. With that >>> constraint, I haven't been able to break the deadlock and get these >>> things to clean up. >>> >>> Hopefully I'm missing something obvious; please look into it. >> I'm curious to see if this affects sequence parsing (i.e. >> SwissProt DB parsing). Does anyone know? It sounds pretty serious. > > Any time you create lots of Bio::Species objects the memory leak > ought to arise. > > >> Sendu, could you commit a bug report for this? I don't think this >> should hold up rel 1.5.2 (it's a dev release) but it would be nice >> to get it fixed. > > http://bugzilla.open-bio.org/show_bug.cgi?id=2149 -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From biology0046 at hotmail.com Sun Nov 26 08:19:45 2006 From: biology0046 at hotmail.com (=?gb2312?B?va0gzsTi/Q==?=) Date: Sun, 26 Nov 2006 13:19:45 +0000 Subject: [Bioperl-l] PAML problem Message-ID: I use scripts at PAML Howto page to caculate M7 or M8 model. but it always report errors: ------------------------------------------------- Error: err: incorrect model for pairwise comparison.check NSsites, alpha, aaDist.. ------------------------------------------------- Can't call method "next_result" on an undefined value at pamtest.txt line 65. ---------------------------------------------------------- use Bio::Tools::Run::Phylo::PAML::Codeml; use Bio::Tools::Run::Alignment::Clustalw; # for projecting alignments from protein to R/DNA space use Bio::Align::Utilities qw(aa_to_dna_aln); # for input of the sequence data use Bio::SeqIO; use Bio::AlignIO; my $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new; #my $seqdata = shift || 'cds.fa'; my $seqio = new Bio::SeqIO(-file =>"CG4686.cds", -format => 'fasta'); my %seqs; my @prots; # process each sequence while ( my $seq = $seqio->next_seq ) { $seqs{$seq->display_id} = $seq; # translate them into protein my $protein = $seq->translate(); my $pseq = $protein->seq(); if( $pseq =~ /\*/ && $pseq !~ /\*$/ ) { warn("provided a CDS sequence with a stop codon, PAML will choke!"); #exit(0); } # Tcoffee can't handle '*' even if it is trailing $pseq =~ s/\*//g; $protein->seq($pseq); push @prots, $protein; } if( @prots < 2 ) { warn("Need at least 2 CDS sequences to proceed"); exit(0); } open(OUT, ">align_output.txt") || die("cannot open output align_output for writing"); # Align the sequences with clustalw my $aa_aln = $aln_factory->align(\@prots); # project the protein alignment back to CDS coordinates my $dna_aln = aa_to_dna_aln($aa_aln, \%seqs); my @each = $dna_aln->each_seq(); my $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new ( -params => { 'NSsites' => 7, 'ncatG'=>10, 'seqtype' => 1, } ); #I change the parameters here # set the alignment object $kaks_factory->alignment($dna_aln); # run the KaKs analysis my ($rc,$parser) = $kaks_factory->run(); my $result = $parser->next_result; Seqfile:>D_pseudoobscuraATGATGGACACATTGGACTACATCACCCTCAGCAATCCCGTGAGCAAGGCGGTTATATATTCGGGATCGGCTATCTTCCGAGCCCTTGGGCTGCGTCCGAAACAGTTGGTTCCGAAGGAGACCCAGACAGTGCGTCCGGTAATGACTCAGTACATGTCGCCGGGTGCTGGCTCGCTGCATAATTTGGCCGGCCGGTACTATCATTTCGTGCGACTGGCTGGCCTAGGCGGCGCTTCGGCTATTTTCATGGGAGCCTACTGCAAATACGTCCTGAAGGAGATCAAGAACGAAAAGGAGCAGCTGGACTCGCAGGCCTTTGCCGATGTCGCCAATCGCATACACTTTTTGCATTCGTTTGCACTGATGGCCATGCCACTGGCCCACTATCCCATAATCACGGGCTCTTTGATGACCACTGGCACACTGCTCTTCAGCGGCTGCATGTACTATCGTGCATTGACGGGCGAGAAGCGCTTCCAGCCGTTTGCCACCGTTGGAGGCTTCTGTCTGATAGCCGCTTGGCTGACGCTGATATTT >D_willistoniATGTCAATAGTTGATACATTGGACTATATAACCCTGGGTAATCCAGTGAGTCGCTTGGTCATATCTTCAACATCGGCATTAATGCGTACAATTGGTCTGCGCCCCAAGCAGGTGCCTATAAAGGATACAGAAATAGCTGGATTGCCACAGCAGGTCCATCATTTCGGAAATCCAAATGGCCCATCCTTATATACAATTGCCGGCTCTCATTATAACTTTATTCGTCTAGCTGGAATTGGCGGAGCATCGGCTATATTTATGGGAGCGTATTGTAAATATTTTCTTAAGGATATCAATGATCCCAAGGAACAGTTGGATTCACAAGCCTTTGCCGATGTGGCCAATCGTATACATTTTCTCCACTCATTTGCATTAATGGCGATGCCCTTGGCTCATTATCCAGTTTTTACTGGCGCCCTTATGACCACCGGCACATTACTTTTCAGTGGGTGTATGTACTATCGCGCTTTAACCGGTGATAAGAGACTTCAACATTATGCCACAATTGGTGGCTTCTGTCTAATGGCTGCTTGGTTATCCTTGGTTTTG >D_melanogasterATGTCAGTCGCTGACACCATTGAATACGTGACCCTGGGCAATCCTGTCAGCAAGATGGTAGCCTCGTCCGCATCCGCCCTGCTCCGCACGCTTGGTCTGCGTCCCAAGAAGGTGCCGGTGCAGGAGACGAGTATGGCGGTGCTCCCTGCCGCCCACAGCTACGCGCATTCACACGGATCACTCTATCGACTGGCCGGCTGCCATTACCACTTCATTCGGCTGGCCGGGATCGTCGGCGCGTCGGCCATCTTTATGGGCGCCTACTGCAAGTACGTCCTGAAGGACGTCAGCGATCCCAAGGAGCAGGTGGACTCGCAGGCCTTTGCTGATGTGGCCAATCGCATCCACTTTCTGCACTCCTTTGCCATGATGGCCATGCCTCTGGCCCACTATCCCGTATTCACTGGCACTTTGATGATTACGGGCATGATGCTTTTCAGCGGCTGCATGTACTACCGCGCTTTGACTGGCGAGAAGCGTCTGCAACCGTACGCGACCGTCGGAGGATTCTGCCTGATGGCCGCGTGGCTGTCGCTGGTCCTG _________________________________________________________________ ???????????????????????????? MSN Messenger: http://messenger.msn.com/cn From chhalling at verizon.net Sun Nov 26 16:00:18 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 26 Nov 2006 16:00:18 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456A0062.6080103@verizon.net> I attempted to use CPAN to install BioPerl 1.5.2 RC5 into a fresh installation of Perl 5.8.8 under Mac OS X 10.4.8 with all dependencies installed. The tests fail for t/SearchIO. An edited record of the output is shown below. cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz [*snip*] *** Optional dependencies section *** All dependencies are installed [*snip*] Running make test PERL_DL_NONLAZY=1 /test/perl/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t [*snip*] t/SearchIO...................ok 1/1340 -------------------- WARNING --------------------- MSG: XML::SAX::Expat not currently supported; must have local copies of NCBI DTD docs! --------------------------------------------------- -------------------- WARNING --------------------- MSG: error in parsing a report: 404 File `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/NCBI_BlastOutput.dtd' does not exist file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/NCBI_BlastOutput.dtd Handler couldn't resolve external entity at line 2, column 82, byte 104 error in processing external entity reference at line 2, column 82, byte 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm line 187 --------------------------------------------------- t/SearchIO...................NOK 5/1340 # Failed test 'The object isa Bio::Search::Result::ResultI' # in t/SearchIO.t at line 65. # The object isn't defined Can't call method "database_name" on an undefined value at t/SearchIO.t line 66. # Looks like you planned 1340 tests but only ran 5. # Looks like you failed 1 test of 5 run. # Looks like your test died just after 5. t/SearchIO...................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-1340 Failed 1336/1340 tests, 0.30% okay [*snip*] Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/SearchIO.t 255 65280 1340 2671 5-1340 2 tests and 126 subtests skipped. Failed 1/235 test scripts. 1336/11940 subtests failed. Files=235, Tests=11940, 321 wallclock secs (154.44 cusr + 24.28 csys = 178.72 CPU) Failed 1/235 test programs. 1336/11940 subtests failed. make: *** [test_dynamic] Error 255 /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Everyone: > Even though 1.5.2 is a 'developer' release, we consider it the most > stable and capable version of Bioperl, and recommend that you use > it in all but the most critical production environments. Please > try it out and let us know of any problems or difficulties you run > into. > > Please try the new Build.PL installation script and report back how > you get on. Also try installing using CPAN. Your CPAN mirrors may > not be current enough, so you may have delete all entries in your > urllist first. > > > Developers: > Please experiment with installation, especially via CPAN. If you > already have all/most prerequisite external modules installed, > try uninstalling some and report how effective the system is at > reinstalling them for you. > > RC5 may form the final release for some of the packages (probably > all except for bioperl-run), so any further commits made, even to > branch-1-5-2, may not make final release. If you think you've > committed an important bug fix that should be part of final release, > let me know. > > > Thank you, > Sendu. > > > PS. What happened to RC4? I didn't announce it, but it was available on > CPAN where I did some testing on it. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Conrad Halling chhalling at verizon.net From cjfields at uiuc.edu Sun Nov 26 17:04:59 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 16:04:59 -0600 Subject: [Bioperl-l] EntrezGene test failures Message-ID: I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ Build test --test_files t/entrezgene.t --verbose': .. ok 1367 ok 1368 - correct number of loops for T18 # Looks like you planned 1417 tests but only ran 1368. # Looks like you failed 22 tests of 1368 run. dubious Test returned status 22 (wstat 5632, 0x1600) DIED. FAILED tests 56, 162, 182, 184, 367, 512, 603, 631, 667, 711, 766, 920, 998, 1107, 1140, 1192, 1225, 1248, 1270, 1297, 1320, 1345, 1369-1417 Failed 71/1417 tests, 94.99% okay Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------ ------- t/entrezgene.t 22 5632 1417 120 56 162 182 184 367 512 603 631 667 711 766 920 998 1107 1140 1192 1225 1248 1270 1297 1320 1345 1369-1417 Failed 1/1 test scripts. 71/1417 subtests failed. Files=1, Tests=1417, 3 wallclock secs ( 3.06 cusr + 0.09 csys = 3.15 CPU) Failed 1/1 test programs. 71/1417 subtests failed. Looks like not all tests are run. Of the tests that fail, all are from unmatched values. A few examples: # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '14' # expected: '16' not ok 56 - correct number of loops for T15 ... # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '28' # expected: '30' ... not ok 162 - correct number of loops for T15 # Failed test in t/entrezgene.t at line 456. # got: '0' # expected: '1' # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '6' # expected: '5' chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Sun Nov 26 17:17:30 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 16:17:30 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456A0062.6080103@verizon.net> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> Message-ID: <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: > I attempted to use CPAN to install BioPerl 1.5.2 RC5 into a fresh > installation of Perl 5.8.8 under Mac OS X 10.4.8 with all dependencies > installed. > > The tests fail for t/SearchIO. An edited record of the output is shown > below. > > > cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz > > [*snip*] > > *** Optional dependencies section *** > All dependencies are installed > > [*snip*] > > Running make test > PERL_DL_NONLAZY=1 /test/perl/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > > [*snip*] > > t/SearchIO...................ok > 1/1340 > -------------------- WARNING --------------------- > MSG: XML::SAX::Expat not currently supported; must have local > copies of > NCBI DTD docs! > --------------------------------------------------- > > -------------------- WARNING --------------------- > MSG: error in parsing a report: > > 404 File > `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ > NCBI_BlastOutput.dtd' > does not exist > file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ > NCBI_BlastOutput.dtd > Handler couldn't resolve external entity at line 2, column 82, byte > 104 > error in processing external entity reference at line 2, column 82, > byte > 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm > line 187 > > --------------------------------------------------- > t/SearchIO...................NOK > 5/1340 > # Failed test 'The object isa Bio::Search::Result::ResultI' > # in t/SearchIO.t at line 65. > # The object isn't defined > Can't call method "database_name" on an undefined value at t/ > SearchIO.t > line 66. > # Looks like you planned 1340 tests but only ran 5. > # Looks like you failed 1 test of 5 run. > # Looks like your test died just after 5. > t/SearchIO...................dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-1340 > Failed 1336/1340 tests, 0.30% okay > > [*snip*] > > Failed Test Stat Wstat Total Fail List of Failed > ---------------------------------------------------------------------- > --------- > t/SearchIO.t 255 65280 1340 2671 5-1340 > 2 tests and 126 subtests skipped. > Failed 1/235 test scripts. 1336/11940 subtests failed. > Files=235, Tests=11940, 321 wallclock secs (154.44 cusr + 24.28 csys = > 178.72 CPU) > Failed 1/235 test programs. 1336/11940 subtests failed. > make: *** [test_dynamic] Error 255 > /usr/bin/make test -- NOT OK > Running make install > make test had returned bad status, won't install without force > ... There is an eval{} block set up to catch that error but apparently it doesn't work. I'll have a look at it. Like the warning states, XML::SAX::Expat is not supported for BLASTXML parsing unless you have the NCBI DTDs installed as well (blame this on NCBI since their BLAST DTDs don't have the explicit web address). Saying that I don't recommend using XML::SAX::Expat at all (it is no longer actively maintained). Pretty much any other XML::SAX backend works; I recommend using XML::SAX::ExpatXS or XML::LibXML for speedier parsing, though XML::SAX::PurePerl also works. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Sun Nov 26 17:56:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 26 Nov 2006 22:56:28 +0000 Subject: [Bioperl-l] EntrezGene test failures In-Reply-To: References: Message-ID: <456A1B9C.5000105@sendu.me.uk> Chris Fields wrote: > I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ > Build test --test_files t/entrezgene.t --verbose': Yes, Stefan is in the middle of bug fixing/ improvements. I changed the test script recently to highlight the problems. From cjfields at uiuc.edu Sun Nov 26 18:48:23 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 17:48:23 -0600 Subject: [Bioperl-l] EntrezGene test failures In-Reply-To: <2ac232dd4a.2dd4a2ac23@bms.com> References: <2ac232dd4a.2dd4a2ac23@bms.com> Message-ID: On Nov 26, 2006, at 5:44 PM, Stefan Kirov wrote: > I thought Sendu rolled back some changes I've made. I was planning to > commit changes both to the module and the tests, but I am not done > yet. > Stefan Not a problem, just wanted to check. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Sun Nov 26 18:44:29 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Sun, 26 Nov 2006 18:44:29 -0500 Subject: [Bioperl-l] EntrezGene test failures Message-ID: <2ac232dd4a.2dd4a2ac23@bms.com> I thought Sendu rolled back some changes I've made. I was planning to commit changes both to the module and the tests, but I am not done yet. Stefan ----- Original Message ----- From: Chris Fields Date: Sunday, November 26, 2006 5:04 pm Subject: [Bioperl-l] EntrezGene test failures > I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ > Build test --test_files t/entrezgene.t --verbose': > > .. > ok 1367 > ok 1368 - correct number of loops for T18 > # Looks like you planned 1417 tests but only ran 1368. > # Looks like you failed 22 tests of 1368 run. > dubious > Test returned status 22 (wstat 5632, 0x1600) > DIED. FAILED tests 56, 162, 182, 184, 367, 512, 603, 631, 667, 711, > > 766, 920, 998, 1107, 1140, 1192, 1225, 1248, 1270, 1297, 1320, > 1345, > 1369-1417 > Failed 71/1417 tests, 94.99% okay > Failed Test Stat Wstat Total Fail List of Failed > -------------------------------------------------------------------- > ---- > ------- > t/entrezgene.t 22 5632 1417 120 56 162 182 184 367 512 603 > 631 > 667 711 > 766 920 998 1107 1140 1192 > 1225 1248 1270 > 1297 1320 1345 1369-1417 > Failed 1/1 test scripts. 71/1417 subtests failed. > Files=1, Tests=1417, 3 wallclock secs ( 3.06 cusr + 0.09 csys = > 3.15 CPU) > Failed 1/1 test programs. 71/1417 subtests failed. > > > > Looks like not all tests are run. Of the tests that fail, all are > from unmatched values. A few examples: > > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '14' > # expected: '16' > not ok 56 - correct number of loops for T15 > > ... > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '28' > # expected: '30' > > ... > > not ok 162 - correct number of loops for T15 > > # Failed test in t/entrezgene.t at line 456. > # got: '0' > # expected: '1' > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '6' > # expected: '5' > > > > chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at uiuc.edu Sun Nov 26 23:14:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 22:14:32 -0600 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4568BEFB.4070201@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> <4568BEFB.4070201@sendu.me.uk> Message-ID: <34BAD635-8C9F-4A22-B114-B3EFB5B544DD@uiuc.edu> On Nov 25, 2006, at 4:08 PM, Sendu Bala wrote: > Jason Stajich wrote: >> >> The circular ref is from Bio::Species when you have >> $self->{tree} = Bio::Tree::Tree->new(-root => $self); >> >> I added a weaken call in Bio::Species code explicitly -- we can't >> generally weaken the ref to the root node in Bio::Tree::Tree as that >> breaks some other things as you saw. > > Thanks. Though there's still the issue with > Bio::Tree::Node::node_cleanup not doing anything. > > >> I'm not sure I am digging what you've done with Bio::Tree::Tree. Why >> didn't you make a specialized Tree object for Taxonomy stuff so >> that you >> can add methods like lineage_node, etc? > > http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree > > get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because > it's > a Tree function. It goes hand in hand with get_lca(), which was > already > there. > > I suppose you're saying it would have been more appropriate to have a > new Tree-based object that only differed in its new() instead of > adding > an option to Tree's new()? > > My thinking was that both the -node option and get_lineage_nodes() are > useful for trees in general, not just Bio::Taxon. Jason's fixes seem to fix the problem (I tested on Mac OS X). However, does Scalar::Utils come as core with perl 5.6.1? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Sun Nov 26 23:58:14 2006 From: jason at bioperl.org (Jason Stajich) Date: Sun, 26 Nov 2006 20:58:14 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4568BEFB.4070201@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> <4568BEFB.4070201@sendu.me.uk> Message-ID: On Nov 25, 2006, at 2:08 PM, Sendu Bala wrote: > Jason Stajich wrote: >> The circular ref is from Bio::Species when you have >> $self->{tree} = Bio::Tree::Tree->new(-root => $self); >> I added a weaken call in Bio::Species code explicitly -- we can't >> generally weaken the ref to the root node in Bio::Tree::Tree as >> that breaks some other things as you saw. > > Thanks. Though there's still the issue with > Bio::Tree::Node::node_cleanup not doing anything. > right - well I am not sure that it is going to get called if you have to remove the cleanup_methods from the object (or does this mean at all?). I don't have any time to debug it any more so we'll just have to wait till later to figure it out. I'd really like to re-visit the tree bjects to see about making them faster anyways so maybe the memory cycle issue can be revisited as well. > >> I'm not sure I am digging what you've done with Bio::Tree::Tree. >> Why didn't you make a specialized Tree object for Taxonomy stuff >> so that you can add methods like lineage_node, etc? > > http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree > > get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because > it's a Tree function. It goes hand in hand with get_lca(), which > was already there. > > I suppose you're saying it would have been more appropriate to have > a new Tree-based object that only differed in its new() instead of > adding an option to Tree's new()? > > My thinking was that both the -node option and get_lineage_nodes() > are useful for trees in general, not just Bio::Taxon. > I guess I was talking about this code in new() - seems like a Tree::Taxon object could have been made to deal with the special case, but probably I am just not seeing the whole picture so no worries. # to stop us pulling in entire database of a Bio::Taxon when we later do # get_nodes() or similar, specifically set ancestor() for each node if ($node->isa('Bio::Taxon')) { push(@lineage, $node) unless $node eq $root; my $ancestor = $root; foreach my $lineage_node (@lineage) { $lineage_node->ancestor($ancestor); } continue { $ancestor = $lineage_node; } } -- Jason Stajich jason at bioperl.org http://jason.open-bio.org/ From anhthu.tieu at gsf.de Mon Nov 27 03:38:36 2006 From: anhthu.tieu at gsf.de (Anh-Thu Tieu) Date: Mon, 27 Nov 2006 09:38:36 +0100 Subject: [Bioperl-l] exention files for bioperl1.5.2 Message-ID: <456AA40C.3050207@gsf.de> Hi, I noticed there has been a new release for bioperl1.5.2 and I wondered whether there is/ will also be an extension file for this version also (as for version 1.4 or 1.5.1). Until now I have only found the core, network, db and the run files. Is it sufficient to install those four packages (+ various additional perl modules) to make bioperl1.5.2 run or do I need any exention files. Thank you. Best regards, Anh Thu From n.haigh at sheffield.ac.uk Mon Nov 27 04:52:39 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 09:52:39 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456AB567.2010601@sheffield.ac.uk> I just checked out RC5 and ran "perl Build.PL" I get: Can't locate object method "new" via package "Module::Build::Notes" (perhaps you forgot to load "Module::Build::Notes"?) at /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. Nath From bix at sendu.me.uk Mon Nov 27 09:50:08 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 14:50:08 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456AB567.2010601@sheffield.ac.uk> References: <4566B3AF.2050305@sendu.me.uk> <456AB567.2010601@sheffield.ac.uk> Message-ID: <456AFB20.4050102@sendu.me.uk> Nathan Haigh wrote: > I just checked out RC5 and ran "perl Build.PL" I get: > > Can't locate object method "new" via package "Module::Build::Notes" > (perhaps you forgot to load "Module::Build::Notes"?) at > /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. What version of Module::Build do you have installed? Does your Module/Build/Base.pm not 'use Modules::Build::Notes' somewhere near the top? Try upgrading to v0.2805 of Module::Build and let me know if that solves the problem. (If you don't have Module::Build installed at all, didn't you get some kind of prompt to install it?) Thank you, Sendu. From bix at sendu.me.uk Mon Nov 27 11:01:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 16:01:16 +0000 Subject: [Bioperl-l] exention files for bioperl1.5.2 In-Reply-To: <456AA40C.3050207@gsf.de> References: <456AA40C.3050207@gsf.de> Message-ID: <456B0BCC.2020202@sendu.me.uk> Anh-Thu Tieu wrote: > Hi, > > I noticed there has been a new release for bioperl1.5.2 and I wondered > whether there is/ will also be an extension file for this version also > (as for version 1.4 or 1.5.1). Until now I have only found the core, > network, db and the run files. Is it sufficient to install those four > packages (+ various additional perl modules) to make bioperl1.5.2 run or > do I need any exention files. What do you mean by 'extension' file? If you mean the bioperl-ext package then hopefully whatever old version you have will still work. It hasn't been tested, nor will it be updated for 1.5.2 From n.haigh at sheffield.ac.uk Mon Nov 27 11:05:40 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 16:05:40 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456AFB20.4050102@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456AB567.2010601@sheffield.ac.uk> <456AFB20.4050102@sendu.me.uk> Message-ID: <456B0CD4.1060602@sheffield.ac.uk> Sendu Bala wrote: > Nathan Haigh wrote: >> I just checked out RC5 and ran "perl Build.PL" I get: >> >> Can't locate object method "new" via package "Module::Build::Notes" >> (perhaps you forgot to load "Module::Build::Notes"?) at >> /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. > > What version of Module::Build do you have installed? Does your > Module/Build/Base.pm not 'use Modules::Build::Notes' somewhere near > the top? > > Try upgrading to v0.2805 of Module::Build and let me know if that > solves the problem. > > (If you don't have Module::Build installed at all, didn't you get some > kind of prompt to install it?) > > > Thank you, > Sendu. I have v0.2612 installed. Upgrading to Module::Build 0.2805 fixed the problem. Nath From bix at sendu.me.uk Mon Nov 27 11:18:35 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 16:18:35 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> Message-ID: <456B0FDB.9020208@sendu.me.uk> Chris Fields wrote: > On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: [snip] >> t/SearchIO...................ok >> 1/1340 >> -------------------- WARNING --------------------- >> MSG: XML::SAX::Expat not currently supported; must have local >> copies of >> NCBI DTD docs! >> --------------------------------------------------- >> >> -------------------- WARNING --------------------- >> MSG: error in parsing a report: >> >> 404 File >> `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >> NCBI_BlastOutput.dtd' >> does not exist >> file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >> NCBI_BlastOutput.dtd >> Handler couldn't resolve external entity at line 2, column 82, byte >> 104 >> error in processing external entity reference at line 2, column 82, >> byte >> 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm >> line 187 [snip] > There is an eval{} block set up to catch that error but apparently it > doesn't work. I'll have a look at it. The test script has nothing to catch in the eval because blastxml.pm catches the error and emits a warning. You'll either have to make blastxml.pm throw (instead of returning undef + warn), or figure something else out. It's a behaviour change, but would anyone care if it threw thanks to this problem? From cjfields at uiuc.edu Mon Nov 27 11:41:53 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 27 Nov 2006 10:41:53 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B0FDB.9020208@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> <456B0FDB.9020208@sendu.me.uk> Message-ID: On Nov 27, 2006, at 10:18 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: > [snip] >>> t/SearchIO...................ok >>> 1/1340 >>> -------------------- WARNING --------------------- >>> MSG: XML::SAX::Expat not currently supported; must have local >>> copies of >>> NCBI DTD docs! >>> --------------------------------------------------- >>> >>> -------------------- WARNING --------------------- >>> MSG: error in parsing a report: >>> >>> 404 File >>> `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >>> NCBI_BlastOutput.dtd' >>> does not exist >>> file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >>> NCBI_BlastOutput.dtd >>> Handler couldn't resolve external entity at line 2, column 82, >>> byte 104 >>> error in processing external entity reference at line 2, column >>> 82, byte >>> 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/ >>> Parser.pm line 187 > > [snip] > >> There is an eval{} block set up to catch that error but apparently >> it doesn't work. I'll have a look at it. > > The test script has nothing to catch in the eval because > blastxml.pm catches the error and emits a warning. You'll either > have to make blastxml.pm throw (instead of returning undef + warn), > or figure something else out. > > It's a behaviour change, but would anyone care if it threw thanks > to this problem? Ah, that's my fault. I had changed that to a throw but didn't commit it. In a nutshell, we can't/won't support XML::SAX::Expat for a number of reasons. One is the problem with the BLAST DTDs (no explicit web address, so XML validation fails). There may be a way to turn validation off. However, the other, more serious issue is that it is no longer maintained (it hasn't been updated in three years). There were plans a year ago for XML::SAX::ExpatXS to take over the XML::SAX::Expat namespace but no one has bothered to make the changeover, apparently. I have committed the change from warn to throw and made the error message more explicit. You can look it over and merge to 1.5.2 at your discretion. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cain.cshl at gmail.com Mon Nov 27 12:39:09 2006 From: cain.cshl at gmail.com (Scott Cain) Date: Mon, 27 Nov 2006 12:39:09 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <45657C65.50200@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> Message-ID: <1164649150.2575.57.camel@localhost.localdomain> Hi Sendu, I won't have time to do testing on Windows until much later in the day, but I at least want to throw out a little more information. In ActivePerl 819, DBI appears to be installed by default, but the method 'available_drivers' doesn't appear to be available (not implemented? returns something invalid when there are none? not sure at the moment). Anyway, as a result, when I run perl Build.PL and there are no drivers installed, it crashes. I'll try to tease out what is going on later tonight. Scott On Thu, 2006-11-23 at 10:48 +0000, Sendu Bala wrote: > Sendu Bala wrote: > > Scott Cain wrote: > >> Hello, > >> > >> I just wanted to mention that I made a few minor changes to Build.PL so > >> that I could get `perl Build.PL` to complete successfully. I am using > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > >> present either. The main thing I did was to have the BioDBGFF test > >> subroutine quit without asking any questions if Build.PL detected that > >> it was running on Windows. > > > > Is it completely impossible for it to pass under Windows? I find that > > quite a shame! > > > > I'm surprised it was necessary to make your changes, because it already > > had to return true from: > [snip] > > Sorry, that all made no sense because I didn't pay attention to what > changes you actually made. > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > being on mswin still causes a problem, or can the excludes_os > restriction on line 78 of Build.PL be lifted now? > > > Cheers, > Sendu. -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain.cshl at gmail.com GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From n.haigh at sheffield.ac.uk Mon Nov 27 12:48:59 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 17:48:59 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456B250B.4050607@sheffield.ac.uk> When running ./Build test for bioperl-run, the tests for DrawGram and DrawTree require me to manually close the window that is opened and press return in the console in order for the test to complete. Nath From bix at sendu.me.uk Mon Nov 27 12:54:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 17:54:58 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B250B.4050607@sheffield.ac.uk> References: <4566B3AF.2050305@sendu.me.uk> <456B250B.4050607@sheffield.ac.uk> Message-ID: <456B2672.5030405@sendu.me.uk> Nathan Haigh wrote: > When running ./Build test for bioperl-run, the tests for DrawGram and > DrawTree require me to manually close the window that is opened and > press return in the console in order for the test to complete. Hasn't that always been the case in the past? Or did you only recently install some optional pre-req? Does anyone know a way around this? From n.haigh at sheffield.ac.uk Mon Nov 27 13:31:18 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 18:31:18 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B2672.5030405@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456B250B.4050607@sheffield.ac.uk> <456B2672.5030405@sendu.me.uk> Message-ID: <456B2EF6.10808@sheffield.ac.uk> Sendu Bala wrote: > Nathan Haigh wrote: >> When running ./Build test for bioperl-run, the tests for DrawGram and >> DrawTree require me to manually close the window that is opened and >> press return in the console in order for the test to complete. > > Hasn't that always been the case in the past? Or did you only recently > install some optional pre-req? > > Does anyone know a way around this? I've always had Phylip installed, and I know I've run the tests remotely without X11 forwarding - which obviously wouldn't allow the windows to appear (tests were still successful). I'm also sure I've run the test locally previously - but I've not noticed it before - starting to think I'm going mad! :-P Nath From cjfields at uiuc.edu Mon Nov 27 16:47:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 27 Nov 2006 15:47:12 -0600 Subject: [Bioperl-l] DBSOURCE parsing Message-ID: Jason, I am working on stockholm and GenPept format parsing, both which have DBLink objects. I have a couple of questions. First, (not a huge issue really, more like a curiosity), is it possible to pass a callback to Annotation objects for the overloaded operators? I'm just thinking of situations where the data is displayed differently in other formats (like Stockholm). Also, would it be feasible to have DBLink objects also contain annotations (comments, other DBLink objects, etc) for more complex data? In particular this regards GenPept stuff, like the following examples: DBSOURCE swissprot: locus BRCA1_HUMAN, accession P38398; class: standard. created: Oct 1, 1994. sequence updated: Feb 1, 1995. annotation updated: Nov 14, 2006. xrefs: U14680.1, AAA73985.1, L78833.1, AAC37594.1, AY273801.1, AAP12647.1, A58881, 1JM7A, 1JNXX, 1N5OX, 1OQAA, 1T15A, 1T29A, 1T2UA, 1T2VA, 1T2VB, 1T2VC, 1T2VD, 1T2VE, 1Y98A xrefs (non-sequence databases): UniGene:Hs.194143, IntAct:P38398, TRANSFAC:T04074, Ensembl:ENSG00000012048, KEGG:hsa:672, HGNC:1100, MIM:113705, MIM:114480, Reactome:P38398, ArrayExpress:P38398, GO:0031436, GO:0008274, GO:0005634, GO:0000151, GO:0050681, GO:0003677, GO:0019899, GO:0003713, GO:0015631, GO:0008270, GO:0030521, GO:0007059, GO:0006978, GO:0008630, GO:0042759, GO:0046600, GO:0016481, GO:0045739, GO:0031398, GO:0045893, GO:0016567, GO:0042981, GO:0042127, GO:0006357, GO:0006359, InterPro:IPR011364, InterPro:IPR001357, InterPro:IPR002378, InterPro:IPR001841, PANTHER:PTHR13763, Pfam:PF00533, Pfam:PF00097, PIRSF:PIRSF001734, PRINTS:PR00493, SMART:SM00292, SMART:SM00184, PROSITE:PS50172, PROSITE:PS00518, PROSITE:PS50089 ... DBSOURCE pdb: molecule 1T2U, chain 65, release Apr 22, 2004; deposition: Apr 22, 2004; class: Antitumor Protein; source: Mol_id: 1; Organism_scientific: Homo Sapiens; Organism_common: Human; Gene: Brca1; Expression_system: Escherichia Coli; Expression_system_common: Bacteria; Exp. method: X-Ray Diffraction. ... DBSOURCE pir: locus I49350; summary: #length 1812 #molecular-weight 198788 #checksum 8813 ; genetic: #gene Brca1 ; superfamily: transcriptional regulator, BRCA1 type; RING finger homology ; PIR dates: 02-Jul-1996 #sequence_revision 02-Jul-1996 #text_change 09-May-2004 . ... DBSOURCE prf: locus 2202221A; state: hepatoma/colonic tumor; taxonomy: Mammalia. My thought is, the first line would be the main DBLink object data, with all subsequent lines as annotation objects (comments, DBLinks, etc) in an annotation collection contained within the main DBLink object. I don't think there would be any danger of circular references if handled correctly. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From chhalling at verizon.net Mon Nov 27 22:25:00 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:25:00 -0500 Subject: [Bioperl-l] A procedure for efficient testing of the installation of BioPerl Message-ID: <456BAC0C.10503@verizon.net> I have devised the following procedure that lets me repeatedly install BioPerl release candidates for testing the installation process. I am performing these tests under Mac OS X 10.4.8. I thought it would be useful to document this process for anyone else who is testing the installation process. I downloaded the tarball for Perl 5.8.8 and ran the following commands to set up the code for installation: cd /Volumes/CHHalling/Perl/Perl-5.8.8 tar -xzf perl-5.8.8.tgz cd perl-5.8.8 sh Configure -Dprefix=/test/perl -Dcc=gcc -des make make test For each round of testing, I run the following commands to install a fresh copy of Perl 5.8.8 and then initialize the cpan utility: cd /Volumes/CHHalling/Perl/Perl-5.8.8/perl-5.8.8 sudo rm -rf /test sudo mkdir /test sudo make install sudo rm -rf ~/.cpan export PATH=/test/perl/bin:$PATH sudo cpan Then I run my cpan commands. For installing BioPerl without having installed the dependencies, I enter the command: cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz For installing the dependencies, then installing BioPerl, I enter the commands: cpan> install Bundle::BioPerl cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz For testing modifications to Bundle::BioPerl (the subject of my next post), I execute the following commands (which exit the cpan utility after I have initialized it, create the Bundle subdirectory, copy the BioPerl.pm file that contains the Bundle::BioPerl package to the .cpan/Bundle directory, start the cpan utility, and install Bundle::BioPerl and BioPerl 1.5.2 RC5): cpan> exit $ sudo mkdir ~/.cpan/Bundle $ sudo cp /Volumes/CHHalling/Perl/BioPerl/BioPerl.pm ~/.cpan/Bundle/ $ sudo cpan cpan> install Bundle::BioPerl cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz When I have finished testing the installation, I loop back to step 2, where I remove the /test directory and reinstall Perl 5.8.8. A note: I was going to use the same procedure to test installing BioPerl 1.5.2 under Perl 5.6.1, but I discovered that Perl 5.6.1 is *so old* that there is no Makefile for Mac OS X. -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Mon Nov 27 22:02:59 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:02:59 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456BA6E3.3010908@verizon.net> I compiled and installed Perl 5.8.8 under Mac OS X 10.4.8 into a directory named /test/perl. Then I used the cpan utility to attempt to install BioPerl 1.5.2 RC5 without having installed any of its dependencies. The installation failed because of the following test failures: t/SeqFeature t/SeqHound_DB t/SeqVersion Here are the pertinent details: t/SeqFeature.................IO::String or LWP::UserAgent or HTTP::Request not installed - skipping DB tests... Can't locate URI/Escape.pm in @INC (@INC contains: t /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/arch /test/perl/lib/5.8.8/darwin-2level /test/perl/lib/5.8.8 /test/perl/lib/site_perl/5.8.8/darwin-2level /test/perl/lib/site_perl/5.8.8 /test/perl/lib/site_perl .) at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/SeqFeature/Annotated.pm line 86. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/SeqFeature/Annotated.pm line 86. Compilation failed in require at t/SeqFeature.t line 52. BEGIN failed--compilation aborted at t/SeqFeature.t line 52. t/SeqFeature.................dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/SeqHound_DB................ok 1/14Can't locate LWP/UserAgent.pm in @INC (@INC contains: /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/arch /test/perl/lib/5.8.8/darwin-2level /test/perl/lib/5.8.8 /test/perl/lib/site_perl/5.8.8/darwin-2level /test/perl/lib/site_perl/5.8.8 /test/perl/lib/site_perl .) at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/WebDBSeqI.pm line 78. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/WebDBSeqI.pm line 78. Compilation failed in require at (eval 19) line 3. ...propagated at /test/perl/lib/5.8.8/base.pm line 85. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/SeqHound.pm line 88. Compilation failed in require at t/SeqHound_DB.t line 41. BEGIN failed--compilation aborted at t/SeqHound_DB.t line 41. Use of uninitialized value in -f at t/SeqHound_DB.t line 34. t/SeqHound_DB................dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/SeqVersion.................NOK 1 # Failed test 'use Bio::DB::SeqVersion;' # in t/SeqVersion.t at line 21. # Tried to use 'Bio::DB::SeqVersion'. # Error: Base class package "LWP::UserAgent" is empty. # (Perhaps you need to 'use' the module which defines that package first.) # at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/WebAgent.pm line 90 # BEGIN failed--compilation aborted at t/SeqVersion.t line 21. # Compilation failed in require at (eval 4) line 3. # ...propagated at /test/perl/lib/5.8.8/base.pm line 85. # BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/SeqVersion.pm line 71. # Compilation failed in require at (eval 3) line 2. # BEGIN failed--compilation aborted at (eval 3) line 2. Can't locate object method "new" via package "Bio::DB::SeqVersion" at t/SeqVersion.t line 23. # Looks like you planned 10 tests but only ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test died just after 1. t/SeqVersion.................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-10 Failed 10/10 tests, 0.00% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/SeqFeature.t 2 512 211 0 0.00% ?? t/SeqHound_DB.t 2 512 14 0 0.00% ?? t/SeqVersion.t 255 65280 10 19 190.00% 1-10 9 tests and 228 subtests skipped. Failed 3/235 test scripts, 98.72% okay. 10/11535 subtests failed, 99.91% okay. make: *** [test_dynamic] Error 255 /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > [*snip*] > Thank you, > Sendu. -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Mon Nov 27 22:51:14 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:51:14 -0500 Subject: [Bioperl-l] A new Bundle::BioPerl Message-ID: <456BB232.4020808@verizon.net> After experimenting with the existing Bundle::BioPerl version 2.1.8 under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install all of the BioPerl dependencies unless run multiple times. I edited the the order that the dependencies were listed so I could get all the dependencies to install on the first try. Then I got carried away and ran some grep commands on the bioperl-live source code to identify all of the dependencies that are use'd or require'd, and I added these dependencies to the Bundle::BioPerl package. Many of these dependencies are core Perl modules, which it doesn't hurt to update. After a few rounds of testing during Thanksgiving weekend festivities, I have completed a new Bundle::BioPerl package that installs virtually all of the dependencies on the first try. There are two modules that won't install. The first is Bio::ASN1::EntrezGene, and the second is CORBA::ORBit. Bio::ASN1::EntrezGene won't install because it is dependent on Bio::Index::AbstractSeq, which is part of BioPerl. CORBA::ORBit won't install because its tarball appears to be corrupted. The cpan utility also reports that Math::Trig and Text::Balanced didn't install, but this is an error, because they are installed correctly. The cpan commands for installing the BioPerl dependencies, Bio::ASN1::EntrezGene, and BioPerl 1.5.2 RC5, will become: cpan> install Bundle::BioPerl cpan> force install Bio::ASN1::EntrezGene cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz I have filed a Bugzilla bug report (bug #2153) and attached my Bundle::BioPerl package (attachment #508) to it for consideration. -- Conrad Halling chhalling at verizon.net From DGroskreutz at twt.com Tue Nov 28 02:00:40 2006 From: DGroskreutz at twt.com (DGroskreutz at twt.com) Date: Tue, 28 Nov 2006 01:00:40 -0600 Subject: [Bioperl-l] CN=Deb Groskreutz/OU=MSN/O=TWT is out of the office. Message-ID: I will be out of the office starting 11/27/2006 and will not return until 12/04/2006. NOTICE OF CONFIDENTIALITY: The information contained in this communication, including attachments, is intended for the specific delivery to and use by the individual(s) to whom it is addressed. This email includes confidential information that may be attorney-client privileged. Any review, retransmission, dissemination, or unauthorized use of this communication is strictly prohibited and may be unlawful. If you have received this communication in error, please reply to the sender immediately and delete the original communication and any copy of it from your computer system, including all attachments. From bix at sendu.me.uk Tue Nov 28 05:53:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 10:53:10 +0000 Subject: [Bioperl-l] A new Bundle::BioPerl In-Reply-To: <456BB232.4020808@verizon.net> References: <456BB232.4020808@verizon.net> Message-ID: <456C1516.5050900@sendu.me.uk> Conrad Halling wrote: > After experimenting with the existing Bundle::BioPerl version 2.1.8 > under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install > all of the BioPerl dependencies unless run multiple times. > > I edited the the order that the dependencies were listed so I could get > all the dependencies to install on the first try. Thank you so much for all your hard work. Its extremely valuable. That said, I'm no longer recommending the usage of Bundle::BioPerl. Instead what I'll do is apply your discovered order to the new Build.PL installation system. You're welcome of course to contact Chris Dagdigian to make sure he knows about your new version of Bundle::BioPerl. He can then upload it to CPAN if he's happy with it, and people who choose to still use the Makefile.PL installation process will surely appreciate the new version of Bundle::BioPerl. Thanks again, Sendu. From st537 at york.ac.uk Tue Nov 28 06:02:07 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Tue, 28 Nov 2006 11:02:07 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... Message-ID: <456C172F.4060008@york.ac.uk> Hi, I am trying to learn bioperl and I'm attempting a few basic thing! I seem to be ok with reading in and outputting sequences and files now I am trying to do a simple BLAST search using a sequence (a sequence object in fact). The code I am attempting to run is at the bottom of the message... I am probably making a dumb mistake and don't understand the capabilities of the objects well enough, but the info for the remoteblast->submit_blast function says that it can take sequences as an argument, I've also tried sending the fasta file name containing my sequence as an argument to submit_blast, with the same result.... I have also tried sending $seqio_obj->next_seq........... i.e the following error message displayed on my terminal: Can't call method "submit_blast" on an undefined value at bioptest2.pl line 22, line 1. I haven't got around to figuring out how to process the returned data from this yet, just trying to get the function to run first! Thanks for any help that anyone can offer me with this... Samantha Thompson #******************************** use Bio::Seq; use Bio::SeqIO; use Bio::Tools::Run::RemoteBlast; use Bio::SearchIO; #seq bit $seq_obj = Bio::Seq->new(-format => 'fasta'); $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); $seq_obj = $seqio_obj->next_seq; #blast bit $remote_blast = Bio::Tools::Run::RemoteBlast->new ( -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); #end From bix at sendu.me.uk Tue Nov 28 07:39:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 12:39:29 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C172F.4060008@york.ac.uk> References: <456C172F.4060008@york.ac.uk> Message-ID: <456C2E01.5070805@sendu.me.uk> Samantha Thompson wrote: > Hi, > I am trying to learn bioperl and I'm attempting a few basic thing! I > seem to be ok with reading in and outputting sequences and files now I > am trying to do a simple BLAST search using a sequence (a sequence > object in fact). The code I am attempting to run is at the bottom of the > message... > I am probably making a dumb mistake and don't understand the > capabilities of the objects well enough, but the info for the > remoteblast->submit_blast function says that it can take sequences as an > argument, I've also tried sending the fasta file name containing my > sequence as an argument to submit_blast, with the same result.... I > have also tried sending $seqio_obj->next_seq........... i.e the > following error message displayed on my terminal: > > Can't call method "submit_blast" on an undefined value at bioptest2.pl > line 22, line 1. Always start your perl scripts with 'use strict;'. This will help you find and fix the main problem with your script, that you made a RemoteBlast object and stored it as $remote_blast, but then tried to use submit_blast() on $remoteBlast which doesn't exist. I've rewritten your code below: use strict; > use Bio::Seq; > use Bio::SeqIO; > > use Bio::Tools::Run::RemoteBlast; > use Bio::SearchIO; > > #seq bit > # $seq_obj = Bio::Seq->new(-format => 'fasta'); # above line doesn't do anything, $seq_obj gets overwritten below > my $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > my $seq_obj = $seqio_obj->next_seq; > > > > #blast bit > my $remote_blast = Bio::Tools::Run::RemoteBlast->new(-prog => 'blastp', -db => 'nr', -expect => '1e-15' ); # submit_blast takes the sequence object, not the sequence string my $blastreturn_obj = $remote_blast->submit_blast($seq_obj); From n.haigh at sheffield.ac.uk Tue Nov 28 08:10:45 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 28 Nov 2006 13:10:45 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C172F.4060008@york.ac.uk> References: <456C172F.4060008@york.ac.uk> Message-ID: <456C3555.3040807@sheffield.ac.uk> Samantha Thompson wrote: > Hi, > I am trying to learn bioperl and I'm attempting a few basic thing! I > seem to be ok with reading in and outputting sequences and files now I > am trying to do a simple BLAST search using a sequence (a sequence > object in fact). The code I am attempting to run is at the bottom of the > message... > I am probably making a dumb mistake and don't understand the > capabilities of the objects well enough, but the info for the > remoteblast->submit_blast function says that it can take sequences as an > argument, I've also tried sending the fasta file name containing my > sequence as an argument to submit_blast, with the same result.... I > have also tried sending $seqio_obj->next_seq........... i.e the > following error message displayed on my terminal: > > Can't call method "submit_blast" on an undefined value at bioptest2.pl > line 22, line 1. > > I haven't got around to figuring out how to process the returned data > from this yet, just trying to get the function to run first! > Thanks for any help that anyone can offer me with this... > > Samantha Thompson > > #******************************** > > > use Bio::Seq; > use Bio::SeqIO; > > use Bio::Tools::Run::RemoteBlast; > use Bio::SearchIO; > > #seq bit > > $seq_obj = Bio::Seq->new(-format => 'fasta'); > > $seqio_obj = Bio::SeqIO->new(-file => > "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > > $seq_obj = $seqio_obj->next_seq; > > > > #blast bit > > $remote_blast = Bio::Tools::Run::RemoteBlast->new ( > -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); > > $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); > > > > > #end > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > Hi Samantha, At first glance and without running any code, the first thing I can see that is incorrect is: $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); I believe that submit_blast() would be likely to take the actual sequence object ($seq_obj) as the argument and not the actual sequence string itself (e.g. "ACTGCTG") that you get by calling $seq_obj->seq. So swap this line for: $blastreturn_obj = $remoteBlast->submit_blast($seq_obj); And see how you get on. Nath From hlapp at gmx.net Tue Nov 28 11:20:59 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 28 Nov 2006 11:20:59 -0500 Subject: [Bioperl-l] load_seqdatabase.pl question In-Reply-To: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> Message-ID: <53C6D534-6E36-4061-B955-E74537839265@gmx.net> Hi Derek, first off, I'd recommend to always post such questions to the mailing list; sometimes I may not have a chance to check my email for a while or respond right away but someone else may know the answer too. In your case it looks like you didn't install bioperl-db. You need to install bioperl-db from CVS (using the main trunk). Instructions for how to do this are on the bioperl web site. Let me (and the list) know if you have trouble finding those. Let me know if you did install bioperl-db. (If you did, did you also set PERL5LIB if you installed it in non-standard place, such as your home directory?) -hilmar On Nov 27, 2006, at 12:07 PM, Derek Buchfink wrote: > Hi, I am new to BioSQL and I am looking to use the > load_seqdatabase.pl script to load some data into a PostgreSQL > 8.1.4 database. I am using version 1.24 of the script. However, I > am getting the following error: > > Can't locate Bio/DB/BioDB.pm in @INC (@INC contains: /usr/lib/ > perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/ > perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/ > site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/ > 5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386- > linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread- > multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/ > lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/ > perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/ > site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/ > site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi / > usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/ > perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/ > vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/ > vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/ > vendor_perl .) at load_seqdatabase.pl line 337. > BEGIN failed--compilation aborted at load_seqdatabase.pl line 337. > > Do you know how to solve this issue or do you have any helpful > suggestions? Thank you very much. > > Derek Buchfink -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cain at cshl.edu Tue Nov 28 11:42:23 2006 From: cain at cshl.edu (Scott Cain) Date: Tue, 28 Nov 2006 11:42:23 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164649150.2575.57.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> Message-ID: <1164732143.2584.33.camel@localhost.localdomain> Hi Sendu, It looks like what you've done did the trick--bioperl installed on both ActivePerl 817 and 819 using Module::Build (though I must admit I didn't look at the tests--I just wanted `perl Build.PL` to work). Nice work! Scott On Mon, 2006-11-27 at 12:39 -0500, Scott Cain wrote: > Hi Sendu, > > I won't have time to do testing on Windows until much later in the day, > but I at least want to throw out a little more information. In > ActivePerl 819, DBI appears to be installed by default, but the method > 'available_drivers' doesn't appear to be available (not implemented? > returns something invalid when there are none? not sure at the moment). > Anyway, as a result, when I run perl Build.PL and there are no drivers > installed, it crashes. I'll try to tease out what is going on later > tonight. > > Scott > > > On Thu, 2006-11-23 at 10:48 +0000, Sendu Bala wrote: > > Sendu Bala wrote: > > > Scott Cain wrote: > > >> Hello, > > >> > > >> I just wanted to mention that I made a few minor changes to Build.PL so > > >> that I could get `perl Build.PL` to complete successfully. I am using > > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > > >> present either. The main thing I did was to have the BioDBGFF test > > >> subroutine quit without asking any questions if Build.PL detected that > > >> it was running on Windows. > > > > > > Is it completely impossible for it to pass under Windows? I find that > > > quite a shame! > > > > > > I'm surprised it was necessary to make your changes, because it already > > > had to return true from: > > [snip] > > > > Sorry, that all made no sense because I didn't pay attention to what > > changes you actually made. > > > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > > being on mswin still causes a problem, or can the excludes_os > > restriction on line 78 of Build.PL be lifted now? > > > > > > Cheers, > > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From bix at sendu.me.uk Tue Nov 28 11:56:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 16:56:04 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164732143.2584.33.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> <1164732143.2584.33.camel@localhost.localdomain> Message-ID: <456C6A24.5090105@sendu.me.uk> Scott Cain wrote: > Hi Sendu, > > It looks like what you've done did the trick--bioperl installed on both > ActivePerl 817 and 819 using Module::Build (though I must admit I didn't > look at the tests--I just wanted `perl Build.PL` to work). Nice work! ... I didn't do anything yet :O Can you check on an export of bioperl-release-1-5-2-rc5 and compare to an export of branch-1-5-2 and let me know if you see the bug in the former and no bug in the latter? From gwu at molbio.mgh.harvard.edu Tue Nov 28 16:13:11 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 28 Nov 2006 16:13:11 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <53C6D534-6E36-4061-B955-E74537839265@gmx.net> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> Message-ID: <456CA667.6010609@molbio.mgh.harvard.edu> Hi everyone, I'm using load_seqdatabase.pl to upload some Genbank genome sequences to my Oracle BioSQL database. I saw some errors(See attached warning message) related to seqfeature_qualifier_value (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data type of maximum 4000 bytes. Did anybody mention this issue before? Should I just modify the column to a type being able store more data such as LONG or CLOB? Thanks. Gang Log information: ============================================ load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank /genomeseq/arabidopsis//NC_003070.gbk Loading /genomeseq/arabidopsis//NC_003070.gbk ... -------------------- WARNING --------------------- MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement execution: ORA-01461: can bind a LONG value only for insert into a LONG column (DBD ERROR: error possibly near <*> indicator at char 12 in 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, rank) VALUES (:p1, :p2, :p3, :p4)') name: INSERT ASSOC [2] Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue values: FK[Bio::SeqFeature::Generic]:14898, FK[Bio::Annotation::SimpleValue]:800, value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFVGTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADRGTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEILASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFPWEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERASVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRYIQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEAEDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDINQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDWRLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFALDIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDNQGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRYMRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYTFESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGLVQATYQASAPLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKVHLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAYTDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFVSVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSEKETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLGNFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEVTAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQLEVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTLSVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVTILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRLMLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAVPDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEYTYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVDISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLRVKLDFNFMYASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQSQVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSNTYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCLSIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWDILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSEIAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASVTRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGLHGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSSKPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDFQTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGLHIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVARLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCLLISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRNGRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVENSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPLWLSVGADASVLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVYLTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITNDSYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQESAGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTSDRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSVFSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESWQFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIVRISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMSVQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRVYPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAMSPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDILGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAKSSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLRPYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMGQRKFIPAKDACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQAINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", rank:"1" -------------------------------------------------- ============================================= From cain.cshl at gmail.com Tue Nov 28 15:18:02 2006 From: cain.cshl at gmail.com (Scott Cain) Date: Tue, 28 Nov 2006 15:18:02 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <456C6A24.5090105@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> <1164732143.2584.33.camel@localhost.localdomain> <456C6A24.5090105@sendu.me.uk> Message-ID: <536f21b00611281218v3e6fd7a1ia2c9e81ef7ad678c@mail.gmail.com> Sendu, I've tried exports of both branches and they both work. Scott On 11/28/06, Sendu Bala wrote: > > Scott Cain wrote: > > Hi Sendu, > > > > It looks like what you've done did the trick--bioperl installed on both > > ActivePerl 817 and 819 using Module::Build (though I must admit I didn't > > look at the tests--I just wanted `perl Build.PL` to work). Nice work! > > ... > > I didn't do anything yet :O > > Can you check on an export of bioperl-release-1-5-2-rc5 and compare to > an export of branch-1-5-2 and let me know if you see the bug in the > former and no bug in the latter? > > From lincoln.stein at gmail.com Tue Nov 28 21:15:38 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 28 Nov 2006 21:15:38 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph Message-ID: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> Hi, I had to back out a change I made to Bio/Graphics/Glyph recently (on both live and 1.52 branches). It caused a bizarre problem in which some features had twice the expected height. Lincoln On 11/23/06, Sendu Bala wrote: > > Sendu Bala wrote: > > Scott Cain wrote: > >> Hello, > >> > >> I just wanted to mention that I made a few minor changes to Build.PL so > >> that I could get `perl Build.PL` to complete successfully. I am using > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > >> present either. The main thing I did was to have the BioDBGFF test > >> subroutine quit without asking any questions if Build.PL detected that > >> it was running on Windows. > > > > Is it completely impossible for it to pass under Windows? I find that > > quite a shame! > > > > I'm surprised it was necessary to make your changes, because it already > > had to return true from: > [snip] > > Sorry, that all made no sense because I didn't pay attention to what > changes you actually made. > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > being on mswin still causes a problem, or can the excludes_os > restriction on line 78 of Build.PL be lifted now? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From hlapp at gmx.net Tue Nov 28 23:54:53 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 28 Nov 2006 23:54:53 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <456CA667.6010609@molbio.mgh.harvard.edu> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> Message-ID: These are the protein translations stored in the feature table as tags of features, right? You can change the type of the column (although there may be some issues when you update the column because the NVL() clause won't work if I recall that correctly), but doing so will deprive you of any 'normal' searches against that column. (You can still use functions from the DBMS_LOB package, but they will be much slower and are completely non-standard.) It is up to you whether that is too big of a price to pay for having some redundant protein translations (translating the feature's DNA sequence should give you the same) in the database. I always trimmed those feature tags off (using a custom SeqProcessor). An alternative is to convert these feature tags into actual bioentries (i.e., Bio::Seq objects; again, a custom SeqProcessor will allow you to do that). -hilmar On Nov 28, 2006, at 4:13 PM, gang wu wrote: > Hi everyone, > > I'm using load_seqdatabase.pl to upload some Genbank genome > sequences to > my Oracle BioSQL database. I saw some errors(See attached warning > message) related to seqfeature_qualifier_value > (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data > type of maximum 4000 bytes. Did anybody mention this issue before? > Should I just modify the column to a type being able store more data > such as LONG or CLOB? > > Thanks. > > Gang > > > Log information: > ============================================ > > load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser > biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank > /genomeseq/arabidopsis//NC_003070.gbk > > > Loading /genomeseq/arabidopsis//NC_003070.gbk ... > > > -------------------- WARNING --------------------- > MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement > execution: ORA-01461: can bind a LONG value only for insert into a > LONG > column (DBD ERROR: error possibly near <*> indicator at char 12 in > 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, > rank) VALUES (:p1, :p2, :p3, :p4)') > name: INSERT ASSOC [2] > Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue > values: FK[Bio::SeqFeature::Generic]:14898, > FK[Bio::Annotation::SimpleValue]:800, > value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFV > GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADR > GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEI > LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFP > WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERA > SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRY > IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEA > EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDI > NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDW > RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFAL > DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDN > QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRY > MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYT > FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGL > VQATYQASA! > > PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKV > HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAY > TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFV > SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSE > KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLG > NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEV > TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQL > EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTL > SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVT > ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRL > MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAV > PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEY > TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVD > ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLR > VKLDFNFM! > > YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQS > QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSN > TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCL > SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWD > ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSE > IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASV > TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGL > HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSS > KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDF > QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGL > HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVA > RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCL > LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRN > GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVE > NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPL > WLSVGADAS! > > VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVY > LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITND > SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQES > AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTS > DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSV > FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESW > QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIV > RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMS > VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRV > YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAM > SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDI > LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAK > SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLR > PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMG > QRKFIPAK! > > DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQ > AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", > rank:"1" > -------------------------------------------------- > > > ============================================= > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Wed Nov 29 04:32:24 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 09:32:24 +0000 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> Message-ID: <456D53A8.80800@sendu.me.uk> Lincoln Stein wrote: > Hi, > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > both live and 1.52 branches). It caused a bizarre problem in which some > features had twice the expected height. Exactly which recent commits are the necessary reversion? Just 'fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height'? I'm confused by 'removed debugging warning' since you did different things during that named commit in HEAD (you removed a warn()) vs branch-1-5-2 (you added a bunch of non-warn related stuff). From lincoln.stein at gmail.com Wed Nov 29 09:41:25 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 29 Nov 2006 09:41:25 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <456D53A8.80800@sendu.me.uk> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> Message-ID: <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> There were two branch-1-5-2 commits last night. Both are needed to back out the changes. Lincoln On 11/29/06, Sendu Bala wrote: > > Lincoln Stein wrote: > > Hi, > > > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > > both live and 1.52 branches). It caused a bizarre problem in which some > > features had twice the expected height. > > Exactly which recent commits are the necessary reversion? Just 'fixed > minor bug which caused some features drawn with the "box" glyph to have > an unexpected height'? > > I'm confused by 'removed debugging warning' since you did different > things during that named commit in HEAD (you removed a warn()) vs > branch-1-5-2 (you added a bunch of non-warn related stuff). > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From lincoln.stein at gmail.com Wed Nov 29 09:38:18 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 29 Nov 2006 09:38:18 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <456D53A8.80800@sendu.me.uk> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> Message-ID: <6dce9a0b0611290638h46dc7d95o7ce5f7977fddfc81@mail.gmail.com> Uh oh. Perhaps I made a mistake during the commits. I will check what's up. Lincoln On 11/29/06, Sendu Bala wrote: > > Lincoln Stein wrote: > > Hi, > > > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > > both live and 1.52 branches). It caused a bizarre problem in which some > > features had twice the expected height. > > Exactly which recent commits are the necessary reversion? Just 'fixed > minor bug which caused some features drawn with the "box" glyph to have > an unexpected height'? > > I'm confused by 'removed debugging warning' since you did different > things during that named commit in HEAD (you removed a warn()) vs > branch-1-5-2 (you added a bunch of non-warn related stuff). > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bix at sendu.me.uk Wed Nov 29 10:53:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 15:53:04 +0000 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> Message-ID: <456DACE0.5060401@sendu.me.uk> Lincoln Stein wrote: > There were two branch-1-5-2 commits last night. Both are needed to back > out the changes. I'm not seeing the changes as a true revert. cvs diff -r 1.113.4.6 Bio/Graphics/Glyph.pm Index: Bio/Graphics/Glyph.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph.pm,v retrieving revision 1.113.4.6 retrieving revision 1.113.4.9 diff -r1.113.4.6 -r1.113.4.9 3c3 < # $Id: Glyph.pm,v 1.113.4.6 2006/11/19 17:18:45 lstein Exp $ --- > # $Id: Glyph.pm,v 1.113.4.9 2006/11/29 02:38:33 lstein Exp $ 126a127,128 > my $feature = $self->feature; > return 1 if $feature->can('compound') && $feature->compound; 1636a1639 > cvs diff -r 1.40.2.2 Bio/Graphics/Glyph/generic.pm Index: Bio/Graphics/Glyph/generic.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/generic.pm,v retrieving revision 1.40.2.2 retrieving revision 1.40.2.4 diff -r1.40.2.2 -r1.40.2.4 113,115c113,115 < my $md = $self->SUPER::maxdepth; < return $md if defined $md; < return 0; --- > my $maxdepth = $self->option('maxdepth'); > return $maxdepth if defined $maxdepth; > return 1; cvs diff -r 1.6.8.1 Bio/Graphics/Glyph/box.pm Index: Bio/Graphics/Glyph/box.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/box.pm,v retrieving revision 1.6.8.1 retrieving revision 1.6.8.2 diff -r1.6.8.1 -r1.6.8.2 14a15,21 > sub maxdepth { > my $self = shift; > my $maxdepth = $self->option('maxdepth'); > return $maxdepth if defined $maxdepth; > return 0; > } > Is this intended? Are you sure this is safe to go into final release for 1.5.2? From cjfields at uiuc.edu Wed Nov 29 10:55:33 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 09:55:33 -0600 Subject: [Bioperl-l] URI, Graph, and Module::Build Message-ID: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> Sendu, For the Build.PL dependencies, do we want to use the absolute module requirements (URI::Escape, Graph::Directed, XML::SAX::Base) or the distributions they are in (URI, Graph, XML::SAX)? Or does it really make a difference? Also, you had mentioned that Bundle::Bioperl is no longer needed since you can have them installed via Build. Does that also hold true for Windows (since CPAN is, at best, very testy installing on Windows)? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 29 11:04:07 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 16:04:07 +0000 Subject: [Bioperl-l] URI, Graph, and Module::Build In-Reply-To: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> References: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> Message-ID: <456DAF77.6050609@sendu.me.uk> Chris Fields wrote: > Sendu, > > For the Build.PL dependencies, do we want to use the absolute module > requirements (URI::Escape, Graph::Directed, XML::SAX::Base) or the > distributions they are in (URI, Graph, XML::SAX)? Or does it really > make a difference? It makes a difference right now only where the absolute module doesn't have a version (because in Build.PL we ask for at least version 0, which fails if version in the modules is actually undef). I'll fix that in the future, so it is best to use the absolute module for clarity. > Also, you had mentioned that Bundle::Bioperl is no longer needed since > you can have them installed via Build. Does that also hold true for > Windows (since CPAN is, at best, very testy installing on Windows)? In what way is it testy? I set up a new WinXP machine today and installed ActiveState. My Build.PL script happily offered to install Module::Build for me with CPAN and it almost worked up until CPAN needed nmake. After installing nmake I upgraded CPAN with no problems and then everything worked after that (I only tried to install one optional dep with Build.PL via CPAN, and that worked fine). So yes, I'd say it holds true for Windows. Though I haven't sorted out the ppd stuff yet. From cjfields at uiuc.edu Wed Nov 29 12:06:37 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 11:06:37 -0600 Subject: [Bioperl-l] URI, Graph, and Module::Build In-Reply-To: <456DAF77.6050609@sendu.me.uk> References: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> <456DAF77.6050609@sendu.me.uk> Message-ID: On Nov 29, 2006, at 10:04 AM, Sendu Bala wrote: > Chris Fields wrote: >> Sendu, >> For the Build.PL dependencies, do we want to use the absolute >> module requirements (URI::Escape, Graph::Directed, XML::SAX::Base) >> or the distributions they are in (URI, Graph, XML::SAX)? Or does >> it really make a difference? > > It makes a difference right now only where the absolute module > doesn't have a version (because in Build.PL we ask for at least > version 0, which fails if version in the modules is actually > undef). I'll fix that in the future, so it is best to use the > absolute module for clarity. That sounds fine to me. If I remember correctly, at least one example (XML::SAX::Base) used to be a separate distribution, but it should install XML::SAX now. >> Also, you had mentioned that Bundle::Bioperl is no longer needed >> since you can have them installed via Build. Does that also hold >> true for Windows (since CPAN is, at best, very testy installing on >> Windows)? > > In what way is it testy? I set up a new WinXP machine today and > installed ActiveState. My Build.PL script happily offered to > install Module::Build for me with CPAN and it almost worked up > until CPAN needed nmake. After installing nmake I upgraded CPAN > with no problems and then everything worked after that (I only > tried to install one optional dep with Build.PL via CPAN, and that > worked fine). It all depends on the modules installed. For instance, a few that include C code or required external compiled libraries had generally been much harder to install, or they were historically; I admittedly haven't tried them recently. GD, (I think) DBD::mysql, and anything using precompiled dynamic libraries were the most problematic, but PPMs and Win-compatible dynamic libraries were always available somewhere which made installing them via nmake a non-issue. One thing I noticed (and mentioned previously) is that using 'Build' also generated HTML docs on WinXP (I didn't see this on Mac OS X); I don't know if this still occurs, so I'll give it a run today. This may be a problem since the pod2html-generated formatting differs significantly from the PPM-generated docs. I'm not even sure they install in the same location as the PPM-generated pages or whether this will cause any issues. Do you also see this on your local WinXP? > So yes, I'd say it holds true for Windows. Though I haven't sorted > out the ppd stuff yet. I think recommending PPM for BioPerl installation on Windows is still the best option for now, at least until we are sure about CPAN installation and the HTML issue above. Frankly, there will just be too much demand for it just for the HTML docs alone (they are quite nice). If the prereqs are listed correctly it should install those first, but who knows with PPM4! It will also generate HTML on the fly and install it in the doc tree as expected, which I have tested. As for a new PPD/PPM, I haven't tried generating it yet via Module::Build (I thought maybe Nathan was doing this). I may give it a go today on WinXP with a fresh ActiveState install (most of my important work is now on Mac OS X, so that shouldn't interfere). My guess is the PPD will be in old PPM3 XML format. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From chhalling at verizon.net Wed Nov 29 20:25:45 2006 From: chhalling at verizon.net (Conrad Halling) Date: Wed, 29 Nov 2006 20:25:45 -0500 Subject: [Bioperl-l] A new Bundle::BioPerl In-Reply-To: <456C1516.5050900@sendu.me.uk> References: <456BB232.4020808@verizon.net> <456C1516.5050900@sendu.me.uk> Message-ID: <456E3319.5090703@verizon.net> Sendu Bala wrote: > Conrad Halling wrote: > >> After experimenting with the existing Bundle::BioPerl version 2.1.8 >> under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install >> all of the BioPerl dependencies unless run multiple times. >> >> I edited the the order that the dependencies were listed so I could get >> all the dependencies to install on the first try. >> > > Thank you so much for all your hard work. Its extremely valuable. That > said, I'm no longer recommending the usage of Bundle::BioPerl. Instead > what I'll do is apply your discovered order to the new Build.PL > installation system. > > You're welcome of course to contact Chris Dagdigian to make sure he > knows about your new version of Bundle::BioPerl. He can then upload it > to CPAN if he's happy with it, and people who choose to still use the > Makefile.PL installation process will surely appreciate the new version > of Bundle::BioPerl. > Good. Having Build.PL do all the work is the best solution. -- Conrad -- Conrad Halling chhalling at verizon.net From hlapp at gmx.net Wed Nov 29 23:03:08 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 29 Nov 2006 23:03:08 -0500 Subject: [Bioperl-l] release timetable Message-ID: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Sendu - what is the timetable in your mind for getting the release out? The NESCent phyloinformatics hackathon is impending and if at all possible I'd really like to see the release be out of the way when it starts so that all new code can simply go the main trunk and has no chance of interfering with the release. Do you think this won't be a problem, or should we start thinking about how to expedite the release in a sensible manner? If anyone else on the list has any concerns about that code going right into the main trunk, please let me know. We (the hackathon attendees) may have to relax the must-pass-all- tests rule, so it may take until a couple days after the end of the event until some sharp edges are smoothened out. I would rather not make any guarantees as to what we will not break, and instead focus on getting the work committed. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Wed Nov 29 23:59:50 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 22:59:50 -0600 Subject: [Bioperl-l] release timetable In-Reply-To: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Message-ID: <8BA20ADA-5114-4DAA-A95F-CBD22C80CC26@uiuc.edu> On Nov 29, 2006, at 10:03 PM, Hilmar Lapp wrote: > Sendu - > > what is the timetable in your mind for getting the release out? The > NESCent phyloinformatics hackathon is impending and if at all > possible I'd really like to see the release be out of the way when it > starts so that all new code can simply go the main trunk and has no > chance of interfering with the release. > > Do you think this won't be a problem, or should we start thinking > about how to expedite the release in a sensible manner? > > If anyone else on the list has any concerns about that code going > right into the main trunk, please let me know. > > We (the hackathon attendees) may have to relax the must-pass-all- > tests rule, so it may take until a couple days after the end of the > event until some sharp edges are smoothened out. I would rather not > make any guarantees as to what we will not break, and instead focus > on getting the work committed. > > -hilmar I think most everyone would agree that the final rel. 1.5.2 should be out soon. I vote for a release before the hackathon, essentially for the same reasons you already outlined. This will get the 1.5.2 code out in the wild for testing, which will (hopefully) iron out any kinks with Module::Build and other residual bugs. If needed we could always have another developer release in the spring to clean up anything from the hackathon, fix bugs from this release, etc. Like you mentioned before, this is (and should be considered by all) a developer release, so not all tests need to pass. Saying that, I applaud Sendu and Nathan (and everyone else) for their hard work. I think this is the first time I can remember where all tests pass for all systems (though I only used since rel 1.0). Even if it's for a finite period of time. -chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 30 02:50:06 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 07:50:06 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Message-ID: <456E8D2E.60908@sendu.me.uk> Hilmar Lapp wrote: > Sendu - > > what is the timetable in your mind for getting the release out? The > NESCent phyloinformatics hackathon is impending and if at all possible > I'd really like to see the release be out of the way when it starts so > that all new code can simply go the main trunk and has no chance of > interfering with the release. I'm going to do one final merge from HEAD to branch-1-5-2 and then set the final release tags later today, so a) anything done at the hackathon won't make any difference, and b) the release should go out soon. The release will go ahead when I've sorted out the Windows PPM and the Change Log (neither of which require code changes on the branch). On this schedule I won't be able to implement Conrad's pre-req installation order in Build.PL since that would require a substantial change to ModuleBuildBioperl.pm and another RC. I'll do that after release so that 1.5.3 benefits. From n.haigh at sheffield.ac.uk Thu Nov 30 03:35:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 08:35:08 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E8D2E.60908@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> Message-ID: <456E97BC.9000800@sheffield.ac.uk> Sendu Bala wrote: > Hilmar Lapp wrote: > >> Sendu - >> >> what is the timetable in your mind for getting the release out? The >> NESCent phyloinformatics hackathon is impending and if at all possible >> I'd really like to see the release be out of the way when it starts so >> that all new code can simply go the main trunk and has no chance of >> interfering with the release. >> > > I'm going to do one final merge from HEAD to branch-1-5-2 and then set > the final release tags later today, so a) anything done at the hackathon > won't make any difference, and b) the release should go out soon. > > The release will go ahead when I've sorted out the Windows PPM and the > Change Log (neither of which require code changes on the branch). > > On this schedule I won't be able to implement Conrad's pre-req > installation order in Build.PL since that would require a substantial > change to ModuleBuildBioperl.pm and another RC. I'll do that after > release so that 1.5.3 benefits. > > _______________________________________________ > I've not had the time to test out the new CPAN installation until now. I've just tried it on a clan install of ActivePerl 5.8.8.819 and it didn't install: Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/RemoteBlast.t 9 2304 13 0 0.00% ?? t/rnamotif.t 2 512 72 144 200.00% 1-72 2 tests and 197 subtests skipped. How can I get the test output from CPAN to go to a log file so I can look at the errors more closely? Nath p.s. I think nmake will need to be installed for windows but I'll doublecheck. --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-0, 29/11/2006 Tested on: 30/11/2006 08:35:09 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From bix at sendu.me.uk Thu Nov 30 03:46:44 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 08:46:44 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E97BC.9000800@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> Message-ID: <456E9A74.9020404@sendu.me.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: >> Hilmar Lapp wrote: >> >>> Sendu - >>> >>> what is the timetable in your mind for getting the release out? The >>> NESCent phyloinformatics hackathon is impending and if at all >>> possible I'd really like to see the release be out of the way when it >>> starts so that all new code can simply go the main trunk and has no >>> chance of interfering with the release. >>> >> >> I'm going to do one final merge from HEAD to branch-1-5-2 and then set >> the final release tags later today, so a) anything done at the >> hackathon won't make any difference, and b) the release should go out >> soon. >> >> The release will go ahead when I've sorted out the Windows PPM and the >> Change Log (neither of which require code changes on the branch). >> >> On this schedule I won't be able to implement Conrad's pre-req >> installation order in Build.PL since that would require a substantial >> change to ModuleBuildBioperl.pm and another RC. I'll do that after >> release so that 1.5.3 benefits. >> >> _______________________________________________ >> > > I've not had the time to test out the new CPAN installation until now. > I've just tried it 'it' being RC5? On Windows? > on a clan install of ActivePerl 5.8.8.819 and it > didn't install: > Failed Test Stat Wstat Total Fail Failed List of Failed > ------------------------------------------------------------------------------- > > t/RemoteBlast.t 9 2304 13 0 0.00% ?? > t/rnamotif.t 2 512 72 144 200.00% 1-72 > 2 tests and 197 subtests skipped. > > How can I get the test output from CPAN to go to a log file so I can > look at the errors more closely? I don't know about log files, but you can configure the cmd window to have a large history and then just copy/paste the results. You can also go into the directory that CPAN extracted the archive to and run the tests there manually. Please send me the results of those tests. From n.haigh at sheffield.ac.uk Thu Nov 30 04:28:36 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 09:28:36 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456EA444.1010705@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sendu Bala wrote: >>> Hilmar Lapp wrote: >>> >>>> Sendu - >>>> >>>> what is the timetable in your mind for getting the release out? The >>>> NESCent phyloinformatics hackathon is impending and if at all >>>> possible I'd really like to see the release be out of the way when >>>> it starts so that all new code can simply go the main trunk and has >>>> no chance of interfering with the release. >>>> >>> >>> I'm going to do one final merge from HEAD to branch-1-5-2 and then >>> set the final release tags later today, so a) anything done at the >>> hackathon won't make any difference, and b) the release should go >>> out soon. >>> >>> The release will go ahead when I've sorted out the Windows PPM and >>> the Change Log (neither of which require code changes on the branch). >>> >>> On this schedule I won't be able to implement Conrad's pre-req >>> installation order in Build.PL since that would require a >>> substantial change to ModuleBuildBioperl.pm and another RC. I'll do >>> that after release so that 1.5.3 benefits. >>> >>> _______________________________________________ >>> >> >> I've not had the time to test out the new CPAN installation until >> now. I've just tried it > > 'it' being RC5? On Windows? > > >> on a clan install of ActivePerl 5.8.8.819 and it didn't install: >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ------------------------------------------------------------------------------- >> >> t/RemoteBlast.t 9 2304 13 0 0.00% ?? >> t/rnamotif.t 2 512 72 144 200.00% 1-72 >> 2 tests and 197 subtests skipped. >> >> How can I get the test output from CPAN to go to a log file so I can >> look at the errors more closely? > > I don't know about log files, but you can configure the cmd window to > have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the archive to > and run the tests there manually. > > Please send me the results of those tests. > > While I figure this out, I've come across the following: The version of CPAN that ships with ActivePerl 5.8.8.819 is 1.7602 and the first version of CPAN to support setting the preference of Module::Build over MakeMaker with "o conf prefer_installer MB" is 1.81 according to their change log. As a result, the default installation of Bioperl on ActivePerl 5.8.8.819 will always use Makefile.PL if it's available. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-0, 29/11/2006 Tested on: 30/11/2006 09:28:37 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From n.haigh at sheffield.ac.uk Thu Nov 30 07:50:57 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 12:50:57 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456ED3B1.9060208@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sendu Bala wrote: >>> Hilmar Lapp wrote: >>> >>>> Sendu - >>>> >>>> what is the timetable in your mind for getting the release out? The >>>> NESCent phyloinformatics hackathon is impending and if at all >>>> possible I'd really like to see the release be out of the way when >>>> it starts so that all new code can simply go the main trunk and has >>>> no chance of interfering with the release. >>>> >>> >>> I'm going to do one final merge from HEAD to branch-1-5-2 and then >>> set the final release tags later today, so a) anything done at the >>> hackathon won't make any difference, and b) the release should go >>> out soon. >>> >>> The release will go ahead when I've sorted out the Windows PPM and >>> the Change Log (neither of which require code changes on the branch). >>> >>> On this schedule I won't be able to implement Conrad's pre-req >>> installation order in Build.PL since that would require a >>> substantial change to ModuleBuildBioperl.pm and another RC. I'll do >>> that after release so that 1.5.3 benefits. >>> >>> _______________________________________________ >>> >> >> I've not had the time to test out the new CPAN installation until >> now. I've just tried it > > 'it' being RC5? On Windows? > > >> on a clan install of ActivePerl 5.8.8.819 and it didn't install: >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ------------------------------------------------------------------------------- >> >> t/RemoteBlast.t 9 2304 13 0 0.00% ?? >> t/rnamotif.t 2 512 72 144 200.00% 1-72 >> 2 tests and 197 subtests skipped. >> >> How can I get the test output from CPAN to go to a log file so I can >> look at the errors more closely? > > I don't know about log files, but you can configure the cmd window to > have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the archive to > and run the tests there manually. > > Please send me the results of those tests. > > > Hi Sendu, Installation on a clean install of ActivePerl 5.8.8.819 n WindowsXP: 1) nmake is required for CPAN installations 2) I updated CPAN to the latest version 3) Restarted CPAN and did "o conf prefer_installer MB" and "o conf commit" 4) Restarted CPAN and tried the install of bioperl 1.5.2 RC5. I still get the message saying it's using Makefile.PL and not Build.PL - not sure why! I'm going to see if updating Module::Build helps. For the time being I installed anyway..... 5) towards the end of dependency checking I get this: -- snip -- Checking if your kit is complete... Looks good Warning: prerequisite DB_File 0 not found. Writing Makefile for Bio ---- Unsatisfied dependencies detected during [S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz] ----- DB_File Shall I follow them and prepend them to the queue of modules we are processing right now? [yes] -- snip -- 6) When running the install, DB_File fails to install and that appears to be the root of the rnamotif test failing: -- snip -- t/rnamotif...................Can't locate DB_File.pm in @INC (@INC contains: t/lib C:\Perl\cpan \build\bioperl-1.5.2_005-RC\blib\lib C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\arch C:/Perl/ site/lib C:/Perl/lib .) at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SeqFeature/Coll ection.pm line 133. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SeqFe ature/Collection.pm line 133. Compilation failed in require at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Tools/RNA Motif.pm line 145. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Tools /RNAMotif.pm line 145. Compilation failed in require at t/rnamotif.t line 27. BEGIN failed--compilation aborted at t/rnamotif.t line 27. t/rnamotif...................dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-72 Failed 72/72 tests, 0.00% okay -- snip -- 7) The RemoteBlast seems to fail due to XML/SAX not being installed: --s nip t/RemoteBlast................ok 10/13Bio::SearchIO: blastxml cannot be found Exception ------------- EXCEPTION ------------- MSG: Failed to load module Bio::SearchIO::blastxml. Can't locate XML/SAX.pm in @INC (@INC conta ins: t C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib C:\Perl\cpan\build\bioperl-1.5.2_005-RC \blib\arch C:/Perl/site/lib C:/Perl/lib .) at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/ Bio\SearchIO\blastxml.pm line 112. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio\Searc hIO\blastxml.pm line 112. Compilation failed in require at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Root/Root .pm line 425. STACK Bio::Root::Root::_load_module C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Root/R oot.pm:427 STACK (eval) C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm:397 STACK Bio::SearchIO::_load_format_module C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/S earchIO.pm:396 STACK Bio::SearchIO::new C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm:176 STACK Bio::Tools::Run::RemoteBlast::retrieve_blast C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib \lib/Bio/Tools/Run/RemoteBlast.pm:603 STACK toplevel t/RemoteBlast.t:185 -------------------------------------- For more information about the SearchIO system please see the SearchIO docs. This includes ways of checking for formats at compile time, not run time Use of uninitialized value in numeric lt (<) at t/RemoteBlast.t line 187. Can't locate object method "new" via package "Bio::SearchIO::blastxml" at C:\Perl\cpan\build\bi operl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm line 177. t/RemoteBlast................dubious Test returned status 9 (wstat 2304, 0x900) after all the subtests completed successfully -- snip -- HTH, Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-1, 30/11/2006 Tested on: 30/11/2006 12:50:59 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From n.haigh at sheffield.ac.uk Thu Nov 30 07:58:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 12:58:08 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456ED560.1020001@sheffield.ac.uk> More updates: After the failed install I updating Module::Build, and re-ran the install, I get: -- snip -- Creating new 'Build' script for 'bioperl' version '1.005002005' Warning: while trying to determine prerequisites for S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi th the help of Module::Build the following error occurred: 'Failed to re-load 'ModuleBuildBiope rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: _build\lib C:\Perl\site\lib C:\ Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. ' Falling back to META.yml for prerequisites 'YAML' not installed, cannot parse 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' -- snip -- Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-1, 30/11/2006 Tested on: 30/11/2006 12:58:09 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From djupiter at tamu.edu Thu Nov 30 01:22:57 2006 From: djupiter at tamu.edu (Daniel Jupiter) Date: Thu, 30 Nov 2006 00:22:57 -0600 Subject: [Bioperl-l] Large databases Message-ID: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> Hi all. I'm new to this list, so if my question is misdirected, or inappropriate, please let me know. The question concerns databases/hashes. I would like to have a rather large hash file. Say 10,000 keys, each with a data field containing roughly 50,000 integers. For whatever reason, the dbm implementation on Mac OSX does not seem to like things of this size. Several strange things happen. First, file size seem to increase exponentially, as I increase the data field size. Additionally, in certain situations, I am returned a rather strange error concerning an uninitialized variable, which has in fact been initialized. In great confusion, I'm just curious as to whether there is a work around for dealing with such large amounts of data, or somewhere with good documentation on using hashes. Thanks. Daniel C. Jupiter, Ph.D. Postdoctoral Research Associate Department of Systems Biology and Translational Medicine College of Medicine Texas A&M University Health Science Center 702 SW H.K. Dodgen Loop Temple, TX 76504 979.997.2106 | Fax 254.742.7145 djupitern at tamu.edu | www.tamhsc.edu ? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: -1.jpeg Type: image/jpeg Size: 19402 bytes Desc: not available URL: From cjfields at uiuc.edu Thu Nov 30 11:13:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 10:13:58 -0600 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> Message-ID: <01b801c7149a$8a9777d0$15327e82@pyrimidine> > Nathan S. Haigh wrote: ... > > How can I get the test output from CPAN to go to a log file > so I can > > look at the errors more closely? > > I don't know about log files, but you can configure the cmd > window to have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the > archive to and run the tests there manually. > > Please send me the results of those tests. Like Sendu, I usually copy from the buffer in the terminal window when running from CPAN (you can set the buffer size for Windows cmd.exe). When running tests manually, I may redirect all output to a temp file, which is a bit easier to scan through since it doesn't wrap text like a cut&paste from the terminal: # Mac OS X ./Build tests &> results.txt # WinXP Build tests > results.txt 2>&1 With Windows I find it sometimes easier to just redirect STDOUT, to avoid all of the 'Subroutine x redefined' warnings. If the CPAN tests go to STDERR you could try redirectly only that stream to a temp file. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Thu Nov 30 11:29:51 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 11:29:51 -0500 Subject: [Bioperl-l] Large databases In-Reply-To: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> References: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> Message-ID: You are aware that you are getting close (or possibly beyond, depending on the exact numbers and if there is any overhead for each integer) the 2GB signed int boundary? Did you make sure that your dbm version is 64-bit enabled and supports 64 bit for filesize? -hilmar On Nov 30, 2006, at 1:22 AM, Daniel Jupiter wrote: > Hi all. > > I'm new to this list, so if my question is misdirected, or > inappropriate, please let me know. > > The question concerns databases/hashes. I would like to have a > rather large hash file. Say 10,000 keys, each with a data field > containing roughly 50,000 integers. For whatever reason, the dbm > implementation on Mac OSX does not seem to like things of this size. > > Several strange things happen. First, file size seem to increase > exponentially, as I increase the data field size. Additionally, in > certain situations, I am returned a rather strange error concerning > an uninitialized variable, which has in fact been initialized. > > In great confusion, I'm just curious as to whether there is a work > around for dealing with such large amounts of data, or somewhere > with good documentation on using hashes. > > Thanks. > > > > Daniel C. Jupiter, Ph.D. > Postdoctoral Research Associate > Department of Systems Biology and Translational Medicine > College of Medicine > Texas A&M University Health Science Center > 702 SW H.K. Dodgen Loop > Temple, TX 76504 > > 979.997.2106 | Fax 254.742.7145 > djupitern at tamu.edu | www.tamhsc.edu > > > <-1.jpeg> > > > > > > > <-1.jpeg> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From st537 at york.ac.uk Thu Nov 30 11:52:27 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Thu, 30 Nov 2006 16:52:27 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C2E01.5070805@sendu.me.uk> References: <456C172F.4060008@york.ac.uk> <456C2E01.5070805@sendu.me.uk> Message-ID: <456F0C4B.2000502@york.ac.uk> Hi, Thanks for helping me with the BLAST code, when I made the corections in ran fine, I'm assuming the returned object $blast_result is a kind of searchio object, although I'm not sure. I tried the code on the bioperl tutorial page for processing a searchio object returned from blast.... http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FASTA_reports_with_Search_and_SearchIO this seems to be the next stage after blasting in the bioperl tutorial but I'm sure how to process it correctly to get hit and alignment information regards, Samantha Thompson Sendu Bala wrote: >Samantha Thompson wrote: > > >>Hi, >>I am trying to learn bioperl and I'm attempting a few basic thing! I >>seem to be ok with reading in and outputting sequences and files now I >>am trying to do a simple BLAST search using a sequence (a sequence >>object in fact). The code I am attempting to run is at the bottom of the >>message... >>I am probably making a dumb mistake and don't understand the >>capabilities of the objects well enough, but the info for the >>remoteblast->submit_blast function says that it can take sequences as an >>argument, I've also tried sending the fasta file name containing my >>sequence as an argument to submit_blast, with the same result.... I >>have also tried sending $seqio_obj->next_seq........... i.e the >>following error message displayed on my terminal: >> >>Can't call method "submit_blast" on an undefined value at bioptest2.pl >>line 22, line 1. >> >> > >Always start your perl scripts with 'use strict;'. This will help you >find and fix the main problem with your script, that you made a >RemoteBlast object and stored it as $remote_blast, but then tried to use >submit_blast() on $remoteBlast which doesn't exist. > >I've rewritten your code below: > >use strict; > > >>use Bio::Seq; >>use Bio::SeqIO; >> >>use Bio::Tools::Run::RemoteBlast; >>use Bio::SearchIO; >> >>#seq bit >> >> >> ># $seq_obj = Bio::Seq->new(-format => 'fasta'); ># above line doesn't do anything, $seq_obj gets overwritten below > > >my $seqio_obj = Bio::SeqIO->new(-file => >"/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > > >my $seq_obj = $seqio_obj->next_seq; > > >> >>#blast bit >> >> >> >my $remote_blast = Bio::Tools::Run::RemoteBlast->new(-prog => 'blastp', >-db => 'nr', -expect => '1e-15' ); > ># submit_blast takes the sequence object, not the sequence string >my $blastreturn_obj = $remote_blast->submit_blast($seq_obj); > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at uiuc.edu Thu Nov 30 12:12:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 11:12:32 -0600 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456F0C4B.2000502@york.ac.uk> Message-ID: <01ba01c714a2$b9659c10$15327e82@pyrimidine> > Hi, > Thanks for helping me with the BLAST code, when I made the > corections in ran fine, I'm assuming the returned object > $blast_result is a kind of searchio object, although I'm not > sure. I tried the code on the bioperl tutorial page for > processing a searchio object returned from blast.... > http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FA > STA_reports_with_Search_and_SearchIO > this seems to be the next stage after blasting in the bioperl > tutorial but I'm sure how to process it correctly to get hit > and alignment information regards, > > Samantha Thompson It is a SearchIO object. FYI, you also have the option of saving the raw BLAST output to a file if needed (it should be described in the RemoteBlast POD). There is also a great HOWTO which goes into more detail about hits/HSPs and how to get alignments: http://www.bioperl.org/wiki/HOWTO:SearchIO chris From bix at sendu.me.uk Thu Nov 30 12:44:38 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 17:44:38 +0000 Subject: [Bioperl-l] Please help with the change log Message-ID: <456F1886.2090708@sendu.me.uk> I'm hoping someone out there is willing to help add summaries for each release to the Change Log: http://bioperl.org/wiki/Change_log Basically, just add a few bullet points about what was new or especially interesting in each release. Thank you, Sendu. From cjfields at uiuc.edu Thu Nov 30 12:50:03 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 11:50:03 -0600 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <438954.89098.qm@web50815.mail.yahoo.com> Message-ID: <000001c714a7$f6ee1300$15327e82@pyrimidine> Katie, Make sure you keep the posts on the mail list, just in case I can't respond but someone else can. > Hi all. > > I just ran the following test script: > > use strict; > use Bio::SearchIO; > my $in = new Bio::SearchIO(-format => 'blast', > -file => 'report.bls'); > while( my $result = $in->next_result ) { > while( my $hit = $result->next_hit ) { > while( my $hsp = $hit->next_hsp ) { > if( $hsp->length('total') > 100 ) { > if ( $hsp->percent_identity >= 75 ) { > print "Hit= ", $hit->name, > ",Length=", $hsp->length('total'), > ",Percent_id=", $hsp->percent_identity, "\n"; > } > } > } > } > } > > and saw the following output: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Could not open report.bls: No such file or directory > STACK: Error::throw > STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:350 > STACK: Bio::Root::IO::_initialize_io > C:/Perl/site/lib/Bio/Root/IO.pm:310 > STACK: Bio::Root::IO::new C:/Perl/site/lib/Bio/Root/IO.pm:223 > STACK: Bio::SearchIO::new C:/Perl/site/lib/Bio/SearchIO.pm:145 > STACK: Bio::SearchIO::new C:/Perl/site/lib/Bio/SearchIO.pm:177 > STACK: test.pl:3 > ----------------------------------------------------------- > > I'm using BioPerl 1.5.2 RC2 > Perl 5.8.8 (Build 819). > WinXP (SP2) > > Thanks, > > ~Katie Is there a BLAST report file named 'report.bls' in the same directory as your script? That's what the error indicates. Chris From n.haigh at sheffield.ac.uk Thu Nov 30 13:24:59 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 18:24:59 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456F2017.8000008@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> <456F2017.8000008@sendu.me.uk> Message-ID: <456F21FB.7090702@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> More updates: >> >> After the failed install I updating Module::Build, and re-ran the >> install, I get: >> >> -- snip -- >> Creating new 'Build' script for 'bioperl' version '1.005002005' >> Warning: while trying to determine prerequisites for >> S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi >> th the help of Module::Build the following error occurred: 'Failed to >> re-load 'ModuleBuildBiope >> rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: >> _build\lib C:\Perl\site\lib C:\ >> Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. >> ' >> >> Falling back to META.yml for prerequisites >> 'YAML' not installed, cannot parse >> 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' >> -- snip -- > > I had that problem fleetingly and it drove me crazy because later I > couldn't reproduce it. Is it reproducible on your end? > I've seen it several time and i'm sure I could reproduce it....give me a few mins and i'll see what I can report. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 18:25:01 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From bix at sendu.me.uk Thu Nov 30 13:16:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 18:16:55 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456ED560.1020001@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> Message-ID: <456F2017.8000008@sendu.me.uk> Nathan S. Haigh wrote: > More updates: > > After the failed install I updating Module::Build, and re-ran the > install, I get: > > -- snip -- > Creating new 'Build' script for 'bioperl' version '1.005002005' > Warning: while trying to determine prerequisites for > S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi > th the help of Module::Build the following error occurred: 'Failed to > re-load 'ModuleBuildBiope > rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: > _build\lib C:\Perl\site\lib C:\ > Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. > ' > > Falling back to META.yml for prerequisites > 'YAML' not installed, cannot parse > 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' > -- snip -- I had that problem fleetingly and it drove me crazy because later I couldn't reproduce it. Is it reproducible on your end? From cjfields at uiuc.edu Thu Nov 30 14:11:47 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 13:11:47 -0600 Subject: [Bioperl-l] Intermittent MySQL problems on BioPerl wiki Message-ID: <000201c714b3$6198e4e0$15327e82@pyrimidine> I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and WinXP): Database error >From BioPerl Jump to: navigation, search A database query syntax error has occurred. This may indicate a bug in the software. The last attempted database query was: (SQL query hidden) from within function "MediaWikiBagOStuff::_doquery". MySQL returned error "1205: Lock wait timeout exceeded; try restarting transaction (localhost)". This occurs intermittently when editting pages, logging in, etc. Also, pages loading to the browser seem much slower. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 30 14:19:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 13:19:34 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl5.8.8.819 In-Reply-To: <456F2017.8000008@sendu.me.uk> Message-ID: <000301c714b4$7846e790$15327e82@pyrimidine> > Nathan S. Haigh wrote: > > More updates: > > > > After the failed install I updating Module::Build, and re-ran the > > install, I get: > > > > -- snip -- > > Creating new 'Build' script for 'bioperl' version '1.005002005' > > Warning: while trying to determine prerequisites for > > S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi th the help of > > Module::Build the following error occurred: 'Failed to re-load > > 'ModuleBuildBiope > > rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: > > _build\lib C:\Perl\site\lib C:\ > > Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. > > ' > > > > Falling back to META.yml for prerequisites 'YAML' not installed, > > cannot parse 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' > > -- snip -- > > I had that problem fleetingly and it drove me crazy because > later I couldn't reproduce it. Is it reproducible on your end? During Module::Build installation I see this: ... t\metadata........ok 8/43 skipped: YAML_support feature is not enabled t\metadata2.......ok 4/18 skipped: YAML_support feature is not enabled t\moduleinfo......ok t\notes...........ok t\parents.........ok t\pod_parser......ok t\ppm.............skipped all skipped: C_support not enabled t\runthrough......ok 7/32 skipped: YAML_support feature is not enabled t\signature.......skipped all skipped: $ENV{TEST_SIGNATURE} is not set t\tilde...........ok t\versions........ok t\xs..............skipped all skipped: C_support not enabled All tests successful, 3 tests and 27 subtests skipped. Files=21, Tests=679, 262 wallclock secs ( 0.00 cusr + 0.00 csys = 0.00 CPU) C:\WINDOWS\nmake.EXE test -- OK Running make install ... Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From st537 at york.ac.uk Thu Nov 30 13:50:17 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Thu, 30 Nov 2006 18:50:17 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <01ba01c714a2$b9659c10$15327e82@pyrimidine> References: <01ba01c714a2$b9659c10$15327e82@pyrimidine> Message-ID: <456F27E9.70205@york.ac.uk> Chris Fields wrote: >>Hi, >>Thanks for helping me with the BLAST code, when I made the >>corections in ran fine, I'm assuming the returned object >>$blast_result is a kind of searchio object, although I'm not >>sure. I tried the code on the bioperl tutorial page for >>processing a searchio object returned from blast.... >>http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FA >>STA_reports_with_Search_and_SearchIO >>this seems to be the next stage after blasting in the bioperl >>tutorial but I'm sure how to process it correctly to get hit >>and alignment information regards, >> >>Samantha Thompson >> >> > >It is a SearchIO object. FYI, you also have the option of saving the raw >BLAST output to a file if needed (it should be described in the RemoteBlast >POD). > >There is also a great HOWTO which goes into more detail about hits/HSPs and >how to get alignments: > >http://www.bioperl.org/wiki/HOWTO:SearchIO > > >chris > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/bioper > > Hi, OK, I tried the code at the SearchIO HOWTO, I've pasted it below, you can see where I've added the SearchIO handling part I've changed $in to the $blast_report as this is returned from the submit_blast ... what happens when I run this however is that I get the following error: Can't call method "next_result" without a package or object reference at bioptest2.pl line 31, line 1. Line 31 being: while( my $result = $blast_report->next_result ) { Not sure why this is happening. Thanks for any help... Samantha Thompson use strict; use Bio::Perl; use Bio::Seq; use Bio::SeqIO; use Bio::Tools::Run::RemoteBlast; use Bio::SearchIO; #seq bit #$seq_obj = Bio::Seq->new(-format => 'fasta'); my $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); my $seq_obj = $seqio_obj->next_seq; #blast bit my $remote_blast = Bio::Tools::Run::RemoteBlast->new ( -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); my $blast_report = $remote_blast->submit_blast($seq_obj); #new part for SearchIO... while( my $result = $blast_report->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { if( $hsp->length('total') > 100 ) { if ( $hsp->percent_identity >= 75 ) { print "Hit= ", $hit->name, ",Length=", $hsp->length('total'), ",Percent_id=", $hsp->percent_identity, "\n"; } } } } } From dag at sonsorol.org Thu Nov 30 14:25:16 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 30 Nov 2006 14:25:16 -0500 Subject: [Bioperl-l] [Root-l] Intermittent MySQL problems on BioPerl wiki In-Reply-To: <000201c714b3$6198e4e0$15327e82@pyrimidine> References: <000201c714b3$6198e4e0$15327e82@pyrimidine> Message-ID: Reports like this need to go to support at helpdesk.open-bio.org so that they enter our RT helpdesk queue -- the main reason is that sometimes emails to the root-l at open-bio.org administrators mailing list can get lost in the shuffle. I am going to bounce this message into RT and will restart mysql on the portal box. This is probably something we should be doing anyway to free up memory -- the wikis in particular seem to be pretty hard on mysql and free memory. -Chris On Nov 30, 2006, at 2:11 PM, Chris Fields wrote: > I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and > WinXP): > > Database error >> From BioPerl > Jump to: navigation, search > A database query syntax error has occurred. This may indicate a bug > in the > software. The last attempted database query was: > > (SQL query hidden) > > from within function "MediaWikiBagOStuff::_doquery". MySQL returned > error > "1205: Lock wait timeout exceeded; try restarting transaction > (localhost)". > > > This occurs intermittently when editting pages, logging in, etc. > Also, > pages loading to the browser seem much slower. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > _______________________________________________ > Root-l mailing list > Root-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/root-l From n.haigh at sheffield.ac.uk Thu Nov 30 15:07:24 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 20:07:24 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456F21FB.7090702@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> <456F2017.8000008@sendu.me.uk> <456F21FB.7090702@sheffield.ac.uk> Message-ID: <456F39FC.9070805@sheffield.ac.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: > >> Nathan S. Haigh wrote: >> >>> More updates: >>> >>> After the failed install I updating Module::Build, and re-ran the >>> install, I get: >>> >>> -- snip -- >>> Creating new 'Build' script for 'bioperl' version '1.005002005' >>> Warning: while trying to determine prerequisites for >>> S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi >>> th the help of Module::Build the following error occurred: 'Failed to >>> re-load 'ModuleBuildBiope >>> rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: >>> _build\lib C:\Perl\site\lib C:\ >>> Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. >>> ' >>> >>> Falling back to META.yml for prerequisites >>> 'YAML' not installed, cannot parse >>> 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' >>> -- snip -- >>> >> I had that problem fleetingly and it drove me crazy because later I >> couldn't reproduce it. Is it reproducible on your end? >> >> > > I've seen it several time and i'm sure I could reproduce it....give me a > few mins and i'll see what I can report. > > Nath > > > --- > avast! Antivirus: Outbound message clean. > Virus Database (VPS): 0652-2, 30/11/2006 > Tested on: 30/11/2006 18:25:01 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > --- > avast! Antivirus: Inbound message clean. > Virus Database (VPS): 0652-2, 30/11/2006 > Tested on: 30/11/2006 18:50:39 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > > Reproduce: 1) clean install of ActivePerl 5.8.8.819 on WinXP 2) Install nmake in path 3) run "cpan CPAN" to install the latest version of CPAN module 4) ran cpan, accepted default for new CPAN configuration, ran "o conf prefer_installer MB" and "o conf commit" then "q" 5) run "cpan Module::Build" to install the latest version of Module::Build 6) run "cpan" and then "install S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" 7) Choose not to install optional modules 8) Error shows here Installing all optional modules doesn't produce the error. However, It produces the problem i've told you about missing "scripts" dir (actually, it's not just the scripts dir - it's all but the base dir it was unpacked into). Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 20:07:25 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From cjfields at uiuc.edu Thu Nov 30 15:48:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 14:48:26 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXPActivePerl 5.8.8.819 In-Reply-To: <456F39FC.9070805@sheffield.ac.uk> Message-ID: <000801c714c0$e26eff70$15327e82@pyrimidine> > Nathan S. Haigh wrote: > Reproduce: > 1) clean install of ActivePerl 5.8.8.819 on WinXP > 2) Install nmake in path > 3) run "cpan CPAN" to install the latest version of CPAN module > 4) ran cpan, accepted default for new CPAN configuration, ran > "o conf prefer_installer MB" and "o conf commit" then "q" > 5) run "cpan Module::Build" to install the latest version of > Module::Build > 6) run "cpan" and then "install > S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" > 7) Choose not to install optional modules > 8) Error shows here > > Installing all optional modules doesn't produce the error. > However, It produces the problem i've told you about missing > "scripts" dir (actually, it's not just the scripts dir - it's > all but the base dir it was unpacked into). > > Nath Confirmed, using same setup as Nathan. chris From cjfields at uiuc.edu Thu Nov 30 16:27:17 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 15:27:17 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <000801c714c0$e26eff70$15327e82@pyrimidine> Message-ID: <002401c714c6$53f65080$15327e82@pyrimidine> > > Nathan S. Haigh wrote: > > Reproduce: > > 1) clean install of ActivePerl 5.8.8.819 on WinXP > > 2) Install nmake in path > > 3) run "cpan CPAN" to install the latest version of CPAN module > > 4) ran cpan, accepted default for new CPAN configuration, > ran "o conf > > prefer_installer MB" and "o conf commit" then "q" > > 5) run "cpan Module::Build" to install the latest version of > > Module::Build > > 6) run "cpan" and then "install > > S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" > > 7) Choose not to install optional modules > > 8) Error shows here > > > > Installing all optional modules doesn't produce the error. > > However, It produces the problem i've told you about > missing "scripts" > > dir (actually, it's not just the scripts dir - it's all but > the base > > dir it was unpacked into). > > > > Nath > > Confirmed, using same setup as Nathan. > > chris Okay, revise that. I get the message you mentioned, but installation only fails after tests are run. The single failed test (rnamotif.t) is due to DB_File not being installed, which Sendu has corrected in CVS and (I think) the 1.5.2 branch. However, I can't get DB_File to install via CPAN (I have VC++ Express Edition installed). I think XML::SAX and a few others fail as well. Chris From n.haigh at sheffield.ac.uk Thu Nov 30 16:41:30 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 21:41:30 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <002401c714c6$53f65080$15327e82@pyrimidine> References: <002401c714c6$53f65080$15327e82@pyrimidine> Message-ID: <456F500A.7010707@sheffield.ac.uk> Chris Fields wrote: >>> Nathan S. Haigh wrote: >>> Reproduce: >>> 1) clean install of ActivePerl 5.8.8.819 on WinXP >>> 2) Install nmake in path >>> 3) run "cpan CPAN" to install the latest version of CPAN module >>> 4) ran cpan, accepted default for new CPAN configuration, >>> >> ran "o conf >> >>> prefer_installer MB" and "o conf commit" then "q" >>> 5) run "cpan Module::Build" to install the latest version of >>> Module::Build >>> 6) run "cpan" and then "install >>> S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" >>> 7) Choose not to install optional modules >>> 8) Error shows here >>> >>> Installing all optional modules doesn't produce the error. >>> However, It produces the problem i've told you about >>> >> missing "scripts" >> >>> dir (actually, it's not just the scripts dir - it's all but >>> >> the base >> >>> dir it was unpacked into). >>> >>> Nath >>> >> Confirmed, using same setup as Nathan. >> >> chris >> > > Okay, revise that. I get the message you mentioned, but installation only > fails after tests are run. The single failed test (rnamotif.t) is due to > DB_File not being installed, which Sendu has corrected in CVS and (I think) > the 1.5.2 branch. However, I can't get DB_File to install via CPAN (I have > VC++ Express Edition installed). I think XML::SAX and a few others fail as > well. > > Chris > > > Yes that's correct, I get the message but things then seem to proceed normally (not that I know what normal is!). I had to install DB_File via PPM and install XML::SAX explicitly in CPAN. That then seems to have cleared things up and the tests pass and bioperl core is installed. However, there are other optional dependencies that didn't install successfully - I suppose I should investigate those tomorrow. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 21:41:31 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From gwu at molbio.mgh.harvard.edu Thu Nov 30 17:08:08 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Thu, 30 Nov 2006 17:08:08 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> Message-ID: <456F5648.6070207@molbio.mgh.harvard.edu> Thanks Hilmar. Do you mean the NVL() clause will make load_seqdatabase.pl not work when update? I have problem with updating. Seems load_seqdatabase.pl only tries to insert instead of update. I used one of the test genbank file coming whith bioperl-db. Please take a look at the attached output. Thanks. Gang ========================================= >perl load_seqdatabase.pl -lookup -host elegans -driver Oracle -dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank -namespace test /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/AP000868.gb Loading /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/AP000868.gb ... -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("This sequence was reannotated via the Ensembl system. Please visit the Ensembl web site, http://www.ensembl.org/ for more information. ","1") FKs (389109) ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) violated (DBD ERROR: OCIStmtExecute) --------------------------------------------------- -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("The /gene indicates a unique id for a gene, /cds a unique id for a translation and a /exon a unique id for an exon. These ids are maintained wherever possible between versions. For more information on how to interpret the feature table, please visit http://www.ensembl.org/Docs/embl.html. ","2") FKs (389109) ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) violated (DBD ERROR: OCIStmtExecute) --------------------------------------------------- ... ... ========================================================== Hilmar Lapp wrote: > These are the protein translations stored in the feature table as > tags of features, right? > > You can change the type of the column (although there may be some > issues when you update the column because the NVL() clause won't work > if I recall that correctly), but doing so will deprive you of any > 'normal' searches against that column. (You can still use functions > from the DBMS_LOB package, but they will be much slower and are > completely non-standard.) > > It is up to you whether that is too big of a price to pay for having > some redundant protein translations (translating the feature's DNA > sequence should give you the same) in the database. I always trimmed > those feature tags off (using a custom SeqProcessor). An alternative > is to convert these feature tags into actual bioentries (i.e., > Bio::Seq objects; again, a custom SeqProcessor will allow you to do > that). > > -hilmar > > On Nov 28, 2006, at 4:13 PM, gang wu wrote: > > >> Hi everyone, >> >> I'm using load_seqdatabase.pl to upload some Genbank genome >> sequences to >> my Oracle BioSQL database. I saw some errors(See attached warning >> message) related to seqfeature_qualifier_value >> (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data >> type of maximum 4000 bytes. Did anybody mention this issue before? >> Should I just modify the column to a type being able store more data >> such as LONG or CLOB? >> >> Thanks. >> >> Gang >> >> >> Log information: >> ============================================ >> >> load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser >> biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank >> /genomeseq/arabidopsis//NC_003070.gbk >> >> >> Loading /genomeseq/arabidopsis//NC_003070.gbk ... >> >> >> -------------------- WARNING --------------------- >> MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement >> execution: ORA-01461: can bind a LONG value only for insert into a >> LONG >> column (DBD ERROR: error possibly near <*> indicator at char 12 in >> 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, >> rank) VALUES (:p1, :p2, :p3, :p4)') >> name: INSERT ASSOC [2] >> Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue >> values: FK[Bio::SeqFeature::Generic]:14898, >> FK[Bio::Annotation::SimpleValue]:800, >> value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFV >> GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADR >> GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEI >> LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFP >> WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERA >> SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRY >> IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEA >> EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDI >> NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDW >> RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFAL >> DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDN >> QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRY >> MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYT >> FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGL >> VQATYQASA! >> >> PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKV >> HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAY >> TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFV >> SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSE >> KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLG >> NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEV >> TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQL >> EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTL >> SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVT >> ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRL >> MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAV >> PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEY >> TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVD >> ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLR >> VKLDFNFM! >> >> YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQS >> QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSN >> TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCL >> SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWD >> ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSE >> IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASV >> TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGL >> HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSS >> KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDF >> QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGL >> HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVA >> RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCL >> LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRN >> GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVE >> NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPL >> WLSVGADAS! >> >> VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVY >> LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITND >> SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQES >> AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTS >> DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSV >> FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESW >> QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIV >> RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMS >> VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRV >> YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAM >> SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDI >> LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAK >> SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLR >> PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMG >> QRKFIPAK! >> >> DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQ >> AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", >> rank:"1" >> -------------------------------------------------- >> >> >> ============================================= >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > From cjfields at uiuc.edu Thu Nov 30 17:16:02 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 16:16:02 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <456F500A.7010707@sheffield.ac.uk> References: <002401c714c6$53f65080$15327e82@pyrimidine> <456F500A.7010707@sheffield.ac.uk> Message-ID: <202B1F50-E905-46DE-9EB5-5F206AC04523@uiuc.edu> On Nov 30, 2006, at 3:41 PM, Nathan S. Haigh wrote: > ... >> >> Okay, revise that. I get the message you mentioned, but >> installation only >> fails after tests are run. The single failed test (rnamotif.t) is >> due to >> DB_File not being installed, which Sendu has corrected in CVS and >> (I think) >> the 1.5.2 branch. However, I can't get DB_File to install via >> CPAN (I have >> VC++ Express Edition installed). I think XML::SAX and a few >> others fail as >> well. >> >> Chris >> >> >> > > Yes that's correct, I get the message but things then seem to > proceed normally (not that I know what normal is!). > I had to install DB_File via PPM and install XML::SAX explicitly in > CPAN. That then seems to have cleared things up and the tests pass > and bioperl core is installed. However, there are other optional > dependencies that didn't install successfully - I suppose I should > investigate those tomorrow. > > Nath The DB_File failure is due to compilation problems. BTW, I can get XML::SAX to install, so that shouldn't be an issue. I know that setting up the PPM is a pain, but I have to say it is much faster, and all required PPMs are available. Which makes me curious: why bother with trying out a CPAN installation process at this point, especially when you have to use PPM to install some of the prereqs properly anyway? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From pelikan at cs.pitt.edu Thu Nov 30 17:19:29 2006 From: pelikan at cs.pitt.edu (pelikan at cs.pitt.edu) Date: Thu, 30 Nov 2006 17:19:29 -0500 (EST) Subject: [Bioperl-l] Error with supplied lineages importing uniprot data Message-ID: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> Hello all, I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows, without Cygwin. The "make test"s have all completed without error. This is my first time dealing with bioperl, so bear with me. I've successfully loaded the most recent taxonomy information using the biosql-schema scripts. After this, I attempted to load the most recent release of the uniprot flat file dataset with the following command: load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat I am subsequently greeted by many of the following errors: Could not store Q7N3Q6: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: The supplied lineage does not start near 'Photorhabdus luminescens subsp. laumondii' STACK: Error::throw STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio\Root\Root.pm:359 STACK: Bio::Species::classification C:/Perl/site/lib/Bio\Species.pm:166 STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:55 STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row C:/Perl/site/lib/Bio\DB\BioSQL\SpeciesAdaptor.pm:281 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key C:/Perl/site/lib/Bio/DB/BioSQL/BasePersisten STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenc STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: STACK: Bio::DB::Persistent::PersistentObject::create C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:244 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:2 STACK: Bio::DB::Persistent::PersistentObject::store C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:271 STACK: C:\DATA\MYSQL\cvs\src\bioperl\bioperl-db-1.5.2_005-RC\scripts\biosql\load_seqdatabase.pl:620 ----------------------------------------------------------- Can someone shed some light on why this may be taking place? -Richard From hlapp at gmx.net Thu Nov 30 18:28:40 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 18:28:40 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <456F5648.6070207@molbio.mgh.harvard.edu> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> <456F5648.6070207@molbio.mgh.harvard.edu> Message-ID: <70B28FBB-0250-4EB8-8775-CD0537369A3D@gmx.net> Right. You need to tell it to lookup sequences first if you know that you are loading sequences which may be in the database already (see the POD of load_seqdatabase.pl, switch --lookup; there are several other command line options that control what will happen if a sequence entry is already present in the database.). The messages in you report are warnings, not errors. It looks like some of the comments are duplicated for a sequence, it doesn't look like reason for concern. Is not so good if you get errors thrown. -hilmar On Nov 30, 2006, at 5:08 PM, gang wu wrote: > Thanks Hilmar. Do you mean the NVL() clause will make > load_seqdatabase.pl not work when update? > > I have problem with updating. Seems load_seqdatabase.pl only tries > to insert instead of update. I used one of the test genbank file > coming whith bioperl-db. Please take a look at the attached output. > > Thanks. > > Gang > > ========================================= > >perl load_seqdatabase.pl -lookup -host elegans -driver Oracle - > dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank - > namespace test /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/ > biosql/data/AP000868.gb > Loading /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/ > AP000868.gb ... > > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, > values were ("This sequence was reannotated via the Ensembl system. > Please visit the Ensembl web site, http://www.ensembl.org/ for more > information. ","1") FKs (389109) > ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) > violated (DBD ERROR: OCIStmtExecute) > --------------------------------------------------- > > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, > values were ("The /gene indicates a unique id for a gene, /cds a > unique id for a translation and a /exon a unique id for an exon. > These ids are maintained wherever possible between versions. For > more information on how to interpret the feature table, please > visit http://www.ensembl.org/Docs/embl.html. ","2") FKs (389109) > ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) > violated (DBD ERROR: OCIStmtExecute) > --------------------------------------------------- > ... > ... > ========================================================== > Hilmar Lapp wrote: >> These are the protein translations stored in the feature table as >> tags of features, right? You can change the type of the column >> (although there may be some issues when you update the column >> because the NVL() clause won't work if I recall that correctly), >> but doing so will deprive you of any 'normal' searches against >> that column. (You can still use functions >from the DBMS_LOB >> package, but they will be much slower and are completely non- >> standard.) It is up to you whether that is too big of a price to >> pay for having some redundant protein translations (translating >> the feature's DNA sequence should give you the same) in the >> database. I always trimmed those feature tags off (using a custom >> SeqProcessor). An alternative is to convert these feature tags >> into actual bioentries (i.e., Bio::Seq objects; again, a custom >> SeqProcessor will allow you to do that). -hilmar On Nov 28, 2006, >> at 4:13 PM, gang wu wrote: >>> Hi everyone, I'm using load_seqdatabase.pl to upload some Genbank >>> genome sequences to my Oracle BioSQL database. I saw some errors >>> (See attached warning message) related to >>> seqfeature_qualifier_value (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE >>> column), which has Varchar2 data type of maximum 4000 bytes. Did >>> anybody mention this issue before? Should I just modify the >>> column to a type being able store more data such as LONG or CLOB? >>> Thanks. Gang Log information: >>> ============================================ load_seqdatabase.pl - >>> host elegans -driver Oracle -dbname sparc -dbuser biosqldb- >>> sgowner -dbpass PASS -format genbank -namespace genbank / >>> genomeseq/arabidopsis//NC_003070.gbk Loading /genomeseq/ >>> arabidopsis//NC_003070.gbk ... -------------------- WARNING >>> --------------------- MSG: SimpleValueAdaptor::add_assoc: >>> unexpected failure of statement execution: ORA-01461: can bind a >>> LONG value only for insert into a LONG column (DBD ERROR: error >>> possibly near <*> indicator at char 12 in 'INSERT INTO >>> <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, rank) >>> VALUES (:p1, :p2, :p3, :p4)') name: INSERT ASSOC [2] >>> Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue values: FK >>> [Bio::SeqFeature::Generic]:14898, FK >>> [Bio::Annotation::SimpleValue]:800, >>> value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSG >>> FV >>> GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASA >>> DR >>> GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSS >>> EI >>> LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNS >>> FP >>> WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFE >>> RA >>> SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYT >>> RY >>> IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRT >>> EA >>> EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIV >>> DI >>> NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENI >>> DW >>> RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRF >>> AL >>> DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGS >>> DN >>> QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPT >>> RY >>> MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYL >>> YT >>> FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLR >>> GL VQATYQASA! >>> PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGG >>> KV >>> HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDED >>> AY >>> TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSD >>> FV >>> SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSD >>> SE >>> KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGT >>> LG >>> NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQ >>> EV >>> TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLG >>> QL >>> EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVP >>> TL >>> SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRT >>> VT >>> ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEM >>> RL >>> MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRIL >>> AV >>> PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGID >>> EY >>> TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDG >>> VD >>> ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKL >>> LR VKLDFNFM! >>> YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNL >>> QS >>> QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAV >>> SN >>> TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVY >>> CL >>> SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSG >>> WD >>> ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADD >>> SE >>> IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEA >>> SV >>> TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLD >>> GL >>> HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQ >>> SS >>> KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDED >>> DF >>> QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAK >>> GL >>> HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKG >>> VA >>> RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNG >>> CL >>> LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSM >>> RN >>> GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPK >>> VE >>> NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSK >>> PL WLSVGADAS! >>> VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRP >>> VY >>> LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWIT >>> ND >>> SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQ >>> ES >>> AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNM >>> TS >>> DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPF >>> SV >>> FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSE >>> SW >>> QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKN >>> IV >>> RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILY >>> MS >>> VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDL >>> RV >>> YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSM >>> AM >>> SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGV >>> DI >>> LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEG >>> AK >>> SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSL >>> LR >>> PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNI >>> MG QRKFIPAK! >>> DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAI >>> DQ AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", >>> rank:"1" -------------------------------------------------- >>> ============================================= >>> _______________________________________________ Bioperl-l mailing >>> list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/ >>> mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Nov 30 18:31:41 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 18:31:41 -0500 Subject: [Bioperl-l] Error with supplied lineages importing uniprot data In-Reply-To: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> References: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> Message-ID: <24C694D6-1124-48A9-8C7C-FA58AB598F01@gmx.net> Maybe Sendu can shed light on what might be happening here? On Nov 30, 2006, at 5:19 PM, pelikan at cs.pitt.edu wrote: > Hello all, > > I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows, > without Cygwin. The "make test"s have all completed without error. > This > is my first time dealing with bioperl, so bear with me. > > I've successfully loaded the most recent taxonomy information > using the > biosql-schema scripts. After this, I attempted to load the most recent > release of the uniprot flat file dataset with the following command: > > load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass > ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat > > I am subsequently greeted by many of the following errors: > > Could not store Q7N3Q6: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: The supplied lineage does not start near 'Photorhabdus > luminescens > subsp. laumondii' > STACK: Error::throw > STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio\Root\Root.pm:359 > STACK: Bio::Species::classification C:/Perl/site/lib/Bio\Species.pm: > 166 > STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:55 > STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row > C:/Perl/site/lib/Bio\DB\BioSQL\SpeciesAdaptor.pm:281 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersisten > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenc > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: > STACK: Bio::DB::Persistent::PersistentObject::create > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:244 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:2 > STACK: Bio::DB::Persistent::PersistentObject::store > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:271 > STACK: > C:\DATA\MYSQL\cvs\src\bioperl\bioperl-db-1.5.2_005-RC\scripts\biosql > \load_seqdatabase.pl:620 > ----------------------------------------------------------- > > Can someone shed some light on why this may be taking place? > > -Richard > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From The_Polymorph at rocketmail.com Thu Nov 30 18:58:22 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 30 Nov 2006 15:58:22 -0800 (PST) Subject: [Bioperl-l] Upgrading my BioPerl RC via ppm? In-Reply-To: <000001c714a7$f6ee1300$15327e82@pyrimidine> Message-ID: <519167.29410.qm@web50804.mail.yahoo.com> Hi all. I'm currently using BioPerl 1.5.2 RC2 but I've seen multiple references to 1.5.2 RC5. Can anyone tell me how to upgrade to the latest version? The ppm GUI (ActivePerl Build 819) doesn't include any BioPerl packages among those deemed upgradable. Thanks, ~Katie "Be who you are and say what you feel because those who mind don't matter and those who matter don't mind." - Dr. Seuss, "Oh the Places You'll Go" ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com From arareko at campus.iztacala.unam.mx Thu Nov 30 19:56:02 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Thu, 30 Nov 2006 18:56:02 -0600 Subject: [Bioperl-l] [Root-l] Intermittent MySQL problems on BioPerl wiki In-Reply-To: References: <000201c714b3$6198e4e0$15327e82@pyrimidine> Message-ID: <456F7DA2.7000408@campus.iztacala.unam.mx> Chris & Chris, I've run the maintenance scripts for MediaWiki (just in case they weren't run in the upgrade to 1.8.2), restarted Apache (with no significant changes on website response), then rebooted the machine (seems like MySQL restart didn't do the trick) and apparently its behaving much better. Please check if the reported error still happens. Regards, Mauricio. Chris Dagdigian wrote: > Reports like this need to go to support at helpdesk.open-bio.org so that > they enter our RT helpdesk queue -- the main reason is that > sometimes emails to the root-l at open-bio.org administrators mailing > list can get lost in the shuffle. > > I am going to bounce this message into RT and will restart mysql on > the portal box. This is probably something we should be doing anyway > to free up memory -- the wikis in particular seem to be pretty hard > on mysql and free memory. > > -Chris > > On Nov 30, 2006, at 2:11 PM, Chris Fields wrote: > >> I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and >> WinXP): >> >> Database error >>> From BioPerl >> Jump to: navigation, search >> A database query syntax error has occurred. This may indicate a bug >> in the >> software. The last attempted database query was: >> >> (SQL query hidden) >> >> from within function "MediaWikiBagOStuff::_doquery". MySQL returned >> error >> "1205: Lock wait timeout exceeded; try restarting transaction >> (localhost)". >> >> >> This occurs intermittently when editting pages, logging in, etc. >> Also, >> pages loading to the browser seem much slower. >> >> Christopher Fields >> Postdoctoral Researcher - Switzer Lab >> Dept. of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> _______________________________________________ >> Root-l mailing list >> Root-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/root-l > > _______________________________________________ > Root-l mailing list > Root-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/root-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From huangyi1 at hkusua.hku.hk Wed Nov 1 03:25:10 2006 From: huangyi1 at hkusua.hku.hk (Huang Yi) Date: Wed, 1 Nov 2006 16:25:10 +0800 Subject: [Bioperl-l] bioperl1.5 and GD2.35 - solved In-Reply-To: <1A4207F8295607498283FE9E93B775B4023B5F3C@EX02.asurite.ad.asu.edu> Message-ID: <200611010825.kA18PGWu022850@hkusua.hku.hk> The problem was solved. I re-emerged gd-2.0.33 with png USE flag. Thanks again! Huang Yi -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Kevin Brown Sent: Tuesday, October 31, 2006 11:35 PM To: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] bioperl1.5 and GD2.35 Not really a Bioperl issue per se, but sounds like when you had Gentoo emerge GD it didn't include libpng and so didn't build the needed parts to create PNG type graphics. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Huang Yi > Sent: Monday, October 30, 2006 10:46 PM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] bioperl1.5 and GD2.35 > > Hi, > > > > I just installed bioperl 1.4 from CPAN to my Gentoo linux > computer. But the > installation was failed. I had to install by force. > > > > However, the GD module couldn't be installed for some unknown reasons. > > > > I therefore use "emerge" tool of Gentoo to get bioperl and GD > again. They > are fine. The version of bioperl became upgrade to1.5 and GD was 2.35. > > > > However, when I tested it by using the program in HOWTO wiki page > (http://www.bioperl.org/wiki/HOWTO:Graphics), it always told me: > > > > Can't locate object method "png" via package "GD::Image" at > /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Panel.pm line > 799, <> line 9. > > > > In my other computer, bioperl1.4 and GD2.34 work fine. I > therefore want to > remove the CPAN bioperl from the system and re-install it, > but it seems to > be impossible. > > > > Would you please give me some advices on how to let my GD and > bioperl work. > > > > Thanks! > > > > Huang Yi > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/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 nhansen at nhgri.nih.gov Wed Nov 1 08:43:32 2006 From: nhansen at nhgri.nih.gov (Nancy Hansen) Date: Wed, 1 Nov 2006 08:43:32 -0500 (EST) Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: References: Message-ID: On Tue, 31 Oct 2006, Brian Osborne wrote: > It looks like a good place to start would be the get_header() and > _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that > the author, at some point, wanted get_header to return meaningful > information but stepping through the test shows it returning a lot of UNDEF. > Now I don't know if this is due to the method or the source SCF file, but > you might be able to get these methods to work yourself. > > But to answer your questions, yes, it certainly sounds reasonable that these > values would be extracted by Bio::SeqIO::scf. Sounds great! So, if I make these changes, is there someone I should run them by before checking them into CVS? Is Chad Matsalla still involved in bioperl? I've never contributed to the project, so I'm not sure how things work... Thanks! --Nancy ************************************* Nancy F. Hansen, PhD nhansen at nhgri.nih.gov Bioinformatics Group NIH Intramural Sequencing Center (NISC) 5625 Fishers Lane Rockville, MD 20852 Phone: (301) 435-1560 Fax: (301) 435-6170 From arareko at campus.iztacala.unam.mx Wed Nov 1 09:30:34 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed, 01 Nov 2006 08:30:34 -0600 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: References: Message-ID: <4548AF8A.6090205@campus.iztacala.unam.mx> The usual way is to send your modifications as an 'enhancement' through the Bugzilla system (please add your patches as attachments after creating the report, not into the description field): http://bugzilla.open-bio.org/ Thanks for contributing! Regards, Mauricio. Nancy Hansen wrote: > On Tue, 31 Oct 2006, Brian Osborne wrote: > >> It looks like a good place to start would be the get_header() and >> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that >> the author, at some point, wanted get_header to return meaningful >> information but stepping through the test shows it returning a lot of UNDEF. >> Now I don't know if this is due to the method or the source SCF file, but >> you might be able to get these methods to work yourself. >> >> But to answer your questions, yes, it certainly sounds reasonable that these >> values would be extracted by Bio::SeqIO::scf. > > Sounds great! So, if I make these changes, is there someone I should run > them by before checking them into CVS? Is Chad Matsalla still involved in > bioperl? I've never contributed to the project, so I'm not sure how > things work... > > Thanks! > --Nancy > > ************************************* > Nancy F. Hansen, PhD nhansen at nhgri.nih.gov > Bioinformatics Group > NIH Intramural Sequencing Center (NISC) > 5625 Fishers Lane > Rockville, MD 20852 > Phone: (301) 435-1560 Fax: (301) 435-6170 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From cjfields at uiuc.edu Wed Nov 1 09:39:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 1 Nov 2006 08:39:38 -0600 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: Message-ID: <000c01c6fdc3$8ed54770$15327e82@pyrimidine> > On Tue, 31 Oct 2006, Brian Osborne wrote: > >> It looks like a good place to start would be the get_header() and >> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can >> see that the author, at some point, wanted get_header to return >> meaningful information but stepping through the test shows it >> returning a lot of UNDEF. Now I don't know if this is due to the >> method or the source SCF file, but you might be able to get these >> methods to work yourself. >> >> But to answer your questions, yes, it certainly sounds reasonable >> that these values would be extracted by Bio::SeqIO::scf. > > Sounds great! So, if I make these changes, is there someone > I should run them by before checking them into CVS? Is Chad > Matsalla still involved in bioperl? I've never contributed > to the project, so I'm not sure how things work... > > Thanks! > --Nancy You can check them into Bugzilla as a patch to a bug: http://bugzilla.open-bio.org/ There is a HOWTO for patch submission here: http://www.bioperl.org/wiki/HOWTO:SubmitPatch You could also send them to Brian or me. Bugzilla is probably your best bet as anyone with a developer account can check in the fix. You should also write up some tests for your code changes. You can use the test file mentioned above (t/scf.t) as a start. -chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Wed Nov 1 08:00:53 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 01 Nov 2006 09:00:53 -0400 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: Message-ID: Nancy, I suggest doing this through Bugzilla, http://bugzilla.open-bio.org. First add your proposal as a bug or as an enhancement, sounds like it could be either but I'd say it doesn't matter. Then contribute patches to the "bug" as you work, some one will apply them. Also add tests to t/scf.t, if you're working on scf.pm. Thank you in advance for your contributions. As for Chad, I have no idea but strictly speaking no one "owns" a module in Bioperl. Brian O. On 11/1/06 9:43 AM, "Nancy Hansen" wrote: > Sounds great! So, if I make these changes, is there someone I should run > them by before checking them into CVS? Is Chad Matsalla still involved in > bioperl? I've never contributed to the project, so I'm not sure how > things work... From keithplayer at hotmail.com Wed Nov 1 19:22:07 2006 From: keithplayer at hotmail.com (Keith Player) Date: Thu, 2 Nov 2006 00:22:07 +0000 (UTC) Subject: [Bioperl-l] Article Message-ID: Sorry I didn't attach the article link originally. You can view the full-text for free: http://www.genome.org/cgi/content/abstract/12/10/1599 When I was talking about the R-tree I was talking about the current implementation. I should point out that I didn't actually try the perl module directly but implemented the binning schema straight in mysql. I found that by using the SQL I mentioned previously the database performed better compared to using the binning schema, I assume because of less disk seeks. I tested on a dataset of around 30k records and another the same size as the paper. The binning outperformed the queries as described in the paper, but the SQL I mentioned in the first post outperformed the binning schema by around a factor of 3. The new binning schema might make all this moot, especially if it removes layers so that groups/features next to each other are saved on the same/adjacent pages. The only question then would be whether database optimization is effected by the binning. Also does needing to know the largest length of a group/feature make the SQL statement I created impractical? From limericksean at gmail.com Wed Nov 1 11:28:58 2006 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 1 Nov 2006 17:28:58 +0100 Subject: [Bioperl-l] Can't locate object method "new_instance" via package "Bio::DB::SeqFeature::Store::dbi::mysql" at /project/gbrowse/httpd_perllib_new/Bio/DB/SeqFeature/Store.pm line 336. Message-ID: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> Hi, I am currently in the process of trying testing Gbrowse with the (relatively new) Bio::DB::SeqFeature::Store adaptor method. A couple of teething problems, just wondering if anyone else had encountered the message above. Any insight appreciated. Also the package called (Bio::DB::SeqFeature::Store::dbi::mysql) had to be copied into the lowercase 'dbi' from its original DBI form - don't know if this was a previously reported bug. Thanks, Sean. From ybolo001 at student.ucr.edu Wed Nov 1 19:15:57 2006 From: ybolo001 at student.ucr.edu (Eugene Bolotin) Date: Wed, 1 Nov 2006 16:15:57 -0800 Subject: [Bioperl-l] Check sequence format, question Message-ID: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> Dear bioperl mailing list, I trying to get sequence from a file using Bio::SeqIO, before I do anything, I want to make sure that the file is in a correct Fasta sequence format. I want it to spit out an error message if it is in any other format. What is the easiest way to do it? Thanks, Eugene Bolotin Sladek Lab. From cjfields at uiuc.edu Wed Nov 1 23:28:11 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 1 Nov 2006 22:28:11 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> References: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> Message-ID: <24DED46C-4630-4E95-94D0-87810183F191@uiuc.edu> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: > Dear bioperl mailing list, > I trying to get sequence from a file using Bio::SeqIO, before I do > anything, > I want to make sure that the file is in a correct Fasta sequence > format. I > want it to spit out an error message if it is in any other format. > What is the easiest way to do it? > Thanks, > Eugene Bolotin > Sladek Lab. There is no formal FASTA definition that is universally accepted beyond having the first line start with '>' and an optional description, with the sequence in subsequent lines. http://www.bioperl.org/wiki/FASTA_sequence_format Bio::SeqIO isn't currently set up to validate sequence formats directly, but you could try preparsing the data using Bio::Tools::GuessSeqFormat. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Wed Nov 1 21:21:35 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 1 Nov 2006 21:21:35 -0500 Subject: [Bioperl-l] Can't locate object method "new_instance" via package "Bio::DB::SeqFeature::Store::dbi::mysql" at /project/gbrowse/httpd_perllib_new/Bio/DB/SeqFeature/Store.pm line 336. In-Reply-To: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> References: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> Message-ID: <6dce9a0b0611011821l45cd7f8enb2e77f286f7cf6f5@mail.gmail.com> Hi, DBI should be uppercased in the gbrowse config file: [GENERAL] description = C. elegans GFF3 Database db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn ws164_gff3 You shouldn't have to change anything to lowercase. Lincoln On 11/1/06, Sean O'Keeffe wrote: > > Hi, > I am currently in the process of trying testing Gbrowse with the > (relatively new) Bio::DB::SeqFeature::Store adaptor method. A couple > of teething problems, just wondering if anyone else had encountered > the message above. Any insight appreciated. > Also the package called (Bio::DB::SeqFeature::Store::dbi::mysql) had > to be copied into the lowercase 'dbi' from its original DBI form - > don't know if this was a previously reported bug. > > Thanks, > Sean. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From Bernhard.Schmalhofer at biomax.com Thu Nov 2 03:53:14 2006 From: Bernhard.Schmalhofer at biomax.com (Bernhard Schmalhofer) Date: Thu, 02 Nov 2006 09:53:14 +0100 Subject: [Bioperl-l] Is it possible to parse BLAST output using IO:String? In-Reply-To: <716af09c0610301244q1c6d4cd6y23e72371dda4fa4d@mail.gmail.com> References: <00e301c6fc5f$a36de9e0$e6028a0a@GOLHARMOBILE1> <716af09c0610301244q1c6d4cd6y23e72371dda4fa4d@mail.gmail.com> Message-ID: <4549B1FA.1020506@biomax.com> Bernd Web wrote: > Hi Ryan, > > I parse blastn output using IO::String w/o problems: > > my $stringfh = new IO::String($input); > my $in = new Bio::SearchIO(-format => 'blast', -fh => $stringfh); I do the same with implicitly using IO::String. Works like a charm at leaset with Perl 5.8.0. # get $blast_report from MySQL open my $blast_report_fh, '<', \$blast_report; my $in = Bio::SearchIO->new( -format => 'blast', -fh => $blast_report_fh ); Regards, Bernhard -- ************************************************** Dipl.-Physiker Bernhard Schmalhofer Senior Developer Biomax Informatics AG Lochhamer Str. 11 82152 Martinsried, Germany Tel: +49 89 895574-839 Fax: +49 89 895574-825 eMail: Bernhard.Schmalhofer at biomax.com Website: www.biomax.com ************************************************** From cjfields at uiuc.edu Thu Nov 2 10:11:01 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 09:11:01 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <85304914-322B-46BA-BED2-09722FE08D57@uiuc.edu> Brian, I think the validation issue is worthwhile but I can see logistical nightmares having every SeqIO parser validate sequence while parsing; GenBank and EMBL do this to some extent already but it isn't foolproof. Much of SeqIO (e.g. GenBank/EMBL/Swiss parsing) is already in dire need of an overhaul as is w/o adding validation. I wonder if it would be better if SeqIO has-a validator object instead of acting as a validator itself, i.e. SeqIO would focus on parsing and writing, the validator would focus on validation. It might be easier from the maintenance aspect. It's probably worthwhile exploring using Bio::Tools::GuessSeqFormat within SeqIO, or setting up a new system altogether. Validation using the sequence validator could then be enabled by having a validation option when instantiating SeqIO. We could even enable XML format validation using the DTD/Schema, which should be fairly straightforward. Of course, this all depends on someone writing it up... Chris On Nov 2, 2006, at 6:49 AM, Brian Osborne wrote: > Chris et al., > > As you know the question of whether SeqIO should or should not > validate or > check the given format is still an open one. In fact, some SeqIO > modules do > validate to some extent. See: > > http://bugzilla.open-bio.org/show_bug.cgi?id=1508 > > I can see that you've commented on this enhancement, I'm replying > just to > bring this to the attention of others. > > Brian O. > > > On 11/2/06 12:28 AM, "Chris Fields" wrote: > >> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: >> >>> Dear bioperl mailing list, >>> I trying to get sequence from a file using Bio::SeqIO, before I do >>> anything, >>> I want to make sure that the file is in a correct Fasta sequence >>> format. I >>> want it to spit out an error message if it is in any other format. >>> What is the easiest way to do it? >>> Thanks, >>> Eugene Bolotin >>> Sladek Lab. >> >> There is no formal FASTA definition that is universally accepted >> beyond having the first line start with '>' and an optional >> description, with the sequence in subsequent lines. >> >> http://www.bioperl.org/wiki/FASTA_sequence_format >> >> Bio::SeqIO isn't currently set up to validate sequence formats >> directly, but you could try preparsing the data using >> Bio::Tools::GuessSeqFormat. >> >> Chris >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Thu Nov 2 09:38:36 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 10:38:36 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <85304914-322B-46BA-BED2-09722FE08D57@uiuc.edu> Message-ID: Chris, Yes, and validation should always be optional. SeqIO is not always as fast as some want it to be and sometimes you're certain that your files don't need to be validated. Brian O. On 11/2/06 11:11 AM, "Chris Fields" wrote: > Brian, > > I think the validation issue is worthwhile but I can see logistical > nightmares having every SeqIO parser validate sequence while parsing; > GenBank and EMBL do this to some extent already but it isn't > foolproof. Much of SeqIO (e.g. GenBank/EMBL/Swiss parsing) is > already in dire need of an overhaul as is w/o adding validation. > > I wonder if it would be better if SeqIO has-a validator object > instead of acting as a validator itself, i.e. SeqIO would focus on > parsing and writing, the validator would focus on validation. It > might be easier from the maintenance aspect. It's probably > worthwhile exploring using Bio::Tools::GuessSeqFormat within SeqIO, > or setting up a new system altogether. Validation using the sequence > validator could then be enabled by having a validation option when > instantiating SeqIO. We could even enable XML format validation > using the DTD/Schema, which should be fairly straightforward. > > Of course, this all depends on someone writing it up... > > Chris > > On Nov 2, 2006, at 6:49 AM, Brian Osborne wrote: > >> Chris et al., >> >> As you know the question of whether SeqIO should or should not >> validate or >> check the given format is still an open one. In fact, some SeqIO >> modules do >> validate to some extent. See: >> >> http://bugzilla.open-bio.org/show_bug.cgi?id=1508 >> >> I can see that you've commented on this enhancement, I'm replying >> just to >> bring this to the attention of others. >> >> Brian O. >> >> >> On 11/2/06 12:28 AM, "Chris Fields" wrote: >> >>> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: >>> >>>> Dear bioperl mailing list, >>>> I trying to get sequence from a file using Bio::SeqIO, before I do >>>> anything, >>>> I want to make sure that the file is in a correct Fasta sequence >>>> format. I >>>> want it to spit out an error message if it is in any other format. >>>> What is the easiest way to do it? >>>> Thanks, >>>> Eugene Bolotin >>>> Sladek Lab. >>> >>> There is no formal FASTA definition that is universally accepted >>> beyond having the first line start with '>' and an optional >>> description, with the sequence in subsequent lines. >>> >>> http://www.bioperl.org/wiki/FASTA_sequence_format >>> >>> Bio::SeqIO isn't currently set up to validate sequence formats >>> directly, but you could try preparsing the data using >>> Bio::Tools::GuessSeqFormat. >>> >>> Chris >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > From bosborne11 at verizon.net Thu Nov 2 07:49:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 08:49:01 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <24DED46C-4630-4E95-94D0-87810183F191@uiuc.edu> Message-ID: Chris et al., As you know the question of whether SeqIO should or should not validate or check the given format is still an open one. In fact, some SeqIO modules do validate to some extent. See: http://bugzilla.open-bio.org/show_bug.cgi?id=1508 I can see that you've commented on this enhancement, I'm replying just to bring this to the attention of others. Brian O. On 11/2/06 12:28 AM, "Chris Fields" wrote: > On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: > >> Dear bioperl mailing list, >> I trying to get sequence from a file using Bio::SeqIO, before I do >> anything, >> I want to make sure that the file is in a correct Fasta sequence >> format. I >> want it to spit out an error message if it is in any other format. >> What is the easiest way to do it? >> Thanks, >> Eugene Bolotin >> Sladek Lab. > > There is no formal FASTA definition that is universally accepted > beyond having the first line start with '>' and an optional > description, with the sequence in subsequent lines. > > http://www.bioperl.org/wiki/FASTA_sequence_format > > Bio::SeqIO isn't currently set up to validate sequence formats > directly, but you could try preparsing the data using > Bio::Tools::GuessSeqFormat. > > Chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Thu Nov 2 13:07:45 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 12:07:45 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <93F383D1-6DDF-4238-954A-96CE1218C641@uiuc.edu> On Nov 2, 2006, at 8:38 AM, Brian Osborne wrote: > Chris, > > Yes, and validation should always be optional. SeqIO is not always > as fast > as some want it to be and sometimes you're certain that your files > don't > need to be validated. > > Brian O. Agreed. We could use the original Bugzilla bug (1508?) to track this and maybe gather ideas, but the wiki is probably a better place... Chris > On 11/2/06 11:11 AM, "Chris Fields" wrote: > >> ... Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Thu Nov 2 13:08:45 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 14:08:45 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <93F383D1-6DDF-4238-954A-96CE1218C641@uiuc.edu> Message-ID: Chris, Yes, in the Project priority list page. Speaking of this page, why is all of the text on the bottom half of this page crossed out? Many of these items have _not_ been done. Brian O. On 11/2/06 2:07 PM, "Chris Fields" wrote: > Agreed. We could use the original Bugzilla bug (1508?) to track this > and maybe gather ideas, but the wiki is probably a better place... From cjfields at uiuc.edu Thu Nov 2 14:22:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 13:22:48 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <0DA38665-F4CB-4000-974F-47915F0524A2@uiuc.edu> On Nov 2, 2006, at 12:08 PM, Brian Osborne wrote: > Chris, > > Yes, in the Project priority list page. > > Speaking of this page, why is all of the text on the bottom half of > this > page crossed out? Many of these items have _not_ been done. > > Brian O. You're right; they shouldn't be crossed out unless they are completed. If someone takes on a project then they attach their signature to it, not cross it off the list. I'll change that and add a disclaimer to the top of the page. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stewarta at nmrc.navy.mil Thu Nov 2 15:26:08 2006 From: stewarta at nmrc.navy.mil (Andrew Stewart) Date: Thu, 2 Nov 2006 15:26:08 -0500 Subject: [Bioperl-l] Bio::DB::GFF and feature order Message-ID: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> In attempting to determine some statistics on the distances between CDS features in my Bio::DB::GFF database, I ran a query on all CDS features as follows... my @CDS = $segment->features('CDS'); ...only to find that the features returned are not in order. Is there a way of returning the features in order or sorting them through some internal Bio::DB::GFF related method, aside from the more obvious path of sorting through the array itself (somehow)? -A -- Andrew Stewart Research Assistant, Genomics Team Navy Medical Research Center (NMRC) Biological Defense Research Directorate (BDRD) BDRD Annex 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 email: stewarta at nmrc.navy.mil phone: 301-231-6700 Ext 270 From lincoln.stein at gmail.com Thu Nov 2 15:41:06 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 2 Nov 2006 15:41:06 -0500 Subject: [Bioperl-l] [Gmod-gbrowse] Bio::DB::GFF and feature order In-Reply-To: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> References: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> Message-ID: <6dce9a0b0611021241i35f602f2q6ca59f23738d1013@mail.gmail.com> How do you want them sorted? To sort them by their start positions: my @CDS = sort {$a->start<=>$b->start} $segment->features('CDS'); Other people may want to sort features by end position, length, name, or who knows what. Lincoln On 11/2/06, Andrew Stewart wrote: > > In attempting to determine some statistics on the distances between CDS > features in my Bio::DB::GFF database, I ran a query on all CDS features as > follows... > my @CDS = $segment->features('CDS'); > > ...only to find that the features returned are not in order. Is there a > way of returning the features in order or sorting them through some internal > Bio::DB::GFF related method, aside from the more obvious path of sorting > through the array itself (somehow)? > > > -A > > -- > Andrew Stewart > Research Assistant, Genomics Team > Navy Medical Research Center (NMRC) > Biological Defense Research Directorate (BDRD) > BDRD Annex > 12300 Washington Avenue, 2nd Floor > Rockville, MD 20852 > > email: stewarta at nmrc.navy.mil > phone: 301-231-6700 Ext 270 > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From n.haigh at sheffield.ac.uk Thu Nov 2 17:12:28 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 02 Nov 2006 22:12:28 +0000 Subject: [Bioperl-l] $Bio::Root::Version:VERSION Message-ID: <454A6D4C.3020605@sheffield.ac.uk> When does $Bio::Root::Version::VERSION get incremented? immediately prior to a tag or straight after a tag so that CVS code is seen as more recent than an official release? For example, $VERSION is currently set to 1.52_01 but the code in CVS HEAD is passed 1.5.2 RC2 now so should is read 1.52_02 or be 1.52_03 for the upcoming 1.52 RC3? Cheers Nath From bix at sendu.me.uk Thu Nov 2 18:14:57 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 02 Nov 2006 23:14:57 +0000 Subject: [Bioperl-l] $Bio::Root::Version:VERSION In-Reply-To: <454A6D4C.3020605@sheffield.ac.uk> References: <454A6D4C.3020605@sheffield.ac.uk> Message-ID: <454A7BF1.1060705@sendu.me.uk> Nathan S. Haigh wrote: > When does $Bio::Root::Version::VERSION get incremented? immediately > prior to a tag or straight after a tag so that CVS code is seen as more > recent than an official release? Normally nothing happens. > For example, $VERSION is currently set to 1.52_01 but the code in CVS > HEAD is passed 1.5.2 RC2 now so should is read 1.52_02 or be 1.52_03 for > the upcoming 1.52 RC3? Once I've decided what to do based on the discussion we had, I'll update it. I'll currently leaning toward the 'clean break', pugs-style suggestion from Chris. If you've strong views in another direction, post in that thread. From bernd.web at gmail.com Fri Nov 3 07:57:03 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 3 Nov 2006 13:57:03 +0100 Subject: [Bioperl-l] Bio::DB::Query::GenBank Message-ID: <716af09c0611030457p678f4d30v935215ba3c4dd5dc@mail.gmail.com> Hi, In contrast to the doc of Bio::DB::Query::GenBank at http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Query/GenBank.html this following seems not the case: "If you provide an array reference of IDs in -ids, the query will be ignored and the list of IDs will be used when the query is passed to a Bio::DB::GenBank object's get_Stream_by_query() method" I used # $Id: GenBank.pm,v 1.19 2006/09/26 22:03:07 sendu Exp $ It looks like query always overrules the array(ref) given in -ids. bernd From staffa at niehs.nih.gov Fri Nov 3 11:29:19 2006 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Fri, 03 Nov 2006 12:29:19 -0400 Subject: [Bioperl-l] Bio::Tools::RestrictionEnzyme Message-ID: The module Bio::Tools::RestrictionEnzyme Uses the perl split function to generate the fragments of a digestion, Using the recognition pattern as the delimiter. It then glues onto the resulting strings that part of the pattern representing the sequence before and after the cut. This is fine for non-ambiguous patterns, but starts looking funny for patterns having ambiguities. Worse that in doing a double digest, one enzyme after another, the ambiguity code character can mask a true cut site. I was using BsaHI [GRCGYC] followed by HpaII [CCGG] Below is the example of the CCGG pattern being masked by a Y And the different results of the digestion. CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAA As opposed to the real thing: CGCCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAA Which when cut by HpaII [CCGG] really yields first A_B_frag : CGC Instead of : first A_B_frag = CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAAG ACTTGCTAGTGCTGTTGGGTCTCC TTGACTCTGAGACAATGATAACAATGTTGAAGGTGGTCTAGGCATTTGGGTGCTGTGGAGTTATAAAGAGGAAAAG AAAAGATAAAACAAAAAAAAATAG GAAACAAATGATTAAGCCACTACTAAGGGGTCTAGTCTAATGCCAACTGGGTAAATTCATGGGAACAATGTGTGCC AGTCTTTAGAAACACTGTTTCATA TTGCATATATTATGGCATGGTATTACATTGATTAATTTTACTTTAGAGATGAAGAAGCTGAGATTTGGGGTGAATA GCAATTATCCCAAAGTCTCTCAGA TAGCTGGAGGCAGCAGGGTCTGGGGTATTCACAGTCCCTACTCCATATTGTGTGGTCAGAACCAAATGAGACAGAT AAAGGGCAGACAAAAGAGAAAGTG GGGAGTATGATTTGAAAATGATGGTGTGACCCAGATTTCTGATGGAAATATCTAATGGCTGCAGACTGGATAGCTG TGACCATTTTAGTTACTGAATTCA GGAGATCTTATCTCAATGGAGGCATGTTGTCAACCAAAAGCCAGGATAAGCAAGGGTCAGTGTCTAGACATTGGAG TAAGGTTTGCCTGGATATTTCCAC AGGGAACCAAGTGTCATGGAGTCTTATTCATTGGGAGGTTATCTTTGTTACACACATGGACATATCATCAAGCCAG CAATTCAGCAAAACTGTCAACACA CAAATAGAGATGTATTGACAACGGGGAACCACAAGTCATGCTTATTCCAAGCTAAAGCCCTCATGTGGAACTTGTT TTGTATGGCATTTGTCTCATCTAC ACATTGATGGGAAGGGTAAAAGGAAGTCTTTGGTGGGATTACAGAAGTCAGTAAAAAAGCAAAAGGAAAGATTTAG AAAACAAAGAAAAAGAAAAGGGAG GAAAGGAAAAGAAAAAAGATTTCAGAGATCTCAACATCAATTCAGACCAAGGGTGCCTCTTATACTATGTCCAAGC CAGTAAGTGGGGTTGTTCTTGTTA ACTACAGCCATGTATAGAGGTGAACTTCAGGCTCCTGACTGATCCTCTGAGGTAGAAAGTAAACAGTACTCTTATG ACACACGCAGTTGTTCAGTGCTGA CATGAAAATGTCATTGCTTACAGCGCTAGGAGAC This subroutine yields, I believe, the true sequence, Although I don't know how efficient it is. I'm thinking it must be more efficient than having to turn each fragment from the first digestion into a BioPerl Sequence Object before applying the cut_seq method. sub cut_seq { my $number= 0; my @frags = (); my $bigline = shift @_; my $recognition_site = shift @_; my $cutsite = shift @_; my $pat = &expanded_string($recognition_site); while ($bigline){ #my $offset = index $bigline, $pat; if ($bigline =~/($pat)/){ my $first = substr $&,0,$cutsite; my $last = substr $&,$cutsite; my $frag = $`.$first; push @frags, $frag; $number++; #print "fragment # $number:\n$frag\n"; my $rest_of_bigline = $last.$'; $bigline = $rest_of_bigline;} else {push @frags, $bigline; #Last one $number++; #print "fragment # $number:\n$bigline\n"; $bigline = "";} } return @frags; } Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Information Technology Support Services Contract (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov ) National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From cjfields at uiuc.edu Fri Nov 3 13:28:53 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 3 Nov 2006 12:28:53 -0600 Subject: [Bioperl-l] Bio::Tools::RestrictionEnzyme In-Reply-To: References: Message-ID: <915FE028-7F12-4BCE-AD9D-7D8D7D74AD6F@uiuc.edu> Nick, Could you file this as a bug? Chris On Nov 3, 2006, at 10:29 AM, Staffa, Nick (NIH/NIEHS) wrote: > The module Bio::Tools::RestrictionEnzyme > Uses the perl split function to generate the fragments of a digestion, > Using the recognition pattern as the delimiter. It then glues onto > the > resulting strings that part of the pattern representing the > sequence before > and after the cut. This is fine for non-ambiguous patterns, but > starts > looking funny for patterns having ambiguities. > Worse that in doing a double digest, one enzyme after another, the > ambiguity > code character can mask a true cut site. > I was using BsaHI [GRCGYC] followed by HpaII [CCGG] > Below is the example of the CCGG pattern being masked by a Y > And the different results of the digestion. > > > CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAA > As opposed to the real thing: > CGCCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAA > > Which when cut by HpaII [CCGG] really yields > first A_B_frag : > CGC > > Instead of : > first A_B_frag = > > CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAAG > ACTTGCTAGTGCTGTTGGGTCTCC > TTGACTCTGAGACAATGATAACAATGTTGAAGGTGGTCTAGGCATTTGGGTGCTGTGGAGTTATAAAGAG > GAAAAG > AAAAGATAAAACAAAAAAAAATAG > GAAACAAATGATTAAGCCACTACTAAGGGGTCTAGTCTAATGCCAACTGGGTAAATTCATGGGAACAATG > TGTGCC > AGTCTTTAGAAACACTGTTTCATA > TTGCATATATTATGGCATGGTATTACATTGATTAATTTTACTTTAGAGATGAAGAAGCTGAGATTTGGGG > TGAATA > GCAATTATCCCAAAGTCTCTCAGA > TAGCTGGAGGCAGCAGGGTCTGGGGTATTCACAGTCCCTACTCCATATTGTGTGGTCAGAACCAAATGAG > ACAGAT > AAAGGGCAGACAAAAGAGAAAGTG > GGGAGTATGATTTGAAAATGATGGTGTGACCCAGATTTCTGATGGAAATATCTAATGGCTGCAGACTGGA > TAGCTG > TGACCATTTTAGTTACTGAATTCA > GGAGATCTTATCTCAATGGAGGCATGTTGTCAACCAAAAGCCAGGATAAGCAAGGGTCAGTGTCTAGACA > TTGGAG > TAAGGTTTGCCTGGATATTTCCAC > AGGGAACCAAGTGTCATGGAGTCTTATTCATTGGGAGGTTATCTTTGTTACACACATGGACATATCATCA > AGCCAG > CAATTCAGCAAAACTGTCAACACA > CAAATAGAGATGTATTGACAACGGGGAACCACAAGTCATGCTTATTCCAAGCTAAAGCCCTCATGTGGAA > CTTGTT > TTGTATGGCATTTGTCTCATCTAC > ACATTGATGGGAAGGGTAAAAGGAAGTCTTTGGTGGGATTACAGAAGTCAGTAAAAAAGCAAAAGGAAAG > ATTTAG > AAAACAAAGAAAAAGAAAAGGGAG > GAAAGGAAAAGAAAAAAGATTTCAGAGATCTCAACATCAATTCAGACCAAGGGTGCCTCTTATACTATGT > CCAAGC > CAGTAAGTGGGGTTGTTCTTGTTA > ACTACAGCCATGTATAGAGGTGAACTTCAGGCTCCTGACTGATCCTCTGAGGTAGAAAGTAAACAGTACT > CTTATG > ACACACGCAGTTGTTCAGTGCTGA > CATGAAAATGTCATTGCTTACAGCGCTAGGAGAC > > > This subroutine yields, I believe, the true sequence, > Although I don't know how efficient it is. > I'm thinking it must be more efficient than having to turn each > fragment > from the first digestion into a BioPerl Sequence Object before > applying the > cut_seq method. > > sub cut_seq { > my $number= 0; > my @frags = (); > my $bigline = shift @_; > my $recognition_site = shift @_; > my $cutsite = shift @_; > my $pat = &expanded_string($recognition_site); > while ($bigline){ > #my $offset = index $bigline, $pat; > if ($bigline =~/($pat)/){ > my $first = substr $&,0,$cutsite; > my $last = substr $&,$cutsite; > my $frag = $`.$first; > push @frags, $frag; > $number++; > #print "fragment # $number:\n$frag\n"; > my $rest_of_bigline = $last.$'; > $bigline = $rest_of_bigline;} > else {push @frags, $bigline; #Last one > $number++; > #print "fragment # $number:\n$bigline\n"; > $bigline = "";} > } > return @frags; > } > > > > > Nick Staffa > Telephone: 919-316-4569 (NIEHS: 6-4569) > Scientific Computing Support Group > NIEHS Information Technology Support Services Contract > (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov ) > National Institute of Environmental Health Sciences > National Institutes of Health > Research Triangle Park, North Carolina > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From johnson.biotech at gmail.com Fri Nov 3 11:47:56 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Fri, 3 Nov 2006 11:47:56 -0500 Subject: [Bioperl-l] BioSQL load_seqdatabase.pl -pipeline option Message-ID: Hello guys, I'm populating biosql database using "load_seqdatabase.pl" from genbank release files for primates. However, I only need sequences that belong to humans (taxon id: 9606). I assume that best way to filter the necessary sequences is to use '-pipeline' option of the script. The documentation seems a little vague to me on how to create my own processor to accomplish the task. Can anyone clarify the steps??? -- Best Regards, Seth Johnson Senior Bioinformatics Associate From er at xs4all.nl Fri Nov 3 14:59:47 2006 From: er at xs4all.nl (Erik) Date: Fri, 3 Nov 2006 20:59:47 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error Message-ID: <10596.156.83.1.241.1162583987.squirrel@webmail.xs4all.nl> Hi all, I noticed the parsing is borked with newest swisprot files: UniProt Knowledgebase Release 9 consists of: UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines in swissprot/trembl according to the new specification (see http://expasy.org/sprot/relnotes/sp_news.html). Basically, the change is as follows: ID EntryName DataClass; MoleculeType; SequenceLength. is changed to: ID EntryName DataClass; SequenceLength. The change I made was only in the regex capturing the entry name: method next_seq (Bio/SeqIO/swiss.pm) : =============== unless( m/ ^ ID \s+ # (\S+) \s+ # $1 entryname ([^\s;]+); \s+ # $2 DataClass [0-9]+[ ]AA \. # Sequencelength (capture?) $ /ox ) { $self->throw("swissprot stream with no ID. Not swissprot in my book"); } =============== I tested this (=entry parsable and SeqIO created) against several hundred Swissprot and Trembl entries. Of course, files with the older format are now broken - it may be better to leave old and new format, and try both (newest first). hth, Erik From er at xs4all.nl Fri Nov 3 15:56:47 2006 From: er at xs4all.nl (Erik) Date: Fri, 3 Nov 2006 21:56:47 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error - Message-ID: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> I should have mentioned two more changes needed in Bio/SeqIO/swiss.pm for the new Swissprot format: In Bio/SeqIO/swiss.pm, next_seq(): =============== $params{'-namespace'} = ($2 eq 'Reviewed' ) ? 'Swiss-Prot' : ($2 eq 'Unreviewed' ) ? 'TrEMBL' : # ($2 eq 'STANDARD' ) ? 'Swiss-Prot' : # ($2 eq 'PRELIMINARY') ? 'TrEMBL' : $2; =============== and in Bio/SeqIO/swiss.pm, write_seq(): =============== $div = ($ns eq 'Swiss-Prot') ? 'Reviewed' : ($ns eq 'TrEMBL') ? 'Unreviewed' : # ($ns eq 'Swiss-Prot') ? 'STANDARD' : # ($ns eq 'TrEMBL') ? 'PRELIMINARY' : $ns; =============== above, the old lines are shown as outcommented. again, hth, Erik From pllv_shrm at yahoo.com Fri Nov 3 16:14:14 2006 From: pllv_shrm at yahoo.com (pallavi sharma) Date: Fri, 3 Nov 2006 13:14:14 -0800 (PST) Subject: [Bioperl-l] need help Message-ID: <20061103211414.56111.qmail@web31712.mail.mud.yahoo.com> hii could ny one plz tell me how to convert bioperl module like Bio::SearchIO n Bio::alignIO module into perl lang --------------------------------- Check out the New Yahoo! Mail - Fire up a more powerful email and get things done faster. From hlapp at gmx.net Fri Nov 3 17:54:08 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 3 Nov 2006 17:54:08 -0500 Subject: [Bioperl-l] BioSQL load_seqdatabase.pl -pipeline option In-Reply-To: References: Message-ID: Close. It's not the --pipeline option you want to use for this purpose but the --seqfilter option. For example, to retain only sequence with taxon id 9606 you would say --seqfilter 'sub {my $s=shift->{"-species"}; return 1 unless $s; return 1 unless $s->ncbi_taxid; return 1 if $s->ncbi_taxid == 9606; return 0;}' Note that when formulating the conditions upon which to accept or reject the object you need to take into account that the closure may be called multiple times for one object, at various stages of completion of the properties hash. So, the above sequence of logic says, accept the object if there is no species attached (yet), or if the species doesn't have a taxon ID (yet; in Genbank format, the taxon ID is actually in the feature table, and hence will only be populated later, after parsing the organism lines), or if the taxon ID is 9606. Otherwise (i.e., there is a species object, it has a taxon ID defined, and the taxon ID is not 9606) reject the object. (Note that --seqfilter will read and parse a file if the argument refers to an existing and readable file. So if you are going to use this construct often, you may want to put into a file.) -hilmar On Nov 3, 2006, at 11:47 AM, Seth Johnson wrote: > Hello guys, > > I'm populating biosql database using "load_seqdatabase.pl" from > genbank release files for primates. However, I only need sequences > that belong to humans (taxon id: 9606). I assume that best way to > filter the necessary sequences is to use '-pipeline' option of the > script. The documentation seems a little vague to me on how to create > my own processor to accomplish the task. Can anyone clarify the > steps??? > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From akozik at atgc.org Fri Nov 3 17:29:49 2006 From: akozik at atgc.org (Alexander Kozik) Date: Fri, 03 Nov 2006 14:29:49 -0800 Subject: [Bioperl-l] SCF files Message-ID: <454BC2DD.5050405@atgc.org> Hi all, There is a contradiction in opinions (I have used google search) what type of data SCF files (sequencing chromatograms) carry. Could you help to clarify following topics: are these statements true or false: 1. SCF files can be generated by Phred program only. 2. new version of Phred can read SCF files produced by older version of Phred and re-do basecalling with new quality scores [new quality scores could be different because of the improvements/changes in a basecalling algorithm] 3. SCF files contain no less information as original AB1 files [in other words, no information lost during conversion of AB1 to SCF] Thanks, -Alex ======================================== Alexander Kozik Bioinformatics Specialist Genome and Biomedical Sciences Facility 451 East Health Sciences Drive University of California Davis, CA 95616-8816 Phone: (530) 754-9127 email: akozik at atgc.org web: http://www.atgc.org/ ======================================== From cjfields at uiuc.edu Sun Nov 5 16:56:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 5 Nov 2006 15:56:08 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error - In-Reply-To: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> References: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> Message-ID: <73A15B2C-A8FE-4F1B-B17E-B43A46B82140@uiuc.edu> We'll try to get these in. THe problem is we need to try and make this backwards compatible. I'll post this as a bug for now as a reminder. Chris On Nov 3, 2006, at 2:56 PM, Erik wrote: > > I should have mentioned two more changes needed > in Bio/SeqIO/swiss.pm for the new Swissprot > format: > > In Bio/SeqIO/swiss.pm, next_seq(): > =============== > $params{'-namespace'} = ($2 eq 'Reviewed' ) ? 'Swiss-Prot' : > ($2 eq 'Unreviewed' ) ? 'TrEMBL' : > # ($2 eq 'STANDARD' ) ? 'Swiss-Prot' : > # ($2 eq 'PRELIMINARY') ? 'TrEMBL' : > $2; > =============== > > > and in Bio/SeqIO/swiss.pm, write_seq(): > =============== > $div = ($ns eq 'Swiss-Prot') ? 'Reviewed' : > ($ns eq 'TrEMBL') ? 'Unreviewed' : > # ($ns eq 'Swiss-Prot') ? 'STANDARD' : > # ($ns eq 'TrEMBL') ? 'PRELIMINARY' : > $ns; > =============== > > above, the old lines are shown as outcommented. > > > again, hth, > > Erik > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From adsj at novozymes.com Mon Nov 6 08:03:21 2006 From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=) Date: Mon, 06 Nov 2006 14:03:21 +0100 Subject: [Bioperl-l] Subclassing Bio::Seq ? Extending Bio::Perl References: <934F95E71B6C9347A873C42AE3C196191299DFBF@NZT0004E.dknz.nzcorp.n et> <934F95E71B6C9347A873C42AE3C196190B84C5FC@NZT0004E.dknz.nzcorp.net> Message-ID: <87zmb4ohgm.fsf@topper.koldfront.dk> On Tue, 24 Oct 2006 14:57:02 -0400, Hilmar wrote: > On Oct 24, 2006, at 1:59 PM, JK ((Jesper Agerbo Krogh)) wrote: >>> The reason that this is a Bio::PrimarySeq and not a Bio::Seq or your >>> extension of the latter is that the Perl garbage collector can't deal >>> with circular references. >> Doesn't Scalar::Util::weaken solve that? > You're welcome to test and try. It should be a simple change in > Bio::Seq::add_SeqFeature(). You will see that it is this method and > not the feature object that makes sure the wrapped primarySeq gets > passed as sequence reference. Just change that to creating a new > reference to the sequence object and make it a weak reference before > passing it to the feature object. > (The feature object has no requirement (or knowledge) that the > referenced sequence object is a PrimarySeq.) I've tried implementing this approach - the only test that failed was FootPrinter.t, which I "solved" by not weakening if the object is a Bio::PrimarySeq. I am not sure how fragile this approach is; any comments (patch attached)? [...] > I'm not following you why this would make any difference (it would be > $seq->message_digest() compared to $seqCompute->message_digest > ($seq)), unless what you are saying is that you would like to cache > the result of the computation. You would have to create, or pass around, a $seqCompute object everywhere your $seq-object's digest was needed, which would be a bit of a pain? Best regards, Adam -- Adam Sj?gren adsj at novozymes.com -------------- next part -------------- A non-text attachment was scrubbed... Name: feature_seq_weaken.patch Type: text/x-patch Size: 3675 bytes Desc: not available URL: From n.haigh at sheffield.ac.uk Mon Nov 6 10:12:37 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 15:12:37 +0000 Subject: [Bioperl-l] return undef Message-ID: <454F50E5.3030702@sheffield.ac.uk> Is there any reason why a "return undef" can't simply be swapped over to just "return"? Cheers Nath From n.haigh at sheffield.ac.uk Mon Nov 6 11:19:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 16:19:08 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F5BED.6040406@sendu.me.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> Message-ID: <454F607C.5020808@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Is there any reason why a "return undef" can't simply be swapped over to >> just "return"? > > No, in fact if you see any 'return undef's, please change them to > 'return' since the former can lead to subtle bugs. We did do an audit > earlier to fix most of those; presumably there was some kind of issue > with the remainder (or they just weren't caught), so check that no > problems arise when you make the change. > Just been checking the bioperl-run modules and changed the ones I found. Running "make test" doesn't seem to show up any errors so I'll commit them shortly. On a similar note, is it safe to simply substitute "use vars" for "our" and correctly commenting the list of variables if qw() was previously used? e.g.: use vars qw($variable1 @array1 %hash1); # to: our ($variable1, @array1, %hash1); If so, there are 340+ "use vars" in the bioperl-run......any wise ideas on a generic script that can do an intelligent search and replace. Bearing in mind that these lists can span multiple lines? I set up the following page a couple of days ago to house some scripts that can be used to do audit checks of code: http://www.bioperl.org/wiki/Auditing If anyone has any scripts, Perl, shell or otherwise fell free to add them! :-) Cheers Nath -- > A: Yes. >> Q: Are you sure? >> >>> A: Because it reverses the logical flow of conversation. >>> >>>> Q: Why is top posting frowned upon? >>>> Get Thunderbird From bix at sendu.me.uk Mon Nov 6 10:59:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 15:59:41 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F50E5.3030702@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> Message-ID: <454F5BED.6040406@sendu.me.uk> Nathan S. Haigh wrote: > Is there any reason why a "return undef" can't simply be swapped over to > just "return"? No, in fact if you see any 'return undef's, please change them to 'return' since the former can lead to subtle bugs. We did do an audit earlier to fix most of those; presumably there was some kind of issue with the remainder (or they just weren't caught), so check that no problems arise when you make the change. From cjfields at uiuc.edu Mon Nov 6 11:35:52 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 10:35:52 -0600 Subject: [Bioperl-l] AlignIO::stockholm write_aln() Message-ID: I have added some experimental write_aln() support for Stockholm format to CVS along with some basic tests to AlignIO.t. I plan on cleaning it up a bit and adding more tests, along with possibly adding a builder option (similar to SeqIO::genbank) to have annotation parsing optional. Right now it is always on by default. It doesn't print meta data yet but does parse and store it; I'll probably add that in the next day or two. Be forewarned if testing this: I haven't tried clustal/msf/etc- >stockholm conversions yet so don't know if that works, but it should (it just won't print annotations). I'll add tests for that when I get time. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 6 11:55:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 16:55:55 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F607C.5020808@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> Message-ID: <454F691B.3090900@sendu.me.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: >> Nathan S. Haigh wrote: >>> Is there any reason why a "return undef" can't simply be swapped over to >>> just "return"? >> >> No, in fact if you see any 'return undef's, please change them to >> 'return' since the former can lead to subtle bugs. We did do an audit >> earlier to fix most of those; presumably there was some kind of issue >> with the remainder (or they just weren't caught), so check that no >> problems arise when you make the change. > > Just been checking the bioperl-run modules and changed the ones I found. > Running "make test" doesn't seem to show up any errors so I'll commit > them shortly. Thanks. > On a similar note, is it safe to simply substitute "use vars" for "our" > and correctly commenting the list of variables if qw() was previously used? Should be. But note that we didn't officially agree on having the Run package require Perl 5.6... Is there a particular person who maintains the Run package, or does that fall to the pumpkin of Core? > If so, there are 340+ "use vars" in the bioperl-run......any wise ideas > on a generic script that can do an intelligent search and replace. > Bearing in mind that these lists can span multiple lines? It'll need a little futzing, just be very careful it is working perfectly before applying it to everything. All of Core and the other packages need the same work done on them... > I set up the following page a couple of days ago to house some scripts > that can be used to do audit checks of code: > http://www.bioperl.org/wiki/Auditing > > If anyone has any scripts, Perl, shell or otherwise fell free to add > them! :-) I created a one-off for the conversion to 'use base', but its a bit of delirium-induced hack. I'll add it when I get the chance; its essentially a more complex version of what you want to do. It also ought to be applied to all the other Bioperl packages... (You should make mention of the existing audit scripts in CVS for bioperl-live in maintenance/) From cjfields at uiuc.edu Mon Nov 6 12:58:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 11:58:27 -0600 Subject: [Bioperl-l] return undef In-Reply-To: <454F691B.3090900@sendu.me.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> <454F691B.3090900@sendu.me.uk> Message-ID: <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> >> On a similar note, is it safe to simply substitute "use vars" for >> "our" >> and correctly commenting the list of variables if qw() was >> previously used? > > Should be. But note that we didn't officially agree on having the Run > package require Perl 5.6... Is there a particular person who maintains > the Run package, or does that fall to the pumpkin of Core? I believe Albert Vilella was taking care of bioperl-run, but I'm not absolutely sure. I think we can assume that, if core rel. 1.5.2 requires perl 5.6.1, anything that requires bioperl rel. 1.5.2 should likewise require perl 5.6.1 as well. Probably should make that explicitly stated somewhere. >> If so, there are 340+ "use vars" in the bioperl-run......any wise >> ideas >> on a generic script that can do an intelligent search and replace. >> Bearing in mind that these lists can span multiple lines? > > It'll need a little futzing, just be very careful it is working > perfectly before applying it to everything. All of Core and the other > packages need the same work done on them... I have gone through a few and manually switched 'use vars' over to 'our'. You can always try making the necessary changes globally but I think you'll see a lot of failed tests. >> I set up the following page a couple of days ago to house some >> scripts >> that can be used to do audit checks of code: >> http://www.bioperl.org/wiki/Auditing >> >> If anyone has any scripts, Perl, shell or otherwise fell free to add >> them! :-) > > I created a one-off for the conversion to 'use base', but its a bit of > delirium-induced hack. I'll add it when I get the chance; its > essentially a more complex version of what you want to do. It also > ought > to be applied to all the other Bioperl packages... > > (You should make mention of the existing audit scripts in CVS for > bioperl-live in maintenance/) Not sure how much more global code auditing should be done before the 1.5.2 final release, but if it passes tests then I don't have a problem. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 6 13:08:38 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 18:08:38 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> <454F691B.3090900@sendu.me.uk> <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> Message-ID: <454F7A26.9090800@sendu.me.uk> Chris Fields wrote: >>> I set up the following page a couple of days ago to house some scripts >>> that can be used to do audit checks of code: >>> http://www.bioperl.org/wiki/Auditing >>> >>> If anyone has any scripts, Perl, shell or otherwise fell free to add >>> them! :-) >> >> I created a one-off for the conversion to 'use base', but its a bit of >> delirium-induced hack. I'll add it when I get the chance; its >> essentially a more complex version of what you want to do. It also ought >> to be applied to all the other Bioperl packages... >> >> (You should make mention of the existing audit scripts in CVS for >> bioperl-live in maintenance/) > > Not sure how much more global code auditing should be done before the > 1.5.2 final release None; I won't add any to the branch (bug fixes and documentation only, for the most part). It is still valuable to do for the next release though! From n.haigh at sheffield.ac.uk Mon Nov 6 15:29:23 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 20:29:23 +0000 Subject: [Bioperl-l] StandAloneFasta::version Message-ID: <454F9B23.8010302@sheffield.ac.uk> Hi Sendu, I've written a version method for StandAloneFasta.pm. However, because of the way in which FASTA is versioned, it makes for difficult version comparisons i.e. they contain non-numeric characters e.g. 3.4t26. I have employed a private function that does a conversion of the non-numeric characters into their ascii value representation to build a float. e.g. the above version would result in: 3.411626 which can then be compared easily. At the moment, this is accessed via $factory->version like other modules as this will give access to a version number that is easily comparable. However, should there be a different function to return the unconverted version string e.g. 3.4t26? Or should there be a function that does a compare internally so it can be accessed something like: print "we have met the min version requirement\n" if $factory->at_least_version('3.4t26'); Ideas welcome! Nath From cjfields at uiuc.edu Mon Nov 6 16:21:10 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 15:21:10 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <454F9B23.8010302@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> Message-ID: <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> Nathan, Weren't the problems with the reported StandAloneFasta.pm test fails due to differences in the returned order of the Hits/HSPs in the FASTA reports from the different versions? The test results you posted on the wiki (where I commented on this) seem to indicate that: not ok 11 # Test 11 got: "0" (t/StandAloneFasta.t at line 75) # Expected: "994" # t/StandAloneFasta.t line 75 is: ok $hsp->num_identical, 994; not ok 12 # Test 12 got: "1977" (t/StandAloneFasta.t at line 76) # Expected: "994" # t/StandAloneFasta.t line 76 is: ok $hsp->length, 994; ok 13 not ok 14 # Test 14 got: "0" (t/StandAloneFasta.t at line 88) # Expected: "994" # t/StandAloneFasta.t line 88 is: ok $hsp->num_identical, 994; not ok 15 # Test 15 got: "1977" (t/StandAloneFasta.t at line 89) # Expected: "994" # t/StandAloneFasta.t line 89 is: ok $hsp->length, 994; It looks like a value is returned for the tests, so parsing isn't broken. They just aren't returned in the order specified, so the tests are faulty, not the parsing. The tests could be fixed by using id/score key/value pairs in a hash or something similar. We probably shouldn't limit to a specific version unless parsing is actually broken. Chris On Nov 6, 2006, at 2:29 PM, Nathan S. Haigh wrote: > Hi Sendu, > > I've written a version method for StandAloneFasta.pm. However, because > of the way in which FASTA is versioned, it makes for difficult version > comparisons i.e. they contain non-numeric characters e.g. 3.4t26. > > I have employed a private function that does a conversion of the > non-numeric characters into their ascii value representation to > build a > float. e.g. the above version would result in: 3.411626 which can then > be compared easily. At the moment, this is accessed via > $factory->version like other modules as this will give access to a > version number that is easily comparable. However, should there be a > different function to return the unconverted version string e.g. > 3.4t26? > Or should there be a function that does a compare internally so it can > be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26'); > > Ideas welcome! > Nath > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From torsten.seemann at infotech.monash.edu.au Mon Nov 6 15:41:24 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Tue, 07 Nov 2006 07:41:24 +1100 Subject: [Bioperl-l] return undef In-Reply-To: <454F607C.5020808@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> Message-ID: <454F9DF4.80702@infotech.monash.edu.au> > I set up the following page a couple of days ago to house some scripts > that can be used to do audit checks of code: > http://www.bioperl.org/wiki/Auditing Your 'grep' patterns should probably have "\s+" rather than " " between keywords as often coders have used multiple spaces or tabs. Your 'die/confess/...' patterns require a "(" after them. I'd say those functions are used without parentheses about half the time, eg. die "ech!"; Explicit "return undef" aren't too hard to find. It's the hidden ones where it's "my $value; ...lots of code...; return $value;" which are hard to identify. -- Torsten Seemann Victorian Bioinformatics Consortium, Monash University, Australia From n.appleby at uq.edu.au Mon Nov 6 21:11:06 2006 From: n.appleby at uq.edu.au (Nikki Appleby) Date: Tue, 7 Nov 2006 12:11:06 +1000 Subject: [Bioperl-l] go-perl error: ')' missing Message-ID: <005d01c70211$fbaf55a0$1b776682@IMBPC.AD> Thanks for being there when things go wrong. I have installed required modules as listed in Chris' instructions, then get stuck on this. C:\Perl\go-perl\go-perl-0.05>perl Makefile.PL The system cannot find the path specified. NOTICE: ** You do not have xsltproc ** This tool is not required for go-perl, but it is useful for for certain kinds of format conversion (eg converting to OWL format). You will also need this tool if you are installing go-db-perl You can safely ignore this notification message; Even if you do intend to use go-db-perl later, you can install xsltproc at a later date xsltproc is available as part of libxslt. See http://xmlsoft.org/XSLT/ for details Writing Makefile for GO C:\Perl\go-perl\go-perl-0.05>nmake Microsoft (R) Program Maintenance Utility Version 1.50 Copyright (c) Microsoft Corp 1988-94. All rights reserved. makefile(1706) : fatal error U1000: syntax error : ')' missing in macro invocati on Stop. Nikki Appleby. 07 334 62634 From n.haigh at sheffield.ac.uk Tue Nov 7 02:05:40 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 07 Nov 2006 07:05:40 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> Message-ID: <45503044.30000@sheffield.ac.uk> Chris Fields wrote: > Nathan, > > Weren't the problems with the reported StandAloneFasta.pm test fails > due to differences in the returned order of the Hits/HSPs in the FASTA > reports from the different versions? The test results you posted on > the wiki (where I commented on this) seem to indicate that: > > not ok 11 > # Test 11 got: "0" (t/StandAloneFasta.t at line 75) > # Expected: "994" > # t/StandAloneFasta.t line 75 is: ok $hsp->num_identical, 994; > not ok 12 > # Test 12 got: "1977" (t/StandAloneFasta.t at line 76) > # Expected: "994" > # t/StandAloneFasta.t line 76 is: ok $hsp->length, 994; > ok 13 > not ok 14 > # Test 14 got: "0" (t/StandAloneFasta.t at line 88) > # Expected: "994" > # t/StandAloneFasta.t line 88 is: ok $hsp->num_identical, 994; > not ok 15 > # Test 15 got: "1977" (t/StandAloneFasta.t at line 89) > # Expected: "994" > # t/StandAloneFasta.t line 89 is: ok $hsp->length, 994; > > It looks like a value is returned for the tests, so parsing isn't > broken. They just aren't returned in the order specified, so the > tests are faulty, not the parsing. The tests could be fixed by using > id/score key/value pairs in a hash or something similar. We probably > shouldn't limit to a specific version unless parsing is actually broken. > > Chris > Chris, I agree, I was going to update the tests later this morning :-P Any thoughts about version() or should I just leave it be for now? Cheers Nath From bix at sendu.me.uk Tue Nov 7 04:15:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 09:15:41 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45503044.30000@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> Message-ID: <45504EBD.2000708@sendu.me.uk> Nathan S. Haigh wrote: > I agree, I was going to update the tests later this morning :-P Any > thoughts about version() or should I just leave it be for now? If its no trouble, go ahead with a version() method. Its nice to have in any case. I'd suggest your latter option of 'there be a function that does a compare internally so it can be accessed something like: print "we have met the min version requirement\n" if $factory->at_least_version('3.4t26');' In fact, it ought to work with '34t26b3' as well (I guess the method would try what it was given, and on failure, try again with the last 2 characters removed, then try both cases again with a decimal added if there wasn't one). From n.haigh at sheffield.ac.uk Tue Nov 7 04:50:52 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 07 Nov 2006 09:50:52 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45504EBD.2000708@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> Message-ID: <455056FC.90608@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> I agree, I was going to update the tests later this morning :-P Any >> thoughts about version() or should I just leave it be for now? > > If its no trouble, go ahead with a version() method. Its nice to have > in any case. I'd suggest your latter option of 'there be a function > that does a compare internally so it can be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26');' > In fact, it ought to work with '34t26b3' as well (I guess the method > would try what it was given, and on failure, try again with the last 2 > characters removed, then try both cases again with a decimal added if > there wasn't one). I've contacted Bill Pearson to clarify his versioning scheme. Ideally, we could do as you say, compare variants of '34t26b3'. However, the software doesn't report the b3 part of the version string only 3.4t26 followed by a date. Therefore, I'm not sure it's possible to distinguish between 3.4t26b1 and 3.4t26b3 - unless we consider the date also returned by the software :-( . Bill said he is currently busy with a course at Cold Spring Harbor but will respond in full later. Therefore, until he's informed me of how he versions his releases, I'll hold off with the version() method for the time being. Nath From cjfields at uiuc.edu Tue Nov 7 10:58:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 09:58:48 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45504EBD.2000708@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> Message-ID: <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> On Nov 7, 2006, at 3:15 AM, Sendu Bala wrote: > Nathan S. Haigh wrote: >> I agree, I was going to update the tests later this morning :-P Any >> thoughts about version() or should I just leave it be for now? > > If its no trouble, go ahead with a version() method. Its nice to > have in > any case. I'd suggest your latter option of 'there be a function that > does a compare internally so it can be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26');' > In fact, it ought to work with '34t26b3' as well (I guess the method > would try what it was given, and on failure, try again with the last 2 > characters removed, then try both cases again with a decimal added if > there wasn't one). Is it possible to have the interface base class contain an abstract program_version() (or similar) method? One that could be implemented to just grab the current version of the program? I was thinking about something like this for the RNA-based wrappers I want to add but it seems to be something that most Run modules would benefit from. Just haven't had time to look into it with much detail. Almost wonder if it would be easier to have all bioperl-run modules have a Run-specific Root object for common methods, regardless of the other interfaces used. Maybe something inheriting Bio::Root::Root... chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Nov 7 11:54:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 10:54:48 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550AF3B.8000807@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> Message-ID: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: ... >> Is it possible to have the interface base class contain an >> abstract program_version() (or similar) method? One that could be >> implemented to just grab the current version of the program? I >> was thinking about something like this for the RNA-based wrappers >> I want to add but it seems to be something that most Run modules >> would benefit from. Just haven't had time to look into it with >> much detail. > > What's wrong with version() ? Didn't realize there was a version() already. >> Almost wonder if it would be easier to have all bioperl-run >> modules have a Run-specific Root object for common methods, >> regardless of the other interfaces used. Maybe something >> inheriting Bio::Root::Root... > > What's wrong with Bio::Tools::Run::WrapperBase ? I agree that WrapperBase fulfills most of this functionality. However, don't a few bioperl-run wrappers 'roll their own', i.e. not implement WrapperBase? Requiring all bioperl-run module inherit the same Run-specific base object would integrate them a bit more and distinguish them from the core modules (which would inherit Bio::Root::Root). Anyway, it's just a suggestion. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Tue Nov 7 10:54:06 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 07 Nov 2006 10:54:06 -0500 Subject: [Bioperl-l] Bio::SeqIO::gcg bug Message-ID: <4550AC1E.2070500@bms.com> Bio::SeqIO::gcg is checking the checksum against the GCG generated one. There is a problem with the way this is done: 1. Bio::SeqIO::gcg removes all characters, except [A-Za-z] (which by the way is always wrong). 2. GCG calculates the checksum on uppercase I assume Hilmar removed the $_ = uc($_); line for a very good reason, but the call to validate should be: _validate_checksum(uc($sequence),$chksum)) Also I believe the regexp for checking the alphabet should remove explicitly numbers and whitespaces. Removing everything else is not a good idea because gaps, end of translation are removed also and possible parsing errors might be suppressed incorrectly. Let me know if I am missing some other considerations here. If not I will commit these changes. Stefan From bix at sendu.me.uk Tue Nov 7 12:25:22 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 17:25:22 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> Message-ID: <4550C182.3000308@sendu.me.uk> Chris Fields wrote: > > On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: > >>> Almost wonder if it would be easier to have all bioperl-run modules >>> have a Run-specific Root object for common methods, regardless of the >>> other interfaces used. Maybe something inheriting Bio::Root::Root... >> >> What's wrong with Bio::Tools::Run::WrapperBase ? > > I agree that WrapperBase fulfills most of this functionality. However, > don't a few bioperl-run wrappers 'roll their own', i.e. not implement > WrapperBase? Requiring all bioperl-run module inherit the same > Run-specific base object would integrate them a bit more and distinguish > them from the core modules (which would inherit Bio::Root::Root). > Anyway, it's just a suggestion. Well, how would you 'require' them to use anything at all? There's not even anything 'requiring' that a core module inherit from Bio::Root::Root(I). We just (very strongly) advise that you inherit from there. So we can also advise that bioperl-run wrappers do not roll their own but use Bio::Tools::Run::WrapperBase. From cjfields at uiuc.edu Tue Nov 7 12:40:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 11:40:32 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C182.3000308@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> Message-ID: <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> > Well, how would you 'require' them to use anything at all? There's not > even anything 'requiring' that a core module inherit from > Bio::Root::Root(I). We just (very strongly) advise that you inherit > from > there. So we can also advise that bioperl-run wrappers do not roll > their > own but use Bio::Tools::Run::WrapperBase. Like I said, it's a suggestion. No need to get snippy. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Tue Nov 7 11:07:23 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 16:07:23 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> Message-ID: <4550AF3B.8000807@sendu.me.uk> Chris Fields wrote: > > On Nov 7, 2006, at 3:15 AM, Sendu Bala wrote: > >> Nathan S. Haigh wrote: >>> I agree, I was going to update the tests later this morning :-P Any >>> thoughts about version() or should I just leave it be for now? >> >> If its no trouble, go ahead with a version() method. Its nice to have in >> any case. I'd suggest your latter option of 'there be a function that >> does a compare internally so it can be accessed something like: >> print "we have met the min version requirement\n" if >> $factory->at_least_version('3.4t26');' >> In fact, it ought to work with '34t26b3' as well (I guess the method >> would try what it was given, and on failure, try again with the last 2 >> characters removed, then try both cases again with a decimal added if >> there wasn't one). > > Is it possible to have the interface base class contain an abstract > program_version() (or similar) method? One that could be implemented to > just grab the current version of the program? I was thinking about > something like this for the RNA-based wrappers I want to add but it > seems to be something that most Run modules would benefit from. Just > haven't had time to look into it with much detail. What's wrong with version() ? > Almost wonder if it would be easier to have all bioperl-run modules have > a Run-specific Root object for common methods, regardless of the other > interfaces used. Maybe something inheriting Bio::Root::Root... What's wrong with Bio::Tools::Run::WrapperBase ? From n.haigh at sheffield.ac.uk Tue Nov 7 12:48:56 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 07 Nov 2006 17:48:56 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> Message-ID: <4550C708.5060209@sheffield.ac.uk> Chris Fields wrote: > On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: > ... > > >>> Is it possible to have the interface base class contain an >>> abstract program_version() (or similar) method? One that could be >>> implemented to just grab the current version of the program? I >>> was thinking about something like this for the RNA-based wrappers >>> I want to add but it seems to be something that most Run modules >>> would benefit from. Just haven't had time to look into it with >>> much detail. >>> >> What's wrong with version() ? >> > > Didn't realize there was a version() already. > > >>> Almost wonder if it would be easier to have all bioperl-run >>> modules have a Run-specific Root object for common methods, >>> regardless of the other interfaces used. Maybe something >>> inheriting Bio::Root::Root... >>> >> What's wrong with Bio::Tools::Run::WrapperBase ? >> > > I agree that WrapperBase fulfills most of this functionality. > However, don't a few bioperl-run wrappers 'roll their own', i.e. not > implement WrapperBase? Requiring all bioperl-run module inherit the > same Run-specific base object would integrate them a bit more and > distinguish them from the core modules (which would inherit > Bio::Root::Root). Anyway, it's just a suggestion. > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > >From what i've seen of Bioperl-run there is not a whole lot of consistency between modules. I think it would be a good idea to have all run modules inherit WrapperBase - would this be a big change?? Nath From bix at sendu.me.uk Tue Nov 7 12:49:09 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 17:49:09 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> Message-ID: <4550C715.5090608@sendu.me.uk> Chris Fields wrote: >> Well, how would you 'require' them to use anything at all? There's not >> even anything 'requiring' that a core module inherit from >> Bio::Root::Root(I). We just (very strongly) advise that you inherit from >> there. So we can also advise that bioperl-run wrappers do not roll their >> own but use Bio::Tools::Run::WrapperBase. > > Like I said, it's a suggestion. No need to get snippy. You took that completely the wrong way. I am applying absolutely no value judgment on your suggestion. It may be an excellent one. I was simply explaining we have no programmatic way of requiring that modules use other modules - we rely on people following the advice/ status quo. Given that, are you still suggesting that it would be better to advise people to use Bio::Root::SomeNewRunThing, or is Bio::Tools::Run::WrapperBase satisfactory? From hlapp at gmx.net Tue Nov 7 12:55:12 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 7 Nov 2006 12:55:12 -0500 Subject: [Bioperl-l] Bio::SeqIO::gcg bug In-Reply-To: <4550AC1E.2070500@bms.com> References: <4550AC1E.2070500@bms.com> Message-ID: On Nov 7, 2006, at 10:54 AM, Stefan Kirov wrote: > I assume Hilmar removed the $_ = uc($_); line for a very good reason, > but the call to validate should be: > _validate_checksum(uc($sequence),$chksum)) I agree. The case of the sequence letters should remain untouched though for other purposes. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Tue Nov 7 12:55:22 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 11:55:22 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C708.5060209@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C708.5060209@sheffield.ac.uk> Message-ID: <8132EB4F-2FE0-4A46-A96D-E406CCB0F047@uiuc.edu> On Nov 7, 2006, at 11:48 AM, Nathan Haigh wrote: ... > From what i've seen of Bioperl-run there is not a whole lot of > consistency between modules. I think it would be a good idea to > have all > run modules inherit WrapperBase - would this be a big change?? > > Nath We really have no idea how many wrappers don't implement WrapperBase at the moment; until then we don't know how much work it would take. This might be a job for a maintenance script... Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From natalia.grabar at club-internet.fr Tue Nov 7 12:48:53 2006 From: natalia.grabar at club-internet.fr (natalia.grabar at club-internet.fr) Date: Tue, 7 Nov 2006 18:48:53 +0100 Subject: [Bioperl-l] perl conference in Paris Message-ID: hi all, are you fine? next 25 & 26 November there will be a Perl conference in Paris http://conferences.mongueurs.net/fpw2006/ I wonder if it would be possible to have a presentation (tutorial?) of the bioperl package during this conference. thanks have a nice day natalia From cjfields at uiuc.edu Tue Nov 7 14:49:47 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 13:49:47 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C715.5090608@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> <4550C715.5090608@sendu.me.uk> Message-ID: <4AC53CE6-20EC-4841-A28C-E083823F8487@uiuc.edu> On Nov 7, 2006, at 11:49 AM, Sendu Bala wrote: >> Like I said, it's a suggestion. No need to get snippy. > > You took that completely the wrong way. I am applying absolutely no > value judgment on your suggestion. It may be an excellent one. I > was simply explaining we have no programmatic way of requiring that > modules use other modules - we rely on people following the advice/ > status quo. There may not be a programmatic way of enforcing one to use WrapperBase or other base classes beyond using maintenance scripts. However, if we as a community agree on following a basic set of bioperl coding standards (Best Practices, using Bio::Root::Root/ RootI, POD, etc), then anyone should reasonably expect that their code may be changed to conform more with those standards, at least within reason. We recently enforced this with Bio::Root::Root/RootI, 'return undef', 'use base', and others, so I don't see the problem with doing so here. There will always be some controversial or grey areas (use of AUTOLOAD comes to mind), but in my opinion it is very reasonable to require that new modules use a particular base class or implement a specific interface if the new code is expected to interact properly with other BioPerl classes/objects. One could always use the mail list to express their opinions if they disagree or want some clarification or guidance. Sorry, Election Day in the States. Lots of snippiness around on this end (overdosed of negative ads)! > Given that, are you still suggesting that it would be better to > advise people to use Bio::Root::SomeNewRunThing, or is > Bio::Tools::Run::WrapperBase satisfactory? Either way will work, but.... I was thinking of something like this: Run-based |---WrapperBase Root class---| |---Non-WrapperBase (web apps and others) Bio::Root::Root works in this capacity already, but I was thinking of a base class unique to bioperl-run classes which could integrate similar methods from WrapperBase and non-WrapperBase'd modules. I suppose we could also have it as a simple interface; modules which implement it could be distinguished from core if needed. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Tue Nov 7 14:58:10 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 7 Nov 2006 11:58:10 -0800 Subject: [Bioperl-l] (no subject) Message-ID: Lincoln - I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql which call $sth->finish in the offset_boundary call and the fetch_sequence method as my code which does GFF3 -> CDS dumping was getting lots of " statement handle DBI::st=HASH(0x189bf8c) still Active at" Changes are here: http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/Bio/DB/ SeqFeature/Store/DBI/mysql.pm.diff?r1=1.25&r2=1.26 These changes should be migrated to the branch before the release if all is okay. Please let me know. -jason From jason at bioperl.org Tue Nov 7 13:27:27 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 7 Nov 2006 10:27:27 -0800 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C708.5060209@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C708.5060209@sheffield.ac.uk> Message-ID: <4A984083-23FA-42F6-8C73-901FD87DB5F6@bioperl.org> i think it is important - we just have not had a dedicated developer who enforced these requirements by auditing the code. I had tried to establish a standard through WrapperBase but some contributions ignored this and some modules had grown up before the wrapperbase was in place. I also think the ontology of applications is a bit screwed up so people were putting modules in directories willy-nilly. I think bioperl-run is even more cat-herding than the other aspects of the project because applications change and there are very many combinations of parameters and version of applications. There was a flurry of contributions and no good way to marshall them initially. So what to do - I guess make do with how it is but not rename anything at this point but try and standardize things - it will depend on your desire to really take this on. The PISE modules may need to be re-evaluated to insure they are still working - there was hope that some of them could be simplified through some automated class generation from the XML they are based on, but that was never developed. We will try and a have an open-bio linux server available as a platform where we can have a consistent testing environment but I am not sure if we want this to represent every possible version of apps or just the most recent. -jason On Nov 7, 2006, at 9:48 AM, Nathan Haigh wrote: > Chris Fields wrote: >> On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: >> ... >> >> >>>> Is it possible to have the interface base class contain an >>>> abstract program_version() (or similar) method? One that could be >>>> implemented to just grab the current version of the program? I >>>> was thinking about something like this for the RNA-based wrappers >>>> I want to add but it seems to be something that most Run modules >>>> would benefit from. Just haven't had time to look into it with >>>> much detail. >>>> >>> What's wrong with version() ? >>> >> >> Didn't realize there was a version() already. >> >> >>>> Almost wonder if it would be easier to have all bioperl-run >>>> modules have a Run-specific Root object for common methods, >>>> regardless of the other interfaces used. Maybe something >>>> inheriting Bio::Root::Root... >>>> >>> What's wrong with Bio::Tools::Run::WrapperBase ? >>> >> >> I agree that WrapperBase fulfills most of this functionality. >> However, don't a few bioperl-run wrappers 'roll their own', i.e. not >> implement WrapperBase? Requiring all bioperl-run module inherit the >> same Run-specific base object would integrate them a bit more and >> distinguish them from the core modules (which would inherit >> Bio::Root::Root). Anyway, it's just a suggestion. >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> From what i've seen of Bioperl-run there is not a whole lot of > consistency between modules. I think it would be a good idea to > have all > run modules inherit WrapperBase - would this be a big change?? > > Nath > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Wed Nov 8 05:24:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 08 Nov 2006 10:24:41 +0000 Subject: [Bioperl-l] (no subject) Message-ID: <4551B069.6060305@sendu.me.uk> [forwarded on behalf of Dave Howorth] Jason Stajich wrote: > Lincoln - > I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql > which call $sth->finish in the offset_boundary call and the > fetch_sequence method as my code which does GFF3 -> CDS dumping was > getting lots of " statement handle DBI::st=HASH(0x189bf8c) still > Active at" What version of DBD::mysql are you using? It sounds like this: http://rt.cpan.org/Public/Bug/Display.html?id=20464 Cheers, Dave From bix at sendu.me.uk Wed Nov 8 06:12:12 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 08 Nov 2006 11:12:12 +0000 Subject: [Bioperl-l] Bioperl versioning In-Reply-To: <6dce9a0b0610311224x79256b29sf102eb5c35865caf@mail.gmail.com> References: <453E309B.9090007@sendu.me.uk> <000001c6f78b$d1c65a30$15327e82@pyrimidine> <6dce9a0b0610311224x79256b29sf102eb5c35865caf@mail.gmail.com> Message-ID: <4551BB8C.5040606@sendu.me.uk> Lincoln Stein wrote: > Are you going to go ahead with 1.52_XX ? If so, I will code GBrowse to > look for 1.52 or higher. You should do the equivalent of use Bio::Root::Version 1.5.2; Eg. unless (eval{"require $Bio::Root::Version;" || ${Bio::Root::Version::VERSION'} < 1.005002) { #complain } Since most core modules get their version from Bio::Root::Version, you could also check the core module you're actually using in GBrowse, instead of asking Bio::Root::Version itself. So, if you do actually need to use Bio::Whatever in your module, the best thing to do is say: use Bio::Whatever 1.5.2; From jason at bioperl.org Wed Nov 8 10:56:55 2006 From: jason at bioperl.org (Jason Stajich) Date: Wed, 8 Nov 2006 07:56:55 -0800 Subject: [Bioperl-l] (no subject) In-Reply-To: <4551B069.6060305@sendu.me.uk> References: <4551B069.6060305@sendu.me.uk> Message-ID: <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> sounds like it. I am running 3.0006 The added sth->finish did take care of it for now since I assume a fair number of people are stuck with these vers? On Nov 8, 2006, at 2:24 AM, Sendu Bala wrote: > [forwarded on behalf of Dave Howorth] > > > Jason Stajich wrote: >> Lincoln - >> I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql >> which call $sth->finish in the offset_boundary call and the >> fetch_sequence method as my code which does GFF3 -> CDS dumping was >> getting lots of " statement handle DBI::st=HASH(0x189bf8c) still >> Active at" > > What version of DBD::mysql are you using? It sounds like this: > > http://rt.cpan.org/Public/Bug/Display.html?id=20464 > > Cheers, Dave > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California Dept of Plant and Microbial Biology 321 Koshland Hall #3102 Berkeley, CA 94720-3102 lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From dhoworth at mrc-lmb.cam.ac.uk Wed Nov 8 11:16:05 2006 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Wed, 08 Nov 2006 16:16:05 +0000 Subject: [Bioperl-l] (no subject) In-Reply-To: <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> References: <4551B069.6060305@sendu.me.uk> <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> Message-ID: <455202C5.9060609@mrc-lmb.cam.ac.uk> Jason Stajich wrote: > sounds like it. > > I am running 3.0006 > > The added sth->finish did take care of it for now since I assume a fair > number of people are stuck with these vers? Well, the current version on CPAN is fixed and the bug breaks lots of applications so upgrading DBD::mysql is a better cure. Or even downgrading to the one before it broke :) Cheers, Dave From bix at sendu.me.uk Thu Nov 9 05:28:34 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 10:28:34 +0000 Subject: [Bioperl-l] bptutorial.pl 0 In-Reply-To: <000601c6fc4a$c3e43450$15327e82@pyrimidine> References: <000601c6fc4a$c3e43450$15327e82@pyrimidine> Message-ID: <455302D2.1000901@sendu.me.uk> Chris Fields wrote: > What version of Bioperl are you running? > > As a warning, the bptutorial.pl script has been removed from CVS and will > not be included in future versions of Bioperl. It can be found on the > bioperl wiki instead: > > http://www.bioperl.org/wiki/Bptutorial It hasn't been removed, but should it be? AFAIK there was still a request from at least one person to keep it. But is it still out of date wrt the wiki version? From bix at sendu.me.uk Thu Nov 9 05:31:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 10:31:16 +0000 Subject: [Bioperl-l] bptutorial.pl 0 In-Reply-To: <455302D2.1000901@sendu.me.uk> References: <000601c6fc4a$c3e43450$15327e82@pyrimidine> <455302D2.1000901@sendu.me.uk> Message-ID: <45530374.1010001@sendu.me.uk> Sendu Bala wrote: > Chris Fields wrote: >> What version of Bioperl are you running? >> As a warning, the bptutorial.pl script has been removed from CVS and will >> not be included in future versions of Bioperl. It can be found on the >> bioperl wiki instead: >> >> http://www.bioperl.org/wiki/Bptutorial > > It hasn't been removed, but should it be? AFAIK there was still a > request from at least one person to keep it. But is it still out of date > wrt the wiki version? Scratch that, it was still in the 1.5.2 branch but I've removed it. From bix at sendu.me.uk Thu Nov 9 07:04:56 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 12:04:56 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 Message-ID: <45531968.6080607@sendu.me.uk> Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. See http://www.bioperl.org/wiki/Release_1.5.2 for instructions on getting and testing this RC. Developers: Once again I'm hopeful that this is the last RC. If all goes well expect final release in about a weeks time. Please check and update documentation. Users: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into. Thank you, Sendu. From avilella at gmail.com Thu Nov 9 07:15:20 2006 From: avilella at gmail.com (Albert Vilella) Date: Thu, 9 Nov 2006 12:15:20 +0000 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln Message-ID: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> Hi, I am musing on how to add trees to the AlignIO::Nexus objects. In PAML we have this "add_tree" method, and "get_rst_trees", which we could also apply to this case. I also would like to hear some feedback on how to write_aln nexus files that contain one or more trees in the object instance. Do we want this by default? Only if a "with_trees" parameter is set? Cheers, Albert. From n.haigh at sheffield.ac.uk Thu Nov 9 08:55:59 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Thu, 09 Nov 2006 13:55:59 +0000 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> Message-ID: <4553336F.2000000@sheffield.ac.uk> Albert Vilella wrote: > Hi, > > I am musing on how to add trees to the AlignIO::Nexus objects. > > In PAML we have this "add_tree" method, and "get_rst_trees", which we > could also apply to this case. > > I also would like to hear some feedback on how to write_aln nexus > files that contain one or more trees in the object instance. Do we > want this by default? Only if a "with_trees" parameter is set? > > Cheers, > > Albert. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > Hi Albert, I don't know if you are aware of this resource, so here it is: http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all I would suggest that if there are trees in the object instance, then write_aln should print them by default and then have a "no_trees" option. Nath From cjfields at uiuc.edu Thu Nov 9 09:13:09 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 08:13:09 -0600 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <4553336F.2000000@sheffield.ac.uk> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> <4553336F.2000000@sheffield.ac.uk> Message-ID: <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> On Nov 9, 2006, at 7:55 AM, Nathan Haigh wrote: > Albert Vilella wrote: >> Hi, >> >> I am musing on how to add trees to the AlignIO::Nexus objects. >> >> In PAML we have this "add_tree" method, and "get_rst_trees", which we >> could also apply to this case. >> >> I also would like to hear some feedback on how to write_aln nexus >> files that contain one or more trees in the object instance. Do we >> want this by default? Only if a "with_trees" parameter is set? >> >> Cheers, >> >> Albert. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > Hi Albert, > > I don't know if you are aware of this resource, so here it is: > http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all > > I would suggest that if there are trees in the object instance, then > write_aln should print them by default and then have a "no_trees" > option. > > Nath Another option is to store them in the SimpleAlign object as a queue of Tree objects. Stockholm format allows trees in the annotation section, so it makes sense that if some alignments contain this data then we should have a way of parsing and storing it, as long as we read/write support the particular tree format. Something like: my $aln = $alnin->next_aln(); # iterate... while (my $tree = $aln->next_tree()) { ... } # or SimpleAlign-like for my $tree ($aln->each_tree()) { ... } # all trees @trees = $aln->each_tree(); etc. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 9 10:28:45 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 09:28:45 -0600 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> <4553336F.2000000@sheffield.ac.uk> <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> Message-ID: <112C051C-0868-4933-A1CE-87E773B7FD05@uiuc.edu> On Nov 9, 2006, at 8:13 AM, Chris Fields wrote: > On Nov 9, 2006, at 7:55 AM, Nathan Haigh wrote: > >> Albert Vilella wrote: >>> Hi, >>> >>> I am musing on how to add trees to the AlignIO::Nexus objects. >>> >>> In PAML we have this "add_tree" method, and "get_rst_trees", >>> which we >>> could also apply to this case. >>> >>> I also would like to hear some feedback on how to write_aln nexus >>> files that contain one or more trees in the object instance. Do we >>> want this by default? Only if a "with_trees" parameter is set? >>> >>> Cheers, >>> >>> Albert. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> Hi Albert, >> >> I don't know if you are aware of this resource, so here it is: >> http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all >> >> I would suggest that if there are trees in the object instance, then >> write_aln should print them by default and then have a "no_trees" >> option. >> >> Nath > > Another option is to store them in the SimpleAlign object as a queue > of Tree objects. Stockholm format allows trees in the annotation > section, so it makes sense that if some alignments contain this data > then we should have a way of parsing and storing it, as long as we > read/write support the particular tree format. .... Forgot to mention the option of using a builder object, analogous to the one used for Bio::SeqIO::genbank (Bio::Seq::SeqBuilder); this would be similar to Nathan's suggestion but would tell the parser what data you want parsed (alignment annotation, tree data, sequences, accession/id, etc) based on 'slots' and particular conditions, and therefore determines what data is stored in SimpleAlign objects. I planned on setting one up for Bio::AlignIO::stockholm in the near future for optional annotation parsing, but tree parsing could be included as well. Were you thinking of something along those lines? Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bernd.web at gmail.com Thu Nov 9 18:07:48 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 10 Nov 2006 00:07:48 +0100 Subject: [Bioperl-l] Blast Writer Message-ID: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> Hi, I am using Bio::SearchIO and Bio::SearchIO::Writer::HTMLResultWriter and its filter, as my $writer = new Bio::SearchIO::Writer::HTMLResultWriter(); $writer->filter('hsp', \&hsp_filter); Can I change the contents of the HSP objects (apart from true/false filtering)? I would like to change some HSP values. Would it be possible to do so with HTMLResultWriter's filters? And if so, how to access the Hit/HSP objects in the filter? I'd be grateful for any suggestions. Best regards, Bernd From jason at bioperl.org Thu Nov 9 18:21:34 2006 From: jason at bioperl.org (Jason Stajich) Date: Thu, 9 Nov 2006 15:21:34 -0800 Subject: [Bioperl-l] Blast Writer In-Reply-To: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> References: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> Message-ID: <15C2FE1E-F0C8-43DD-96E7-FADA3421AA82@bioperl.org> You can always do this before you pass the Result object to the writer. The for loop will pass back the actual hit or hsp objects and so any updates should be stored. for my $hit ( $result->hits ) { for my $hsp ( $hit->hsps ) { # change the HSP } } -jason On Nov 9, 2006, at 3:07 PM, Bernd Web wrote: > Hi, > > I am using Bio::SearchIO and Bio::SearchIO::Writer::HTMLResultWriter > and its filter, as > my $writer = new Bio::SearchIO::Writer::HTMLResultWriter(); > $writer->filter('hsp', \&hsp_filter); > > Can I change the contents of the HSP objects (apart from true/ > false filtering)? > I would like to change some HSP values. Would it be possible to do so > with HTMLResultWriter's filters? And if so, how to access the Hit/HSP > objects in the filter? > > I'd be grateful for any suggestions. > > Best regards, > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California Dept of Plant and Microbial Biology 321 Koshland Hall #3102 Berkeley, CA 94720-3102 lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From James.Rose at UCHSC.edu Thu Nov 9 17:56:00 2006 From: James.Rose at UCHSC.edu (James.Rose at UCHSC.edu) Date: Thu, 9 Nov 2006 15:56:00 -0700 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI Message-ID: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Hi- apologies if this subject has been addressed before, but I can't seem to find a way to search prior threads short of downloading the entire archives. I'm trying to use Bioperl to do something I thought would be fairly simple: Ingredients: one file containing a list of GI numbers for various proteins 1) Read GI number from file. 2) run a remote tblastn search against the sequenced Spermophilus tridecemlineatus genome with the GI number as query. 3) save resultant BLAST file to disk for later parsing. As it stands, several hours of browsing and scripting has failed to turn up anything that might be useful in this regard. Any advice is very much appreciated. Thanks, James From ak at ebi.ac.uk Thu Nov 9 19:01:55 2006 From: ak at ebi.ac.uk (Andreas Kahari) Date: Fri, 10 Nov 2006 00:01:55 +0000 Subject: [Bioperl-l] Archive searching (was Re: Remote tblastn against a sequenced genome at NCBI) In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: <20061110000155.GA27524@ebi.ac.uk> On Thu, Nov 09, 2006 at 03:56:00PM -0700, James.Rose at UCHSC.edu wrote: > > > Hi- apologies if this subject has been addressed before, but I can't > seem to find a way to search prior threads short of downloading the > entire archives. [cut] See here: http://www.bioperl.org/wiki/Mailing_lists -- Andreas K?h?ri :: Ensembl Software Developer European Bioinformatics Institute (EMBL-EBI) -------------------------------------------- contentsofsignaturemightsettleduringtransfer From cjfields at uiuc.edu Thu Nov 9 19:46:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 18:46:35 -0600 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: <43D47332-B9A9-4D01-87FD-433D86B68853@uiuc.edu> > Hi- apologies if this subject has been addressed before, but I > can't seem to find a way to search prior threads short of > downloading the entire archives. I'm trying to use Bioperl to do > something I thought would be fairly simple: > > Ingredients: one file containing a list of GI numbers for various > proteins > > 1) Read GI number from file. > 2) run a remote tblastn search against the sequenced Spermophilus > tridecemlineatus genome with the GI number as query. > 3) save resultant BLAST file to disk for later parsing. > > As it stands, several hours of browsing and scripting has failed to > turn up anything that might be useful in this regard. > > Any advice is very much appreciated. > > Thanks, > > James NCBI has a little-known (but very useful) list of databases available for remote BLAST searches: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastdblist.html If you replace the database parameter with the exact string listed under the table, then it should work. 'Trace/ Spermophilus_tridecemlineatus_WGS' for the WGS sequences is probably what you want. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 9 19:49:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 18:49:24 -0600 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: On Nov 9, 2006, at 4:56 PM, wrote: > > > Hi- apologies if this subject has been addressed before, but I > can't seem to find a way to search prior threads short of > downloading the entire archives. I'm trying to use Bioperl to do > something I thought would be fairly simple: > > Ingredients: one file containing a list of GI numbers for various > proteins > > 1) Read GI number from file. > 2) run a remote tblastn search against the sequenced Spermophilus > tridecemlineatus genome with the GI number as query. > 3) save resultant BLAST file to disk for later parsing. > > As it stands, several hours of browsing and scripting has failed to > turn up anything that might be useful in this regard. > > Any advice is very much appreciated. > > Thanks, > > James Oops, sent you an old page. Here's the more up-to-date one: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/ remote_accessible_blastdblist.html Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sayali_salodkar at persistent.co.in Fri Nov 10 00:10:35 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Fri, 10 Nov 2006 10:40:35 +0530 Subject: [Bioperl-l] Bioperl parser for PolyPhred? Message-ID: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> Hi, I want to parse the output of polyphred http://droog.gs.washington.edu/PolyPhred.html. Is there a parser already available in Bioperl which would help me in doing the same. Thanks, Sayali DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From bix at sendu.me.uk Fri Nov 10 05:15:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 10:15:41 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) Message-ID: <4554514D.2020001@sendu.me.uk> Hi all, Since I'm seeing inadequacies with the current Makefile.PL scripts we have, I'm thinking of converting from ExtUtils::MakeMaker and the Makefile.PL scripts to Module::Build Build.PL scripts. The advantages this will bring would be creation and installation of documentation, sane handling of required and optional dependencies, and hopefully good META.yml output, for CPAN compatibility wrt version numbers. I'll be able to use Module::Build::Compat to automatically generate Makefile.PL scripts in 'passthrough' style (if an end-user tries to use Makefile.PL without having Module::Build installed, it will offer to install Module::Build for them) when it comes time to make distributions, but Makefile.PL would no longer be in CVS. One thing I'm not clear on with the current situation is what is supposed to happen when the user chooses to install scripts. Where are they supposed to get installed to, and where do end-users normally run them from and how? How does this compare to expectations from other perl module distributions that have installable scripts? Please comment and discuss, but I'd like to get this done for the 1.5.2 release so that the CPAN distribution will be happy. From Derek.Fairley at bll.n-i.nhs.uk Fri Nov 10 05:15:52 2006 From: Derek.Fairley at bll.n-i.nhs.uk (Fairley, Derek) Date: Fri, 10 Nov 2006 10:15:52 -0000 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: James, Try the nabble.com mirror of this forum for easy searching of prior threads: http://www.nabble.com/BioPerl-f13596.html Derek. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of James.Rose at UCHSC.edu Sent: 09 November 2006 22:56 To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI Hi- apologies if this subject has been addressed before, but I can't seem to find a way to search prior threads short of downloading the entire archives. I'm trying to use Bioperl to do something I thought would be fairly simple: Ingredients: one file containing a list of GI numbers for various proteins 1) Read GI number from file. 2) run a remote tblastn search against the sequenced Spermophilus tridecemlineatus genome with the GI number as query. 3) save resultant BLAST file to disk for later parsing. As it stands, several hours of browsing and scripting has failed to turn up anything that might be useful in this regard. Any advice is very much appreciated. Thanks, James _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Fri Nov 10 07:31:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 12:31:29 +0000 Subject: [Bioperl-l] Distribution files, versions Message-ID: <45547121.6040904@sendu.me.uk> Does anyone know what the following files are supposed to do and if they still used/needed? bioperl.lisp maintenance/symlink_scripts.pl maintenance/symlink_scripts.PLS doc/makedoc.PL scripts/install_bioperl_scripts.pl Most modules in the distribution take their version from Bio::Root::Version, but some do not. Is there some reason they must keep the version they currently have, or can they be made like the others? These are the modules that seem to define their own version (based on a quick grep): Bio/DB/NCBIHelper.pm Bio/DB/Expression/geo.pm Bio/DB/EUtilities/elink.pm Bio/SeqIO/tinyseq.pm Bio/Graphics/Glyph/cds.pm Bio/Graphics/Glyph/translation.pm Bio/Graphics/Glyph/so_transcript.pm Bio/Index/Blast.pm Bio/Index/Hmmer.pm Bio/Tools/WebBlat.pm Bio/Tools/HMM.pm Bio/Tools/dpAlign.pm From JK at novozymes.com Fri Nov 10 07:41:19 2006 From: JK at novozymes.com (JK (Jesper Agerbo Krogh)) Date: Fri, 10 Nov 2006 13:41:19 +0100 Subject: [Bioperl-l] Bio::SeqIO::fasta patch. Message-ID: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> Hi. Just a small patch for outputting stuff on the descriptionline i fasta format. Stuff like: DE test DE test2 DE test3 converted to fasta becomes: > testtest2test3 and not > test test2 test3 Index: fasta.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/fasta.pm,v retrieving revision 1.60 diff -r1.60 fasta.pm 203c203 < $desc =~ s/\n//g; --- > $desc =~ s/\n/ /g; Should probably be applied to the stable-branch . Jesper From arareko at campus.iztacala.unam.mx Fri Nov 10 10:14:18 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Fri, 10 Nov 2006 09:14:18 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: <4554974A.4010206@campus.iztacala.unam.mx> Sendu Bala wrote: > Does anyone know what the following files are supposed to do and if they > still used/needed? > > bioperl.lisp This a module template for Emacs users. > maintenance/symlink_scripts.pl > maintenance/symlink_scripts.PLS The 1st is created by Makefile.PL (basically its a rename of the 2nd) and is run during 'make install'. From the POD: "This script will create a symlink in the 'installscript' directory (as defined during install) to a script in that same directory. It was written to create a symlink with the name 'bp_pg_bulk_load_gff.pl' that targeted 'bp_bulk_load_gff.pl' but can be extended by adding files to the %symlink_scripts hash. Perl function 'symlink' is used to keep the script from crashing on systems that don't allow symbolic linking." > doc/makedoc.PL I have no idea :) > scripts/install_bioperl_scripts.pl This is also run automatically on 'make install'. Cheers, Mauricio. -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From aaron.j.mackey at gsk.com Fri Nov 10 08:59:55 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Fri, 10 Nov 2006 08:59:55 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> Message-ID: > bioperl.lisp This is a set of convenience macros for developers who use Emacs, but it's pretty out of date. Some may still use it, though. It's of no use being in the package distribution, however. > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must keep > the version they currently have, or can they be made like the others? if their current version is greater than the bioperl version, then they must keep it for backwards compatibility (as otherwise a "require" statement for a certain version of Bio::SeqIO::tinyseq won't work properly). -Aaron From dmessina at wustl.edu Fri Nov 10 09:55:44 2006 From: dmessina at wustl.edu (David Messina) Date: Fri, 10 Nov 2006 08:55:44 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: <256AAE6A-2ACC-4CFE-B66E-F94C536FA8C5@wustl.edu> > bioperl.lisp This is the emacs template for bioperl module writing. Should be kept I think. http://www.bioperl.org/wiki/Emacs_template > maintenance/symlink_scripts.pl > maintenance/symlink_scripts.PLS Don't know if they're still needed, but Makefile.PL still refers to them. > doc/makedoc.PL I think this does similar to what you propose below, namely redefining modules' version strings to be the same as Bio::Root::Version's. I don't see any reason to remove it, but I like your suggestion to have all the modules get their version from Bio::Root::Version. > scripts/install_bioperl_scripts.pl Does what it says. Don't know if it's still needed; I think Makefile.PL handles script installation. Re your other post about switching over to Build.PL, I think scripts go into /usr/local/bin by default, or wherever specified if PREFIX or the like is set when the user runs 'perl Makefile.PL'. That seems to fit with other CPAN distros' model, and is what I (as an end-user) would expect. Dave > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must > keep > the version they currently have, or can they be made like the others? > > These are the modules that seem to define their own version (based > on a > quick grep): > Bio/DB/NCBIHelper.pm > Bio/DB/Expression/geo.pm > Bio/DB/EUtilities/elink.pm > Bio/SeqIO/tinyseq.pm > Bio/Graphics/Glyph/cds.pm > Bio/Graphics/Glyph/translation.pm > Bio/Graphics/Glyph/so_transcript.pm > Bio/Index/Blast.pm > Bio/Index/Hmmer.pm > Bio/Tools/WebBlat.pm > Bio/Tools/HMM.pm > Bio/Tools/dpAlign.pm From cjfields at uiuc.edu Fri Nov 10 10:50:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 09:50:58 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > Hi all, > > Since I'm seeing inadequacies with the current Makefile.PL scripts we > have, I'm thinking of converting from ExtUtils::MakeMaker and the > Makefile.PL scripts to Module::Build Build.PL scripts. > > The advantages this will bring would be creation and installation of > documentation, sane handling of required and optional dependencies, > and > hopefully good META.yml output, for CPAN compatibility wrt version > numbers. > > I'll be able to use Module::Build::Compat to automatically generate > Makefile.PL scripts in 'passthrough' style (if an end-user tries to > use > Makefile.PL without having Module::Build installed, it will offer to > install Module::Build for them) when it comes time to make > distributions, but Makefile.PL would no longer be in CVS. > > > One thing I'm not clear on with the current situation is what is > supposed to happen when the user chooses to install scripts. Where are > they supposed to get installed to, and where do end-users normally run > them from and how? How does this compare to expectations from other > perl > module distributions that have installable scripts? > > > Please comment and discuss, but I'd like to get this done for the > 1.5.2 > release so that the CPAN distribution will be happy. I don't have a problem with this as long as it works for all systems. It sounds like a good long-term solution, esp. for CPAN developer releases. However, we've already had three RC's using the regular old Makefile.PL setup, which seems to work fine for now. It also sounds like we will need to update all relevant installation documentation (since we can't run 'perl Makefile.PL' w/o Makefile.PL, unless I'm missing something). Hence I'm a bit worried about adding something new like this after three RCs and just before a final release. I think it's something we should do, but I'm not sure we should have it for this release. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From dmessina at wustl.edu Fri Nov 10 10:40:21 2006 From: dmessina at wustl.edu (David Messina) Date: Fri, 10 Nov 2006 09:40:21 -0600 Subject: [Bioperl-l] Bioperl parser for PolyPhred? In-Reply-To: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> References: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> Message-ID: Sayali, I don't believe there is a BioPerl polyphred parser yet. This question came up on the list previously, however, and there was mention of a Perl script that appears to parse polyphred output: http://portal.open-bio.org/pipermail/bioperl-l/2003-December/014206.html Dave From bix at sendu.me.uk Fri Nov 10 10:59:54 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 15:59:54 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> Message-ID: <4554A1FA.6080003@sendu.me.uk> Chris Fields wrote: > On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > >> Hi all, >> >> Since I'm seeing inadequacies with the current Makefile.PL scripts we >> have, I'm thinking of converting from ExtUtils::MakeMaker and the >> Makefile.PL scripts to Module::Build Build.PL scripts. [snip] > I don't have a problem with this as long as it works for all systems. > It sounds like a good long-term solution, esp. for CPAN developer releases. > > However, we've already had three RC's using the regular old Makefile.PL > setup, which seems to work fine for now. It also sounds like we will > need to update all relevant installation documentation (since we can't > run 'perl Makefile.PL' w/o Makefile.PL, unless I'm missing something). > Hence I'm a bit worried about adding something new like this after three > RCs and just before a final release. > > I think it's something we should do, but I'm not sure we should have it > for this release. Now that I'm looking into it, it seems like quite a job, and yes, especially with all the documentation updates that need to be carefully looked at. Though to answer your question, Makefile.PL would be auto-generated by Build.PL immediately prior to a release and included in the distribution file for end users to use, but it wouldn't be in CVS. Such a Makefile.PL is essentially a front-end to the Build.PL for backwards-compatibility. For 1.5.2 I may just manually create a META.yml (the one generated via Makefile.PL isn't good enough) which only affects CPAN behaviour and nothing else we've been testing in the RCs. From bix at sendu.me.uk Fri Nov 10 11:03:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 16:03:04 +0000 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554974A.4010206@campus.iztacala.unam.mx> References: <45547121.6040904@sendu.me.uk> <4554974A.4010206@campus.iztacala.unam.mx> Message-ID: <4554A2B8.4010207@sendu.me.uk> Mauricio Herrera Cuadra wrote: > Sendu Bala wrote: >> Does anyone know what the following files are supposed to do and if >> they still used/needed? >> >> bioperl.lisp > > This a module template for Emacs users. I propose moving it to the wiki and removing it from CVS. >> maintenance/symlink_scripts.pl >> maintenance/symlink_scripts.PLS > The 1st is created by Makefile.PL (basically its a rename of the 2nd) > and is run during 'make install'. From the POD: > > "This script will create a symlink in the 'installscript' directory (as > defined during install) to a script in that same directory. It was > written to create a symlink with the name 'bp_pg_bulk_load_gff.pl' that > targeted 'bp_bulk_load_gff.pl' but can be extended by adding files to > the %symlink_scripts hash. > > Perl function 'symlink' is used to keep the script from crashing on > systems that don't allow symbolic linking." The question is, do we need this symlink? Is the bulk_load_gff stuff still relevant? Why was it needed in the first place? For me, it doesn't seem to do anything useful; it just creates a broken symlink in PREFIX/bin. >> scripts/install_bioperl_scripts.pl > This is also run automatically on 'make install'. Not any more it isn't. Makefile.PL has (some of, at least) this script's methods. Does anyone use it manually? I propose removing it from CVS. AFAICT, Makefile.PL only ever installs to scripts_temp? How would people normally expect to define the script installation directory? Maybe it used to install scripts to user-defined or typical places (eg. /usr/local/bin as David Messina suggests) but that got broken in a recent commit? Can anyone confirm if script installation works properly for them, and how they got it to work? From cjfields at uiuc.edu Fri Nov 10 11:11:17 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:11:17 -0600 Subject: [Bioperl-l] Bio::SeqIO::fasta patch. In-Reply-To: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> References: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> Message-ID: <7BBF2CEB-B012-4145-9818-6B69D10C7E8F@uiuc.edu> On Nov 10, 2006, at 6:41 AM, JK ((Jesper Agerbo Krogh)) wrote: > Hi. > > Just a small patch for outputting stuff on the descriptionline i > fasta format. > > Stuff like: > > DE test > DE test2 > DE test3 > > converted to fasta becomes: > >> testtest2test3 > > and not > >> test test2 test3 ... Actually, this should be fixed in the original input parser, not in fasta.pm. Was this from EMBL format? Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Fri Nov 10 11:16:24 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Fri, 10 Nov 2006 11:16:24 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> Message-ID: <4554A5D8.8000700@bms.com> I personally like the idea. Why not have both for this release to ensure smooth transition? Sendu, would having Makefile.PL (I mean the old one) along with the build script be a problem? I am not very familiar with both modules, but from the pdoc it seems it should not be too hard: Note that if you want to provide both a Makefile.PL and a Build.PL for your distribution, you probably want to add the following to "WriteMakefile" in your Makefile.PL so that MakeMaker doesn?t try to run your Build.PL as a nor? mal .PL file: PL_FILES => {}, Stefan Chris Fields wrote: > On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > > >> Hi all, >> >> Since I'm seeing inadequacies with the current Makefile.PL scripts we >> have, I'm thinking of converting from ExtUtils::MakeMaker and the >> Makefile.PL scripts to Module::Build Build.PL scripts. >> >> The advantages this will bring would be creation and installation of >> documentation, sane handling of required and optional dependencies, >> and >> hopefully good META.yml output, for CPAN compatibility wrt version >> numbers. >> >> I'll be able to use Module::Build::Compat to automatically generate >> Makefile.PL scripts in 'passthrough' style (if an end-user tries to >> use >> Makefile.PL without having Module::Build installed, it will offer to >> install Module::Build for them) when it comes time to make >> distributions, but Makefile.PL would no longer be in CVS. >> >> >> One thing I'm not clear on with the current situation is what is >> supposed to happen when the user chooses to install scripts. Where are >> they supposed to get installed to, and where do end-users normally run >> them from and how? How does this compare to expectations from other >> perl >> module distributions that have installable scripts? >> >> >> Please comment and discuss, but I'd like to get this done for the >> 1.5.2 >> release so that the CPAN distribution will be happy. >> > > I don't have a problem with this as long as it works for all > systems. It sounds like a good long-term solution, esp. for CPAN > developer releases. > > However, we've already had three RC's using the regular old > Makefile.PL setup, which seems to work fine for now. It also sounds > like we will need to update all relevant installation documentation > (since we can't run 'perl Makefile.PL' w/o Makefile.PL, unless I'm > missing something). Hence I'm a bit worried about adding something > new like this after three RCs and just before a final release. > > I think it's something we should do, but I'm not sure we should have > it for this release. > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at uiuc.edu Fri Nov 10 11:21:07 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:21:07 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: ... > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must > keep > the version they currently have, or can they be made like the others? > > These are the modules that seem to define their own version (based > on a > quick grep): > Bio/DB/NCBIHelper.pm > Bio/DB/Expression/geo.pm > Bio/DB/EUtilities/elink.pm > Bio/SeqIO/tinyseq.pm > Bio/Graphics/Glyph/cds.pm > Bio/Graphics/Glyph/translation.pm > Bio/Graphics/Glyph/so_transcript.pm > Bio/Index/Blast.pm > Bio/Index/Hmmer.pm > Bio/Tools/WebBlat.pm > Bio/Tools/HMM.pm > Bio/Tools/dpAlign.pm They probably shouldn't have their own unless there is a good reason (and I can't really think of one). The elink $VERSION is for the NCBI elink DTD, not the bioperl version, but that should be changed in elinks to something else beside $VERSION (my bad). The same reasoning may be relevant for the other modules; we'll just have to check them one-by-one. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Nov 10 11:29:42 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:29:42 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554A5D8.8000700@bms.com> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> Message-ID: On Nov 10, 2006, at 10:16 AM, Stefan Kirov wrote: > I personally like the idea. Why not have both for this release to > ensure smooth transition? Sendu, would having Makefile.PL (I mean > the old one) along with the build script be a problem? I am not > very familiar with both modules, but from the pdoc it seems it > should not be too hard: > > Note that if you want to provide both a Makefile.PL and a > Build.PL for your distribution, you probably want to add > the following to "WriteMakefile" in your Makefile.PL so > that MakeMaker doesn?t try to run your Build.PL as a nor > mal .PL file: > > PL_FILES => {}, > > > Stefan ... Sounds like a good compromise to me. Like I said, the only problem I had is introducing something drastically new after three RCs (and just prior to a final release; I think Sendu wanted to release the final 1.5.2 next week, just before Thanksgiving here.). There is no problem though if we have the old Makefile.PL to fall back to for this release. In fact, you could remove it from HEAD when needed; the file still exists on the 1.5.2 branch, right? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bernd.web at gmail.com Fri Nov 10 12:39:30 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 10 Nov 2006 18:39:30 +0100 Subject: [Bioperl-l] Bio::Graphics Message-ID: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> Hi, Lincoln made an excellent help on Graphics. Thanks for that!(http://www.bioperl.org/wiki/HOWTO:Graphics) I am just looking at the imagemap creation with my $map=$panel->create_web_map('mapname',\&linkrule,'bbb'); and would like to connect the PNG from a blast report to the blast results. I just realize that this likely has been done many times. Does someone have a pointer to code for creating an imagemap from a BLAST report and also write the blast results with links? Bernd From bosborne11 at verizon.net Fri Nov 10 13:10:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Fri, 10 Nov 2006 13:10:01 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554A2B8.4010207@sendu.me.uk> Message-ID: Sendu, No, no scripts installed either by bioperl-live or by 1.5.2-RC3 (Mac OS X, Perl 5.8.6). But yes, bioperl-live has certainly been capable of installing scripts in the past. Brian O. On 11/10/06 11:03 AM, "Sendu Bala" wrote: > Can anyone confirm if script installation works properly for them, and > how they got it to work? From hlapp at gmx.net Fri Nov 10 18:33:48 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:33:48 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: On Nov 10, 2006, at 7:31 AM, Sendu Bala wrote: > bioperl.lisp This is the macros file for emacs. Do not delete it from the repository ... -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Nov 10 18:37:32 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:37:32 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: References: Message-ID: <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: >> bioperl.lisp > > This is a set of convenience macros for developers who use Emacs, > but it's > pretty out of date. What is out of date in there? > Some may still use it, though. E.g., dinosaurs like me. > It's of no use being in the package distribution, however. I agree. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Nov 10 18:40:40 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:40:40 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554A2B8.4010207@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> <4554974A.4010206@campus.iztacala.unam.mx> <4554A2B8.4010207@sendu.me.uk> Message-ID: <2E617B21-BBFA-4865-AC50-6D6694B6CE2F@gmx.net> On Nov 10, 2006, at 11:03 AM, Sendu Bala wrote: >>> bioperl.lisp >> >> This a module template for Emacs users. > > I propose moving it to the wiki and removing it from CVS. This is not a good idea because the wiki is a bad platform for version controlling source code files, and this is a source code file. I don't have a problem with putting it up on the wiki, too. Better yet, link to the version in CVS. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Nov 10 19:35:06 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 19:35:06 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: Sounds like a good thing to do to me - I'd just be hesitant to do this for the 1.5.2 release. But I'm not the release master. -hilmar On Nov 10, 2006, at 5:15 AM, Sendu Bala wrote: > Hi all, > > Since I'm seeing inadequacies with the current Makefile.PL scripts we > have, I'm thinking of converting from ExtUtils::MakeMaker and the > Makefile.PL scripts to Module::Build Build.PL scripts. > > The advantages this will bring would be creation and installation of > documentation, sane handling of required and optional dependencies, > and > hopefully good META.yml output, for CPAN compatibility wrt version > numbers. > > I'll be able to use Module::Build::Compat to automatically generate > Makefile.PL scripts in 'passthrough' style (if an end-user tries to > use > Makefile.PL without having Module::Build installed, it will offer to > install Module::Build for them) when it comes time to make > distributions, but Makefile.PL would no longer be in CVS. > > > One thing I'm not clear on with the current situation is what is > supposed to happen when the user chooses to install scripts. Where are > they supposed to get installed to, and where do end-users normally run > them from and how? How does this compare to expectations from other > perl > module distributions that have installable scripts? > > > Please comment and discuss, but I'd like to get this done for the > 1.5.2 > release so that the CPAN distribution will be happy. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From kaboroev at sfu.ca Fri Nov 10 17:51:21 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Fri, 10 Nov 2006 14:51:21 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical Message-ID: <45550269.9050407@sfu.ca> Hi, I am attempting to add a few methods (ie. matching_bands_list) to the fpc map class but I am having a hard time inheriting the class properly. My first attempt was to inherit the "Bio::Map::Physical" class but the "next_map" package is not found. So I tried inheriting "Bio::MapIO" instead, and get a cannot find "matching_bands_list" via package "Bio::Map::Physical" The only way I can get it to work is with no inheritance and passing the map class variable to the function, but this isn't very elegant. Is there a correct way to inherit these classes that will allow me to execute this properly? keith From bernd.web at gmail.com Fri Nov 10 18:10:09 2006 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 11 Nov 2006 00:10:09 +0100 Subject: [Bioperl-l] POD HTML ResultWriter Message-ID: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> Hi, I just found the POD for HTMLResultWriter is truncated in Internet Explorer. http://doc.bioperl.org/bioperl-live/Bio/SearchIO/Writer/HTMLResultWriter.html. It stops with start_report. I think this is due to the tag (and , <BODY> tags in the text of start_report. In Firefox the page is rendered OK. Bernd From bix at sendu.me.uk Sat Nov 11 03:38:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 11 Nov 2006 08:38:27 +0000 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45550269.9050407@sfu.ca> References: <45550269.9050407@sfu.ca> Message-ID: <45558C03.8020903@sendu.me.uk> Keith Anthony Boroevich wrote: > Hi, > > I am attempting to add a few methods (ie. matching_bands_list) to the > fpc map class but I am having a hard time inheriting the class properly. > > My first attempt was to inherit the "Bio::Map::Physical" class but the > "next_map" package is not found. > So I tried inheriting "Bio::MapIO" instead, and get a cannot find > "matching_bands_list" via package "Bio::Map::Physical" > The only way I can get it to work is with no inheritance and passing the > map class variable to the function, but this isn't very elegant. Is > there a correct way to inherit these classes that will allow me to > execute this properly? It's hard to diagnose the problem without knowing exactly what you've tried. Please post some relevant code. Also, what version of Bioperl are you using? From bernd.web at gmail.com Sat Nov 11 08:53:55 2006 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 11 Nov 2006 14:53:55 +0100 Subject: [Bioperl-l] Bio::DB::Fasta index Message-ID: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Hi, A maybe strange question: is it possible to force Bio::DB::Fasta NOT to index the fasta file at any time (if there is already an index)? In the doc (http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Fasta.html), I read: " If one of the source fasta files is updated, the module reindexes just that one file. (You can also force reindexing manually)." Can I also switch off reindexing? (I realize that with Bio::Index::Fasta indexing can be separated). bernd From mkiwala at watson.wustl.edu Sat Nov 11 10:54:55 2006 From: mkiwala at watson.wustl.edu (mkiwala at watson.wustl.edu) Date: Sat, 11 Nov 2006 09:54:55 -0600 (CST) Subject: [Bioperl-l] Bio::DB::Fasta index In-Reply-To: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> References: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Message-ID: <58605.24.107.18.143.1163260495.squirrel@gscmail.wustl.edu> > A maybe strange question: is it possible to force Bio::DB::Fasta NOT > to index the fasta file at any time (if there is already an index)? I don't think so, but you could set the time stamp on the index file just before you run your script that uses the index. On a unix-like machine you would use the touch command. From cjfields at uiuc.edu Sat Nov 11 11:26:31 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 11 Nov 2006 10:26:31 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> References: <OF981FA506.80BA9953-ON85257222.004C99FF-85257222.004CE6C4@gsk.com> <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> Message-ID: <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> On Nov 10, 2006, at 5:37 PM, Hilmar Lapp wrote: > > On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: > >>> bioperl.lisp >> >> This is a set of convenience macros for developers who use Emacs, >> but it's >> pretty out of date. > > What is out of date in there? > >> Some may still use it, though. > > E.g., dinosaurs like me. > >> It's of no use being in the package distribution, however. > > I agree. > > -hilmar Maybe move it to it's own folder? It would be convenient if anyone else has helper macros (Komodo, vim, etc) or other developer stuff donated that we don't want included in the package distribution. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Sat Nov 11 11:31:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 11 Nov 2006 10:31:26 -0600 Subject: [Bioperl-l] POD HTML ResultWriter In-Reply-To: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> References: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> Message-ID: <27593A76-29AE-4295-A229-36A92F9F92F6@uiuc.edu> Bernd, Could you submit this as a bug? It likely has to do with PDOC. Include the IE version etc. Chris On Nov 10, 2006, at 5:10 PM, Bernd Web wrote: > Hi, > > I just found the POD for HTMLResultWriter is truncated in Internet > Explorer. > http://doc.bioperl.org/bioperl-live/Bio/SearchIO/Writer/ > HTMLResultWriter.html. > It stops with start_report. > I think this is due to the <HTML> tag (and <TITLE>, <BODY> tags in the > text of start_report. In Firefox the page is rendered OK. > > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Sat Nov 11 13:02:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 11 Nov 2006 13:02:18 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> References: <OF981FA506.80BA9953-ON85257222.004C99FF-85257222.004CE6C4@gsk.com> <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> Message-ID: <6E07DFB4-4D2A-4D66-9FAA-FEC20F6DE1B2@gmx.net> On Nov 11, 2006, at 11:26 AM, Chris Fields wrote: > > On Nov 10, 2006, at 5:37 PM, Hilmar Lapp wrote: > >> >> On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: >> >>>> bioperl.lisp >> >>> It's of no use being in the package distribution, however. >> >> I agree. >> >> -hilmar > > Maybe move it to it's own folder? It would be convenient if anyone > else has helper macros (Komodo, vim, etc) or other developer stuff > donated that we don't want included in the package distribution. Good idea, I agree. -hilmar > > chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From chhalling at verizon.net Sun Nov 12 13:11:54 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 12 Nov 2006 13:11:54 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC Message-ID: <455763EA.8080300@verizon.net> Quick summary: 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but not by Bio::Restriction::Enzyme. Should 'X' be removed from Bio::Tools::IUPAC or should it be added to Bio::Restriction::Enzyme? Detailed explanation: I tried to use the Bio::Restriction modules to perform a simple restriction analysis of some sequences I'm using at work, and I found the documentation and code confusing. So I'm volunteering to overhaul and redocument these modules. As part of this effort, I am also volunteering to fix the Bio::Restriction::IO::bairoch module. I have begun writing a test suite, RestrictionEnzyme.t, for the Bio::Restriction::Enzyme module. For one of the tests, I created a Bio::Restriction::Enzyme object with a recognition sequence that includes all of the IUPAC base symbols along with the caret ('^') symbol. A code excerpt is: use Bio::Tools::IUPAC; my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); ok $enzyme = Bio::Restriction::Enzyme->new( -name => 'IUPAC-IUB', -site => $site ); This test fails because Bio::Tools::IUPAC module includes 'X' as a valid base symbol, whereas Bio::Restriction::Enzyme does not. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 STACK: t/RestrictionEnzyme.t:184 ----------------------------------------------------------- The symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC need to be synchronized. Since 'X' is not recommended by "Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences" (see http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it stands for xanthine), I am in favor of removing it as a valid symbol. But I have a feeling that if 'X' is removed as a valid symbol from Bio::Tools::IUPAC, this will break a lot of existing code. So the simplest solution seems to be to add 'X' to the symbols recognized by Bio::Restriction::Enzyme. Does anyone have a recommendation? -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Sun Nov 12 17:21:06 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 12 Nov 2006 17:21:06 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> References: <455763EA.8080300@verizon.net> Message-ID: <45579E52.3010606@verizon.net> A followup: Bio::Tools::IUPAC::iupac_iub() also returns 'U' as a valid base. My idea of getting an authoritative set of base symbols from Bio::Tools::IUPAC does not work well. I will leave the valid bases in Bio::Restriction::Enzyme set to what is already used in the module ('ABCDGHKMNRSTVWY'). -- Conrad Conrad Halling wrote: > Quick summary: > > 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but not by > Bio::Restriction::Enzyme. Should 'X' be removed from Bio::Tools::IUPAC > or should it be added to Bio::Restriction::Enzyme? > > Detailed explanation: > > I tried to use the Bio::Restriction modules to perform a simple > restriction analysis of some sequences I'm using at work, and I found > the documentation and code confusing. So I'm volunteering to overhaul > and redocument these modules. As part of this effort, I am also > volunteering to fix the Bio::Restriction::IO::bairoch module. > > I have begun writing a test suite, RestrictionEnzyme.t, for the > Bio::Restriction::Enzyme module. For one of the tests, I created a > Bio::Restriction::Enzyme object with a recognition sequence that > includes all of the IUPAC base symbols along with the caret ('^') > symbol. A code excerpt is: > > use Bio::Tools::IUPAC; > my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); > my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); > ok $enzyme = > Bio::Restriction::Enzyme->new( > -name => 'IUPAC-IUB', > -site => $site ); > > This test fails because Bio::Tools::IUPAC module includes 'X' as a valid > base symbol, whereas Bio::Restriction::Enzyme does not. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 > STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 > STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 > STACK: t/RestrictionEnzyme.t:184 > ----------------------------------------------------------- > > The symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC > need to be synchronized. Since 'X' is not recommended by "Nomenclature > for Incompletely Specified Bases in Nucleic Acid Sequences" (see > http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it > stands for xanthine), I am in favor of removing it as a valid symbol. > > But I have a feeling that if 'X' is removed as a valid symbol from > Bio::Tools::IUPAC, this will break a lot of existing code. So the > simplest solution seems to be to add 'X' to the symbols recognized by > Bio::Restriction::Enzyme. > > Does anyone have a recommendation? > > -- Conrad Halling chhalling at verizon.net From dmessina at wustl.edu Sun Nov 12 17:30:59 2006 From: dmessina at wustl.edu (David Messina) Date: Sun, 12 Nov 2006 16:30:59 -0600 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> References: <455763EA.8080300@verizon.net> Message-ID: <C5C56BF0-8135-4CBE-BF30-B931E79B39C7@wustl.edu> > The symbols recognized by Bio::Restriction::Enzyme and > Bio::Tools::IUPAC > need to be synchronized. Since 'X' is not recommended by "Nomenclature > for Incompletely Specified Bases in Nucleic Acid Sequences" (see > http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it > stands for xanthine), I am in favor of removing it as a valid symbol. > > But I have a feeling that if 'X' is removed as a valid symbol from > Bio::Tools::IUPAC, this will break a lot of existing code. So the > simplest solution seems to be to add 'X' to the symbols recognized by > Bio::Restriction::Enzyme. How about adding a -strict option which would require valid IUPAC symbols (i.e. not 'X')? And the permissive, 'X'-okay behavior would be the default. Dave From cjfields at uiuc.edu Sun Nov 12 19:15:37 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 12 Nov 2006 18:15:37 -0600 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <45579E52.3010606@verizon.net> References: <455763EA.8080300@verizon.net> <45579E52.3010606@verizon.net> Message-ID: <59337785-5E63-4FD3-A490-FA9AC4715BBE@uiuc.edu> On Nov 12, 2006, at 4:21 PM, Conrad Halling wrote: > A followup: > > Bio::Tools::IUPAC::iupac_iub() also returns 'U' as a valid base. My > idea > of getting an authoritative set of base symbols from Bio::Tools::IUPAC > does not work well. > > I will leave the valid bases in Bio::Restriction::Enzyme set to > what is > already used in the module ('ABCDGHKMNRSTVWY'). > > -- Conrad Conrad, You could grab a hash of DNA/RNA codes from Bio::Tools::IUPAC using iupac_iub(), then modify that for internal use in Bio::Restriction modules by adding/deleting what you want. Or add a method to Bio::Tools::IUPAC that adds/deletes key-value pairs in the object to your specifications. If there are non-IUPAC symbols present in the module we should consider the reasons why they are there. Were they added as a quick fix, or for other reasons? Strictly speaking, I would say a module named Bio::Tools::IUPAC should not contain non-IUPAC symbols, and modifications should be made on a case-by-case basis (in objects), vs. universally (in classes). You could always remove any non- standard symbols and see what breaks. By the way, I think I can speak for many here by saying that we are happy you will take up the Bio::Restriction classes. They definitely need some work! Chris > Conrad Halling wrote: >> Quick summary: >> >> 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but >> not by >> Bio::Restriction::Enzyme. Should 'X' be removed from >> Bio::Tools::IUPAC >> or should it be added to Bio::Restriction::Enzyme? >> >> Detailed explanation: >> >> I tried to use the Bio::Restriction modules to perform a simple >> restriction analysis of some sequences I'm using at work, and I found >> the documentation and code confusing. So I'm volunteering to overhaul >> and redocument these modules. As part of this effort, I am also >> volunteering to fix the Bio::Restriction::IO::bairoch module. >> >> I have begun writing a test suite, RestrictionEnzyme.t, for the >> Bio::Restriction::Enzyme module. For one of the tests, I created a >> Bio::Restriction::Enzyme object with a recognition sequence that >> includes all of the IUPAC base symbols along with the caret ('^') >> symbol. A code excerpt is: >> >> use Bio::Tools::IUPAC; >> my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); >> my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); >> ok $enzyme = >> Bio::Restriction::Enzyme->new( >> -name => 'IUPAC-IUB', >> -site => $site ); >> >> This test fails because Bio::Tools::IUPAC module includes 'X' as a >> valid >> base symbol, whereas Bio::Restriction::Enzyme does not. >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 >> STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 >> STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 >> STACK: t/RestrictionEnzyme.t:184 >> ----------------------------------------------------------- >> >> The symbols recognized by Bio::Restriction::Enzyme and >> Bio::Tools::IUPAC >> need to be synchronized. Since 'X' is not recommended by >> "Nomenclature >> for Incompletely Specified Bases in Nucleic Acid Sequences" (see >> http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it >> stands for xanthine), I am in favor of removing it as a valid symbol. >> >> But I have a feeling that if 'X' is removed as a valid symbol from >> Bio::Tools::IUPAC, this will break a lot of existing code. So the >> simplest solution seems to be to add 'X' to the symbols recognized by >> Bio::Restriction::Enzyme. >> >> Does anyone have a recommendation? >> >> > > -- > Conrad Halling > chhalling at verizon.net > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Mon Nov 13 04:59:34 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 13 Nov 2006 09:59:34 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 Message-ID: <45584206.2040506@sheffield.ac.uk> I've done a test of the bioperl-run 1.5.2 RC3. I've posted results etc to the wiki. I have quite a lot of changes to commit regarding changing "return undef" to "return" and other issues about "bioperl best practices" - they are mainly only obvious changes. I also, moved some tests over to Test::More and added a few further tests for those modules. The test suite passes OK for me (other than the same issues for 1.5.2 RC3). Should It be OK to commit the to HEAD? or shall I wait till after the 1.5.2 release? Cheers Nath From avilella at gmail.com Mon Nov 13 08:25:44 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 13 Nov 2006 13:25:44 +0000 Subject: [Bioperl-l] new methods -- wiki or bugzilla? Message-ID: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Hi, Should the new methods/features be declared as ENH bugs in bugzilla or using the wiki? Cheers, Albert. From cjfields at uiuc.edu Mon Nov 13 10:10:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 09:10:27 -0600 Subject: [Bioperl-l] new methods -- wiki or bugzilla? In-Reply-To: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Message-ID: <013f01c70735$dbc09140$15327e82@pyrimidine> > Hi, > > Should the new methods/features be declared as ENH bugs in > bugzilla or using the wiki? > > Cheers, > > Albert. Historically we have used Bugzilla so we can keep track of them (the enhancement tag is also available there for that reason). You could use the wiki, but I personally think the wiki better serves as primarily a documentation site, both for current code and for the direction we plan on taking Bioperl. We could add a code requests page, though. We already have a Projects Priority page that details what we think are the top issues with Bioperl that need to be addressed; there have been a number of things added to that page that should be separated out into a code request page. However, I don't know how much will be implemented unless someone interested takes it up. Frankly, there are quite a number of requests in bugzilla that haven't been added b/c of lack of interest/time by the other developers. Either that, or we have a lack of knowledge about a certain format or program, as I had with the XMFA and ARP AlignIO parsers (see the POD for my comments; the parsing is pretty minimal). Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Mon Nov 13 10:17:03 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 09:17:03 -0600 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <45584206.2040506@sheffield.ac.uk> Message-ID: <014001c70736$c6e20c80$15327e82@pyrimidine> > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Nathan S. Haigh > Sent: Monday, November 13, 2006 4:00 AM > To: bioperl-l; sendu Bala > Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 > > I've done a test of the bioperl-run 1.5.2 RC3. I've posted > results etc to the wiki. > > I have quite a lot of changes to commit regarding changing > "return undef" to "return" and other issues about "bioperl > best practices" - they are mainly only obvious changes. I > also, moved some tests over to Test::More and added a few > further tests for those modules. The test suite passes OK for > me (other than the same issues for 1.5.2 RC3). > Should It be OK to commit the to HEAD? or shall I wait till after the > 1.5.2 release? > > Cheers > Nath I would say, if the tests pass, commit away. As an aside, I'm not sure how versioning works in the other bioperl distributions. We generally package them up at the same time but I don't remember them getting a specific version number upon release. For instance, bioperl-db was considered at version 0.1 for a long time, but I can't remember if it was officially assigned that. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 13 10:18:43 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 15:18:43 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <014001c70736$c6e20c80$15327e82@pyrimidine> References: <014001c70736$c6e20c80$15327e82@pyrimidine> Message-ID: <45588CD3.5020407@sendu.me.uk> Chris Fields wrote: > > As an aside, I'm not sure how versioning works in the other bioperl > distributions. We generally package them up at the same time but I don't > remember them getting a specific version number upon release. For instance, > bioperl-db was considered at version 0.1 for a long time, but I can't > remember if it was officially assigned that. I'm making their versions match that of core, which seems appropriate. From avilella at gmail.com Mon Nov 13 08:36:44 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 13 Nov 2006 13:36:44 +0000 Subject: [Bioperl-l] new methods -- wiki or bugzilla? In-Reply-To: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> References: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Message-ID: <358f4d650611130536sd99bc51u9df42f8bd71cb3a8@mail.gmail.com> and related to the previous question: can an email (presumably with a certain template format) be sent somewhere so that either one or the other system create a new feature ticket somewhere? I've been told that it can be done with wikis, but never seen it done. On 11/13/06, Albert Vilella <avilella at gmail.com> wrote: > Hi, > > Should the new methods/features be declared as ENH bugs in bugzilla or > using the wiki? > > Cheers, > > Albert. > From cjfields at uiuc.edu Mon Nov 13 11:51:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 10:51:24 -0600 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <45588CD3.5020407@sendu.me.uk> Message-ID: <000001c70743$f45b5ce0$15327e82@pyrimidine> > Chris Fields wrote: > > > > As an aside, I'm not sure how versioning works in the other bioperl > > distributions. We generally package them up at the same time but I > > don't remember them getting a specific version number upon > release. > > For instance, bioperl-db was considered at version 0.1 for a long > > time, but I can't remember if it was officially assigned that. > > I'm making their versions match that of core, which seems appropriate. Sounds good to me. We could at least state that run, db, and network 1.5.2 releases require bioperl rel. 1.5.2 (i.e. they are not guaranteed to work with older bioperl core versions), since that's what they were tested against. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 13 11:52:15 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 16:52:15 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <000001c70743$f45b5ce0$15327e82@pyrimidine> References: <000001c70743$f45b5ce0$15327e82@pyrimidine> Message-ID: <4558A2BF.7000405@sendu.me.uk> Chris Fields wrote: >> Chris Fields wrote: >>> As an aside, I'm not sure how versioning works in the other bioperl >>> distributions. We generally package them up at the same time but I >>> don't remember them getting a specific version number upon >> release. >>> For instance, bioperl-db was considered at version 0.1 for a long >>> time, but I can't remember if it was officially assigned that. >> I'm making their versions match that of core, which seems appropriate. > > Sounds good to me. We could at least state that run, db, and network 1.5.2 > releases require bioperl rel. 1.5.2 (i.e. they are not guaranteed to work > with older bioperl core versions), since that's what they were tested > against. Yes, they will (do already) require core 1.5.2 for Makefile.PL (Build.PL) to succeed. From alessandro.botton at unipd.it Mon Nov 13 13:10:36 2006 From: alessandro.botton at unipd.it (Alessandro Botton) Date: Mon, 13 Nov 2006 19:10:36 +0100 Subject: [Bioperl-l] Installation problems... Message-ID: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Sorry to disturb you... I tried to install BioPerl by means of cpan. I have previously installed Bundle::BioPerl and everything was ok, and then tried to force the Bioperl installation. Anyway, I attach the "make test" part taken from my shell during Bioperl installation and the result of the second test (tut1.pl, also in attachment) suggested to detect a good installation of Biopelr (the first one was ok). if you need further information please ask me. Thank you in advance for your precious help. Best wishes, A.Botton ??? ======================================= ALESSANDRO BOTTON, PhD student Department of Environmental Agronomy and Crop Science University of Padova AGRIPOLIS - V.le dell'Universit?, 16 35020 Legnaro (PD)-ITALY Fax ++39 049 8272850 Phone ++39 049 8272889 E-mail: alessandro.botton at unipd.it _______________________________________ Doctorate School of Crop Science www.daapv.unipd.it/spv _______________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0012.html> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: make_test_part.txt URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0006.txt> -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0013.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: tut1.pl Type: text/x-perl-script Size: 137 bytes Desc: not available URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0003.bin> -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0014.html> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: test_tut1.pl.txt URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0007.txt> -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0015.html> From bix at sendu.me.uk Mon Nov 13 14:16:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 19:16:58 +0000 Subject: [Bioperl-l] Installation problems... In-Reply-To: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> References: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Message-ID: <4558C4AA.6020004@sendu.me.uk> Alessandro Botton wrote: > Sorry to disturb you... > I tried to install BioPerl by means of cpan. I have previously installed > Bundle::BioPerl and everything was ok, and then tried to force the > Bioperl installation. Anyway, I attach the "make test" part taken from > my shell during Bioperl installation and the result of the second test > (tut1.pl, also in attachment) suggested to detect a good installation of > Biopelr (the first one was ok). if you need further information please > ask me. Unfortunately Bioperl 1.4 (the latest 'stable' edition in CPAN) is very old and yes, you're likely to get all sorts of failures. tut1.pl tries to do something that indeed no longer works in 1.4. We have a 'developer' release called 1.5.2 soon to be released which should in fact be suitable for use by everyone and everything should work. You can download a pre-release version and install it manually: http://bioperl.org/wiki/Release_1.5.2 Or wait a week or two and you'll be able to find the final release on CPAN. Hope that helps, Sendu. From n.haigh at sheffield.ac.uk Mon Nov 13 14:50:53 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 13 Nov 2006 19:50:53 +0000 Subject: [Bioperl-l] Installation problems... In-Reply-To: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> References: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Message-ID: <4558CC9D.2050507@sheffield.ac.uk> Alessandro Botton wrote: > Sorry to disturb you... > I tried to install BioPerl by means of cpan. I have previously > installed Bundle::BioPerl and everything was ok, and then tried to > force the Bioperl installation. Anyway, I attach the "make test" part > taken from my shell during Bioperl installation and the result of the > second test (tut1.pl, also in attachment) suggested to detect a good > installation of Biopelr (the first one was ok). if you need further > information please ask me. > Thank you in advance for your precious help. > Best wishes, > A.Botton > Hi Alessandro, The Bioperl 1.4 release is now somewhat out-of-date and you might be better to install the latest 1.5.x developer release. We are currently working towards a 1.5.2 release, which should be out within the next week or so. The latest version is 1.5.2 release candidate 3 - it should be installable via CPAN. I will refer you to what has been said about the 1.5.2 RC3 release: "Users: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into." At the moment CPAN doesn't see 1.5.x as a developer release (which should be fixed shortly). Therefore you should still be able to install it with: prompt> perl -MCPAN -e shell CPAN> install Bioperl Once the 1.5.2 RC3 distribution file is fixed, the above will not work. Let me know how you get on and if you get 1.5.2 RC3 installed. Cheers Nathan From jdw at ou.edu Mon Nov 13 18:50:15 2006 From: jdw at ou.edu (James D. White) Date: Mon, 13 Nov 2006 17:50:15 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> Message-ID: <455904B7.50504@ou.edu> "Erik" <er at xs4all.nl> wrote: >Hi all, > >I noticed the parsing is borked with newest swisprot files: > UniProt Knowledgebase Release 9 consists of: > UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 > UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 > > >I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines >in swissprot/trembl according to the new specification (see >http://expasy.org/sprot/relnotes/sp_news.html). > >Basically, the change is as follows: > ID EntryName DataClass; MoleculeType; SequenceLength. >is changed to: > ID EntryName DataClass; SequenceLength. > > > >The change I made was only in the regex capturing the entry name: >method next_seq (Bio/SeqIO/swiss.pm) : > >=============== > > unless( m/ > ^ > ID \s+ # > (\S+) \s+ # $1 entryname > ([^\s;]+); \s+ # $2 DataClass > [0-9]+[ ]AA \. # Sequencelength (capture?) > $ > /ox ) > { > $self->throw("swissprot stream with no ID. Not swissprot in my book"); > } > >=============== > > How about something like the following to recognize both old and new formats =============== unless( m/ ^ ID \s+ # (\S+) \s+ # $1 entryname ( (: [^\s;]+; \s+ )? ) # $2 DataClass (including ";\s+") [0-9]+[ ]AA \. # Sequencelength (capture?) $ /ox ) { $self->throw("swissprot stream with no ID. Not swissprot in my book"); } # Because $2 now contains a trailing ";\s+" in the new format, it needs to be fixed $DataClass = $2 || 'default DataClass'; # provide default for old file format $DataClass =~ s/;\s+$//; # remove trailing ";\s+" =============== The code trailing the unless block should be modified to use the appropriate variable names. This is provided only to show what post-match modification is needed. > >I tested this (=entry parsable and SeqIO created) against several >hundred Swissprot and Trembl entries. > >Of course, files with the older format are now broken - it may be better >to leave old and new format, and try both (newest first). > >hth, > >Erik > > > > > > From lincoln.stein at gmail.com Mon Nov 13 12:43:50 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 13 Nov 2006 12:43:50 -0500 Subject: [Bioperl-l] Bio::DB::Fasta index In-Reply-To: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> References: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Message-ID: <6dce9a0b0611130943n28600d66xb3fa37f7bb4a68b6@mail.gmail.com> You can always remove write permissions from the index file, in which case the attempted reindexing will fail quickly. Lincoln On 11/11/06, Bernd Web <bernd.web at gmail.com> wrote: > > Hi, > > A maybe strange question: is it possible to force Bio::DB::Fasta NOT > to index the fasta file at any time (if there is already an index)? In > the doc ( > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Fasta.html > ), > I read: " If one of the source fasta files is updated, the module > reindexes just that one file. (You can also force reindexing > manually)." > > Can I also switch off reindexing? (I realize that with > Bio::Index::Fasta indexing can be separated). > > bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Mon Nov 13 23:44:09 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 22:44:09 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <455904B7.50504@ou.edu> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> Message-ID: <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> On Nov 13, 2006, at 5:50 PM, James D. White wrote: > "Erik" <er at xs4all.nl> wrote: > >> Hi all, >> >> I noticed the parsing is borked with newest swisprot files: >> UniProt Knowledgebase Release 9 consists of: >> UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 >> UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 >> >> >> I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines >> in swissprot/trembl according to the new specification (see >> http://expasy.org/sprot/relnotes/sp_news.html). >> >> Basically, the change is as follows: >> ID EntryName DataClass; MoleculeType; SequenceLength. >> is changed to: >> ID EntryName DataClass; SequenceLength. >> >> >> >> The change I made was only in the regex capturing the entry name: >> method next_seq (Bio/SeqIO/swiss.pm) : >> >> =============== >> >> unless( m/ >> ^ >> ID \s+ # >> (\S+) \s+ # $1 entryname >> ([^\s;]+); \s+ # $2 DataClass >> [0-9]+[ ]AA \. # Sequencelength >> (capture?) >> $ >> /ox ) >> { >> $self->throw("swissprot stream with no ID. Not swissprot in my >> book"); >> } >> >> =============== >> >> > > How about something like the following to recognize both old and > new formats > > =============== > > unless( m/ > ^ > ID \s+ # > (\S+) \s+ # $1 entryname > ( (: [^\s;]+; \s+ )? ) # $2 DataClass > (including ";\s+") > [0-9]+[ ]AA \. # > Sequencelength (capture?) > $ > /ox ) > { > $self->throw("swissprot stream with no ID. Not swissprot in my > book"); > } > # Because $2 now contains a trailing ";\s+" in the new format, it > needs to be fixed > $DataClass = $2 || 'default DataClass'; # provide default > for old file format > $DataClass =~ s/;\s+$//; # remove trailing "; > \s+" > > =============== > > The code trailing the unless block should be modified to use the > appropriate > variable names. This is provided only to show what post-match > modification is > needed. > >> >> I tested this (=entry parsable and SeqIO created) against several >> hundred Swissprot and Trembl entries. >> >> Of course, files with the older format are now broken - it may be >> better >> to leave old and new format, and try both (newest first). >> >> hth, >> >> Erik This has been fixed to match old and new formats in CVS and passes all tests so far. You can try it out if you want. The regex is made to match up to (but not include) the ';', so there is no need to remove the extra space. ... unless( m{^ ID \s+ # (\S+) \s+ # $1 entryname ([^\s;]+); \s+ # $2 DataClass (?:PRT;)? \s+ # Molecule Type (optional) [0-9]+[ ]AA \. # Sequencelength (capture?) $ }ox ) { ... The molecule type was always PRT and was a carryover from EMBL format divisions. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From kaboroev at sfu.ca Tue Nov 14 00:55:46 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Mon, 13 Nov 2006 21:55:46 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45558C03.8020903@sendu.me.uk> References: <45550269.9050407@sfu.ca> <45558C03.8020903@sendu.me.uk> Message-ID: <45595A62.7090704@sfu.ca> Hi, I am using an up-to-date bioperl-live. The precise code is insignificant so I wrote some additional (shorter) code to attempt to explain my problem. What I want to do is the following. I want to add some functionality to the Bio::Map::Physical module so i created a module that inherits Physical module, Extended::FPC.pm. #----Test.pl-BEGIN---# use strict; use diagnostics; use Extended::FPC; my $mapio = new Extended::FPC(-format => "fpc",-file => $ARGV[0],-readcor => 1); my $map = $mapio->next_map(); $map->fpc_test(); exit 0; #---Test.pl-END------# #----Extended::FPC.pm-BEGIN---# package Extended::FPC; use strict; use base qw(Bio::Map::Physical Bio::MapIO); sub fpc_test { print STDERR "testing\n"; return 0; } 1; #----Extended::FPC.pm-END-----# The execution of test.pl results in a "Can't locate object method "next_map" via package "Extended::FPC"" error; Then I added the "Bio::MapIO" module to the "use base qw(Bio::Map::Physical Bio::MapIO);", because that is the module in which next_map is declared. When I again execute test.pl I now get the exception: Uncaught exception from user code: #-------- EXCEPTION ------- # ------------- EXCEPTION: Bio::Root::NotImplemented ------------- MSG: Abstract method "Bio::Factory::MapFactoryI::next_map" is not implemented by package Extended::FPC. This is not your fault - author of Extended::FPC should be blamed! STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.7/Bio/Root/Root.pm:359 STACK: Bio::Root::RootI::throw_not_implemented /usr/lib/perl5/site_perl/5.8.7/Bio/Root/RootI.pm:522 STACK: Bio::Factory::MapFactoryI::next_map /usr/lib/perl5/site_perl/5.8.7/Bio/Factory/MapFactoryI.pm:84 STACK: ./fpc.pl:12 ---------------------------------------------------------------- at /usr/lib/perl5/site_perl/5.8.7/Error.pm line 187 Error::throw('Bio::Root::NotImplemented', '-class', 'Bio::Root::NotImplemented', '-object', 'Extended::FPC=HASH(0x109ce10)', '-text', 'Abstract method "Bio::Factory::MapFactoryI::next_map" is not ...') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Root/Root.pm line 359 Bio::Root::Root::throw('Extended::FPC=HASH(0x109ce10)', '-text', 'Abstract method "Bio::Factory::MapFactoryI::next_map" is not ...', '-class', 'Bio::Root::NotImplemented') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Root/RootI.pm line 522 Bio::Root::RootI::throw_not_implemented('Extended::FPC=HASH(0x109ce10)') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Factory/MapFactoryI.pm line 84 Bio::Factory::MapFactoryI::next_map('Extended::FPC=HASH(0x109ce10)') called at ./fpc.pl line 12 #---- EXCEPTION END ----# This is where I am now and have no real idea of where to begin. I suppose the easiest way is to pass the $map variable to the function of interest and not to bother with inheriting any modules. Sendu Bala wrote: > Keith Anthony Boroevich wrote: > >> Hi, >> >> I am attempting to add a few methods (ie. matching_bands_list) to the >> fpc map class but I am having a hard time inheriting the class properly. >> >> My first attempt was to inherit the "Bio::Map::Physical" class but the >> "next_map" package is not found. >> So I tried inheriting "Bio::MapIO" instead, and get a cannot find >> "matching_bands_list" via package "Bio::Map::Physical" >> The only way I can get it to work is with no inheritance and passing the >> map class variable to the function, but this isn't very elegant. Is >> there a correct way to inherit these classes that will allow me to >> execute this properly? >> > > It's hard to diagnose the problem without knowing exactly what you've > tried. Please post some relevant code. Also, what version of Bioperl are > you using? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- ><)))?> -cGRASP- <?(((>< Keith Anthony Boroevich Simon Fraser University Tel: 604-268-7276 From bix at sendu.me.uk Tue Nov 14 03:49:52 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 14 Nov 2006 08:49:52 +0000 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45595A62.7090704@sfu.ca> References: <45550269.9050407@sfu.ca> <45558C03.8020903@sendu.me.uk> <45595A62.7090704@sfu.ca> Message-ID: <45598330.20400@sendu.me.uk> Keith Anthony Boroevich wrote: > Hi, > > I am using an up-to-date bioperl-live. The precise code is > insignificant so I wrote some additional (shorter) code to attempt to > explain my problem. What I want to do is the following. I want to add > some functionality to the Bio::Map::Physical module so i created a > module that inherits Physical module, Extended::FPC.pm. > > #----Test.pl-BEGIN---# > use strict; > use diagnostics; > use Extended::FPC; > my $mapio = new Extended::FPC(-format => "fpc",-file => > $ARGV[0],-readcor => 1); > my $map = $mapio->next_map(); > $map->fpc_test(); > exit 0; > #---Test.pl-END------# > > #----Extended::FPC.pm-BEGIN---# > package Extended::FPC; > use strict; > use base qw(Bio::Map::Physical Bio::MapIO); > > sub fpc_test { > print STDERR "testing\n"; > return 0; > } > > 1; > #----Extended::FPC.pm-END-----# > > The execution of test.pl results in a "Can't locate object method > "next_map" via package "Extended::FPC"" error; > Then I added the "Bio::MapIO" module to the "use base > qw(Bio::Map::Physical Bio::MapIO);", because that is the module in which > next_map is declared. Well I think alarm bells should have been ringing at that point. I think you're trying to inherit from the wrong module to do whatever it is you want to do. Bio::Map::Physical has no next_map() because it isn't a Map::IO module. It represents a /single/ map (only), and is the sort of object you might /receive/ as the result of calling next_map() on an actual Map::IO module. So perhaps you should take another look at the various Map modules and figure out the correct thing to inherit from, or you just need to correct your usage (only call next_map() on a Map::IO). From er at xs4all.nl Tue Nov 14 04:40:20 2006 From: er at xs4all.nl (Erik) Date: Tue, 14 Nov 2006 10:40:20 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> Message-ID: <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> Btw and FYI: I have run this regex through SwissProt and Trembl and a previous version of those two files (to be version-precise: swissprot 51 and 50; trembl 33 and 34). It matched all ID lines. Thanks :) Erik > ... > unless( m{^ > ID \s+ # > (\S+) \s+ # $1 entryname > ([^\s;]+); \s+ # $2 DataClass > (?:PRT;)? \s+ # Molecule Type (optional) > [0-9]+[ ]AA \. # Sequencelength (capture?) > $ > }ox ) { > ... > > The molecule type was always PRT and was a carryover from EMBL format > divisions. From cjfields at uiuc.edu Tue Nov 14 07:35:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 14 Nov 2006 06:35:24 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> Message-ID: <B5AD2308-6CC0-4250-ABFA-1E728196693F@uiuc.edu> On Nov 14, 2006, at 3:40 AM, Erik wrote: > Btw and FYI: > > I have run this regex through SwissProt and Trembl and a previous > version > of those two files (to be version-precise: swissprot 51 and 50; > trembl 33 > and 34). > > It matched all ID lines. > > Thanks :) > > Erik ... Thanks for letting us know. We like success stories! Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From gcarbajosa at cnio.es Tue Nov 14 05:39:41 2006 From: gcarbajosa at cnio.es (guillermo) Date: Tue, 14 Nov 2006 11:39:41 +0100 Subject: [Bioperl-l] Error while indexing whole genbank Message-ID: <80337800c106ece5f0c78ed0b098b8f8@cnio.es> Hello, I am trying to index the whole of genbank nucleotide (release number 156, October 15 2006), with the script (which uses Bio::Index::GenBank) that is attached at the end of this message the process crashes with this error message: sdbm store returned -1, errno 9, key "BF460808" at /usr/local/lib/perl5/site_perl/5.8.8/Bio/Index/Abstract.pm line 714, <GenBank> line 164732819. why could this be? Thanks, Guillermo #!/usr/local/bin/perl -w # Perl pragma to restrict unsafe constructs use strict; # Issue warnings about suspicious programming. use warnings; # Use the code module that contains BioPerl Services. use Bio::Index::GenBank; # Use to index GenBank file use Bio::SeqIO; # be prepare for command-line options/arguments use Getopt::Std; sub help { return<<"END_HELP"; Description: Make index from GenBank database Usage: createGenBankIndex.pl -d {index file} -g {GenBank database} -d path and file name of index database -g GenBank database path END_HELP } BEGIN { # Determines the options with values from program use vars qw/$opt_d $opt_g/; # these are switches taking an argument (a value) my $switches = 'dg'; # Get the switches getopt($switches); # If the user does not write nothing, skip to help unless (defined($opt_d) || defined($opt_g)){ print help; exit 0; } } ######################################################################## ####### # # DESCRIPTION: The next program creates an BioPerl index aside GenBank database. # # INPUT (BY CONSOLE): - (-d) Path where the Uniprot index is going to store. # - (-g) Path where GenBank database is located # # OUTPUT: - O => The program has finished sucessfully # - 1 => Some of database files has not founded # - 2 => There was an error while the process was running # # AUTHOR: Jos?? Manuel Rodr??guez Carrasco -jmrc at cnb.uam.es- (INB-CNB) ######################################################################## ####### # Check if the path of GenBank database is able to read unless (-f $opt_g && -r $opt_g) { # The GenBank database has not been found print "Error of createGenBankIndex program: The GenBank database has not been found\n"; # Return an error exit 1; } # Store the database paths my @DBList = ($opt_g); # Create new instance to index file. It is used the option my $indexSW = Bio::Index::GenBank->new ('-filename' => $opt_d, '-write_flag' => 1); # Make the index my $numFiles = $indexSW->make_index(@DBList); # Check how many databases have been indexed if ($numFiles == 1) { # There has been not exist error. print "\nThe creation of GenBank index has been executed successfully\n"; exit 0; } else { # There has been exist an process error print "\nThere was a problem while the creation of GenBank index was running\n"; exit 2; } **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From gcarbajosa at cnio.es Tue Nov 14 05:57:01 2006 From: gcarbajosa at cnio.es (guillermo) Date: Tue, 14 Nov 2006 11:57:01 +0100 Subject: [Bioperl-l] indexing with several processors Message-ID: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> Hello, While using the Bio::Index::GenBank module for indexing Genbank, is there any option to run the process with more than one processor. Thanks **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From lincoln.stein at gmail.com Tue Nov 14 11:08:55 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 14 Nov 2006 11:08:55 -0500 Subject: [Bioperl-l] Bio::Graphics In-Reply-To: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> References: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> Message-ID: <6dce9a0b0611140808md4edbe7ye2632714621da52d@mail.gmail.com> I don't think the dots have been connected on this. It should be straightforward following the example in the BioGraphics HOWTO. Lincoln On 11/10/06, Bernd Web <bernd.web at gmail.com> wrote: > > Hi, > > Lincoln made an excellent help on Graphics. Thanks for > that!(http://www.bioperl.org/wiki/HOWTO:Graphics) > I am just looking at the imagemap creation with > my $map=$panel->create_web_map('mapname',\&linkrule,'bbb'); > and would like to connect the PNG from a blast report to the blast > results. > > I just realize that this likely has been done many times. Does someone > have a pointer to code for creating an imagemap from a BLAST report > and also write the blast results with links? > > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bosborne11 at verizon.net Tue Nov 14 16:54:25 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 14 Nov 2006 16:54:25 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> Message-ID: <C17FA541.B55D%bosborne11@verizon.net> Conrad, The typical solution is to declare an alphabet, as in: my $seq = Bio::Seq->new(-seq => "xxxx", -alphabet => "dna") Then Bioperl will not check your sequence. This works since you'll know that the alphabet, in this case, has to be "dna". Brian O. On 11/12/06 1:11 PM, "Conrad Halling" <chhalling at verizon.net> wrote: > This test fails because Bio::Tools::IUPAC module includes 'X' as a valid > base symbol, whereas Bio::Restriction::Enzyme does not. From stewarta at nmrc.navy.mil Tue Nov 14 17:47:26 2006 From: stewarta at nmrc.navy.mil (Andrew Stewart) Date: Tue, 14 Nov 2006 17:47:26 -0500 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast Message-ID: <8AF15F1F-0C81-4506-97C4-D25A12804731@nmrc.navy.mil> Anyone have any opinions as to how easy/difficult it would be to incorporate mpiblast into Bio::Tools::Run::StandAloneBlast? It runs essentially the same way as blastall, and its output is nearly identical. -A -- Andrew Stewart Research Assistant, Genomics Team Navy Medical Research Center (NMRC) Biological Defense Research Directorate (BDRD) BDRD Annex 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 email: stewarta at nmrc.navy.mil phone: 301-231-6700 Ext 270 From bosborne11 at verizon.net Tue Nov 14 22:10:00 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 14 Nov 2006 22:10:00 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <45531968.6080607@sendu.me.uk> Message-ID: <C17FEF38.B565%bosborne11@verizon.net> Sendu, RC3 can't be released as it doesn't install its scripts and some of these scripts are critical (e.g. the bp_*load_gff.pl and bp_process*.pl scripts, used by GMOD and chado users). I believe I've fixed this though, the problem was in Makefile.PL, no surprise. BIO On 11/9/06 7:04 AM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Developers: > Once again I'm hopeful that this is the last RC. If all goes well > expect final release in about a weeks time. Please check and update > documentation. > > Users: > Even though 1.5.2 is a 'developer' release, we consider it the most > stable and capable version of Bioperl, and recommend that you use > it in all but the most critical production environments. Please > try it out and let us know of any problems or difficulties you run > into. > > > Thank you, > Sendu. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sayali_salodkar at persistent.co.in Wed Nov 15 09:15:52 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Wed, 15 Nov 2006 19:45:52 +0530 Subject: [Bioperl-l] Help needed urgently Message-ID: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> I wish to fetch consensus sequence and the names of the trace (chromat) files used in the assembly from the .ace file For this purpose, I am using Bio::Assembly::IO. But I am unable to find the appropriate methods which would enable me to fetch this information. Note: The BS line (base segment) in the .ace file indicates which read phrap has chosen to be the consensus at a particular position. For example: BS 1 515 K26-572c gives BS <padded start consensus position> <padded end consensus position> <read name> respectively. How do I retrieve this information contig wise? Kindly help. Regards, Sayali D Salodkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From cjfields at uiuc.edu Wed Nov 15 09:22:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 08:22:38 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <C17FEF38.B565%bosborne11@verizon.net> Message-ID: <000a01c708c1$80d37300$15327e82@pyrimidine> > Sendu, > > RC3 can't be released as it doesn't install its scripts and > some of these scripts are critical (e.g. the bp_*load_gff.pl > and bp_process*.pl scripts, used by GMOD and chado users). I > believe I've fixed this though, the problem was in > Makefile.PL, no surprise. > > BIO ... This is definitely something to think about with Sendu's proposed changeover to Module::Build, which would obviate having a Makefile.PL. The issue with broken script installation was raised previously, but there were few responses (probably b/c itr came up somewhat indirectly in relation to other files in CVS). Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 09:24:25 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 08:24:25 -0600 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast In-Reply-To: <8AF15F1F-0C81-4506-97C4-D25A12804731@nmrc.navy.mil> Message-ID: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> > Anyone have any opinions as to how easy/difficult it would be > to incorporate mpiblast into > Bio::Tools::Run::StandAloneBlast? It runs essentially the > same way as blastall, and its output is nearly identical. > > > -A > > -- > Andrew Stewart > Research Assistant, Genomics Team > Navy Medical Research Center (NMRC) > Biological Defense Research Directorate (BDRD) BDRD Annex > 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 > > email: stewarta at nmrc.navy.mil > phone: 301-231-6700 Ext 270 I think plans were to rewrite StandAloneBlast and RemoteBlast to make them more 'generic' (i.e. capable of running other BLAST-related programs), though I'm not sure at what stage everything is. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From sayali_salodkar at persistent.co.in Wed Nov 15 09:15:52 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Wed, 15 Nov 2006 19:45:52 +0530 Subject: [Bioperl-l] Help needed urgently Message-ID: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> I wish to fetch consensus sequence and the names of the trace (chromat) files used in the assembly from the .ace file For this purpose, I am using Bio::Assembly::IO. But I am unable to find the appropriate methods which would enable me to fetch this information. Note: The BS line (base segment) in the .ace file indicates which read phrap has chosen to be the consensus at a particular position. For example: BS 1 515 K26-572c gives BS <padded start consensus position> <padded end consensus position> <read name> respectively. How do I retrieve this information contig wise? Kindly help. Regards, Sayali D Salodkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From bix at sendu.me.uk Wed Nov 15 10:35:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 15:35:29 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: <455B33C1.1010800@sendu.me.uk> Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I propose removing it from CVS. Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL when a user does a normal install of Bioperl? Or can it safely be ignored, only run manually by people who want to install Deobfuscator? From nhansen at nhgri.nih.gov Wed Nov 15 10:52:05 2006 From: nhansen at nhgri.nih.gov (Nancy Hansen) Date: Wed, 15 Nov 2006 10:52:05 -0500 (EST) Subject: [Bioperl-l] Inheritance Bio::Map::Physical Message-ID: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Keith Anthony Boroevich wrote: > > I am using an up-to-date bioperl-live. The precise code is > insignificant so I wrote some additional (shorter) code to attempt to > explain my problem. What I want to do is the following. I want to add > some functionality to the Bio::Map::Physical module so i created a > module that inherits Physical module, Extended::FPC.pm. > > #----Test.pl-BEGIN---# > use strict; > use diagnostics; > use Extended::FPC; > my $mapio = new Extended::FPC(-format => "fpc",-file => > $ARGV[0],-readcor => 1); > my $map = $mapio->next_map(); > $map->fpc_test(); > exit 0; > #---Test.pl-END------# You're right that your Extended::FPC should inherit from Bio::Map::Physical, but you really don't want to use it to parse the fpc file (Bio::MapIO does that just fine, and gets all the data you need into the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical object using Bio::MapIO, then forcing it to be an Extended::FPC, which will allow it to use your method(s): my $mapio = Bio::MapIO->new(-format => 'fpc', -file => $ARGV[0], -readcor => 1); my $fpc_map = $mapio->next_map(); bless $fpc_map, Extended::FPC; my $ra_bands = $fpc_map->my_new_extended_method(); I've actually written my own method to return the band sizes as well, so it would probably make a good enhancement to Bio::Map::Physical, which already has a "matching_bands" method that returns the (scalar) number of bands that match at a given tolerance. If that method were "enhanced" to return an array of matching band sizes rather than the scalar number of bands, it would still return the number in scalar context, but give you the matching band info in list context. I'd be happy to submit a patch for this if others think it's backwardly-compatible enough. --Nancy ************************************* Nancy F. Hansen, PhD nhansen at nhgri.nih.gov Bioinformatics Group NIH Intramural Sequencing Center (NISC) 5625 Fishers Lane Rockville, MD 20852 Phone: (301) 435-1560 Fax: (301) 435-6170 From cjfields at uiuc.edu Wed Nov 15 11:24:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 10:24:57 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> Message-ID: <000001c708d2$97c9d610$15327e82@pyrimidine> > Does anyone know what purpose Bio/DB/Makefile.PL serves? If > none, I propose removing it from CVS. > > Dave: Do you need anything to happen with > doc/Deobfuscator/Makefile.PL when a user does a normal > install of Bioperl? Or can it safely be ignored, only run > manually by people who want to install Deobfuscator? The Bio/DB/Makefile.PL and MANIFEST could be GMOD- or Chado-related (they are both related to Bio::DB::GFF). I'm not sure though; I'm cc'ing this to Lincoln to see if they are still needed. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From arareko at campus.iztacala.unam.mx Wed Nov 15 11:23:45 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed, 15 Nov 2006 10:23:45 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> Message-ID: <455B3F11.6070102@campus.iztacala.unam.mx> I think Deobfuscator code should be manually installed only. Mauricio. Sendu Bala wrote: > Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I > propose removing it from CVS. > > Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL > when a user does a normal install of Bioperl? Or can it safely be > ignored, only run manually by people who want to install Deobfuscator? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From kaboroev at sfu.ca Wed Nov 15 12:14:14 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Wed, 15 Nov 2006 09:14:14 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> References: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Message-ID: <455B4AE6.509@sfu.ca> Thanks, this is exactly what I was looking for. I didn't know how to get Bio::MapIO to return "my" class and I was unaware that bless could be used in such a manner. Not to nit-pick, but just in case anyone else has such a problem, quotes are required around the class. bless $fpc_map "Extended::FPC"; Nancy Hansen wrote: > > > You're right that your Extended::FPC should inherit from > Bio::Map::Physical, but you really don't want to use it to parse the fpc > file (Bio::MapIO does that just fine, and gets all the data you need into > the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical > object using Bio::MapIO, then forcing it to be an Extended::FPC, which > will allow it to use your method(s): > > my $mapio = Bio::MapIO->new(-format => 'fpc', > -file => $ARGV[0], > -readcor => 1); > > my $fpc_map = $mapio->next_map(); > > bless $fpc_map, Extended::FPC; > my $ra_bands = $fpc_map->my_new_extended_method(); > -- ><)))?> -cGRASP- <?(((>< Keith Anthony Boroevich Simon Fraser University Tel: 604-268-7276 From pmiguel at purdue.edu Wed Nov 15 12:00:50 2006 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 15 Nov 2006 12:00:50 -0500 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <455B47C2.8020400@purdue.edu> Sayali wrote: > I wish to fetch consensus sequence and the names of the trace (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar > Hi Sayali, I don't think there is a pre-rolled bioperl method to do what you ask. (But it seems like one is under construction?) You can extract the contig sequences from a phrap .ace file with the following plain perl code: my $print_it = 0; while (<>){ $print_it = /^CO / ? 1 : /^$/ ? 0 : $print_it ; s/^CO />/; s/\*//g; #removes "pads"--optional print if $print_it; } To find the reads that went into each contig, you do *not* want the BS tagged records. My understanding is that BS is just what consed uses to populate its consensus line from the ace file. The simplest way is: egrep '^CO|AF' acefilename if you are on a unix system. Or with perl while (<>) { print if (/^CO|AF/); } -- Phillip Purdue Genomics Core Facility From cjfields at uiuc.edu Wed Nov 15 12:00:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:00:05 -0600 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> > I wish to fetch consensus sequence and the names of the trace > (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to > find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read > phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus > position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar It looks like the relevant part of the Bio::Assembly::IO::ace parser responsible for parsing this is commented out: # Loading base segments definitions (Base Segment field) # /^BS (\d+) (\d+) (\S+)/ && do { # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} {'segments'})) { # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . " " . $2; # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = $1 . " " . $2 } # }; I'm not sure why to be honest as I'm not very familiar with the Bio::Assembly. Have you tried removing the comments to see what happens? You could file a bug report noting this using Bugzilla: http://bugzilla.open-bio.org/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 12:00:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:00:05 -0600 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> > I wish to fetch consensus sequence and the names of the trace > (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to > find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read > phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus > position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar It looks like the relevant part of the Bio::Assembly::IO::ace parser responsible for parsing this is commented out: # Loading base segments definitions (Base Segment field) # /^BS (\d+) (\d+) (\S+)/ && do { # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} {'segments'})) { # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . " " . $2; # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = $1 . " " . $2 } # }; I'm not sure why to be honest as I'm not very familiar with the Bio::Assembly. Have you tried removing the comments to see what happens? You could file a bug report noting this using Bugzilla: http://bugzilla.open-bio.org/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 12:37:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:37:35 -0600 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> References: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Message-ID: <D7DFA98D-2107-4C4C-9BBA-8B029DD9CC41@uiuc.edu> On Nov 15, 2006, at 9:52 AM, Nancy Hansen wrote: > Keith Anthony Boroevich wrote: >> >> I am using an up-to-date bioperl-live. The precise code is >> insignificant so I wrote some additional (shorter) code to attempt to >> explain my problem. What I want to do is the following. I want >> to add >> some functionality to the Bio::Map::Physical module so i created a >> module that inherits Physical module, Extended::FPC.pm. >> >> #----Test.pl-BEGIN---# >> use strict; >> use diagnostics; >> use Extended::FPC; >> my $mapio = new Extended::FPC(-format => "fpc",-file => >> $ARGV[0],-readcor => 1); >> my $map = $mapio->next_map(); >> $map->fpc_test(); >> exit 0; >> #---Test.pl-END------# > > You're right that your Extended::FPC should inherit from > Bio::Map::Physical, but you really don't want to use it to parse > the fpc > file (Bio::MapIO does that just fine, and gets all the data you > need into > the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical > object using Bio::MapIO, then forcing it to be an Extended::FPC, which > will allow it to use your method(s): > > my $mapio = Bio::MapIO->new(-format => 'fpc', > -file => $ARGV[0], > -readcor => 1); > > my $fpc_map = $mapio->next_map(); > > bless $fpc_map, Extended::FPC; > my $ra_bands = $fpc_map->my_new_extended_method(); > > I've actually written my own method to return the band sizes as > well, so > it would probably make a good enhancement to Bio::Map::Physical, which > already has a "matching_bands" method that returns the (scalar) > number of > bands that match at a given tolerance. If that method were > "enhanced" to > return an array of matching band sizes rather than the scalar > number of > bands, it would still return the number in scalar context, but give > you > the matching band info in list context. I'd be happy to submit a > patch > for this if others think it's backwardly-compatible enough. > > --Nancy Keith, Nancy, Sendu Bala has taken over maintenance of the Bio::Map modules. I have cc'd him this in case he has missed it (he's in the middle of getting a bioperl developer release put together). In general we are more than happy to take new modules and patches for current ones. There is a HOWTO on submitting patches and new code: http://www.bioperl.org/wiki/HOWTO:SubmitPatch If you plan on submitting a patch, you should also consider adding some tests as well. I think the relevant tests for Bio::Map modules are in t/Map.t and t/MapIO.t. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 13:15:48 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 18:15:48 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> Message-ID: <455B5954.1080209@sendu.me.uk> Chris Fields wrote: > On Nov 10, 2006, at 10:16 AM, Stefan Kirov wrote: > >> I personally like the idea. Why not have both for this release to >> ensure smooth transition? Sendu, would having Makefile.PL (I mean >> the old one) along with the build script be a problem? [snip] > Sounds like a good compromise to me. Like I said, the only problem I > had is introducing something drastically new after three RCs (and > just prior to a final release; I think Sendu wanted to release the > final 1.5.2 next week, just before Thanksgiving here.). There is no > problem though if we have the old Makefile.PL to fall back to for > this release. In fact, you could remove it from HEAD when needed; > the file still exists on the 1.5.2 branch, right? I think the compromise isn't worth it. The old Makefile.PL is just too inadequate and I don't want to support it. Build.pl is simply far too superior and I really want all users to be using it. I've now made the changeover in HEAD for core only (so far). Can people please try it out, especially wrt to installation in default and user-specified locations? First, clean out your system of the old Makefile.PL stuff: perl Makefile.PL make clean rm Makefile.PL Makefile.old cvs update -d -P Now try out the new Build.PL: perl Build.PL ./Build test ./Build install Try out other things: http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm You'll notice you don't have a Makefile.PL anymore. Distributions will include one, and as a cvs user you can generate one by: ./Build manifest ./Build distmeta Now you can try out the things you used to be able to do: make test make install Please let me know how you get on, Sendu. From bosborne11 at verizon.net Wed Nov 15 13:33:06 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 13:33:06 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> Message-ID: <C180C792.B596%bosborne11@verizon.net> Sendu, I see: 175 ~/bioperl-live>perl Build.PL Checking prerequisites... ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Which is incorrect since there no "modules indicated above". Brian O. On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Please let me know how you get on, From gcarbajosa at cnio.es Wed Nov 15 12:43:10 2006 From: gcarbajosa at cnio.es (guillermo) Date: Wed, 15 Nov 2006 18:43:10 +0100 Subject: [Bioperl-l] Fwd: Error while indexing whole genbank Message-ID: <68874599fabff74a65fcc62568022288@cnio.es> Hello, I just indexed BCT without problems and now I am going to do it in parts, different indexes for each one, for PLN, PRI, ROD, etc. Anyways, I??l try to do it for the whole genbank and if it works I?ll let you know. Thanks for the support, Guille Inicio mensaje reenviado: > De: guillermo <gcarbajosa at cnio.es> > Fecha: 14 de noviembre de 2006 11:39:41 GMT+01:00 > Para: bioperl-l at bioperl.org > Asunto: Error while indexing whole genbank > > Hello, > > I am trying to index the whole of genbank nucleotide (release number > 156, October 15 2006), with the script (which uses > Bio::Index::GenBank) that is attached at the end of this message the > process crashes with this error message: > > sdbm store returned -1, errno 9, key "BF460808" at > /usr/local/lib/perl5/site_perl/5.8.8/Bio/Index/Abstract.pm line 714, > <GenBank> line 164732819. > > why could this be? > > Thanks, > Guillermo > > > #!/usr/local/bin/perl -w > > # Perl pragma to restrict unsafe constructs > use strict; > > # Issue warnings about suspicious programming. > use warnings; > > # Use the code module that contains BioPerl Services. > use Bio::Index::GenBank; # Use to index GenBank file > use Bio::SeqIO; > > # be prepare for command-line options/arguments > use Getopt::Std; > > sub help { > return<<"END_HELP"; > Description: Make index from GenBank database > Usage: > > createGenBankIndex.pl -d {index file} -g {GenBank database} > -d path and file name of index database > -g GenBank database path > > END_HELP > > } > > > BEGIN { > > # Determines the options with values from program > use vars qw/$opt_d $opt_g/; > > # these are switches taking an argument (a value) > my $switches = 'dg'; > > # Get the switches > getopt($switches); > > # If the user does not write nothing, skip to help > unless (defined($opt_d) || defined($opt_g)){ > print help; > exit 0; > } > > } > > ####################################################################### > ######## > # > # DESCRIPTION: The next program creates an BioPerl index aside GenBank > database. > # > # INPUT (BY CONSOLE): - (-d) Path where the Uniprot index is going to > store. > # - (-g) Path where GenBank database is located > # > # OUTPUT: - O => The program has finished sucessfully > # - 1 => Some of database files has not founded > # - 2 => There was an error while the process was running > # > # AUTHOR: Jos?? Manuel Rodr??guez Carrasco -jmrc at cnb.uam.es- (INB-CNB) > ####################################################################### > ######## > > > # Check if the path of GenBank database is able to read > unless (-f $opt_g && -r $opt_g) { > > # The GenBank database has not been found > print "Error of createGenBankIndex program: The GenBank database has > not been found\n"; > > # Return an error > exit 1; > } > > > # Store the database paths > my @DBList = ($opt_g); > > # Create new instance to index file. It is used the option > my $indexSW = Bio::Index::GenBank->new ('-filename' => $opt_d, > '-write_flag' => 1); > > # Make the index > my $numFiles = $indexSW->make_index(@DBList); > > # Check how many databases have been indexed > if ($numFiles == 1) { > > # There has been not exist error. > print "\nThe creation of GenBank index has been executed > successfully\n"; > exit 0; > > > } else { > > # There has been exist an process error > print "\nThere was a problem while the creation of GenBank index was > running\n"; > exit 2; > } > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3585 bytes Desc: not available URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061115/64a3cab3/attachment-0003.bin> From cain at cshl.edu Wed Nov 15 12:45:52 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 15 Nov 2006 12:45:52 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <000001c708d2$97c9d610$15327e82@pyrimidine> References: <000001c708d2$97c9d610$15327e82@pyrimidine> Message-ID: <1163612752.2599.2.camel@localhost.localdomain> I didn't even know those files were in the repository. I suspect they are leftovers from original Bio::DB::GFF development. Given that the last time they were touched was over five years ago, and neither GBrowse nor any other GMOD project use them (that I know of), I think they can be safely removed. Scott On Wed, 2006-11-15 at 10:24 -0600, Chris Fields wrote: > > Does anyone know what purpose Bio/DB/Makefile.PL serves? If > > none, I propose removing it from CVS. > > > > Dave: Do you need anything to happen with > > doc/Deobfuscator/Makefile.PL when a user does a normal > > install of Bioperl? Or can it safely be ignored, only run > > manually by people who want to install Deobfuscator? > > The Bio/DB/Makefile.PL and MANIFEST could be GMOD- or Chado-related (they > are both related to Bio::DB::GFF). I'm not sure though; I'm cc'ing this to > Lincoln to see if they are still needed. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061115/e5f0620c/attachment-0003.bin> From pabignone at gmail.com Wed Nov 15 09:51:43 2006 From: pabignone at gmail.com (Paola Bignone) Date: Wed, 15 Nov 2006 14:51:43 +0000 Subject: [Bioperl-l] reverse complement - and features Message-ID: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Hi all, do you know of an easy way to reverse complement the sequence of an embl entry and the features associated with that sequence. I'm looking at genomic syntenic regions, and in some organisms the gene is in the plus strand while in others is in the minus. Thanks in advance, PAB From cjfields at uiuc.edu Wed Nov 15 14:16:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:16:34 -0600 Subject: [Bioperl-l] Fwd: Error while indexing whole genbank In-Reply-To: <68874599fabff74a65fcc62568022288@cnio.es> References: <68874599fabff74a65fcc62568022288@cnio.es> Message-ID: <E99B3889-1800-4A69-9F40-FEED774FD653@uiuc.edu> On Nov 15, 2006, at 11:43 AM, guillermo wrote: > Hello, > > I just indexed BCT without problems and now I am going to do it in > parts, different indexes for each one, for PLN, PRI, ROD, etc. > Anyways, I??l try to do it for the whole genbank and if it works I > ?ll let you know. > > Thanks for the support, > Guille My guess is that the full genbank file was way too large, so breaking them up by division is probably the way to go. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 14:18:18 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:18:18 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> <455B5954.1080209@sendu.me.uk> Message-ID: <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> On Nov 15, 2006, at 12:15 PM, Sendu Bala wrote: > ... > I think the compromise isn't worth it. The old Makefile.PL is just too > inadequate and I don't want to support it. Build.pl is simply far too > superior and I really want all users to be using it. > > I've now made the changeover in HEAD for core only (so far). > > Can people please try it out, especially wrt to installation in > default > and user-specified locations? > > First, clean out your system of the old Makefile.PL stuff: > perl Makefile.PL > make clean > rm Makefile.PL Makefile.old > cvs update -d -P > > Now try out the new Build.PL: > perl Build.PL > ./Build test > ./Build install > > Try out other things: > http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm > > You'll notice you don't have a Makefile.PL anymore. Distributions will > include one, and as a cvs user you can generate one by: > ./Build manifest > ./Build distmeta > > Now you can try out the things you used to be able to do: > make test > make install > > > Please let me know how you get on, > Sendu. Will do. We'll need to change all docs in CVS/wiki to conform with the new install routine. You'll probably want to post another interim RC before a final release just to make sure any residual bugs are worked out, unless you are just doing this in CVS HEAD. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 14:22:08 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:22:08 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> <455B5954.1080209@sendu.me.uk> <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> Message-ID: <455B68E0.9090308@sendu.me.uk> Chris Fields wrote: > Will do. We'll need to change all docs in CVS/wiki to conform with the > new install routine. You'll probably want to post another interim RC > before a final release just to make sure any residual bugs are worked > out, unless you are just doing this in CVS HEAD. There needs to be another RC for 1.5.2 for the remaining run package problems, so what I'll do is wait a little while longer for Build.PL feedback and when all seems well it'll go into 1.5.2 branch and become part of RC4. From bix at sendu.me.uk Wed Nov 15 14:33:33 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:33:33 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <OFAAF39FAB.9EB9DA23-ON85257227.00675002-85257227.00676C9E@gsk.com> References: <OFAAF39FAB.9EB9DA23-ON85257227.00675002-85257227.00676C9E@gsk.com> Message-ID: <455B6B8D.30508@sendu.me.uk> Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: > What actual needs prompted the change from ExtUtils::MakeMaker to > Module::Build? For the old Makefile.PL: At the time I started, script installation was broken. Documentation installation hasn't worked in a very long time. Handling of true requirements and optional pre-requisites is completely inadequate. It can't generate a suitable META.yml, and leaves the package non-ideal for distribution on CPAN. It was also a nightmare keeping the Makefile.PL scripts in each cvs module (live, run, db, network) in sync with each other. Now they can have simple module-specific Build.PL scripts, with all the advanced functionality in a rarely-updated and unchanged-between-modules ModuleBuildBioperl.pm. > It seems that the switch was made without a complete understanding of > all the bits and bobs in the existing Makefile.PL I hope that's not the case; I tried to understand everything. Please let me know if I've missed something. (To tidy up a question I asked about the symlink script, I've resolved that and the symlink should also work given the proviso outlined in the POD for maintenance/symlink_script.pl) > For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered > by the main Makefile.PL) such that users can choose whether to test > the install vs. a live database or not. The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such functionality. Letting the user choose to do live database tests was a function of the main Makefile.PL, which I have carried over to the new Build.PL. (And made it better in the process.) > This is an example of encapsulation: the specializied testing/install > process for a module is kept with the module, and not in the > monolithic main script. From a maintenance point of view, it seems to me to be much easier if all install-related things are in one place rather than scattered where you might miss things. > For two, it seems that the ability to install bp_*.pl scripts was > "lost" in the transition. What makes you say that? It certainly shouldn't be. What should happen is you get asked what scripts you'd like to install (the same question as before), but again its done in a much nicer way. (The major difference, I suppose, is that scripts_temp is no longer generated; prior to "./Build install" you'll find the scripts in blib/script/) > For three, there's certainly a lot more that I can't remember right > now. Please try and remember. I spent a lot of time trying to make sure that Build.PL does everything Makefile.PL did, but much much better. Thank you, Sendu. From bix at sendu.me.uk Wed Nov 15 14:09:01 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:09:01 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180CA3A.B599%bosborne11@verizon.net> References: <C180CA3A.B599%bosborne11@verizon.net> Message-ID: <455B65CD.3020400@sendu.me.uk> Brian Osborne wrote: > Sendu, > > 177 ~/bioperl-live>./Build test > scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Can't copy('scripts/utilities/bp_sreformat.PLS', > 'blib/script/bp_sreformat.PLS'): Permission denied at > /Library/Perl/5.8.6/Module/Build/Base.pm line 3977. That's an odd one. Did you first start out with a clean bioperl-live (ie. one without a blib directory made by something else)? Is it consistent? If you run ./Build test again, does it keep happening? Does blib/script/bp_sreformat.PLS exist and what are its permissions? Did it manage to put anything at all in blib? Is ~/bioperl-live writable? From bix at sendu.me.uk Wed Nov 15 14:09:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:09:41 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <455B65F5.1030207@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > > Which is incorrect since there no "modules indicated above". Thanks, I'll look into it. Just to confirm, do you suppose that you have all pre-reqs installed? From cjfields at uiuc.edu Wed Nov 15 14:36:11 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:36:11 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <0FCFCA18-8FDC-4463-BF3B-1586145743CE@uiuc.edu> On Nov 15, 2006, at 12:33 PM, Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this > installation > > > Which is incorrect since there no "modules indicated above". > > > Brian O. > > > On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > >> Please let me know how you get on, Same here (Mac OS X). All tests pass, though (setting BIOPERLDEBUG=1): All tests successful, 6 subtests skipped. Files=236, Tests=12817, 398 wallclock secs (86.03 cusr + 14.12 csys = 100.15 CPU) I'll give WinXP a test to see how it fares. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Wed Nov 15 11:44:19 2006 From: jason at bioperl.org (Jason Stajich) Date: Wed, 15 Nov 2006 08:44:19 -0800 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> Message-ID: <1965DDC8-DC2E-4895-A6C9-BD7A15FACDF1@bioperl.org> On Nov 15, 2006, at 7:35 AM, Sendu Bala wrote: > Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I > propose removing it from CVS. this was from when Lincoln imported Bio::DB::GFF into Bioperl from a separate code base. I don't know that it serves any purpose but I would get an okay from Lincoln first. > > Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL > when a user does a normal install of Bioperl? Or can it safely be > ignored, only run manually by people who want to install Deobfuscator? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From bosborne11 at verizon.net Wed Nov 15 13:44:26 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 13:44:26 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> Message-ID: <C180CA3A.B599%bosborne11@verizon.net> Sendu, 177 ~/bioperl-live>./Build test scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Can't copy('scripts/utilities/bp_sreformat.PLS', 'blib/script/bp_sreformat.PLS'): Permission denied at /Library/Perl/5.8.6/Module/Build/Base.pm line 3977. Brian O. On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Please let me know how you get on, From bix at sendu.me.uk Wed Nov 15 15:20:26 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 20:20:26 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <455B768A.8060009@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > > Which is incorrect since there no "modules indicated above". Should be fixed now. From bix at sendu.me.uk Wed Nov 15 15:23:22 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 20:23:22 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C180E071.B5B0%bosborne11@verizon.net> References: <C180E071.B5B0%bosborne11@verizon.net> Message-ID: <455B773A.5080608@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I just looked at the most recent bioperl-db and bioperl-run, I don't see any > Build.pl there. Are you suggesting that the Bioperl core build should be > mediated by Build.pl yet all other packages are built by some Makefile.PL? No, once it seems like Build.PL is ok in core, I'll convert db, run and network over to it as well. From bosborne11 at verizon.net Wed Nov 15 14:24:12 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 14:24:12 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B65F5.1030207@sendu.me.uk> Message-ID: <C180D38C.B5A4%bosborne11@verizon.net> Sendu, According to my install of 1.5.2 RC3 I have all of the dependencies installed: *** Optional dependencies section *** All dependencies are installed So that line "ERRORS/WARNINGS FOUND IN PREREQUISITES.." shouldn't appear. Brian O. On 11/15/06 2:09 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Brian Osborne wrote: >> Sendu, >> >> I see: >> >> 175 ~/bioperl-live>perl Build.PL >> Checking prerequisites... >> >> ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the >> versions >> of the modules indicated above before proceeding with this installation >> >> >> Which is incorrect since there no "modules indicated above". > > Thanks, I'll look into it. Just to confirm, do you suppose that you have > all pre-reqs installed? From cjfields at uiuc.edu Wed Nov 15 15:52:23 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 14:52:23 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B68E0.9090308@sendu.me.uk> Message-ID: <001601c708f7$f441dd50$15327e82@pyrimidine> > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Sendu Bala > Sent: Wednesday, November 15, 2006 1:22 PM > To: bioperl-l > Subject: Re: [Bioperl-l] No more Makefile.PL (MakeMaker -> > Module::Build) > > Chris Fields wrote: > > Will do. We'll need to change all docs in CVS/wiki to conform with > > the new install routine. You'll probably want to post > another interim > > RC before a final release just to make sure any residual bugs are > > worked out, unless you are just doing this in CVS HEAD. > > There needs to be another RC for 1.5.2 for the remaining run > package problems, so what I'll do is wait a little while > longer for Build.PL feedback and when all seems well it'll go > into 1.5.2 branch and become part of RC4. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l All tests pass for WinXP. If anyone wants to install from CVS using WinXP we'll need to get them to install Module::Build, as it doesn't come standard with ActivePerl (although a PPM is available). I'm guessing make/nmake is still required, though not explicitly. One oddity I noticed is if you use: perl Build.PL Build On Mac it manifies the POD; on WinXP it manify's and HTMLifies the POD. No idea why there is a difference between the two. I would suggest that we make this optional, though; not everybody wants the HTML/man pages. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 16:10:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 21:10:27 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <001601c708f7$f441dd50$15327e82@pyrimidine> References: <001601c708f7$f441dd50$15327e82@pyrimidine> Message-ID: <455B8243.4080809@sendu.me.uk> Chris Fields wrote: > All tests pass for WinXP. If anyone wants to install from CVS using > WinXP we'll need to get them to install Module::Build, as it doesn't > come standard with ActivePerl (although a PPM is available). I'm > guessing make/nmake is still required, though not explicitly. I think one of the benefits of Module::Build is that it is more cross-platform, and doesn't rely on a make-like thing. If you tried to install without Module::Build on WinXP, did you get some kind of meaningful error message? > One oddity I noticed is if you use: > > perl Build.PL Build > > On Mac it manifies the POD; on WinXP it manify's and HTMLifies the > POD. Nothing to do with me. I guess WinXP people like HTML docs :) > I would suggest that we make this optional, though; not everybody > wants the HTML/man pages. I disagree with making it optional, default off. I've never been aware of having the option to not install man pages for things that had man pages to install. It just happens and I'm glad of it. Its telling that there doesn't seem to be command line arg to turn doc installation off in Module::Build. Its a new functionality I'd have to add, I think. Is there actually any significant value in not installing docs? From bosborne11 at verizon.net Wed Nov 15 15:19:13 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 15:19:13 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <C180E071.B5B0%bosborne11@verizon.net> Sendu, I just looked at the most recent bioperl-db and bioperl-run, I don't see any Build.pl there. Are you suggesting that the Bioperl core build should be mediated by Build.pl yet all other packages are built by some Makefile.PL? Brian O. On 11/15/06 2:33 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: >> What actual needs prompted the change from ExtUtils::MakeMaker to >> Module::Build? > > For the old Makefile.PL: > At the time I started, script installation was broken. Documentation > installation hasn't worked in a very long time. Handling of true > requirements and optional pre-requisites is completely inadequate. It > can't generate a suitable META.yml, and leaves the package non-ideal for > distribution on CPAN. > > It was also a nightmare keeping the Makefile.PL scripts in each cvs > module (live, run, db, network) in sync with each other. Now they can > have simple module-specific Build.PL scripts, with all the advanced > functionality in a rarely-updated and unchanged-between-modules > ModuleBuildBioperl.pm. > > >> It seems that the switch was made without a complete understanding of >> all the bits and bobs in the existing Makefile.PL > > I hope that's not the case; I tried to understand everything. Please let > me know if I've missed something. (To tidy up a question I asked about > the symlink script, I've resolved that and the symlink should also work > given the proviso outlined in the POD for maintenance/symlink_script.pl) > > >> For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered >> by the main Makefile.PL) such that users can choose whether to test >> the install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such > functionality. Letting the user choose to do live database tests was a > function of the main Makefile.PL, which I have carried over to the new > Build.PL. (And made it better in the process.) > > >> This is an example of encapsulation: the specializied testing/install >> process for a module is kept with the module, and not in the >> monolithic main script. > > From a maintenance point of view, it seems to me to be much easier if > all install-related things are in one place rather than scattered where > you might miss things. > > >> For two, it seems that the ability to install bp_*.pl scripts was >> "lost" in the transition. > > What makes you say that? It certainly shouldn't be. What should happen > is you get asked what scripts you'd like to install (the same question > as before), but again its done in a much nicer way. > > (The major difference, I suppose, is that scripts_temp is no longer > generated; prior to "./Build install" you'll find the scripts in > blib/script/) > > >> For three, there's certainly a lot more that I can't remember right >> now. > > Please try and remember. I spent a lot of time trying to make sure that > Build.PL does everything Makefile.PL did, but much much better. > > > Thank you, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From aaron.j.mackey at gsk.com Wed Nov 15 13:29:30 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Wed, 15 Nov 2006 13:29:30 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" Message-ID: <OFE989A597.3219BF40-ON85257227.0064E293-85257227.00659451@gsk.com> What actual needs prompted the change from ExtUtils::MakeMaker to Module::Build? It seems that the switch was made without a complete understanding of all the bits and bobs in the existing Makefile.PL For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered by the main Makefile.PL) such that users can choose whether to test the install vs. a live database or not. This is an example of encapsulation: the specializied testing/install process for a module is kept with the module, and not in the monolithic main script. For two, it seems that the ability to install bp_*.pl scripts was "lost" in the transition. For three, there's certainly a lot more that I can't remember right now. I know Module::Build is shiny and new and preferred for startup development projects, but that cruddy old Makefile.PL still works, and does a number of clever things that do have reasons for existence, even if the collective wit of the mailing list can't remember all of them right away. -Aaron -- Aaron J. Mackey, Ph.D. Principal Scientist Bioinformatics Discovery & Analysis, Upper Providence GlaxoSmithKline 1250 South Collegeville Road, UP1345 P.O. Box 5089 Collegeville, PA 19426-0989 phone: 610-917-5761/8-282-5761 fax: 610-917-7901 email: Aaron.J.Mackey at gsk.com From bix at sendu.me.uk Wed Nov 15 16:28:30 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 21:28:30 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C180E8B3.B5B6%bosborne11@verizon.net> References: <C180E8B3.B5B6%bosborne11@verizon.net> Message-ID: <455B867E.8010001@sendu.me.uk> Brian Osborne wrote: > Sendu, > > One problem here, as I see it, is the fact that this change has been > introduced just days before the intended release. My intent is to go to RC4 instead, which pushes release a week or two away. God knows I wanted to release over a month ago, but I'm a perfectionist. > http://www.bioperl.org/wiki/Release_1.5.2 > > You won't find any mention of changing the build there, nor of Build.pl, or > Module::Build. This page is a nice example of "best practice", where > everything about the release is lined up and laid out, and making a big > change at the last minute is not best practice. Now, has Bioperl always made > a big deal out of best practice? No, but that's what's been nice about this > particular release so far, an emphasis on doing things correctly. This is assuredly all valid. But I feel this is a case of a necessary last minute addition. Necessary because I don't feel the old Makefile.PL is up to the job. Its merely unfortunate that I only discovered this so late into the RC cycle. Evidently I and all the other testers don't test the installation side of things, only the test scripts in t/. > Also, I understand that you think that your approach is better but such a > central change can't be adopted without discussion and some semblance of > consensus. So far I'm not getting any sense that anyone is agreeing with the > change but I am sensing discomfort with the idea, or resignation. I asked for comments and discussions 5 days ago. The only responses were positive or neutral (with reservations regarding putting it into 1.5.2, but not for the idea itself). If you don't press on and make things happen after positive feedback, nothing will ever get done at all. So to clarify, is anyone actually uncomfortable or 'resigned' to the idea? Does anyone feel strongly in favour of keeping Makefile.PL? > I have no strong opinion one way or another, Makefile or Build, but I do not > want to see significant changes at the last minute and I do not want > significant changes coming unilaterally. I agree. But again, I'm even less happy with the idea of releasing something that I know is inadequate simply because I discovered that too late. From cjfields at uiuc.edu Wed Nov 15 17:33:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 16:33:26 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <001901c70906$1441aa50$15327e82@pyrimidine> > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: .... > > For one, the Bio::DB::GFF Makefile.PL is independent (yet > triggered by > > the main Makefile.PL) such that users can choose whether to > test the > > install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves > no such functionality. Letting the user choose to do live > database tests was a function of the main Makefile.PL, which > I have carried over to the new Build.PL. (And made it better > in the process.) Scott Cain also indicated the Bio/DB Makefile.PL and MANIFEST files were not used anymore. ... > > For three, there's certainly a lot more that I can't remember right > > now. > > Please try and remember. I spent a lot of time trying to make > sure that Build.PL does everything Makefile.PL did, but much > much better. > > > Thank you, > Sendu. We can always reinstate the Makefile.PL if things blow up; I don't think they will, but that's what CVS is good for. I haven't had any problems on WinXP or Mac OS X yet beyond the pre-req error message Brian pointed out (and scripts seem to install fine on both OS's). Personally, I would have liked to wait until after the 1.5.2 final release to avoid any confusion and documentation changes, but that's not my call. We do need to let Scott and Lincoln in on these changes (they only know about the removal of the Bio/DB Makefile.PL). I think various install scripts look for a Makefile.PL, so if it isn't there things will tank on their end. We also need to post this everywhere possible in very big neon-colored letters (with fireworks and so on), since most users are used to 'perl Makefile.PL; make; make install'. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From pabignone at gmail.com Wed Nov 15 09:51:43 2006 From: pabignone at gmail.com (Paola Bignone) Date: Wed, 15 Nov 2006 14:51:43 +0000 Subject: [Bioperl-l] reverse complement - and features Message-ID: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Hi all, do you know of an easy way to reverse complement the sequence of an embl entry and the features associated with that sequence. I'm looking at genomic syntenic regions, and in some organisms the gene is in the plus strand while in others is in the minus. Thanks in advance, PAB From bix at sendu.me.uk Wed Nov 15 18:08:00 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:08:00 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c70906$1441aa50$15327e82@pyrimidine> References: <001901c70906$1441aa50$15327e82@pyrimidine> Message-ID: <455B9DD0.5000409@sendu.me.uk> Chris Fields wrote: > > We do need to let Scott and Lincoln in on these changes (they only know > about the removal of the Bio/DB Makefile.PL). I think various install > scripts look for a Makefile.PL, so if it isn't there things will tank on > their end. We also need to post this everywhere possible in very big > neon-colored letters (with fireworks and so on), since most users are used > to 'perl Makefile.PL; make; make install'. It doesn't need to be neon because most users will still be able to do exactly that; Makefile.PL will be part of the distributions (having been generated by Build.PL). For most people, there's not going to be any significant difference with this change. It'll be more like a behind-the-scenes thing. From lincoln.stein at gmail.com Wed Nov 15 17:43:21 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 15 Nov 2006 17:43:21 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B867E.8010001@sendu.me.uk> References: <C180E8B3.B5B6%bosborne11@verizon.net> <455B867E.8010001@sendu.me.uk> Message-ID: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> > > This is assuredly all valid. But I feel this is a case of a necessary > last minute addition. Necessary because I don't feel the old Makefile.PL > is up to the job. Its merely unfortunate that I only discovered this so > late into the RC cycle. Evidently I and all the other testers don't test > the installation side of things, only the test scripts in t/ > I tested script installation last week and it was all fine as far as I could tell. Are there any details about how installation was failing? Lincoln > Also, I understand that you think that your approach is better but such a > > central change can't be adopted without discussion and some semblance of > > consensus. So far I'm not getting any sense that anyone is agreeing with > the > > change but I am sensing discomfort with the idea, or resignation. > > I asked for comments and discussions 5 days ago. The only responses were > positive or neutral (with reservations regarding putting it into 1.5.2, > but not for the idea itself). If you don't press on and make things > happen after positive feedback, nothing will ever get done at all. Sorry, but I didn't see the discussion. So to clarify, is anyone actually uncomfortable or 'resigned' to the > idea? Does anyone feel strongly in favour of keeping Makefile.PL? I'm sorry we have to push the release back. I was unaware that Makefile.PLwas broken -- my preference would have been to fix it rather than to rewrite things from scratch. Lincoln > I have no strong opinion one way or another, Makefile or Build, but I do > not > > want to see significant changes at the last minute and I do not want > > significant changes coming unilaterally. > > I agree. But again, I'm even less happy with the idea of releasing > something that I know is inadequate simply because I discovered that too > late. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Wed Nov 15 17:31:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 16:31:56 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B8243.4080809@sendu.me.uk> Message-ID: <001801c70905$dbdd7a40$15327e82@pyrimidine> > Chris Fields wrote: > > All tests pass for WinXP. If anyone wants to install from > CVS using > > WinXP we'll need to get them to install Module::Build, as > it doesn't > > come standard with ActivePerl (although a PPM is available). I'm > > guessing make/nmake is still required, though not explicitly. > > I think one of the benefits of Module::Build is that it is > more cross-platform, and doesn't rely on a make-like thing. > > If you tried to install without Module::Build on WinXP, did > you get some kind of meaningful error message? Yes: C:\Perl\src\bioperl\core>perl Build.PL Base class package "Module::Build" is empty. (Perhaps you need to 'use' the module which defines that package first.) at ModuleBuildBioperl.pm line 12 BEGIN failed--compilation aborted at ModuleBuildBioperl.pm line 12. Compilation failed in require at Build.PL line 16. BEGIN failed--compilation aborted at Build.PL line 16. Which clued me in immediately. > > One oddity I noticed is if you use: > > > > perl Build.PL Build > > > > On Mac it manifies the POD; on WinXP it manify's and HTMLifies the > > POD. > > Nothing to do with me. I guess WinXP people like HTML docs :) > > > > I would suggest that we make this optional, though; not everybody > > wants the HTML/man pages. > > I disagree with making it optional, default off. I've never > been aware of having the option to not install man pages for > things that had man pages to install. It just happens and I'm > glad of it. > > Its telling that there doesn't seem to be command line arg to > turn doc installation off in Module::Build. Its a new > functionality I'd have to add, I think. Is there actually any > significant value in not installing docs? HTML docs are made by PPM upon module installation, so there is no need for making HTML at least on WinXP (and the conversion almost triples the time for the Build step). However, oddly, using 'Build test' only manifies the docs on WinXP (using 'Build' does both man and HTML). I have a feeling we will run into this very rarely (the average WinXP user will install using PPM), so it's not an immediate problem. I would like to hear what Mauricio finds on FreeBSD and see how other OS's fare. I see that there is a PPMMaker module with Module::Build, so we'll have to look into that for WinXP PPMs.. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 18:19:47 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:19:47 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> References: <C180E8B3.B5B6%bosborne11@verizon.net> <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> Message-ID: <455BA093.8040603@sendu.me.uk> Lincoln Stein wrote: > Sendu Bala wrote: > This is assuredly all valid. But I feel this is a case of a necessary > last minute addition. Necessary because I don't feel the old Makefile.PL > is up to the job. Its merely unfortunate that I only discovered this so > late into the RC cycle. Evidently I and all the other testers don't test > the installation side of things, only the test scripts in t/ > > I tested script installation last week and it was all fine as far as I > could tell. Are there any details about how installation was failing? Maybe this aspect got broken since after you tested (I don't think so though, judging by the fix), but scripts only got put in scripts_temp and nowhere else. The major prompt for the change was needing a complete META.yml for CPAN... > So to clarify, is anyone actually uncomfortable or 'resigned' to the > idea? Does anyone feel strongly in favour of keeping Makefile.PL? > > I'm sorry we have to push the release back. I was unaware that > Makefile.PL was broken -- my preference would have been to fix it rather > than to rewrite things from scratch. ... I'd have had to do far more rewriting things from scratch to get a complete META.yml out of Makefile.PL. I didn't want to reinvent the wheel, and Module::Build has lots of other benefits as well. I'd already done major adjustments to Makefile.PL previously; the move to Build.PL can be seen as just one more major behind-the-scenes adjustment, since Makefile.PL will still exist in distributions (having been generated by Build.PL) and people can still install the same way they have done in the past. The only real change for most users is that they now need Module::Build installed. From bix at sendu.me.uk Wed Nov 15 18:57:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:57:14 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810D8A.B5D0%bosborne11@verizon.net> References: <C1810D8A.B5D0%bosborne11@verizon.net> Message-ID: <455BA95A.5040404@sendu.me.uk> Brian Osborne wrote: > Sendu, > > This is not right. I just removed all the build stuff, Makefile* and Build*, > and did an update. There's no Makefile.PL, it's not part of the > distribution, there is Build.PL. As I mentioned in the other thread, Makefile.PL isn't in CVS, but it will be generated and included in distributions (ie. in .tar.gz file that you download from the website or via CPAN). As a CVS user you can generate one for yourself by: perl Build.PL ./Build manifest ./Build distmeta You should now have Makefile.PL on which you can do the usual stuff: perl Makefile.PL make make test make install From bosborne11 at verizon.net Wed Nov 15 15:54:27 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 15:54:27 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <C180E8B3.B5B6%bosborne11@verizon.net> Sendu, One problem here, as I see it, is the fact that this change has been introduced just days before the intended release. Take a look at the page that's supposed to describe 1.5.2 and associated work: http://www.bioperl.org/wiki/Release_1.5.2 You won't find any mention of changing the build there, nor of Build.pl, or Module::Build. This page is a nice example of "best practice", where everything about the release is lined up and laid out, and making a big change at the last minute is not best practice. Now, has Bioperl always made a big deal out of best practice? No, but that's what's been nice about this particular release so far, an emphasis on doing things correctly. That, and having enough people to do the work! Also, I understand that you think that your approach is better but such a central change can't be adopted without discussion and some semblance of consensus. So far I'm not getting any sense that anyone is agreeing with the change but I am sensing discomfort with the idea, or resignation. I have no strong opinion one way or another, Makefile or Build, but I do not want to see significant changes at the last minute and I do not want significant changes coming unilaterally. Brian O. On 11/15/06 2:33 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: >> What actual needs prompted the change from ExtUtils::MakeMaker to >> Module::Build? > > For the old Makefile.PL: > At the time I started, script installation was broken. Documentation > installation hasn't worked in a very long time. Handling of true > requirements and optional pre-requisites is completely inadequate. It > can't generate a suitable META.yml, and leaves the package non-ideal for > distribution on CPAN. > > It was also a nightmare keeping the Makefile.PL scripts in each cvs > module (live, run, db, network) in sync with each other. Now they can > have simple module-specific Build.PL scripts, with all the advanced > functionality in a rarely-updated and unchanged-between-modules > ModuleBuildBioperl.pm. > > >> It seems that the switch was made without a complete understanding of >> all the bits and bobs in the existing Makefile.PL > > I hope that's not the case; I tried to understand everything. Please let > me know if I've missed something. (To tidy up a question I asked about > the symlink script, I've resolved that and the symlink should also work > given the proviso outlined in the POD for maintenance/symlink_script.pl) > > >> For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered >> by the main Makefile.PL) such that users can choose whether to test >> the install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such > functionality. Letting the user choose to do live database tests was a > function of the main Makefile.PL, which I have carried over to the new > Build.PL. (And made it better in the process.) > > >> This is an example of encapsulation: the specializied testing/install >> process for a module is kept with the module, and not in the >> monolithic main script. > > From a maintenance point of view, it seems to me to be much easier if > all install-related things are in one place rather than scattered where > you might miss things. > > >> For two, it seems that the ability to install bp_*.pl scripts was >> "lost" in the transition. > > What makes you say that? It certainly shouldn't be. What should happen > is you get asked what scripts you'd like to install (the same question > as before), but again its done in a much nicer way. > > (The major difference, I suppose, is that scripts_temp is no longer > generated; prior to "./Build install" you'll find the scripts in > blib/script/) > > >> For three, there's certainly a lot more that I can't remember right >> now. > > Please try and remember. I spent a lot of time trying to make sure that > Build.PL does everything Makefile.PL did, but much much better. > > > Thank you, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Wed Nov 15 18:59:19 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:59:19 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810E20.B5D2%bosborne11@verizon.net> References: <C1810E20.B5D2%bosborne11@verizon.net> Message-ID: <455BA9D7.6020906@sendu.me.uk> Brian Osborne wrote: > Lincoln, > > All I know was the scripts weren't being installed, I fixed this by adding > "use IO::File" to Makefile.PL. Sendu mentioned a problem with documentation, > I don't know what he meant by this. 'man' docs weren't being generated/installed apparently due to some kind of issue with command line length. That's been a long-standing issue. From cjfields at uiuc.edu Wed Nov 15 19:01:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 18:01:57 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810D8A.B5D0%bosborne11@verizon.net> Message-ID: <001d01c70912$723c8a60$15327e82@pyrimidine> Brian, I think he means the actual releases or the 1.5.2 branch, not CVS. Sendu, I am seeing a general consensus towards not using Module::Build just now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar and I also had stated previously that this should probably wait until after 1.5.2 (which you seemed to agree with). I think we are all for the idea of moving forward, but it's a lot to impose just prior to a release (not to mention Thanksgiving here!). I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we should stick with that for now (i.e. not change over to Module::Build on the 1.5.2 branch). The install script fix that Brian committed to Makefile.PL in CVS HEAD prior to removal could be merged to branch-1.5.2. We could leave the Module::Build stuff in CVS for the next release to work out the bugs. I'm not sure whether we can have both Build.PL and Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl Build.PL' just overwrite the old Makefile.PL anyway? chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign > -----Original Message----- > From: Brian Osborne [mailto:bosborne11 at verizon.net] > Sent: Wednesday, November 15, 2006 5:32 PM > To: Sendu Bala; Chris Fields > Cc: aaron.j.mackey at gsk.com; bioperl-l > Subject: Re: [Bioperl-l] "progress": useful changes vs. > "shiny new thingie" > > Sendu, > > This is not right. I just removed all the build stuff, > Makefile* and Build*, and did an update. There's no > Makefile.PL, it's not part of the distribution, there is Build.PL. > > Brian O. > > > On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > > > exactly that; Makefile.PL will be part of the distributions (having > > been generated by Build.PL). > > From bix at sendu.me.uk Wed Nov 15 19:27:31 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 00:27:31 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001d01c70912$723c8a60$15327e82@pyrimidine> References: <001d01c70912$723c8a60$15327e82@pyrimidine> Message-ID: <455BB073.9040205@sendu.me.uk> Chris Fields wrote: > Brian, > > I think he means the actual releases or the 1.5.2 branch, not CVS. > > Sendu, I am seeing a general consensus towards not using Module::Build just > now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar and I also > had stated previously that this should probably wait until after 1.5.2 > (which you seemed to agree with). I think we are all for the idea of moving > forward, but it's a lot to impose just prior to a release (not to mention > Thanksgiving here!). > > I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we > should stick with that for now (i.e. not change over to Module::Build on the > 1.5.2 branch). The install script fix that Brian committed to Makefile.PL > in CVS HEAD prior to removal could be merged to branch-1.5.2. Its certainly possible to stay with Makefile.PL on the 1.5.2 branch. I /think/ that if I took a META.yml generated from HEAD's Build.PL and added it to the branch that should solve the CPAN issue at least. I would just want clarification that the consensus really is to stay with Makefile.PL for 1.5.2. The primary argument seems to be to not have anything too new and untested in the branch, but Makefile.PL itself has lots of new additions. My Makefile.PL improvements and the change to Build.PL have all been in the name of making 1.5.2 install well. The move to Build.PL was just the most appropriate way to fix some bugs and make needed changes. > We could leave the Module::Build stuff in CVS for the next release to work > out the bugs. I'm not sure whether we can have both Build.PL and > Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl Build.PL' > just overwrite the old Makefile.PL anyway? It would, but why would we want both in CVS? I'd strongly advise the cessation of development on the old Makefile.PL, and if it isn't going to be added to anymore, nor used by anyone, why keep it in CVS? It's just going to cause confusion and problems with people coming across issues in the old Makefile.PL. Wasted development time if someone tries to fix something in Makefile.PL that was already solved in Build.PL. Bizarre behaviour if you were doing something with old Makefile.PL but then managed to overwrite it with Build.PL's Makefile.PL and suddenly you're working with a whole different script. In short, not the most optimal of situations. From bosborne11 at verizon.net Wed Nov 15 18:31:38 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 18:31:38 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B9DD0.5000409@sendu.me.uk> Message-ID: <C1810D8A.B5D0%bosborne11@verizon.net> Sendu, This is not right. I just removed all the build stuff, Makefile* and Build*, and did an update. There's no Makefile.PL, it's not part of the distribution, there is Build.PL. Brian O. On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > exactly that; Makefile.PL will be part of the distributions (having been > generated by Build.PL). From bosborne11 at verizon.net Wed Nov 15 18:34:08 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 18:34:08 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> Message-ID: <C1810E20.B5D2%bosborne11@verizon.net> Lincoln, All I know was the scripts weren't being installed, I fixed this by adding "use IO::File" to Makefile.PL. Sendu mentioned a problem with documentation, I don't know what he meant by this. Brian O. On 11/15/06 5:43 PM, "Lincoln Stein" <lincoln.stein at gmail.com> wrote: > I tested script installation last week and it was all fine as far as I could > tell. Are there any details about how installation was failing? From bosborne11 at verizon.net Wed Nov 15 20:43:32 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 20:43:32 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BA95A.5040404@sendu.me.uk> Message-ID: <C1812C74.B5E3%bosborne11@verizon.net> Sendu, If I'm understanding you correctly you're saying that someone checking out bioperl-live, HEAD, would not see a Makefile.PL if we chose to use Build.PL, yes? And there would be a Makefile.PL in the distributions, yes? Brian O. On 11/15/06 6:57 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Brian Osborne wrote: >> Sendu, >> >> This is not right. I just removed all the build stuff, Makefile* and Build*, >> and did an update. There's no Makefile.PL, it's not part of the >> distribution, there is Build.PL. > > As I mentioned in the other thread, Makefile.PL isn't in CVS, but it > will be generated and included in distributions (ie. in .tar.gz file > that you download from the website or via CPAN). > > As a CVS user you can generate one for yourself by: > perl Build.PL > ./Build manifest > ./Build distmeta > > You should now have Makefile.PL on which you can do the usual stuff: > perl Makefile.PL > make > make test > make install From stefan.kirov at bms.com Wed Nov 15 19:34:02 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Wed, 15 Nov 2006 19:34:02 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" Message-ID: <db32bddda3.ddda3db32b@bms.com> Maybe I will just reiterate myself. I think the idea is good, but timing is bad. Sendu, from purely socialogical point of view Makefile.PL should be there. I bet that significant percent of the users would do cvs checkout, type perl Makefile.PL and start cursing. Perhaps you would not do this, but many of us do not read most of the docs, unless nothing else works. As a result you would have confusion and frustration. Many people would google 'bioperl install' and come up with old docs and wonder why it does not work. In a perfect world it would work. Just my thoughts. Stefan ----- Original Message ----- From: Chris Fields <cjfields at uiuc.edu> Date: Wednesday, November 15, 2006 7:01 pm Subject: Re: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" > Brian, > > I think he means the actual releases or the 1.5.2 branch, not CVS. > > Sendu, I am seeing a general consensus towards not using > Module::Build just > now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar > and I also > had stated previously that this should probably wait until after 1.5.2 > (which you seemed to agree with). I think we are all for the idea > of moving > forward, but it's a lot to impose just prior to a release (not to > mentionThanksgiving here!). > > I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we > should stick with that for now (i.e. not change over to > Module::Build on the > 1.5.2 branch). The install script fix that Brian committed to > Makefile.PLin CVS HEAD prior to removal could be merged to branch- > 1.5.2. > > We could leave the Module::Build stuff in CVS for the next release > to work > out the bugs. I'm not sure whether we can have both Build.PL and > Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl > Build.PL'just overwrite the old Makefile.PL anyway? > > chris > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > -----Original Message----- > > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > Sent: Wednesday, November 15, 2006 5:32 PM > > To: Sendu Bala; Chris Fields > > Cc: aaron.j.mackey at gsk.com; bioperl-l > > Subject: Re: [Bioperl-l] "progress": useful changes vs. > > "shiny new thingie" > > > > Sendu, > > > > This is not right. I just removed all the build stuff, > > Makefile* and Build*, and did an update. There's no > > Makefile.PL, it's not part of the distribution, there is Build.PL. > > > > Brian O. > > > > > > On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > > > > > exactly that; Makefile.PL will be part of the distributions > (having > > > been generated by Build.PL). > > > > > > _______________________________________________ > 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 Nov 15 20:48:43 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 20:48:43 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> Message-ID: <C1812DAB.B5E5%bosborne11@verizon.net> Sendu, That's right. Brian O. On 11/15/06 7:27 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. From joannec at bii.a-star.edu.sg Wed Nov 15 21:11:31 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 02:11:31 +0000 (UTC) Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations Message-ID: <loom.20061116T030106-109@post.gmane.org> Hi, I am a new user to BioPerl and am encountering some problems while parsing location statements. I have read the link http://www.bioperl.org/wiki/FAQ#How_do_I_parse_the_CDS_join_or_complement_statements_in_GenBank_or_EMBL_files_to_get_the_sub-locations.3F and tried to implement this. However I am encountering some problems. Given a testcase: CDS join(752472..752685,752752..753298,753335..754039) CDS complement(637431..639525) CDS 741745..741781 This means that my file has join, complement and simple location statements. Using Bio::Location::SplitLocationI object to get the coordinates, my output is: CDS 752472..752685,752752..753298,753335..754039 CDS CDS The complement and simple location statements were not parsed properly. Am I using the right BioPerl module to parse? Kindly assist on the appropriate steps to retrieve all 3 different location types. Thanks! Joanne From cjfields at uiuc.edu Wed Nov 15 21:33:25 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 20:33:25 -0600 Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations In-Reply-To: <loom.20061116T030106-109@post.gmane.org> References: <loom.20061116T030106-109@post.gmane.org> Message-ID: <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> On Nov 15, 2006, at 8:11 PM, Joanne Chen wrote: > Hi, > I am a new user to BioPerl and am encountering some problems while > parsing > location statements. > > I have read the link > http://www.bioperl.org/wiki/ > FAQ#How_do_I_parse_the_CDS_join_or_complement_statements_in_GenBank_or > _EMBL_files_to_get_the_sub-locations.3F > and tried to implement this. > > However I am encountering some problems. > > Given a testcase: > > CDS join(752472..752685,752752..753298,753335..754039) > > > CDS complement(637431..639525) > > > CDS 741745..741781 > > > This means that my file has join, complement and simple location > statements. > > Using Bio::Location::SplitLocationI object to get the coordinates, > my output is: > > CDS 752472..752685,752752..753298,753335..754039 > > CDS > > CDS > > > The complement and simple location statements were not parsed > properly. Am I > using the right BioPerl module to parse? Kindly assist on the > appropriate steps > to retrieve all 3 different location types. Thanks! > > > Joanne > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l If you are using the loop as shown in the FAQ: foreach my $feature ($seqobj->top_SeqFeatures){ if ( $feature->location->isa('Bio::Location::SplitLocationI') and $feature->primary_tag eq 'CDS' ) { foreach my $location ( $feature->location->sub_Location ) { print $location->start , ".." , $location->end, "\n"; } } } it will skip over simple locations, so the last two are passed over. You probably should use: foreach my $feature ($seqobj->top_SeqFeatures){ if ( $feature->primary_tag eq 'CDS' ) { foreach my $location ( $feature->location->each_Location ) { print $location->start , ".." , $location->end, "\n"; } } } Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 21:44:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 20:44:05 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> Message-ID: <DEAB987E-4700-4677-979B-E5708F6905D3@uiuc.edu> On Nov 15, 2006, at 6:27 PM, Sendu Bala wrote: >> I think the old Makefile.PL is still in the 1.5.2 branch. So >> maybe we >> should stick with that for now (i.e. not change over to >> Module::Build on the >> 1.5.2 branch). The install script fix that Brian committed to >> Makefile.PL >> in CVS HEAD prior to removal could be merged to branch-1.5.2. > > Its certainly possible to stay with Makefile.PL on the 1.5.2 branch. I > /think/ that if I took a META.yml generated from HEAD's Build.PL and > added it to the branch that should solve the CPAN issue at least. > > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. The primary argument seems to be to not > have > anything too new and untested in the branch, but Makefile.PL itself > has > lots of new additions. My Makefile.PL improvements and the change to > Build.PL have all been in the name of making 1.5.2 install well. The > move to Build.PL was just the most appropriate way to fix some bugs > and > make needed changes. Right, but those changes were made w/o much discussion; what discussion there was seemed to end with the agreement this would wait until after rel. 1.5.2. I think that's the main point. That and the timing seems to be a little off for implementing this (after three RC's and just prior to a final release). Everyone seems to think that switching to Module::Build would be a good idea, but the move was made rather arbitrarily and (borrowing Brian's well-chosen word) unilaterally. And, although the Makefile.PL was a bit clunky, it works for now. >> We could leave the Module::Build stuff in CVS for the next release >> to work >> out the bugs. I'm not sure whether we can have both Build.PL and >> Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl >> Build.PL' >> just overwrite the old Makefile.PL anyway? > > It would, but why would we want both in CVS? I'd strongly advise the > cessation of development on the old Makefile.PL, and if it isn't going > to be added to anymore, nor used by anyone, why keep it in CVS? It's > just going to cause confusion and problems with people coming across > issues in the old Makefile.PL. Wasted development time if someone > tries > to fix something in Makefile.PL that was already solved in Build.PL. > Bizarre behaviour if you were doing something with old Makefile.PL but > then managed to overwrite it with Build.PL's Makefile.PL and suddenly > you're working with a whole different script. > > In short, not the most optimal of situations. Stefan has hit upon the problem very succinctly; there is no Makefile.PL in CVS, so anyone checking out bioperl-live will immediately run into problems. Hence, there has to be a Makefile.PL in CVS HEAD, be it the old one or a new one, at least for the time being. And it seems many still want the old Makefile.PL for now (which is why I suggested it). If you left the old Makefile.PL in you could always add a deprecation message indicating the switch. It will at least give everybody some time to get used to using Module::Build and the new system (and hopefully dissuade them from working on it). Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From joannec at bii.a-star.edu.sg Wed Nov 15 22:17:27 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 03:17:27 +0000 (UTC) Subject: [Bioperl-l] =?utf-8?q?Parsing_the_CDS_join_or_complement_statemen?= =?utf-8?q?ts_to=09get_the_sub-locations?= References: <loom.20061116T030106-109@post.gmane.org> <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> Message-ID: <loom.20061116T041551-540@post.gmane.org> Thanks a lot for your help. It works. =) However I have a small problem. Now I would also like to determine its strand-ie. negative strand for complement and positive for all others. Is there a function to determine and print its strand OR a function to determine if it is a complement, join or simple? Joanne. From pmiguel at purdue.edu Wed Nov 15 22:53:02 2006 From: pmiguel at purdue.edu (Phillip SanMiguel) Date: Wed, 15 Nov 2006 22:53:02 -0500 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> Message-ID: <455BE09E.4020408@purdue.edu> Chris Fields wrote: >> I wish to fetch consensus sequence and the names of the trace >> (chromat) >> files used in the assembly from the .ace file >> >> For this purpose, I am using Bio::Assembly::IO. But I am unable to >> find the >> appropriate methods which would enable me to fetch this information. >> >> >> >> [..base segment documentation elided...] >> >> >> How do I retrieve this information contig wise? >> >> Kindly help. >> >> Regards, >> >> Sayali D Salodkar >> > > It looks like the relevant part of the Bio::Assembly::IO::ace parser > responsible for parsing this is commented out: > > # Loading base segments definitions (Base Segment field) > # /^BS (\d+) (\d+) (\S+)/ && do { > # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} > {'segments'})) { > # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . > " " . $2; > # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = > $1 . " " . $2 } > # }; > > I'm not sure why to be honest as I'm not very familiar with the > Bio::Assembly. Have you tried removing the comments to see what > happens? > > Chris, I'm pretty sure that the Base Segment tag (BS) is not the one Sayali wants. At least that is my reading of Sayali's wanting to get the consensus sequence and the traces names used in the assembly. I write this because of an email sent me by David Gordon in 2001 included here without his permission: > Phrap writes BS lines which > indicate, for each consensus position, which read phrap uses at that > position to become the consensus. These BS ("base segments") are > manipulated by Consed when there are changes to the assembly, such as > joins, tears, removing reads, or changing the consensus. Which is basically what Sayali quoted from the documentation from phrap. But it is not consistent with "trace names used in the assembly". -- Phillip From hlapp at gmx.net Thu Nov 16 00:52:23 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Nov 2006 00:52:23 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> Message-ID: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. The primary argument seems to be to not > have > anything too new and untested in the branch, but Makefile.PL itself > has > lots of new additions. My Makefile.PL improvements and the change to > Build.PL have all been in the name of making 1.5.2 install well. The > move to Build.PL was just the most appropriate way to fix some bugs > and > make needed changes. My take on this, aside from having said before that the move to Module::Build is certainly a good one except with not-so-great timing, is that the distribution if at all possible should have a working Makefile.PL. If Build.PL can coexist that'd be great. That would give you the opportunity to have Makefile.PL print out a message right at the beginning that if the installation process messes up one should try Build.PL. This would spare you from fixing any problems in Makefile.PL that are fixed in the Build.PL approach. As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub that just prints out a message telling you to use Build.PL and does nothing else. If you check out bioperl-live from CVS you need to be prepared to having checked out the live edge of the code. Edges can be rough. The key thing is that the build process works. Finally let's not forget that this is still a developer release. That means that a) perfection isn't needed, rather shorter release cycles, and b) development implies change. So the main reason why I find the timing less than optimal is because it prolongs the time until the next release. Implementing changes like this do require a lot of energy. I very much appreciate that Sendu invested the time and energy to make it work, even though unfortunately at the last hour. Who knows who would have had the energy after the release. If Sendu hadn't put in the work now, the next release master may have been stuck with an even messier Makefile.PL system. Instead of Monday morning quarterbacking after no-one stopped him when he asked about it, we should all help him make the release - and the build change - successful now that he has done most if not all of the migration work already. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Thu Nov 16 02:47:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 07:47:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1812C74.B5E3%bosborne11@verizon.net> References: <C1812C74.B5E3%bosborne11@verizon.net> Message-ID: <455C1790.3080408@sendu.me.uk> Brian Osborne wrote: > Sendu, > > If I'm understanding you correctly you're saying that someone checking out > bioperl-live, HEAD, would not see a Makefile.PL if we chose to use Build.PL, > yes? And there would be a Makefile.PL in the distributions, yes? Yes, that is what I had meant. Though now following Hilmar's suggestion, I might create a stub in CVS for Makefile.PL that tells you to use Build.PL. I don't think it appropriate to have a working Makefile.PL in CVS though; not the old one for reasons outlined previously, and not one generated by Build.PL, because generated files don't need version control and only confuse matters when they become controlled. Ok, so the current plan is: # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml # CVS core gets a Makefile.PL stub telling you to use Build.PL # CVS db, run, network stay with Makefile.PL until after final release of 1.5.2, then move to Build.PL with Makefile.PL stub (because they don't have a 1.5.2 branch) Is everyone happy with that, or are there further suggestions for something better? From joannec at bii.a-star.edu.sg Thu Nov 16 02:55:22 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 07:55:22 +0000 (UTC) Subject: [Bioperl-l] =?utf-8?q?Parsing_the_CDS_join_or_complement_statemen?= =?utf-8?q?ts_to=09get_the_sub-locations?= References: <loom.20061116T030106-109@post.gmane.org> <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> <loom.20061116T041551-540@post.gmane.org> Message-ID: <loom.20061116T085446-347@post.gmane.org> Got the strand problem fixed. Thanks. =) From bix at sendu.me.uk Thu Nov 16 02:55:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 07:55:41 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C1790.3080408@sendu.me.uk> References: <C1812C74.B5E3%bosborne11@verizon.net> <455C1790.3080408@sendu.me.uk> Message-ID: <455C197D.6000107@sendu.me.uk> Sendu Bala wrote: > Brian Osborne wrote: >> Sendu, >> >> If I'm understanding you correctly you're saying that someone checking >> out >> bioperl-live, HEAD, would not see a Makefile.PL if we chose to use >> Build.PL, >> yes? And there would be a Makefile.PL in the distributions, yes? > > Yes, that is what I had meant. Though now following Hilmar's suggestion, > I might create a stub in CVS for Makefile.PL that tells you to use > Build.PL. I don't think it appropriate to have a working Makefile.PL in > CVS though; not the old one for reasons outlined previously, and not one > generated by Build.PL, because generated files don't need version > control and only confuse matters when they become controlled. > > Ok, so the current plan is: > # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml Also, # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who read the docs on the website/elsewhere (which will be updated to explain the new Build.PL system) don't get confused when that doesn't work, for wide testing, and to get people used to it for the next release. The old Makefile.PL will have 2 changes: Brians bug-fix and a little message pointing out that Build.PL is now the preferred installation system, but Makefile.PL still works. > # CVS core gets a Makefile.PL stub telling you to use Build.PL > # CVS db, run, network stay with Makefile.PL until after final release > of 1.5.2, then move to Build.PL with Makefile.PL stub (because they > don't have a 1.5.2 branch) > > Is everyone happy with that, or are there further suggestions for > something better? From rvosa at sfu.ca Thu Nov 16 02:19:43 2006 From: rvosa at sfu.ca (Rutger Vos) Date: Wed, 15 Nov 2006 23:19:43 -0800 Subject: [Bioperl-l] indexing with several processors In-Reply-To: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> References: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> Message-ID: <455C110F.4000600@sfu.ca> I notice nobody has responded yet. Without looking at the code I'm guessing here, but I would be very surprised if any part of bioperl is smart enough to be able to switch to some kind of mpi architecture, or any other clever way of parallelizing tasks on multi-processor architectures. If you can split the job up by hand and start scripts on the chunks, that might work. Good luck, Rutger guillermo wrote: > Hello, > > While using the Bio::Index::GenBank module for indexing Genbank, is > there any option to run the process with more than one processor. > > Thanks > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los > ficheros adjuntos, pueden contener informaci?n protegida para el uso > exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n > o cualquier otro tipo de transmisi?n por parte de otra persona que no > sea el destinatario. Si usted recibe por error este correo, se ruega > comunicarlo al remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any > attachments may contain confidential and privileged information for > the sole use of the designated recipient named above. Distribution, > reproduction or any other use of this transmission by any party other > than the intended recipient is prohibited. If you are not the intended > recipient please contact the sender and delete all copies. > > ------------------------------------------------------------------------ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > ------------------------------------------------------------------------ > > No virus found in this incoming message. > Checked by AVG Free Edition. > Version: 7.1.409 / Virus Database: 268.14.5/534 - Release Date: 11/14/2006 > -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Rutger A. Vos Postdoctoral research fellow University of British Columbia Personal site: http://www.sfu.ca/~rvosa CIPRES: http://www.phylo.org Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From n.haigh at sheffield.ac.uk Thu Nov 16 04:14:52 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 09:14:52 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> Message-ID: <455C2C0C.1080403@sheffield.ac.uk> Hilmar Lapp wrote: > On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > > >> I would just want clarification that the consensus really is to stay >> with Makefile.PL for 1.5.2. The primary argument seems to be to not >> have >> anything too new and untested in the branch, but Makefile.PL itself >> has >> lots of new additions. My Makefile.PL improvements and the change to >> Build.PL have all been in the name of making 1.5.2 install well. The >> move to Build.PL was just the most appropriate way to fix some bugs >> and >> make needed changes. >> > > My take on this, aside from having said before that the move to > Module::Build is certainly a good one except with not-so-great > timing, is that the distribution if at all possible should have a > working Makefile.PL. > I was in the process of writing a rather long e-mail to try to stem the tide of Sendu-bashing :-P But, this response serves as a better platform for my comments. I don't see the change to Build.PL as an issue - especially if we have another RC. I think it would be worse to introduce Build.PL in the "stable" 1.6 release than in the 1.5.x developer series. I think one good reason for using Build.PL when Sendu brought the issue up, is that it is more important as far as building a package for CPAN rather than an end user - and since Sendu is the release pumpkin he is the one with the strongest opinion for changing it now, rather than later - it would make his job much easier! I believe Sendu mentioned that a Makefile.PL would be included in the CPAN package but is not in CVS as it would be generated from Build.PL for backward compatibility - is that right Sendu? How does installing via CPAN affect this? Does it give higher priority to Build.PL over Makefile.PL and thus use Build.PL for the install? > If Build.PL can coexist that'd be great. That would give you the > opportunity to have Makefile.PL print out a message right at the > beginning that if the installation process messes up one should try > Build.PL. This would spare you from fixing any problems in > Makefile.PL that are fixed in the Build.PL approach. > Good idea, for anyone downloading the .tar.gz from CPAN if they issue "perl Makefile.PL" without knowing Build.PL was there it should hopefully work, but if not, issue a comment at the end to say try "perl Build.PL" if anything seemed to go wrong. > As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub > that just prints out a message telling you to use Build.PL and does > nothing else. If you check out bioperl-live from CVS you need to be > prepared to having checked out the live edge of the code. Edges can > be rough. The key thing is that the build process works. > I was going to suggest something like this with regard to a Makefile.PL in CVS. This would then be overwritten by the Makefile.PL produced from Build.PL by the release pumpkin when making the CPAN package. > Finally let's not forget that this is still a developer release. That > means that a) perfection isn't needed, rather shorter release cycles, > and b) development implies change. So the main reason why I find the > timing less than optimal is because it prolongs the time until the > next release. > If we go for short release cycles, and regular bug fix release, we will no longer have to say to users: "This is a known bug/issue in release x.y.z, it has been fixed in CVS HEAD so get it from there" we can roll out fixes in regular releases. This way CVS is then used solely by developers and those really wanting to live on the bleeding edge code. Therefore, it is important to get Build.PL in place to let the release cycle and CPAN packages built quickly, easily and without hassle - which I believe is the problem with Makefile.PL as it currently is. > Implementing changes like this do require a lot of energy. I very > much appreciate that Sendu invested the time and energy to make it > work, even though unfortunately at the last hour. Who knows who would > have had the energy after the release. If Sendu hadn't put in the > work now, the next release master may have been stuck with an even > messier Makefile.PL system. Instead of Monday morning quarterbacking > after no-one stopped him when he asked about it, we should all help > him make the release - and the build change - successful now that he > has done most if not all of the migration work already. > > -hilmar > Hear, hear - well done Sendu on all your hard work! Personally, I think the move to Build.PL is a good one - it may be a little late in this particular release, but I think that the problem is not that it is a late change, but that it wasn't picked up sooner. It fits well with the goal of making releases and big fix releases more regular, and if these are made available via CPAN, then the use of CVS is for developers and those wanting to live on the edge. Build.PL helps all this by making is easier and quicker to make CPAN packages. It also means we have a while before the "stable" 1.6 release to ensure it is working effectively - better than dropping it in on the 1.6 release isn't it? I think it's work the delay and an extra RC! Anyway, my 2 pence worth! Nath From n.haigh at sheffield.ac.uk Thu Nov 16 04:04:00 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 09:04:00 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> Message-ID: <455C2980.4000609@sheffield.ac.uk> Hilmar Lapp wrote: > On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > > >> I would just want clarification that the consensus really is to stay >> with Makefile.PL for 1.5.2. The primary argument seems to be to not >> have >> anything too new and untested in the branch, but Makefile.PL itself >> has >> lots of new additions. My Makefile.PL improvements and the change to >> Build.PL have all been in the name of making 1.5.2 install well. The >> move to Build.PL was just the most appropriate way to fix some bugs >> and >> make needed changes. >> > > My take on this, aside from having said before that the move to > Module::Build is certainly a good one except with not-so-great > timing, is that the distribution if at all possible should have a > working Makefile.PL. > I was in the process of writing a rather long e-mail to try to stem the tide of Sendu-bashing :-P But, this response serves as a better platform for my comments. I don't see the change to Build.PL as an issue - especially if we have another RC. I think it would be worse to introduce Build.PL in the "stable" 1.6 release than in the 1.5.x developer series. I think one good reason for using Build.PL when Sendu brought the issue up, is that it is more important as far as building a package for CPAN rather than an end user - and since Sendu is the release pumpkin he is the one with the strongest opinion for changing it now, rather than later - it would make his job much easier! I believe Sendu mentioned that a Makefile.PL would be included in the CPAN package but is not in CVS as it would be generated from Build.PL for backward compatibility - is that right Sendu? How does installing via CPAN affect this? Does it give higher priority to Build.PL over Makefile.PL and thus use Build.PL for the install? > If Build.PL can coexist that'd be great. That would give you the > opportunity to have Makefile.PL print out a message right at the > beginning that if the installation process messes up one should try > Build.PL. This would spare you from fixing any problems in > Makefile.PL that are fixed in the Build.PL approach. > Good idea, for anyone downloading the .tar.gz from CPAN if they issue "perl Makefile.PL" without knowing Build.PL was there it should hopefully work, but if not, issue a comment at the end to say try "perl Build.PL" if anything seemed to go wrong. > As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub > that just prints out a message telling you to use Build.PL and does > nothing else. If you check out bioperl-live from CVS you need to be > prepared to having checked out the live edge of the code. Edges can > be rough. The key thing is that the build process works. > I was going to suggest something like this with regard to a Makefile.PL in CVS. This would then be overwritten by the Makefile.PL produced from Build.PL by the release pumpkin when making the CPAN package. > Finally let's not forget that this is still a developer release. That > means that a) perfection isn't needed, rather shorter release cycles, > and b) development implies change. So the main reason why I find the > timing less than optimal is because it prolongs the time until the > next release. > If we go for short release cycles, and regular bug fix release, we will no longer have to say to users: "This is a known bug/issue in release x.y.z, it has been fixed in CVS HEAD so get it from there" we can roll out fixes in regular releases. This way CVS is then used solely by developers and those really wanting to live on the bleeding edge code. Therefore, it is important to get Build.PL in place to let the release cycle and CPAN packages built quickly, easily and without hassle - which I believe is the problem with Makefile.PL as it currently is. > Implementing changes like this do require a lot of energy. I very > much appreciate that Sendu invested the time and energy to make it > work, even though unfortunately at the last hour. Who knows who would > have had the energy after the release. If Sendu hadn't put in the > work now, the next release master may have been stuck with an even > messier Makefile.PL system. Instead of Monday morning quarterbacking > after no-one stopped him when he asked about it, we should all help > him make the release - and the build change - successful now that he > has done most if not all of the migration work already. > > -hilmar > Here, here - well done Sendu on all your hard work! Personally, I think the move to Build.PL is a good one - it may be a little late in this particular release, but I think that the problem is not that it is a late change, but that it wasn't picked up sooner. It fits well with the goal of making releases and big fix releases more regular, and if these are made available via CPAN, then the use of CVS is for developers and those wanting to live on the edge. Build.PL helps all this by making is easier and quicker to make CPAN packages. It also means we have a while before the "stable" 1.6 release to ensure it is working effectively - better than dropping it in on the 1.6 release isn't it? I think it's work the delay and an extra RC! Anyway, my 2 pence worth! Nath -- > A: Yes. >> Q: Are you sure? >> >>> A: Because it reverses the logical flow of conversation. >>> >>>> Q: Why is top posting frowned upon? >>>> Get Thunderbird <http://www.mozilla.org/products/thunderbird/> From bix at sendu.me.uk Thu Nov 16 04:26:45 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 09:26:45 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2C0C.1080403@sheffield.ac.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> <455C2C0C.1080403@sheffield.ac.uk> Message-ID: <455C2ED5.4060602@sendu.me.uk> Nathan S. Haigh wrote: > I believe Sendu mentioned that a Makefile.PL would be included in the > CPAN package but is not in CVS as it would be generated from > Build.PL for backward compatibility - is that right Sendu? Yes. > How does installing via CPAN affect this? Does it give higher > priority to Build.PL over Makefile.PL and thus use Build.PL for the > install? I don't know about priorities (but assume it would prefer Build.PL), but in any case, the generated Makefile.PL basically just calls Build.PL, so it makes no difference. > Build.PL helps all this by making is easier and quicker to make CPAN > packages. It also means we have a while before the "stable" 1.6 > release to ensure it is working effectively - better than dropping it > in on the 1.6 release isn't it? I think it's work the delay and an > extra RC! Yes, it surely needs to happen before 1.6. As suggested here and originally in the other thread, 1.5.2 can be the transition release with old Makefile.PL and Build.PL as well (set up to not overwrite Makefile.PL). From bix at sendu.me.uk Thu Nov 16 06:35:25 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 11:35:25 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <001801c70905$dbdd7a40$15327e82@pyrimidine> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> Message-ID: <455C4CFD.5080005@sendu.me.uk> Chris Fields wrote: > I see that there is a PPMMaker module with Module::Build, so we'll have to > look into that for WinXP PPMs.. Nathan, does: perl Build.PL ./Build ppmdist create anything useful? For me it generates a tar.gz containing blib, and a ppd file (the contents of which can be adjusted by supplying "an optional argument codebase which is used in the generated ppd file to specify the (usually relative) URL of the distribution. By default, this value is the distribution name without any path information", eg. ./Build ppmdist --codebase "MSWin32-x86-multi-thread/Bioperl....tar.gz"). Is this PPM4 format? What else needs to be done to it to make it suitable? I can easily extend the ppmdist action to do whatever you want, so let me know. From bix at sendu.me.uk Thu Nov 16 06:45:03 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 11:45:03 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <45531968.6080607@sendu.me.uk> References: <45531968.6080607@sendu.me.uk> Message-ID: <455C4F3F.1090901@sendu.me.uk> Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Developers: > Once again I'm hopeful that this is the last RC. If all goes well > expect final release in about a weeks time. Please check and update > documentation. Sadly all didn't go well. Some remaining bugs are present in the Run package which are now being worked on (there was also a WinXP core bug already fixed by Chris). Expect RC4 sometime this week, which will also include a transitional Build.PL as an alternative to installing with Makefile.PL. From bikash_lohia2000 at yahoo.com Thu Nov 16 07:30:04 2006 From: bikash_lohia2000 at yahoo.com (bikash lohia) Date: Thu, 16 Nov 2006 04:30:04 -0800 (PST) Subject: [Bioperl-l] i am new to group, require a help Message-ID: <20061116123004.87840.qmail@web54213.mail.yahoo.com> hello group, I am new to this group and want a help.i have list of accesion id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to manually search gene database of NCBI for converting this accession no. of cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i want to do it through perl programming where the program directly takes the list of id ( such as AK105331,Ak070197) from notepad file and searches in gene database of ncbi. to give results in accession id starting with OS****** .i want only the accession id of corresponding Ak***** id. for example - AK070197 of nucleotide databse = Os02g0669100 of gene database. i want to convert all this AK***** ids to OS***** ids through programming in perl/bioperl as manually not possible for long list. please help. i have no idea how can the code be. with thanks in advance from Bikash --------------------------------- Sponsored Link Degrees for working adults in as fast as 1 year. Bachelors, Masters, Associates. Top schools From n.haigh at sheffield.ac.uk Thu Nov 16 07:45:14 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 12:45:14 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C4CFD.5080005@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> Message-ID: <455C5D5A.5020205@sheffield.ac.uk> Sendu Bala wrote: > Chris Fields wrote: >> I see that there is a PPMMaker module with Module::Build, so we'll >> have to >> look into that for WinXP PPMs.. > > Nathan, does: > > perl Build.PL > ./Build ppmdist > > create anything useful? For me it generates a tar.gz containing blib, > and a ppd file (the contents of which can be adjusted by supplying "an > optional argument codebase which is used in the generated ppd file to > specify the (usually relative) URL of the distribution. By default, > this value is the distribution name without any path information", eg. > ./Build ppmdist --codebase "MSWin32-x86-multi-thread/Bioperl....tar.gz"). > > Is this PPM4 format? What else needs to be done to it to make it > suitable? I can easily extend the ppmdist action to do whatever you > want, so let me know. Sorry, but i've been busy this last week etc so haven't be able to test RC3 on WinXP yet - hopefully Chris' tests have been sufficient. Essentially a PPM dist comprises of the .tar.gz file you described (of the blib dir) and then the XML file (.ppd) which describes the package and it's dependencies. The syntax of the XML has changed for PPM4 (which required me to do these changes by hand on the ppd that was previously output by "make ppd". For PPM4 the XML in the ppd file can be copied over to packages.xml file in our PPM repository. the codebase URL can be relative/absolute and it's exact value depends on the relative position of the XML (whether in the .ppd or package.xml file) and the .tar.gz file. Thus, by default, they would have to reside in the same dir on our server. Without looking at the XML I couldn't say if it was PPM3 or PPM4 compatible. Could you e-mail me the ppd file and I'll take a look. Cheers Nath From cjfields at uiuc.edu Thu Nov 16 07:45:13 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 06:45:13 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C197D.6000107@sendu.me.uk> References: <C1812C74.B5E3%bosborne11@verizon.net> <455C1790.3080408@sendu.me.uk> <455C197D.6000107@sendu.me.uk> Message-ID: <F9D837E4-4614-4905-A171-9738ED1D01D8@uiuc.edu> On Nov 16, 2006, at 1:55 AM, Sendu Bala wrote: ... > Also, > # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who > read the docs on the website/elsewhere (which will be updated to > explain > the new Build.PL system) don't get confused when that doesn't work, > for wide testing, and to get people used to it for the next > release. The > old Makefile.PL will have 2 changes: Brians bug-fix and a little > message > pointing out that Build.PL is now the preferred installation > system, but > Makefile.PL still works. Sounds fine to me. The old Makefile.PL is in the branch along with the new system, we leave a stub in place for Makefile.PL in CVS HEAD, and everybody's happy (hopefully). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 08:08:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 07:08:57 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2980.4000609@sheffield.ac.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> <455C2980.4000609@sheffield.ac.uk> Message-ID: <4723715A-551A-4402-A98C-14B64EEDD80E@uiuc.edu> On Nov 16, 2006, at 3:04 AM, Nathan S. Haigh wrote: > ... >> If Build.PL can coexist that'd be great. That would give you the >> opportunity to have Makefile.PL print out a message right at the >> beginning that if the installation process messes up one should try >> Build.PL. This would spare you from fixing any problems in >> Makefile.PL that are fixed in the Build.PL approach. > > Good idea, for anyone downloading the .tar.gz from CPAN if they issue > "perl Makefile.PL" without knowing Build.PL was there it should > hopefully work, but if not, issue a comment at the end to say try > "perl > Build.PL" if anything seemed to go wrong. That's amazingly similar to the suggestion I made ;> Seriously, when we make any changes in Bioperl they should be made with the community in mind. If I were to download RC3 directly from the website, it uses the old Makefile.PL. Therefore I would expect the new RC and the final release to have a similar installation procedure. Same with CVS. And I'll note that the CVS docs and wiki still state that Makefile.PL is the one to use. If we can redirect them to the current way, all the better. But sudden dramatic changes, even in a developer release, are probably not the way to go. > If we go for short release cycles, and regular bug fix release, we > will > no longer have to say to users: > "This is a known bug/issue in release x.y.z, it has been fixed in CVS > HEAD so get it from there" > we can roll out fixes in regular releases. This way CVS is then used > solely by developers and those really wanting to live on the bleeding > edge code. Therefore, it is important to get Build.PL in place to let > the release cycle and CPAN packages built quickly, easily and without > hassle - which I believe is the problem with Makefile.PL as it > currently is. Shorter developer cycles are definitely better. Like Hilmar suggests, they don't have to be perfect (though relatively bug- free). If you look back through the old releases I don't think you'll find many with all tests passing on all OS's. I would like to get a 1.5.3 out by spring, then start towards cleaning up for a summer-fall rel. 1.6. Maybe that's wishful thinking. >> Implementing changes like this do require a lot of energy. I very >> much appreciate that Sendu invested the time and energy to make it >> work, even though unfortunately at the last hour. Who knows who would >> have had the energy after the release. If Sendu hadn't put in the >> work now, the next release master may have been stuck with an even >> messier Makefile.PL system. Instead of Monday morning quarterbacking >> after no-one stopped him when he asked about it, we should all help >> him make the release - and the build change - successful now that he >> has done most if not all of the migration work already. >> >> -hilmar >> > > Here, here - well done Sendu on all your hard work! > Personally, I think the move to Build.PL is a good one - it may be a > little late in this particular release, but I think that the > problem is > not that it is a late change, but that it wasn't picked up sooner. It > fits well with the goal of making releases and big fix releases more > regular, and if these are made available via CPAN, then the use of CVS > is for developers and those wanting to live on the edge. Build.PL > helps > all this by making is easier and quicker to make CPAN packages. It > also > means we have a while before the "stable" 1.6 release to ensure it is > working effectively - better than dropping it in on the 1.6 release > isn't it? I think it's work the delay and an extra RC! > > Anyway, my 2 pence worth! > Nath I don't think anyone is knocking Sendu for his effort here. I will remind everybody that this was discussed in a previous thread and a decision was made (and agreed to by Sendu) to wait until after this release to implement Build, hence the backlash. Brian summed it up quite well. We all support this; the timimg was just bad. That's all. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 08:21:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 13:21:27 +0000 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? Message-ID: <455C65D7.5060704@sendu.me.uk> Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if the intent was that it not be included in any distribution. I've had a very quick look at it and the docs seem a little out of date. More importantly, I couldn't get it to return any results. I can't find any tests for it in the t/ directory either. Is there any interest in developing this module to get it into a working and tested state, or should I exclude it from the up-coming release of Bioperl? If no one wants to maintain it, should it be deprecated? Thank you, Sendu. From roy at colibase.bham.ac.uk Thu Nov 16 08:18:55 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Thu, 16 Nov 2006 13:18:55 +0000 Subject: [Bioperl-l] reverse complement - and features In-Reply-To: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> References: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Message-ID: <455C653F.7010907@colibase.bham.ac.uk> > do you know of an easy way to reverse complement the sequence of an > embl entry and the features associated with that sequence. > I'm looking at genomic syntenic regions, and in some organisms the > gene is in the plus strand while in others is in the minus. Try the revcom_with_features method from Bio::SeqUtils: $revcom=Bio::SeqUtils->revcom_with_features($seq); (Apparently the documentation isn't correct for this. I have submitted a patch to Bugzilla.) Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From n.haigh at sheffield.ac.uk Thu Nov 16 08:37:33 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 13:37:33 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C6028.3060402@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455C6028.3060402@sendu.me.uk> Message-ID: <455C699D.1040407@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sorry, but i've been busy this last week etc so haven't be able to test >> RC3 on WinXP yet - hopefully Chris' tests have been sufficient. > > No problem, thanks for all your testing effort! > > >> Essentially a PPM dist comprises of the .tar.gz file you described (of >> the blib dir) and then the XML file (.ppd) which describes the package >> and it's dependencies. > > Is the .ppd ever included in the .tar.gz, or is it always separate? > > Nope - always separate. >> The syntax of the XML has changed for PPM4 (which >> required me to do these changes by hand on the ppd that was previously >> output by "make ppd". > > Is there a reference for the format anywhere? > Erm not really - that I know of. There is this thread which I use for reference: http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 > >> For PPM4 the XML in the ppd file can be copied >> over to packages.xml file in our PPM repository. the codebase URL can be >> relative/absolute and it's exact value depends on the relative position >> of the XML (whether in the .ppd or package.xml file) and the .tar.gz >> file. Thus, by default, they would have to reside in the same dir on our >> server. >> >> Without looking at the XML I couldn't say if it was PPM3 or PPM4 >> compatible. Could you e-mail me the ppd file and I'll take a look. > > It's pretty basic: > > <SOFTPKG NAME="bioperl" VERSION="1,005002003,0,0"> > <TITLE>bioperl > Bioinformatics Toolkit > Bioperl Team <bioperl-l at bioperl.org> > > > > > > If I made it output the sort of information in the current > http://bioperl.org/DIST/RC/package.xml, would that be fine? Did you > have any kind of automation for creating that package.xml, or do you > see a good potential way of automating it? This PPD doesn't contain any info about what modules it provides (ideally, it should have a provide tags for all modules in bioperl) or the dependencies via the require tag. I didn't have an automated way of making it. Previously, the output of "make ppd" used PREREQ_PM from makefile.pl to create PPM3 dependency tags for all modules in PREREQ_PM. I just modified the tags to REQUIRE and added '::' to the end of modules that didn't natively have one. This should all be detailed in the above in - here again for convenience: http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 There must be an automated way to generate the PPM4 compatible PPDs - I think there is a way to generate one from the CPAN distribution. I think this might be the way ActiveState does it? Nath From bix at sendu.me.uk Thu Nov 16 08:47:05 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 13:47:05 +0000 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> References: <455C65D7.5060704@sendu.me.uk> <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> Message-ID: <455C6BD9.6090100@sendu.me.uk> Allen Day wrote: > Hi Sendu, > > Several years ago I was asked by Jim Kent to stop maintaining it. He > was concerned it would overload the UCSC servers. It's not in the > distribution for the same reason. Thanks, I'll deprecate it then. From gcarbajosa at cnio.es Thu Nov 16 08:12:58 2006 From: gcarbajosa at cnio.es (guillermo) Date: Thu, 16 Nov 2006 14:12:58 +0100 Subject: [Bioperl-l] indexing whole genbank Message-ID: Hello, I wrote to this list before because I wasn?t able to index the whole of genebank. I?ve tried to do it spliting the work by creating small indexes and it has worked perfectly so that seems the way to do it. Thanks for your comments, Guillermo **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From cjfields at uiuc.edu Thu Nov 16 10:08:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:08:08 -0600 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <455C65D7.5060704@sendu.me.uk> Message-ID: <001501c70991$06b14fe0$15327e82@pyrimidine> > Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if > the intent was that it not be included in any distribution. > I've had a very quick look at it and the docs seem a little > out of date. More importantly, I couldn't get it to return > any results. > > I can't find any tests for it in the t/ directory either. Is > there any interest in developing this module to get it into a > working and tested state, or should I exclude it from the > up-coming release of Bioperl? > > If no one wants to maintain it, should it be deprecated? > > > Thank you, > Sendu. I would definitely exclude it if it doesn't work or have tests. Have you contacted the author (Allen Day)? I wonder if he has updated the code but hasn't committed it. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Thu Nov 16 10:17:23 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Nov 2006 10:17:23 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C197D.6000107@sendu.me.uk> References: <455C1790.3080408@sendu.me.uk> <455C197D.6000107@sendu.me.uk> Message-ID: <75FDB3A6-BFB6-4120-92B1-04D54D708E4C@gmx.net> Sounds great to me. -hilmar On Nov 16, 2006, at 2:55 AM, Sendu Bala wrote: >> Ok, so the current plan is: >> # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml > Also, > # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who > read the docs on the website/elsewhere (which will be updated to > explain > the new Build.PL system) don't get confused when that doesn't work, > for wide testing, and to get people used to it for the next > release. The > old Makefile.PL will have 2 changes: Brians bug-fix and a little > message > pointing out that Build.PL is now the preferred installation > system, but > Makefile.PL still works. > > >> # CVS core gets a Makefile.PL stub telling you to use Build.PL >> # CVS db, run, network stay with Makefile.PL until after final >> release >> of 1.5.2, then move to Build.PL with Makefile.PL stub (because they >> don't have a 1.5.2 branch) >> >> Is everyone happy with that, or are there further suggestions for >> something better? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Thu Nov 16 10:29:31 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:29:31 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C699D.1040407@sheffield.ac.uk> Message-ID: <001601c70994$02da28d0$15327e82@pyrimidine> ... > > > > Is there a reference for the format anywhere? > > > > Erm not really - that I know of. There is this thread which I use for > reference: > http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 Looks like kobes is using PPM::Make (he should; it's his distribution). We'll need to make sure that Module::Build uses that as well, since it seems there are some significant changes. ... > There must be an automated way to generate the PPM4 > compatible PPDs - I think there is a way to generate one from > the CPAN distribution. I think this might be the way > ActiveState does it? > > Nath I think ActiveState has it's own automated build process. For PPM3 they used the PPD section from the regular makefile (from Makefile.PL and ExtUtils::MakeMaker). Notably they still indicate using 'nmake ppd' when generating Makefile.PL, so maybe they use an updated or modified ExtUtils::MakeMaker? Or they add tags for the Makefile.PL: use ExtUtils::MakeMaker; # See lib/ExtUtils/MakeMaker.pm for details of how to influence # the contents of the Makefile that is written. WriteMakefile( 'NAME' => 'Term::Control', 'VERSION_FROM' => 'Control.pm', # finds $VERSION ($] ge '5.005') ? ( 'AUTHOR' => 'Johnny Doel (johnny at doel.org)', 'ABSTRACT' => 'Control the IO for terminals', # extra tags here? ) : (), ); The reason you may not see a certain distribution built into a PPM is b/c a particular dependency is not available for one reason or another, tests fail during the make process, etc. They will try to build specific ones upon request. Many of the ones in Kobes are generated by users who want up-to-date distros or ones not built automatically by ActiveState, though Randy Kobes himself sets up most of them. Significantly, he has already switched over to PPM4; maybe we should contact him about this? Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 10:31:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:31:08 -0600 Subject: [Bioperl-l] indexing whole genbank In-Reply-To: Message-ID: <001701c70994$3d332400$15327e82@pyrimidine> > Hello, > > I wrote to this list before because I wasn?t able to index > the whole of genebank. I?ve tried to do it spliting the work > by creating small indexes and it has worked perfectly so that > seems the way to do it. > > Thanks for your comments, > Guillermo Thanks for the update. I think that the problem was a full GenBank file is way too large for flatfile indexing (I think it's around 800 GB unpacked now). Nice to know doing it by divisions works. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 11:29:33 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 16:29:33 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <17756.36534.549232.263868@satchel.alerce.com> References: <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> <455BA093.8040603@sendu.me.uk> <17756.36534.549232.263868@satchel.alerce.com> Message-ID: <455C91ED.2030008@sendu.me.uk> George Hartzell wrote: > Sendu Bala writes: > > [...] > > The only real change for most users is that they now need Module::Build > > installed. > > Module::Build can be a real pain-in-the_%$* if you're used to > installing perl modules in a specialized place using something like > this: > > perl Makefile.PL PREFIX=~/perl-stuff > > Granted, MakeMaker's handling of that has been inconsistent across > platforms over the years, but on a single system at least it's > manageable. > > If/when bioperl swaps over to a Module::Build based system, PLEASE > make a big&loud reference to the "Installing in the same location as > ExtUtils::MakeMaker" section of the Module::Build::Cookbook so that > folks have a fighting chance of avoiding unpleasant surprises. Thanks, I've added a clarification to the INSTALL file. From hartzell at alerce.com Thu Nov 16 11:15:50 2006 From: hartzell at alerce.com (George Hartzell) Date: Thu, 16 Nov 2006 08:15:50 -0800 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BA093.8040603@sendu.me.uk> References: <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> <455BA093.8040603@sendu.me.uk> Message-ID: <17756.36534.549232.263868@satchel.alerce.com> Sendu Bala writes: > [...] > The only real change for most users is that they now need Module::Build > installed. Module::Build can be a real pain-in-the_%$* if you're used to installing perl modules in a specialized place using something like this: perl Makefile.PL PREFIX=~/perl-stuff Granted, MakeMaker's handling of that has been inconsistent across platforms over the years, but on a single system at least it's manageable. If/when bioperl swaps over to a Module::Build based system, PLEASE make a big&loud reference to the "Installing in the same location as ExtUtils::MakeMaker" section of the Module::Build::Cookbook so that folks have a fighting chance of avoiding unpleasant surprises. That section says, in part: With the introduction of "--prefix" in Module::Build 0.28 and "INSTALL_BASE" in ExtUtils::MakeMaker 6.31 its [sic] easy to get them both to install in the same locations. First, ensure you have at least version 0.28 of Module::Build installed and 6.31 of ExtUtils::MakeMaker. Prior versions have differeing installation behaviours. People may need to upgrade their installations [at least the ExtUtils::MakeMaker and Module::Build bits], but at least they'll see the train barreling down at them. g. From roy at colibase.bham.ac.uk Thu Nov 16 11:49:49 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Thu, 16 Nov 2006 16:49:49 +0000 Subject: [Bioperl-l] reverse complement - and features In-Reply-To: <40d6e6580611160828m5f7047e0gadec36f958a69990@mail.gmail.com> References: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> <455C653F.7010907@colibase.bham.ac.uk> <40d6e6580611160828m5f7047e0gadec36f958a69990@mail.gmail.com> Message-ID: <455C96AD.8030804@colibase.bham.ac.uk> > that method sounds promising, although the documentation seems to be > copy-and-paste from the trunc_with_features() method. Yes, I was a bit lazy with that. It has been fixed in CVS (thanks Chris) and will be included in the new 1.5.2 release. > I included in my script, although it doesn't complaint but no being > there, it doesn't do anything with the file. > I looked at the version of bioperl in the server where I'm running, > and it is 1.5.0 and the SeqUtils.pm does not include the > revcom_with_features(). > Do you know if I can install the SeqUtils.pm module in my directory, > and call it with use lib "/home/xxxx/xxxx/lib/perl"; ? Yes, that should work. You can download the most recent version from: http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioperl-live/Bio/SeqUtils.pm?rev=HEAD&content-type=text/plain You can put that file in the directory /home/xxxx/xxxx/lib/perl/Bio/ and it should then be recognised as the preferred Bio::SeqUtils module if you use lib as you say. Good luck with it. Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From cjfields at uiuc.edu Thu Nov 16 11:55:39 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 10:55:39 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2ED5.4060602@sendu.me.uk> Message-ID: <001901c709a0$0b6a6d50$15327e82@pyrimidine> > Nathan S. Haigh wrote: > > I believe Sendu mentioned that a Makefile.PL would be > included in the > > CPAN package but is not in CVS as it would be generated > from Build.PL > > for backward compatibility - is that right Sendu? > > Yes. > > > > How does installing via CPAN affect this? Does it give > higher priority > > to Build.PL over Makefile.PL and thus use Build.PL for the install? > > I don't know about priorities (but assume it would prefer > Build.PL), but in any case, the generated Makefile.PL > basically just calls Build.PL, so it makes no difference. > > > > Build.PL helps all this by making is easier and quicker to > make CPAN > > packages. It also means we have a while before the "stable" 1.6 > > release to ensure it is working effectively - better than > dropping it > > in on the 1.6 release isn't it? I think it's work the delay and an > > extra RC! > > Yes, it surely needs to happen before 1.6. As suggested here > and originally in the other thread, 1.5.2 can be the > transition release with old Makefile.PL and Build.PL as well > (set up to not overwrite Makefile.PL). So far, we have these modes of installation: 1) Direct installation using CPAN -> INSTALL 2) Regular distribution (either from the Bioperl website or CPAN) using 'make/nmake' ->INSTALL, INSTALL.WIN 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN 4) PPM (Windows-only) -> INSTALL.WIN Anything using make/nmake will need to be changed in docs. Do you want to switch everything over to using 'perl Build.PL'? Also, since the 'manifying' problem is now fixed we can remove the blurb about it from INSTALL and the wiki. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 11:59:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 16:59:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> References: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: <455C98F0.9050909@sendu.me.uk> Chris Fields wrote: > So far, we have these modes of installation: > > 1) Direct installation using CPAN -> INSTALL > 2) Regular distribution (either from the Bioperl website or CPAN) using > 'make/nmake' ->INSTALL, INSTALL.WIN > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > 4) PPM (Windows-only) -> INSTALL.WIN > > Anything using make/nmake will need to be changed in docs. Do you want to > switch everything over to using 'perl Build.PL'? > > Also, since the 'manifying' problem is now fixed we can remove the blurb > about it from INSTALL and the wiki. I've already updated docs in CVS. The emails are just very slow to get through to guts. Do an update and let me know if I missed anything. I'll add the changes to the wiki when I get a chance. From n.haigh at sheffield.ac.uk Thu Nov 16 12:44:28 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 17:44:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> References: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: <455CA37C.3070704@sheffield.ac.uk> --snip-- >> Yes, it surely needs to happen before 1.6. As suggested here >> and originally in the other thread, 1.5.2 can be the >> transition release with old Makefile.PL and Build.PL as well >> (set up to not overwrite Makefile.PL). >> > > So far, we have these modes of installation: > > 1) Direct installation using CPAN -> INSTALL > 2) Regular distribution (either from the Bioperl website or CPAN) using > 'make/nmake' ->INSTALL, INSTALL.WIN > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > Chris, Do you ever have a problem with nmake when doing an install from a regular distribution or CVS? I'm sure I used to get an nmake problem which wouldn't let you proceed further - might have been "nmake test" and it might be a while back now. Nath From cjfields at uiuc.edu Thu Nov 16 12:58:14 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 11:58:14 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455CA37C.3070704@sheffield.ac.uk> Message-ID: <000001c709a8$c9c1b760$15327e82@pyrimidine> > --snip-- > >> Yes, it surely needs to happen before 1.6. As suggested here and > >> originally in the other thread, 1.5.2 can be the > transition release > >> with old Makefile.PL and Build.PL as well (set up to not overwrite > >> Makefile.PL). > >> > > > > So far, we have these modes of installation: > > > > 1) Direct installation using CPAN -> INSTALL > > 2) Regular distribution (either from the Bioperl website or CPAN) > > using 'make/nmake' ->INSTALL, INSTALL.WIN > > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > > > > Chris, > > Do you ever have a problem with nmake when doing an install > from a regular distribution or CVS? I'm sure I used to get an > nmake problem which wouldn't let you proceed further - might > have been "nmake test" > and it might be a while back now. > > Nath I haven't had problems beyond the '-w' paranoia and 'Subroutine x redefined at' warnings, which is an ActivePerl issue. 'nmake test' works for me (that's what I have been using on all the RC's and using bioperl-live). I think 'Build test' also uses nmake, so if that works nmake should also work. I have used both an old version (1.5) and the recent VC++ nmake version (8.00.50727.42) w/o problems. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From pcantalupo at gmail.com Thu Nov 16 11:26:31 2006 From: pcantalupo at gmail.com (Paul Cantalupo) Date: Thu, 16 Nov 2006 11:26:31 -0500 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID Message-ID: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Hello, Is there a way with Bioperl (or some other tool - NCBI EUtils?) to convert a Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's that I need to convert to Mouse GeneIDs so that I can compare them to my Mouse microarray data. Thank you, Paul -- Paul Cantalupo Research Specialist/Systems Programmer 559 Crawford Hall Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Work: 412-624-4687 Fax: 412-624-4759 Ask me about Toastmasters: www.toastmasters.org Midday Club Treasurer From bosborne11 at verizon.net Thu Nov 16 13:09:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 16 Nov 2006 13:09:01 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: Chris, So a package like bioperl-ext, normally requiring a C compiler and make/nmake, now no longer needs make/nmake? I don't recall this coming up in our discussions... Brian O. On 11/16/06 11:55 AM, "Chris Fields" wrote: > Anything using make/nmake will need to be changed in docs. From bix at sendu.me.uk Thu Nov 16 13:14:12 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 18:14:12 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: References: Message-ID: <455CAA74.60500@sendu.me.uk> Brian Osborne wrote: > Chris, > > So a package like bioperl-ext, normally requiring a C compiler and > make/nmake, now no longer needs make/nmake? I don't recall this coming up in > our discussions... I'm sure you'd still need compiler tools to do compilation. I wasn't sure what to say about bioperl-ext in the docs, so I didn't change anything. bioperl-ext isn't my concern (see the thread where I was deciding which packages needed a unified release), so I'll not be trying to change it over to Build.PL From bix at sendu.me.uk Thu Nov 16 13:16:48 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 18:16:48 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: References: Message-ID: <455CAB10.1090703@sendu.me.uk> Brian Osborne wrote: > George, > > But the most recent versions of Module::Build do the installations > correctly? And it's as simple as specifying PREFIX or LIB? In Build.PL's case, it's --prefix or --lib, but yes. For both Module::Build and MakeMaker in recent versions, --install_base is recommended. From cjfields at uiuc.edu Thu Nov 16 13:41:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 12:41:56 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: Message-ID: <000101c709ae$e475bfb0$15327e82@pyrimidine> > Chris, > > So a package like bioperl-ext, normally requiring a C > compiler and make/nmake, now no longer needs make/nmake? I > don't recall this coming up in our discussions... > > Brian O. The makefile setup for bioperl-ext is much more complex than for the others, so I don't know how that would be handled using Module::Build. I tried it earlier on before the RCs on Mac OS X and it installed fine, but Inline complained when running other tests so I tossed it. I don't think it ever worked under Windows using nmake, unless you're using CygWin/GNU make. I believe the Build file must use make/nmake somehow, so there must be a way to compile C code included with the distribution. I just haven't had time to invesitgate yet. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Thu Nov 16 14:05:27 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 19:05:27 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <000101c709ae$e475bfb0$15327e82@pyrimidine> References: <000101c709ae$e475bfb0$15327e82@pyrimidine> Message-ID: <455CB677.6080608@sheffield.ac.uk> Chris Fields wrote: >> Chris, >> >> So a package like bioperl-ext, normally requiring a C >> compiler and make/nmake, now no longer needs make/nmake? I >> don't recall this coming up in our discussions... >> >> Brian O. >> > > The makefile setup for bioperl-ext is much more complex than for the others, > so I don't know how that would be handled using Module::Build. I tried it > earlier on before the RCs on Mac OS X and it installed fine, but Inline > complained when running other tests so I tossed it. I don't think it ever > worked under Windows using nmake, unless you're using CygWin/GNU make. > > I believe the Build file must use make/nmake somehow, so there must be a way > to compile C code included with the distribution. I just haven't had time > to invesitgate yet. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > I was under the impression that Module::Build is pure Perl and thus wouldn't use make/nmake. This page might help, look under "code" in this section: http://search.cpan.org/~kwilliams/Module-Build-0.2805/lib/Module/Build.pm#ACTIONS According to change logs they use ExtUtils::CBuilder to do all compiling of C code (since version 0.27_01) see: http://search.cpan.org/src/KWILLIAMS/Module-Build-0.27_03/Changes HTH Nathan From bosborne11 at verizon.net Thu Nov 16 13:05:15 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 16 Nov 2006 13:05:15 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <17756.36534.549232.263868@satchel.alerce.com> Message-ID: George, But the most recent versions of Module::Build do the installations correctly? And it's as simple as specifying PREFIX or LIB? Brian O. On 11/16/06 11:15 AM, "George Hartzell" wrote: > Module::Build can be a real pain-in-the_%$* if you're used to > installing perl modules in a specialized place using something like > this: > > perl Makefile.PL PREFIX=~/perl-stuff From er at xs4all.nl Thu Nov 16 16:01:12 2006 From: er at xs4all.nl (Erik) Date: Thu, 16 Nov 2006 22:01:12 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch Message-ID: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> Hi all, Using bioperl-live, I noticed a problem with the parsing in Bio/SeqIO/genbank.pm. It occurs in the DBSOURCE section, where the 'dblink' annotation gets its values. I got several values that had a double colon, like InterPro::IPR011000 etc. Not all 'dblink' values were affected. Here is a patch which seems to fix it / it works for me: ======= --- Bio/SeqIO/genbank.pm.orig 2006-11-16 18:33:30.060417520 +0100 +++ Bio/SeqIO/genbank.pm 2006-11-16 20:29:59.014934936 +0100 @@ -504,7 +504,7 @@ my $db; # this is because GenBank dropped the spaces!!! # I'm sure we're not going to get this right - if( $id =~ s/^(EchoBASE|IntAct|SWISS-2DPAGE|ECO2DBASE|ECOGENE|TIGRFAMs|TIGR|GO|InterPro|Pfam|PROSITE|SGD|GermOnline|HSSP|PhosSite)//i ) { + if( $id =~ s/^(EchoBASE|IntAct|SWISS-2DPAGE|ECO2DBASE|ECOGENE|TIGRFAMs|TIGR|GO|InterPro|Pfam|PROSITE|SGD|GermOnline|HSSP|PhosSite)://i ) { $db = $1; } $annotation->add_Annotation======= I also wrote a few tests for the problem, which also needed an extra file in t/data. I will attach the lot hth, Erik -------------- next part -------------- A non-text attachment was scrubbed... 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Name: genbank.pm.diff Type: application/octet-stream Size: 608 bytes Desc: not available URL: From jason at bioperl.org Thu Nov 16 14:45:24 2006 From: jason at bioperl.org (Jason Stajich) Date: Thu, 16 Nov 2006 11:45:24 -0800 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> References: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Message-ID: have you tried ensembl's biomart? http://www.ensembl.org/Multi/martview you will want the ortholog table. -jason On Nov 16, 2006, at 8:26 AM, Paul Cantalupo wrote: > Hello, > > Is there a way with Bioperl (or some other tool - NCBI EUtils?) to > convert a > Human NCBI GeneID to a Mouse GeneID. I have a list of Human > GeneID's that I > need to convert to Mouse GeneIDs so that I can compare them to my > Mouse > microarray data. > > Thank you, > > Paul > > -- > Paul Cantalupo > Research Specialist/Systems Programmer > 559 Crawford Hall > Department of Biological Sciences > University of Pittsburgh > Pittsburgh, PA 15260 > Work: 412-624-4687 > Fax: 412-624-4759 > > Ask me about Toastmasters: www.toastmasters.org > Midday Club Treasurer > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From allenday at ucla.edu Thu Nov 16 08:43:35 2006 From: allenday at ucla.edu (Allen Day) Date: Thu, 16 Nov 2006 05:43:35 -0800 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <455C65D7.5060704@sendu.me.uk> References: <455C65D7.5060704@sendu.me.uk> Message-ID: <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> Hi Sendu, Several years ago I was asked by Jim Kent to stop maintaining it. He was concerned it would overload the UCSC servers. It's not in the distribution for the same reason. -Allen On 11/16/06, Sendu Bala wrote: > Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if the intent > was that it not be included in any distribution. I've had a very quick > look at it and the docs seem a little out of date. More importantly, I > couldn't get it to return any results. > > I can't find any tests for it in the t/ directory either. Is there any > interest in developing this module to get it into a working and tested > state, or should I exclude it from the up-coming release of Bioperl? > > If no one wants to maintain it, should it be deprecated? > > > Thank you, > Sendu. > From torsten.seemann at infotech.monash.edu.au Thu Nov 16 19:42:41 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 17 Nov 2006 11:42:41 +1100 Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch In-Reply-To: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> References: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> Message-ID: <455D0581.4010805@infotech.monash.edu.au> Erik, > Using bioperl-live, I noticed a problem with the parsing in > Bio/SeqIO/genbank.pm. > It occurs in the DBSOURCE section, where the 'dblink' annotation gets its > values. I got several values that had a double colon, like > InterPro::IPR011000 etc. Not all 'dblink' values were affected. > Here is a patch which seems to fix it / it works for me: Thank you very much for your contribution of bug fix and patch and new tests, you have been very thorough. However, these contributions are best done via the Bugzilla tracking system: http://bugzilla.open-bio.org/ For more information see: http://www.bioperl.org/wiki/Bugs -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From cjfields at uiuc.edu Thu Nov 16 08:47:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 07:47:26 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C5D5A.5020205@sheffield.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> Message-ID: On Nov 16, 2006, at 6:45 AM, Nathan S. Haigh wrote: > Sendu Bala wrote: >> Chris Fields wrote: >>> I see that there is a PPMMaker module with Module::Build, so we'll >>> have to >>> look into that for WinXP PPMs.. >> >> Nathan, does: >> >> perl Build.PL >> ./Build ppmdist >> >> create anything useful? For me it generates a tar.gz containing blib, >> and a ppd file (the contents of which can be adjusted by supplying >> "an >> optional argument codebase which is used in the generated ppd file to >> specify the (usually relative) URL of the distribution. By default, >> this value is the distribution name without any path information", >> eg. >> ./Build ppmdist --codebase "MSWin32-x86-multi-thread/ >> Bioperl....tar.gz"). >> >> Is this PPM4 format? What else needs to be done to it to make it >> suitable? I can easily extend the ppmdist action to do whatever you >> want, so let me know. > > Sorry, but i've been busy this last week etc so haven't be able to > test > RC3 on WinXP yet - hopefully Chris' tests have been sufficient. > > Essentially a PPM dist comprises of the .tar.gz file you described (of > the blib dir) and then the XML file (.ppd) which describes the package > and it's dependencies. The syntax of the XML has changed for PPM4 > (which > required me to do these changes by hand on the ppd that was previously > output by "make ppd". For PPM4 the XML in the ppd file can be copied > over to packages.xml file in our PPM repository. the codebase URL > can be > relative/absolute and it's exact value depends on the relative > position > of the XML (whether in the .ppd or package.xml file) and the .tar.gz > file. Thus, by default, they would have to reside in the same dir > on our > server. > > Without looking at the XML I couldn't say if it was PPM3 or PPM4 > compatible. Could you e-mail me the ppd file and I'll take a look. > > Cheers > Nath I'll also try making a PPM here. I noticed that Module::Build has a developer release; I may check with the developers about PPM compatibility. I hate to say it, but we might need to get a PPM3 rolled for this release if people ask for it. There has been some backlash about PPM4 so a lot of people are actually downgrading to an older ActivePerl installations for PPM3. We'll just make a barebones version if this pops up (and no Bundle). One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a developer release, but as the latest release (which implies it is stable): http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Not sure what's going on there, but I don't think that was intended, correct? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 21:51:49 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 20:51:49 -0600 Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations In-Reply-To: References: Message-ID: <277B1C9B-1719-47C5-9A34-9B4E179A78A0@uiuc.edu> On Nov 16, 2006, at 1:55 AM, Joanne Chen wrote: > Got the strand problem fixed. Thanks. =) No problem. Just as a heads up, we plan on making some changes to SplitLocations but nothing too dramatic (hopefully). chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From dmessina at wustl.edu Thu Nov 16 22:54:50 2006 From: dmessina at wustl.edu (David Messina) Date: Thu, 16 Nov 2006 21:54:50 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B3F11.6070102@campus.iztacala.unam.mx> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> <455B3F11.6070102@campus.iztacala.unam.mx> Message-ID: <450674EB-F9CA-4BBF-8EB9-D08423FD16FD@wustl.edu> Sorry, just seeing this now. > ignored, only run manually by people who want to install Deobfuscator? Thanks for asking. As Mauricio said, manual installation only is what I would suggest. Dave From torsten.seemann at infotech.monash.edu.au Thu Nov 16 19:19:42 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 17 Nov 2006 11:19:42 +1100 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast In-Reply-To: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> References: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> Message-ID: <455D001E.4000409@infotech.monash.edu.au> Andrew, >> Anyone have any opinions as to how easy/difficult it would be >> to incorporate mpiblast into >> Bio::Tools::Run::StandAloneBlast? It runs essentially the >> same way as blastall, and its output is nearly identical. > I think plans were to rewrite StandAloneBlast and RemoteBlast to make them > more 'generic' (i.e. capable of running other BLAST-related programs), > though I'm not sure at what stage everything is. Chris is correct is saying there were plans to rewrite the Blast modules - at the time myself, Roger Hall, Chris? and Jason were involved, but unfortunately Roger fell ill in Feb 2006 and had to have urgent heart surgery. (And my wife had a baby :-) Here's some of the early discussion: http://portal.open-bio.org/pipermail/bioperl-l/2006-February/020745.html ANYWAY, I think it might be possible to incorporate mpiblast easily, even without changing Bioperl if we are lucky, via the ->executable() setter method. If not, I added rpsblast support last year which is similar to blastall, so it'd probably be achievable. How does the the output of mpiblast differ to NCBI blastall ? What command line options does mpiblast take? -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From bix at sendu.me.uk Fri Nov 17 02:38:30 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 07:38:30 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> Message-ID: <455D66F6.4070804@sendu.me.uk> Chris Fields wrote: > One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a > developer release, but as the latest release (which implies it is stable): > > http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ > > Not sure what's going on there, but I don't think that was intended, > correct? It wasn't intended. I've deleted the file and if you refresh you should find that page doesn't exist anymore? From bix at sendu.me.uk Fri Nov 17 05:20:11 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 10:20:11 +0000 Subject: [Bioperl-l] Testing with Build.PL Message-ID: <455D8CDB.1070100@sendu.me.uk> Developers, For those not familiar with Module::Build and Build.PL I thought I'd point out some useful testing-related things. To run the whole test suite (the same thing that happens during an install process), say: perl Build.PL (answer 'n' to the script installation question to reduce the amount of output you see later on) ./Build test To run a single test script you can of course continue to do: perl -I. -w t/script.t However to see what would really happen during the full "./Build test" you can say: ./Build test --test_files t/script.t To do the same but see the full test output say: ./Build test --test_files t/script.t --verbose If anyone else has tips, please post them. Cheers, Sendu. From sanges at biogem.it Fri Nov 17 05:14:03 2006 From: sanges at biogem.it (Remo Sanges) Date: Fri, 17 Nov 2006 10:14:03 +0000 Subject: [Bioperl-l] Fellowships for Junior Scientists Message-ID: <455D8B6B.1050108@biogem.it> Apologies for the off topic post... AREA Science Park (http://www.area.trieste.it/opencms/opencms/area/en/) and CBM (http://www.cbm.fvg.it/?lang=en_US) are launching a mobility initiative aimed at attracting international scientists to work with the biomedical research community of Trieste. Research areas: * Biostatistics * Systems Biology * Algorithm Development The fellowships are funded by AREA Science Park and the CBM - Consortium for Molecular Biomedicine as part of an international mobility programme run by AREA Science Park and the CBM. The programme aims at attracting young scientists to the Friuli Venezia Giulia Region and adding them to the community of researchers operating in Trieste in the field of biomedicine. CBM and AREA Science Park are two research institutes recognised by the Ministry of Education, Universities and Research. Here there are laboratories integrating dry and wet lab research and developing a wide research program encompassing functional and comparative genomics, bioinformatics database, software development and algorithm development. The laboratories are already integrated in international collaborative projects tackling non-coding RNA genes, regulatory elements, and bioinformatics workflow management systems. For further information: http://www.cbm.fvg.it/?page=mobility&lang=en_US&id=2 Regards Remo Sanges From er at xs4all.nl Fri Nov 17 05:57:43 2006 From: er at xs4all.nl (Erik) Date: Fri, 17 Nov 2006 11:57:43 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch In-Reply-To: <455D0581.4010805@infotech.monash.edu.au> References: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> <455D0581.4010805@infotech.monash.edu.au> Message-ID: <16667.156.83.0.21.1163761063.squirrel@webmail.xs4all.nl> > However, these contributions are best done via the Bugzilla tracking > system: http://bugzilla.open-bio.org/ ok, I'll do that, but a little later today. Maybe just as well as I later thought of some, err.., imperfections in the tests anyway :) Erik From cjfields at uiuc.edu Fri Nov 17 08:43:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 07:43:38 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455D66F6.4070804@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> Message-ID: <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> On Nov 17, 2006, at 1:38 AM, Sendu Bala wrote: > Chris Fields wrote: >> One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a >> developer release, but as the latest release (which implies it is >> stable): >> >> http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ >> >> Not sure what's going on there, but I don't think that was intended, >> correct? > > It wasn't intended. I've deleted the file and if you refresh you > should > find that page doesn't exist anymore? The page is still there, but the distribution is gone (i.e. the 'Download' link is now dead). http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Fri Nov 17 08:51:03 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 13:51:03 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> Message-ID: <455DBE47.90501@sendu.me.uk> Chris Fields wrote: > > On Nov 17, 2006, at 1:38 AM, Sendu Bala wrote: > >> Chris Fields wrote: >>> One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a >>> developer release, but as the latest release (which implies it is >>> stable): >>> >>> http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ >>> >>> Not sure what's going on there, but I don't think that was intended, >>> correct? >> >> It wasn't intended. I've deleted the file and if you refresh you should >> find that page doesn't exist anymore? > > The page is still there, but the distribution is gone (i.e. the > 'Download' link is now dead). > > http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Hmm, I see just a big 'Not found' message for a non-existing page. I think the old page is still stuck in a cache somewhere for you. In any case, don't whatever you do look in the super-sekrit http://search.cpan.org/~sendu/ because I'm testing out CPAN stuff and getting it horribly wrong. Multiple times. I'll make a post when CPAN stuff is ready to test. From cuiw at ncbi.nlm.nih.gov Fri Nov 17 09:59:15 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Fri, 17 Nov 2006 09:59:15 -0500 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Message-ID: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> You can query HomoloGene DB using NCBI EUtils: ESearch like this: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=homologene& term=BRCA1[gene%20name]&retmode=text Once get HomoloGene id then Then Efetch: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=homologene&i d=5276 Just SOAP it to get the gi and acc via taxid. Good luck. Wenwu Cui -----Original Message----- From: Paul Cantalupo [mailto:pcantalupo at gmail.com] Sent: Thursday, November 16, 2006 11:27 AM To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID Hello, Is there a way with Bioperl (or some other tool - NCBI EUtils?) to convert a Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's that I need to convert to Mouse GeneIDs so that I can compare them to my Mouse microarray data. Thank you, Paul -- Paul Cantalupo Research Specialist/Systems Programmer 559 Crawford Hall Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Work: 412-624-4687 Fax: 412-624-4759 Ask me about Toastmasters: www.toastmasters.org Midday Club Treasurer _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Fri Nov 17 12:43:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 17:43:55 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455DF2BC.9010601@sheffield.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> Message-ID: <455DF4DB.5000808@sendu.me.uk> Nathan S. Haigh wrote: > Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked up as > a developer release? I didn't try that variation, but have decided to go with bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a developer release. I've outlined the numbering scheme here: http://www.bioperl.org/wiki/Making_a_BioPerl_release#Making_the_distribution_directory From cjfields at uiuc.edu Fri Nov 17 13:30:20 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 12:30:20 -0600 Subject: [Bioperl-l] CPAN Versioning, was [something else] In-Reply-To: <455DF4DB.5000808@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> Message-ID: <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> On Nov 17, 2006, at 11:43 AM, Sendu Bala wrote: > Nathan S. Haigh wrote: >> Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked >> up as >> a developer release? > > I didn't try that variation, but have decided to go with > bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a > developer > release. > > I've outlined the numbering scheme here: > http://www.bioperl.org/wiki/ > Making_a_BioPerl_release#Making_the_distribution_directory I noticed that Module::Build now has a developer release that uses this: Module-Build-0.2805_01.tar.gz So the '_###' seems to be key. If so I see a versioning dilemma that depends on what we want to call rel 1.5.2. If we used 'bioperl-1.5.2_004' for the RCs, then logically the final dev release would be 'bioperl-1.5.2', which would not be designated a dev release on CPAN (if the underscore rule holds up, that is). If we plan on having CPAN designate it a developer release (which I think is the consensus among the developers, since 1.6 would be the stable release), then the final 1.5.2 version would be something like 'bioperl-1.5_02' or 'bioperl-1.5_002'. RCs would be '1.5_02-RC#'. Or maybe even '1.5_02_##', which a few modules seem to use. However, even that is tricky; what do we call rel 1.6.1, a point release in the stable series? 'bioperl-1.6_2' would then be a developer release! Argghhh! Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Nov 17 13:51:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 12:51:27 -0600 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> References: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> Message-ID: <55142E31-33F7-442C-B358-E81FA57E9F9E@uiuc.edu> On Nov 17, 2006, at 8:59 AM, Cui, Wenwu ((NIH/NLM/NCBI)) [C] wrote: > You can query HomoloGene DB using NCBI EUtils: > > ESearch like this: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? > db=homologene& > term=BRCA1[gene%20name]&retmode=text > > Once get HomoloGene id then > Then Efetch: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? > db=homologene&i > d=5276 > > Just SOAP it to get the gi and acc via taxid. > > Good luck. > > Wenwu Cui > > > -----Original Message----- > From: Paul Cantalupo [mailto:pcantalupo at gmail.com] > Sent: Thursday, November 16, 2006 11:27 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID > > Hello, > > Is there a way with Bioperl (or some other tool - NCBI EUtils?) to > convert a > Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's > that I > need to convert to Mouse GeneIDs so that I can compare them to my > Mouse > microarray data. > > Thank you, > > Paul > ... You could also use esearch(homologene, using history)->elink (homologene_gene, using history)->esummary(elink 'cookie'). I have set up a (very) experimental BioPerl interface to NCBI eutils (Bio::DB::EUtilities). If you update from CVS (this won't be in the 1.5.2 release), you could do something like this: ------------------------------------------------------ use Bio::DB::EUtilities; my $term = 'BRCA1[gene name]'; # grab BRCA1 homologene UID my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => $term, -usehistory => 'y'); $esearch->get_response; my @h_genes = $esearch->get_ids; # what Gene UIDs are linked to the Homologene UID? my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', -db => 'gene', -cookie => $esearch->next_cookie, -cmd => 'neighbor_history'); $elink->get_response; # what taxids go with which GeneID? my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', -cookie => $elink->next_cookie); $esum->get_response; while (my $docsum = $esum->next_docsum) { print $docsum->esummary_id,"\n"; print "\t\tTaxID: ",$docsum->get_Content_by_name('TaxID'),"\n"; print "\t\tOrganism: ",$docsum->get_Content_by_name ('Orgname'),"\n"; } ------------------------------------------------------ A future bioperl SOAP interface for eutils is also not out of the question either, just haven't had time to play around with it. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Fri Nov 17 14:35:11 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 19:35:11 +0000 Subject: [Bioperl-l] CPAN Versioning, was [something else] In-Reply-To: <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> Message-ID: <455E0EEF.4080806@sendu.me.uk> Chris Fields wrote: > > On Nov 17, 2006, at 11:43 AM, Sendu Bala wrote: > >> Nathan S. Haigh wrote: >>> Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked up as >>> a developer release? >> >> I didn't try that variation, but have decided to go with >> bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a developer >> release. >> >> I've outlined the numbering scheme here: >> http://www.bioperl.org/wiki/Making_a_BioPerl_release#Making_the_distribution_directory >> > > I noticed that Module::Build now has a developer release that uses this: > > Module-Build-0.2805_01.tar.gz > > So the '_###' seems to be key. If so I see a versioning dilemma that > depends on what we want to call rel 1.5.2. [snip] See the page I linked above. It shows what the filenames will be for RCs , releases and point releases for developer and non-developer releases. From gwu at molbio.mgh.harvard.edu Sat Nov 18 01:39:46 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 01:39:46 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455E0EEF.4080806@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> Message-ID: <455EAAB2.4010004@molbio.mgh.harvard.edu> Hi everyone, I saw some problems when installing BioPerl 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could not solve all the dependency issues with one shot of 'install Bundle::BioPerl'. Some packages such as GD-2.35 just could not be installed. And it turned out that CPAN refused to install BioPerl with some test return value 255. Then I went to /root/.cpan/build to configure, test, rebuild those problematic packages. After several more runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl successfully. Below attached is the output of CPAN, which stills complains three packages have issues: Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel. I think the first two are typos somewhere in the Bundle::BioPerl. And the third module is not on the server and could be found on the CPAN site. So my question is : Is this the right way to install BioPerl? It took me two days to figure it out but still not 100% sure all packages are installed properly. Any feedback is appreciated. Gang ================================================= cpan> install Bundle::BioPerl Ace is up to date. Bio::ASN1::EntrezGene is up to date. Class::AutoClass is up to date. Clone is up to date. Convert::Binary::C is up to date. Running install for module Data::Stag::writer The module Data::Stag::writer isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i Data::Stag::writer'. DBD::mysql is up to date. GD::SVG is up to date. GD is up to date. Graph::Directed is up to date. HTML::Parser is up to date. Running install for module HTTP::Request::Common- The module HTTP::Request::Common- isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i HTTP::Request::Common-'. LWP::UserAgent is up to date. Set::Scalar is up to date. SOAP::Lite is up to date. Running install for module Spreadhseet::ParseExcel The module Spreadhseet::ParseExcel isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i Spreadhseet::ParseExcel'. Storable is up to date. SVG is up to date. SVG::Graph is up to date. Text::Shellwords is up to date. XML::DOM::XPath is up to date. XML::Parser::PerlSAX is up to date. XML::SAX is up to date. XML::SAX::Base is up to date. XML::SAX::Writer is up to date. XML::Simple is up to date. XML::Twig is up to date. XML::Writer is up to date. Bundle summary: The following items in bundle Bundle::BioPerl had installation problems: Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel ==================================================== From bix at sendu.me.uk Sat Nov 18 03:04:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 18 Nov 2006 08:04:14 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <455EBE7E.4060105@sendu.me.uk> gang wu wrote: > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. What problems did you run into specifically with GD? > And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. Do you remember what the other problematic packages were, and what you had to do to get them working? > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. All three are typos. We'll get those fixed. > So my question is : Is this the right way to install BioPerl? At the present moment, yes. For 1.5.2 I'll probably be recommending not using Bundle::BioPerl once I fix some other things. > It took me two days to figure it out but still not 100% sure all packages are > installed properly. I'm sorry for the troubles you ran into. We'll try and do better for the final release of 1.5.2. From gwu at molbio.mgh.harvard.edu Sat Nov 18 03:07:47 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:07:47 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <455EBF53.4010701@molbio.mgh.harvard.edu> It turned out that most of the modules of BioPerl were not installed at all. And none of the scripts were installed. I had to download and install bioperl-1.5.2-RC3.tar.gz again. A similar problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually copied all stuff under Bio folder to the corresponding Perl library folder. Is it Ok to do it in this way? Gang gang wu wrote: > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. > > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. > > So my question is : Is this the right way to install BioPerl? It took me > two days to figure it out but still not 100% sure all packages are > installed properly. > > Any feedback is appreciated. > > Gang > > ================================================= > cpan> install Bundle::BioPerl > Ace is up to date. > Bio::ASN1::EntrezGene is up to date. > Class::AutoClass is up to date. > Clone is up to date. > Convert::Binary::C is up to date. > Running install for module Data::Stag::writer > > The module Data::Stag::writer isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Data::Stag::writer'. > DBD::mysql is up to date. > GD::SVG is up to date. > GD is up to date. > Graph::Directed is up to date. > HTML::Parser is up to date. > Running install for module HTTP::Request::Common- > > The module HTTP::Request::Common- isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i HTTP::Request::Common-'. > LWP::UserAgent is up to date. > Set::Scalar is up to date. > SOAP::Lite is up to date. > Running install for module Spreadhseet::ParseExcel > > The module Spreadhseet::ParseExcel isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Spreadhseet::ParseExcel'. > Storable is up to date. > SVG is up to date. > SVG::Graph is up to date. > Text::Shellwords is up to date. > XML::DOM::XPath is up to date. > XML::Parser::PerlSAX is up to date. > XML::SAX is up to date. > XML::SAX::Base is up to date. > XML::SAX::Writer is up to date. > XML::Simple is up to date. > XML::Twig is up to date. > XML::Writer is up to date. > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > ==================================================== > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From N.Haigh at sheffield.ac.uk Sat Nov 18 03:22:00 2006 From: N.Haigh at sheffield.ac.uk (Nathan Haigh) Date: Sat, 18 Nov 2006 08:22:00 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Hi Gang, At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - we are in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things wrong with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such that it may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 and CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as dependencies will fail to install. I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - these will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install process much easier to the users. Thanks Nathan Quoting gang wu : > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. > > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. > > So my question is : Is this the right way to install BioPerl? It took me > two days to figure it out but still not 100% sure all packages are > installed properly. > > Any feedback is appreciated. > > Gang > > ================================================= > cpan> install Bundle::BioPerl > Ace is up to date. > Bio::ASN1::EntrezGene is up to date. > Class::AutoClass is up to date. > Clone is up to date. > Convert::Binary::C is up to date. > Running install for module Data::Stag::writer > > The module Data::Stag::writer isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Data::Stag::writer'. > DBD::mysql is up to date. > GD::SVG is up to date. > GD is up to date. > Graph::Directed is up to date. > HTML::Parser is up to date. > Running install for module HTTP::Request::Common- > > The module HTTP::Request::Common- isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i HTTP::Request::Common-'. > LWP::UserAgent is up to date. > Set::Scalar is up to date. > SOAP::Lite is up to date. > Running install for module Spreadhseet::ParseExcel > > The module Spreadhseet::ParseExcel isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Spreadhseet::ParseExcel'. > Storable is up to date. > SVG is up to date. > SVG::Graph is up to date. > Text::Shellwords is up to date. > XML::DOM::XPath is up to date. > XML::Parser::PerlSAX is up to date. > XML::SAX is up to date. > XML::SAX::Base is up to date. > XML::SAX::Writer is up to date. > XML::Simple is up to date. > XML::Twig is up to date. > XML::Writer is up to date. > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > ==================================================== > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From gwu at molbio.mgh.harvard.edu Sat Nov 18 03:30:30 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:30:30 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EBE7E.4060105@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> Message-ID: <455EC4A6.4040103@molbio.mgh.harvard.edu> Sendu Bala wrote: > gang wu wrote: >> Hi everyone, >> >> I saw some problems when installing BioPerl >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could >> not solve all the dependency issues with one shot of 'install >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >> installed. > > What problems did you run into specifically with GD? If I enable JPEG, GIFS and XPM, none of the test could pass. Since I usually use only PNG for output, I can live without them. I am not sure if it's system related problem. All of them work fine with my 32 bit Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with newer libgd runnig Redhat AS4 AMD/EM64T does not work. > >> And it turned out that CPAN refused to install BioPerl with >> some test return value 255. Then I went to /root/.cpan/build to >> configure, test, rebuild those problematic packages. After several more >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >> successfully. > > Do you remember what the other problematic packages were, and what you > had to do to get them working? > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I guess it should be XML::DOM::XPath.pm. I could not recall what other packages had issues, but basically it's special package configuration issue. >> Below attached is the output of CPAN, which stills complains three >> packages have issues: Data::Stag::writer HTTP::Request::Common- >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in >> the Bundle::BioPerl. And the third module is not on the server and could >> be found on the CPAN site. > > All three are typos. We'll get those fixed. > > >> So my question is : Is this the right way to install BioPerl? > > At the present moment, yes. For 1.5.2 I'll probably be recommending > not using Bundle::BioPerl once I fix some other things. > See my another message for other issues. > >> It took me two days to figure it out but still not 100% sure all >> packages are >> installed properly. > > I'm sorry for the troubles you ran into. We'll try and do better for > the final release of 1.5.2. Actually your hard work is benifiting the whole community and we all owe you a Thank You. From gwu at molbio.mgh.harvard.edu Sat Nov 18 03:44:45 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:44:45 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Message-ID: <455EC7FD.5010707@molbio.mgh.harvard.edu> Hi Nathan, Thanks for your message. I saw the C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you use 'install Bundle::BioPerl', which will definitely frustrate a bunch of users. Can this release be held for a while before most of the bugs are cleared? Thanks again. Gang Gang Nathan Haigh wrote: > Hi Gang, > > At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - we are > in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things wrong > with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). > > I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such that it > may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 and > CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as > dependencies will fail to install. > > I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - these > will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. > > If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install process > much easier to the users. > > Thanks > Nathan > > > Quoting gang wu : > > >> Hi everyone, >> >> I saw some problems when installing BioPerl >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could >> not solve all the dependency issues with one shot of 'install >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >> installed. And it turned out that CPAN refused to install BioPerl with >> some test return value 255. Then I went to /root/.cpan/build to >> configure, test, rebuild those problematic packages. After several more >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >> successfully. >> >> Below attached is the output of CPAN, which stills complains three >> packages have issues: Data::Stag::writer HTTP::Request::Common- >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in >> the Bundle::BioPerl. And the third module is not on the server and could >> be found on the CPAN site. >> >> So my question is : Is this the right way to install BioPerl? It took me >> two days to figure it out but still not 100% sure all packages are >> installed properly. >> >> Any feedback is appreciated. >> >> Gang >> >> ================================================= >> cpan> install Bundle::BioPerl >> Ace is up to date. >> Bio::ASN1::EntrezGene is up to date. >> Class::AutoClass is up to date. >> Clone is up to date. >> Convert::Binary::C is up to date. >> Running install for module Data::Stag::writer >> >> The module Data::Stag::writer isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i Data::Stag::writer'. >> DBD::mysql is up to date. >> GD::SVG is up to date. >> GD is up to date. >> Graph::Directed is up to date. >> HTML::Parser is up to date. >> Running install for module HTTP::Request::Common- >> >> The module HTTP::Request::Common- isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i HTTP::Request::Common-'. >> LWP::UserAgent is up to date. >> Set::Scalar is up to date. >> SOAP::Lite is up to date. >> Running install for module Spreadhseet::ParseExcel >> >> The module Spreadhseet::ParseExcel isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i Spreadhseet::ParseExcel'. >> Storable is up to date. >> SVG is up to date. >> SVG::Graph is up to date. >> Text::Shellwords is up to date. >> XML::DOM::XPath is up to date. >> XML::Parser::PerlSAX is up to date. >> XML::SAX is up to date. >> XML::SAX::Base is up to date. >> XML::SAX::Writer is up to date. >> XML::Simple is up to date. >> XML::Twig is up to date. >> XML::Writer is up to date. >> Bundle summary: The following items in bundle Bundle::BioPerl had >> installation problems: >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >> ==================================================== >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 gwu at molbio.mgh.harvard.edu Sat Nov 18 03:57:49 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:57:49 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <455EC4A6.4040103@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> Message-ID: <455ECB0D.5090606@molbio.mgh.harvard.edu> Hi everyone, I used to use MySQL to host the BioSQL schema and load Genbank into it with the 'load_seqdatabase.pl' without problem(except extremely slow. It took about 12 hours to load Arabidopsis thaliana). I just loaded the BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database without problem. When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with MySQL while always saw an error with Oracle: Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. , where the code is $sth->bind_param(); Any idea what the problem is? Gang From N.Haigh at sheffield.ac.uk Sat Nov 18 04:56:57 2006 From: N.Haigh at sheffield.ac.uk (Nathan Haigh) Date: Sat, 18 Nov 2006 09:56:57 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EC7FD.5010707@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> Message-ID: <1163843817.455ed8e970075@webmail.shef.ac.uk> Hi Chris, Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it contains some errors. I think Sendu *may* have some further instructions regarding this package a bit closer to the 1.5.2 release. Cheers Nathan Quoting gang wu : > Hi Nathan, > > Thanks for your message. I saw the > C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you > use 'install Bundle::BioPerl', which will definitely frustrate a bunch > of users. Can this release be held for a while before most of the bugs > are cleared? > > Thanks again. > Gang > > > Gang > > Nathan Haigh wrote: > > Hi Gang, > > > > At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - > we are > > in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things > wrong > > with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). > > > > I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such > that it > > may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 > and > > CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as > > dependencies will fail to install. > > > > I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - > these > > will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. > > > > If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install > process > > much easier to the users. > > > > Thanks > > Nathan > > > > > > Quoting gang wu : > > > > > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > >> > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in > >> the Bundle::BioPerl. And the third module is not on the server and could > >> be found on the CPAN site. > >> > >> So my question is : Is this the right way to install BioPerl? It took me > >> two days to figure it out but still not 100% sure all packages are > >> installed properly. > >> > >> Any feedback is appreciated. > >> > >> Gang > >> > >> ================================================= > >> cpan> install Bundle::BioPerl > >> Ace is up to date. > >> Bio::ASN1::EntrezGene is up to date. > >> Class::AutoClass is up to date. > >> Clone is up to date. > >> Convert::Binary::C is up to date. > >> Running install for module Data::Stag::writer > >> > >> The module Data::Stag::writer isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i Data::Stag::writer'. > >> DBD::mysql is up to date. > >> GD::SVG is up to date. > >> GD is up to date. > >> Graph::Directed is up to date. > >> HTML::Parser is up to date. > >> Running install for module HTTP::Request::Common- > >> > >> The module HTTP::Request::Common- isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i HTTP::Request::Common-'. > >> LWP::UserAgent is up to date. > >> Set::Scalar is up to date. > >> SOAP::Lite is up to date. > >> Running install for module Spreadhseet::ParseExcel > >> > >> The module Spreadhseet::ParseExcel isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i Spreadhseet::ParseExcel'. > >> Storable is up to date. > >> SVG is up to date. > >> SVG::Graph is up to date. > >> Text::Shellwords is up to date. > >> XML::DOM::XPath is up to date. > >> XML::Parser::PerlSAX is up to date. > >> XML::SAX is up to date. > >> XML::SAX::Base is up to date. > >> XML::SAX::Writer is up to date. > >> XML::Simple is up to date. > >> XML::Twig is up to date. > >> XML::Writer is up to date. > >> Bundle summary: The following items in bundle Bundle::BioPerl had > >> installation problems: > >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > >> ==================================================== > >> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/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 uiuc.edu Sat Nov 18 09:35:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 18 Nov 2006 08:35:38 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163843817.455ed8e970075@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> Message-ID: It probably doesn't need to be pulled, just updated to fix errors, spelling, etc. The problems reported with GD are common and normally are due to libgd issues or C code compilation problems during the test run (the DEPENDENCIES doc and wiki page indicate this). DBI/ DBD::mysql is another one that sometimes requires finessing (I remember it giving problems on CygWin and Mac OS X). Chris D. probably just needs a list of issues that need fixing. You also have to realize we're heading into Thanksgiving so some people may be incommunicado for the time being. Spelling is the main problem. Beyond that there really isn't anything we can do about those requirements beside not requiring them (i.e. removing them then explaining that particular components won't work), but then it wouldn't be a proper Bundle package. It's a catch-22. If there isn't a place in the install docs yet some of these issues could use a bit more detail or explanation, or at least redirect to some proper installation instructions based on the platform. I think, now that this is on CPAN, you'll likely see many more questions popping up. Chris (F.) On Nov 18, 2006, at 3:56 AM, Nathan Haigh wrote: > Hi Chris, > > Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it > contains some errors. I think Sendu *may* have some further > instructions regarding > this package a bit closer to the 1.5.2 release. > > Cheers > Nathan > > > > Quoting gang wu : > >> Hi Nathan, >> >> Thanks for your message. I saw the >> C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you >> use 'install Bundle::BioPerl', which will definitely frustrate a >> bunch >> of users. Can this release be held for a while before most of the >> bugs >> are cleared? >> >> Thanks again. >> Gang >> >> >> Gang >> >> Nathan Haigh wrote: >>> Hi Gang, >>> >>> At the moment we are having a few teathing problems with CPAN >>> packages. I notice that you are trying to install the 1.5.2 >>> release candidate 3 - >> we are >>> in the final stages of getting out the official 1.5.2 developer >>> release (hopefully in the next couple of weeks). There are indeed >>> a few things >> wrong >>> with the latest Bundle::BioPerl package but we thought we'd hold >>> off updating it until the 1.5.2 release (or shortly before). >>> >>> I think that the problem with CPAN installing dependencies is >>> that it has no way to correctly ordering the installation of >>> dependencies, such >> that it >>> may be neccessary to run the install several time in order to get >>> everything installed. For example, if prerequisite 2 depends on >>> prerequisite 1 >> and >>> CPAN installs prerequisite 2 first, then it's test suite will >>> probably fail and thus the installation of the package siting >>> both these as >>> dependencies will fail to install. >>> >>> I believe you are correct in the way you are installing bioperl, >>> but we still have a few issues to sort out with regards to the >>> CPAN packages - >> these >>> will definately be sorted out by the time of the 1.5.2 release in >>> a matter of weeks. >>> >>> If anyone is aware of a way to force CPAN to install modules in a >>> specific order, please let Sendu know - we may be able to make >>> the install >> process >>> much easier to the users. >>> >>> Thanks >>> Nathan >>> >>> >>> Quoting gang wu : >>> >>> >>>> Hi everyone, >>>> >>>> I saw some problems when installing BioPerl >>>> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>>> CPAN could >>>> not solve all the dependency issues with one shot of 'install >>>> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>>> installed. And it turned out that CPAN refused to install >>>> BioPerl with >>>> some test return value 255. Then I went to /root/.cpan/build to >>>> configure, test, rebuild those problematic packages. After >>>> several more >>>> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>>> successfully. >>>> >>>> Below attached is the output of CPAN, which stills complains three >>>> packages have issues: Data::Stag::writer HTTP::Request::Common- >>>> Spreadhseet::ParseExcel. I think the first two are typos >>>> somewhere in >>>> the Bundle::BioPerl. And the third module is not on the server >>>> and could >>>> be found on the CPAN site. >>>> >>>> So my question is : Is this the right way to install BioPerl? It >>>> took me >>>> two days to figure it out but still not 100% sure all packages are >>>> installed properly. >>>> >>>> Any feedback is appreciated. >>>> >>>> Gang >>>> >>>> ================================================= >>>> cpan> install Bundle::BioPerl >>>> Ace is up to date. >>>> Bio::ASN1::EntrezGene is up to date. >>>> Class::AutoClass is up to date. >>>> Clone is up to date. >>>> Convert::Binary::C is up to date. >>>> Running install for module Data::Stag::writer >>>> >>>> The module Data::Stag::writer isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i Data::Stag::writer'. >>>> DBD::mysql is up to date. >>>> GD::SVG is up to date. >>>> GD is up to date. >>>> Graph::Directed is up to date. >>>> HTML::Parser is up to date. >>>> Running install for module HTTP::Request::Common- >>>> >>>> The module HTTP::Request::Common- isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i HTTP::Request::Common-'. >>>> LWP::UserAgent is up to date. >>>> Set::Scalar is up to date. >>>> SOAP::Lite is up to date. >>>> Running install for module Spreadhseet::ParseExcel >>>> >>>> The module Spreadhseet::ParseExcel isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i Spreadhseet::ParseExcel'. >>>> Storable is up to date. >>>> SVG is up to date. >>>> SVG::Graph is up to date. >>>> Text::Shellwords is up to date. >>>> XML::DOM::XPath is up to date. >>>> XML::Parser::PerlSAX is up to date. >>>> XML::SAX is up to date. >>>> XML::SAX::Base is up to date. >>>> XML::SAX::Writer is up to date. >>>> XML::Simple is up to date. >>>> XML::Twig is up to date. >>>> XML::Writer is up to date. >>>> Bundle summary: The following items in bundle Bundle::BioPerl had >>>> installation problems: >>>> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >>>> ==================================================== >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Sat Nov 18 12:13:10 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sat, 18 Nov 2006 12:13:10 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EC4A6.4040103@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> Message-ID: <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> What version of libgd do you have installed? With recent versions of libgd (more recent than two years old) you will not be given the chance to select whether to compile JPEG, GIF and XPM support, since these options are selected automatically by running libgd-config. Lincoln On 11/18/06, gang wu wrote: > > > Sendu Bala wrote: > > gang wu wrote: > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN > could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. > > > > What problems did you run into specifically with GD? > If I enable JPEG, GIFS and XPM, none of the test could pass. Since I > usually use only PNG for output, I can live without them. I am not sure > if it's system related problem. All of them work fine with my 32 bit > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with newer > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > >> And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > > > > Do you remember what the other problematic packages were, and what you > > had to do to get them working? > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > guess it should be XML::DOM::XPath.pm. I could not recall what other > packages had issues, but basically it's special package configuration > issue. > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in > >> the Bundle::BioPerl. And the third module is not on the server and > could > >> be found on the CPAN site. > > > > All three are typos. We'll get those fixed. > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > At the present moment, yes. For 1.5.2 I'll probably be recommending > > not using Bundle::BioPerl once I fix some other things. > > > See my another message for other issues. > > > >> It took me two days to figure it out but still not 100% sure all > >> packages are > >> installed properly. > > > > I'm sorry for the troubles you ran into. We'll try and do better for > > the final release of 1.5.2. > Actually your hard work is benifiting the whole community and we all owe > you a Thank You. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From dag at sonsorol.org Sat Nov 18 12:47:07 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Sat, 18 Nov 2006 12:47:07 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> Message-ID: <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> Hi folks, On November 17th, Victor de Jager filed a bug report with CPAN (thanks Victor!) covering the following issues with the 2.1.6 bundle: > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > > This should be Spreadsheet::ParseExcel of course. > Data::Stag::writer does not exist in CPAN, should be > Data::Stag::Writer > > Hope it helps, meanwhile I got around using the CVS version. > Best regards I immediately fixed the errors and uploaded version 2.1.7 on the same day, by now it has probably propagated through the CPAN mirror system but you can find it directly here: http://search.cpan.org/~craffi/ Please let me know directly (email: dag at sonsorol.org) if there are *other* things that need to be added or updated. Sorry for the problems with 2.1.6 -- the contents of that Bundle were given to me by someone else on Oct 17th :) and I think I was sitting on a plane at the time and did not have time to do a local CPAN test with it. My apologies. Regards, Chris On Nov 18, 2006, at 9:35 AM, Chris Fields wrote: > It probably doesn't need to be pulled, just updated to fix errors, > spelling, etc. The problems reported with GD are common and > normally are due to libgd issues or C code compilation problems > during the test run (the DEPENDENCIES doc and wiki page indicate > this). DBI/DBD::mysql is another one that sometimes requires > finessing (I remember it giving problems on CygWin and Mac OS X). > Chris D. probably just needs a list of issues that need fixing. > You also have to realize we're heading into Thanksgiving so some > people may be incommunicado for the time being. > > Spelling is the main problem. Beyond that there really isn't > anything we can do about those requirements beside not requiring > them (i.e. removing them then explaining that particular components > won't work), but then it wouldn't be a proper Bundle package. It's > a catch-22. If there isn't a place in the install docs yet some of > these issues could use a bit more detail or explanation, or at > least redirect to some proper installation instructions based on > the platform. > > I think, now that this is on CPAN, you'll likely see many more > questions popping up. > > Chris (F.) > > On Nov 18, 2006, at 3:56 AM, Nathan Haigh wrote: > >> Hi Chris, >> >> Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it >> contains some errors. I think Sendu *may* have some further >> instructions regarding >> this package a bit closer to the 1.5.2 release. >> >> Cheers >> Nathan >> >> >> >> Quoting gang wu : >> >>> Hi Nathan, >>> >>> Thanks for your message. I saw the >>> C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if >>> you >>> use 'install Bundle::BioPerl', which will definitely frustrate a >>> bunch >>> of users. Can this release be held for a while before most of the >>> bugs >>> are cleared? >>> >>> Thanks again. >>> Gang >>> >>> >>> Gang >>> >>> Nathan Haigh wrote: >>>> Hi Gang, >>>> >>>> At the moment we are having a few teathing problems with CPAN >>>> packages. I notice that you are trying to install the 1.5.2 >>>> release candidate 3 - >>> we are >>>> in the final stages of getting out the official 1.5.2 developer >>>> release (hopefully in the next couple of weeks). There are >>>> indeed a few things >>> wrong >>>> with the latest Bundle::BioPerl package but we thought we'd hold >>>> off updating it until the 1.5.2 release (or shortly before). >>>> >>>> I think that the problem with CPAN installing dependencies is >>>> that it has no way to correctly ordering the installation of >>>> dependencies, such >>> that it >>>> may be neccessary to run the install several time in order to >>>> get everything installed. For example, if prerequisite 2 depends >>>> on prerequisite 1 >>> and >>>> CPAN installs prerequisite 2 first, then it's test suite will >>>> probably fail and thus the installation of the package siting >>>> both these as >>>> dependencies will fail to install. >>>> >>>> I believe you are correct in the way you are installing bioperl, >>>> but we still have a few issues to sort out with regards to the >>>> CPAN packages - >>> these >>>> will definately be sorted out by the time of the 1.5.2 release >>>> in a matter of weeks. >>>> >>>> If anyone is aware of a way to force CPAN to install modules in >>>> a specific order, please let Sendu know - we may be able to make >>>> the install >>> process >>>> much easier to the users. >>>> >>>> Thanks >>>> Nathan >>>> >>>> >>>> Quoting gang wu : >>>> >>>> >>>>> Hi everyone, >>>>> >>>>> I saw some problems when installing BioPerl >>>>> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>>>> CPAN could >>>>> not solve all the dependency issues with one shot of 'install >>>>> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>>>> installed. And it turned out that CPAN refused to install >>>>> BioPerl with >>>>> some test return value 255. Then I went to /root/.cpan/build to >>>>> configure, test, rebuild those problematic packages. After >>>>> several more >>>>> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>>>> successfully. >>>>> >>>>> Below attached is the output of CPAN, which stills complains three >>>>> packages have issues: Data::Stag::writer HTTP::Request::Common- >>>>> Spreadhseet::ParseExcel. I think the first two are typos >>>>> somewhere in >>>>> the Bundle::BioPerl. And the third module is not on the server >>>>> and could >>>>> be found on the CPAN site. >>>>> >>>>> So my question is : Is this the right way to install BioPerl? >>>>> It took me >>>>> two days to figure it out but still not 100% sure all packages are >>>>> installed properly. >>>>> >>>>> Any feedback is appreciated. >>>>> >>>>> Gang >>>>> >>>>> ================================================= >>>>> cpan> install Bundle::BioPerl >>>>> Ace is up to date. >>>>> Bio::ASN1::EntrezGene is up to date. >>>>> Class::AutoClass is up to date. >>>>> Clone is up to date. >>>>> Convert::Binary::C is up to date. >>>>> Running install for module Data::Stag::writer >>>>> >>>>> The module Data::Stag::writer isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i Data::Stag::writer'. >>>>> DBD::mysql is up to date. >>>>> GD::SVG is up to date. >>>>> GD is up to date. >>>>> Graph::Directed is up to date. >>>>> HTML::Parser is up to date. >>>>> Running install for module HTTP::Request::Common- >>>>> >>>>> The module HTTP::Request::Common- isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i HTTP::Request::Common-'. >>>>> LWP::UserAgent is up to date. >>>>> Set::Scalar is up to date. >>>>> SOAP::Lite is up to date. >>>>> Running install for module Spreadhseet::ParseExcel >>>>> >>>>> The module Spreadhseet::ParseExcel isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i Spreadhseet::ParseExcel'. >>>>> Storable is up to date. >>>>> SVG is up to date. >>>>> SVG::Graph is up to date. >>>>> Text::Shellwords is up to date. >>>>> XML::DOM::XPath is up to date. >>>>> XML::Parser::PerlSAX is up to date. >>>>> XML::SAX is up to date. >>>>> XML::SAX::Base is up to date. >>>>> XML::SAX::Writer is up to date. >>>>> XML::Simple is up to date. >>>>> XML::Twig is up to date. >>>>> XML::Writer is up to date. >>>>> Bundle summary: The following items in bundle Bundle::BioPerl had >>>>> installation problems: >>>>> Data::Stag::writer HTTP::Request::Common- >>>>> Spreadhseet::ParseExcel >>>>> ==================================================== >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/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 > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > From n.haigh at sheffield.ac.uk Sat Nov 18 13:32:17 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Sat, 18 Nov 2006 18:32:17 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> Message-ID: <455F51B1.6000301@sheffield.ac.uk> Chris Dagdigian wrote: > > Hi folks, > > On November 17th, Victor de Jager filed a bug report with CPAN (thanks > Victor!) covering the following issues with the 2.1.6 bundle: > >> Bundle summary: The following items in bundle Bundle::BioPerl had >> installation problems: >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >> >> This should be Spreadsheet::ParseExcel of course. >> Data::Stag::writer does not exist in CPAN, should be Data::Stag::Writer >> >> Hope it helps, meanwhile I got around using the CVS version. >> Best regards > > I immediately fixed the errors and uploaded version 2.1.7 on the same > day, by now it has probably propagated through the CPAN mirror system > but you can find it directly here: > > http://search.cpan.org/~craffi/ > > Please let me know directly (email: dag at sonsorol.org) if there are > *other* things that need to be added or updated. > > Sorry for the problems with 2.1.6 -- the contents of that Bundle were > given to me by someone else on Oct 17th :) and I think I was sitting > on a plane at the time and did not have time to do a local CPAN test > with it. My apologies. > > Regards, > Chris > > That was me - my bad! :-[ Nath From hlapp at gmx.net Sat Nov 18 22:08:00 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 18 Nov 2006 22:08:00 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <455ECB0D.5090606@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> Message-ID: <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> This is very odd. I would mean that preparing the statement failed, i.e., that the generated SQL was not accepted by the server (or the Oracle client library). Which test does this happen with? Could you run the test alone in which it happens with TEST_VERBOSE turned on? E.g., $ make test_03simpleseq TEST_VERBOSE=1 if it's the simpleseq test that's causing the failure. Capture the output in a file and send it to me. -hilmar On Nov 18, 2006, at 3:57 AM, gang wu wrote: > Hi everyone, > > I used to use MySQL to host the BioSQL schema and load Genbank into it > with the 'load_seqdatabase.pl' without problem(except extremely > slow. It > took about 12 hours to load Arabidopsis thaliana). I just loaded the > BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database > without > problem. > > When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with > MySQL while always saw an error with Oracle: > Can't call method "bind_param" on an undefined value at > /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm > line 939. > > , where the code is $sth->bind_param(); > > Any idea what the problem is? > > Gang > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From gwu at molbio.mgh.harvard.edu Sat Nov 18 22:09:08 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 22:09:08 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> Message-ID: <455FCAD4.7050709@molbio.mgh.harvard.edu> Lincoln, Thanks for your message. I have gd-2.0.28-4.4E.1 and gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. Attached is the output. Gang ================================================== [root at elegans GD-2.35]# perl Makefile.PL NOTICE: This module requires libgd 2.0.28 or higher. If you are using Math::Trig 1.01 or lower, it has a bug that causes a "prerequisite not found" warning to be issued. You may safely ignore this warning. Type perl Makefile.PL -h for command-line option summary Where is libgd installed? [/usr/lib] Please choose the features that match how libgd was built: Build JPEG support? [y] Build PNG support? [y] Build FreeType support? [y] Build GIF support? [y] Build support for animated GIFs? [y] Build XPM support? [y] If you experience compile problems, please check the @INC, @LIBPATH and @LIBS arrays defined in Makefile.PL and manually adjust, if necessary. Checking if your kit is complete... Looks good Writing Makefile for GD [root at elegans GD-2.35]# make cp GD/Polyline.pm blib/lib/GD/Polyline.pm cp qd.pl blib/lib/qd.pl cp GD/Image.pm blib/lib/GD/Image.pm cp GD.pm blib/lib/GD.pm AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) cp GD/Simple.pm blib/lib/GD/Simple.pm cp GD/Polygon.pm blib/lib/GD/Polygon.pm /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc && mv GD.xsc GD.c gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c GD.xs: In function `XS_GD__Image_STORABLE_thaw': GD.xs:923: warning: cast from pointer to integer of different size GD.xs: In function `XS_GD__Image_gifanimbegin': GD.xs:990: warning: cast to pointer from integer of different size GD.xs: In function `XS_GD__Image_gifanimadd': GD.xs:1015: warning: cast to pointer from integer of different size GD.xs: In function `XS_GD__Image_gifanimend': GD.xs:1034: warning: cast to pointer from integer of different size Running Mkbootstrap for GD () chmod 644 GD.bs rm -f blib/arch/auto/GD/GD.so gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11 /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11 /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when searching for -lXpm /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when searching for -lXpm /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc chmod 755 blib/arch/auto/GD/GD.so cp GD.bs blib/arch/auto/GD/GD.bs chmod 644 blib/arch/auto/GD/GD.bs cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bdf2gdfont.pl Manifying blib/man1/bdf2gdfont.pl.1 Manifying blib/man3/GD::Polyline.3pm Manifying blib/man3/GD::Image.3pm Manifying blib/man3/GD::Simple.3pm Manifying blib/man3/GD.3pm Manifying blib/man3/GD::Polygon.3pm [root at elegans GD-2.35]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. at t/GD.t line 14 Compilation failed in require at t/GD.t line 14. BEGIN failed--compilation aborted at t/GD.t line 14. t/GD..........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-12 Failed 12/12 tests, 0.00% okay t/Polyline....Can't load '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 Compilation failed in require at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. BEGIN failed--compilation aborted at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. Compilation failed in require at t/Polyline.t line 10. BEGIN failed--compilation aborted at t/Polyline.t line 10. t/Polyline....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED test 1 Failed 1/1 tests, 0.00% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/GD.t 255 65280 12 23 191.67% 1-12 t/Polyline.t 255 65280 1 2 200.00% 1 Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. make: *** [test_dynamic] Error 255 [root at elegans GD-2.35]# =========================================================== Lincoln Stein wrote: > What version of libgd do you have installed? With recent versions of > libgd (more recent than two years old) you will not be given the > chance to select whether to compile JPEG, GIF and XPM support, since > these options are selected automatically by running libgd-config. > > Lincoln > > On 11/18/06, *gang wu* > wrote: > > > Sendu Bala wrote: > > gang wu wrote: > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously > CPAN could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. > > > > What problems did you run into specifically with GD? > If I enable JPEG, GIFS and XPM, none of the test could pass. Since I > usually use only PNG for output, I can live without them. I am not > sure > if it's system related problem. All of them work fine with my 32 bit > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with > newer > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > >> And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After > several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > > > > Do you remember what the other problematic packages were, and > what you > > had to do to get them working? > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > guess it should be XML::DOM::XPath.pm. I could not recall what other > packages had issues, but basically it's special package > configuration issue. > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos > somewhere in > >> the Bundle::BioPerl. And the third module is not on the server > and could > >> be found on the CPAN site. > > > > All three are typos. We'll get those fixed. > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > At the present moment, yes. For 1.5.2 I'll probably be recommending > > not using Bundle::BioPerl once I fix some other things. > > > See my another message for other issues. > > > >> It took me two days to figure it out but still not 100% sure all > >> packages are > >> installed properly. > > > > I'm sorry for the troubles you ran into. We'll try and do better for > > the final release of 1.5.2. > Actually your hard work is benifiting the whole community and we > all owe > you a Thank You. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu From bix at sendu.me.uk Sun Nov 19 10:51:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 19 Nov 2006 15:51:55 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EBF53.4010701@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> Message-ID: <45607D9B.4010703@sendu.me.uk> gang wu wrote: > It turned out that most of the modules of BioPerl were not installed at > all. And none of the scripts were installed. I had to download and > install bioperl-1.5.2-RC3.tar.gz > again. A similar > problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually > copied all stuff under Bio folder to the corresponding Perl library > folder. Is it Ok to do it in this way? It will work, but is hardly good enough from our point of view (you shouldn't have to do that). Can you tell me exactly what you mean by 'were not installed'? What did you do to try and install? How did you determine that installation had failed? With CPAN, if you were still getting errors during testing, what were those remaining errors, and did you do a forced install to ignore the errors? If a forced install didn't actually install anything, what message did CPAN give you about that, if any? With the manual download, after doing "perl Makefile.PL", what is your output of "make install"? Thank you, Sendu. From lincoln.stein at gmail.com Sun Nov 19 10:54:11 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sun, 19 Nov 2006 10:54:11 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455FCAD4.7050709@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> <455FCAD4.7050709@molbio.mgh.harvard.edu> Message-ID: <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> That's very odd. gd.0.28 should install gdlib-config, and the existence of this executable should inhibit the interactive questions. Could you see if there's a gdlib-config executable installed on your system? Lincoln On 11/18/06, gang wu wrote: > > Lincoln, > Thanks for your message. I have gd-2.0.28-4.4E.1 and > gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. > Attached is the output. > > Gang > > ================================================== > [root at elegans GD-2.35]# perl Makefile.PL > NOTICE: This module requires libgd 2.0.28 or higher. > > If you are using Math::Trig 1.01 or lower, it has a bug that > causes a "prerequisite not found" warning to be issued. You may > safely ignore this warning. > > Type perl Makefile.PL -h for command-line option summary > > > Where is libgd installed? [/usr/lib] > > Please choose the features that match how libgd was built: > Build JPEG support? [y] > Build PNG support? [y] > Build FreeType support? [y] > Build GIF support? [y] > Build support for animated GIFs? [y] > Build XPM support? [y] > > If you experience compile problems, please check the @INC, @LIBPATH and > @LIBS > arrays defined in Makefile.PL and manually adjust, if necessary. > > Checking if your kit is complete... > Looks good > Writing Makefile for GD > [root at elegans GD-2.35]# make > cp GD/Polyline.pm blib/lib/GD/Polyline.pm > cp qd.pl blib/lib/qd.pl > cp GD/Image.pm blib/lib/GD/Image.pm > cp GD.pm blib/lib/GD.pm > AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) > cp GD/Simple.pm blib/lib/GD/Simple.pm > cp GD/Polygon.pm blib/lib/GD/Polygon.pm > /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap > /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc > && mv GD.xsc GD.c > gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE > -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g > -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC > "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG > -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c > GD.xs: In function `XS_GD__Image_STORABLE_thaw': > GD.xs:923: warning: cast from pointer to integer of different size > GD.xs: In function `XS_GD__Image_gifanimbegin': > GD.xs:990: warning: cast to pointer from integer of different size > GD.xs: In function `XS_GD__Image_gifanimadd': > GD.xs:1015: warning: cast to pointer from integer of different size > GD.xs: In function `XS_GD__Image_gifanimend': > GD.xs:1034: warning: cast to pointer from integer of different size > Running Mkbootstrap for GD () > chmod 644 GD.bs > rm -f blib/arch/auto/GD/GD.so > gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 > -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 > -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm > /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz > /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz > /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm > /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when > searching for -lX11 > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when > searching for -lX11 > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when > searching for -lXpm > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when > searching for -lXpm > /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc > /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc > chmod 755 blib/arch/auto/GD/GD.so > cp GD.bs blib/arch/auto/GD/GD.bs > chmod 644 blib/arch/auto/GD/GD.bs > cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" > blib/script/bdf2gdfont.pl > Manifying blib/man1/bdf2gdfont.pl.1 > Manifying blib/man3/GD::Polyline.3pm > Manifying blib/man3/GD::Image.3pm > Manifying blib/man3/GD::Simple.3pm > Manifying blib/man3/GD.3pm > Manifying blib/man3/GD::Polygon.3pm > [root at elegans GD-2.35]# make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: > ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at > /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. > at t/GD.t line 14 > Compilation failed in require at t/GD.t line 14. > BEGIN failed--compilation aborted at t/GD.t line 14. > t/GD..........dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-12 > Failed 12/12 tests, 0.00% okay > t/Polyline....Can't load > '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: > /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: > gdImageGifAnimAddPtr at > /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. > at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 > Compilation failed in require at > /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. > BEGIN failed--compilation aborted at > /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. > Compilation failed in require at t/Polyline.t line 10. > BEGIN failed--compilation aborted at t/Polyline.t line 10. > t/Polyline....dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED test 1 > Failed 1/1 tests, 0.00% okay > Failed Test Stat Wstat Total Fail Failed List of Failed > > ------------------------------------------------------------------------------- > t/GD.t 255 65280 12 23 191.67% 1-12 > t/Polyline.t 255 65280 1 2 200.00% 1 > Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. > make: *** [test_dynamic] Error 255 > [root at elegans GD-2.35]# > =========================================================== > > Lincoln Stein wrote: > > What version of libgd do you have installed? With recent versions of > > libgd (more recent than two years old) you will not be given the > > chance to select whether to compile JPEG, GIF and XPM support, since > > these options are selected automatically by running libgd-config. > > > > Lincoln > > > > On 11/18/06, *gang wu* > > wrote: > > > > > > Sendu Bala wrote: > > > gang wu wrote: > > >> Hi everyone, > > >> > > >> I saw some problems when installing BioPerl > > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously > > CPAN could > > >> not solve all the dependency issues with one shot of 'install > > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > > >> installed. > > > > > > What problems did you run into specifically with GD? > > If I enable JPEG, GIFS and XPM, none of the test could pass. Since > I > > usually use only PNG for output, I can live without them. I am not > > sure > > if it's system related problem. All of them work fine with my 32 bit > > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with > > newer > > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > > > >> And it turned out that CPAN refused to install BioPerl with > > >> some test return value 255. Then I went to /root/.cpan/build to > > >> configure, test, rebuild those problematic packages. After > > several more > > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > > >> successfully. > > > > > > Do you remember what the other problematic packages were, and > > what you > > > had to do to get them working? > > > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > > guess it should be XML::DOM::XPath.pm. I could not recall what other > > packages had issues, but basically it's special package > > configuration issue. > > >> Below attached is the output of CPAN, which stills complains > three > > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > > >> Spreadhseet::ParseExcel. I think the first two are typos > > somewhere in > > >> the Bundle::BioPerl. And the third module is not on the server > > and could > > >> be found on the CPAN site. > > > > > > All three are typos. We'll get those fixed. > > > > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > > > At the present moment, yes. For 1.5.2 I'll probably be > recommending > > > not using Bundle::BioPerl once I fix some other things. > > > > > See my another message for other issues. > > > > > >> It took me two days to figure it out but still not 100% sure all > > >> packages are > > >> installed properly. > > > > > > I'm sorry for the troubles you ran into. We'll try and do better > for > > > the final release of 1.5.2. > > Actually your hard work is benifiting the whole community and we > > all owe > > you a Thank You. > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From lincoln.stein at gmail.com Sun Nov 19 12:22:25 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sun, 19 Nov 2006 12:22:25 -0500 Subject: [Bioperl-l] [Gmod-gbrowse] aggregators issue? In-Reply-To: <455CE3CE.4060305@mail.med.upenn.edu> References: <455CE3CE.4060305@mail.med.upenn.edu> Message-ID: <6dce9a0b0611190922h7eb79928y46104c17266eccce@mail.gmail.com> Hi, What you want to do is what the heterogeneous_segments glyph does. The redgreen_box glyph originally only operated on the top level feature and not with aggregated features. However, since what you want to do is reasonable I've added a new color_subparts option, so that you will get the right effect with this modified stanza: [Linkage2] feature = qtl color_subparts = 1 glyph = redgreen_box key = Linkage2 You'll need to update bioperl to get this fix. The xyplot issue that you reported was a real bug in bioperl. This has now been fixed in both the release candidate and HEAD CVS repositories. Lincoln On 11/16/06, mmorley wrote: > > Hello All, > > Not sure where the problem lies but I'm trying to display results from a > Linkage analysis (many really).. > Perhaps my logic on the data structure is wrong but I have a peak > (locus,QTL,etc) that exceeds some defined significance that I have > predefined. > Within each peak there are markers (SNPs in this case) each with a level > of significance(score). Instead of displaying each SNP value as say in > XY plot... I have a score for the SNP to SNP interval.. The idea being > is I'd like to display the data using the redgreen_box glyph. > > To make it easier I created a little small test set which can be placed > on the Volvox tutorial ctgA > > Here is the gff data: > ---------------------------------------- > ctgA test peak 0 40000 . . . peak 3 ; Note > "EIF4G2" > ctgA test signal 0 1 0.4 . . peak 3 ; > ctgA test signal 2 25000 0.7 . . peak 3 ; > ctgA test signal 25000 35000 0.6 . . peak 3 ; > ctgA test signal 35000 40000 0.5 . . peak 3 ; > ctgA test peak 0 40000 . . . peak 10 ; Note "LRAP" > ctgA test signal 0 1 0.3 . . peak 10 ; > ctgA test signal 2 25000 0.4 . . peak 10 ; > ctgA test signal 25000 35000 0.7 . . peak 10 ; > ctgA test signal 35000 40000 0.5 . . peak 10 ; > --------------------------------------------------- > > here is my aggregator: > -------------------------------------- > qtl{signal/peak} > ----------------------------------------- > and my track: > --------------------------------------------- > [Linkage2] > feature = qtl > glyph = redgreen_box > key = Linkage2 > ------------------------------------------- > > right now very basic... the problem is well nothing is displayed using > that track... I do however get the label for each printed.. but no > graphic. If I change the feature to "signal" I do get data plotted but > each signal is on a different line,which is expected but not what I want. > > Also as a side note if I decide to plot the data as an xy_plot using the > following track stanza: > [Linkage] > feature = qtl > glyph = xyplot > graph_type = line > height = 50 > min_score = 0 > max_score = 1 > scale = right > key = Linkage > > I get both peaks plotted but within the same plot... However a second > plot is created it is just empty. > > Hopefully I'm convening this well... and if not hopefully fairly easy to > test... > > > -Mike > > > -- > Michael Morley > Bioinformatics Specialist > University of Pennsylvania > Department of Pediatrics > 3516 Civic Center Blvd., > 510B Abramson Pediatric Research Center, > Philadelphia, PA 19104-4318. > Phone: (215) 590-7673 > FAX: (215) 590-3709 > > > > > > > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From pmiguel at purdue.edu Sun Nov 19 19:58:42 2006 From: pmiguel at purdue.edu (Phillip SanMiguel) Date: Sun, 19 Nov 2006 19:58:42 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <45607D9B.4010703@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> Message-ID: <4560FDC2.4000309@purdue.edu> Sendu Bala wrote: > gang wu wrote: > >> It turned out that most of the modules of BioPerl were not installed at >> all. And none of the scripts were installed. I had to download and >> install bioperl-1.5.2-RC3.tar.gz >> again. A similar >> problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually >> copied all stuff under Bio folder to the corresponding Perl library >> folder. Is it Ok to do it in this way? >> > > It will work, but is hardly good enough from our point of view (you > shouldn't have to do that). > > Can you tell me exactly what you mean by 'were not installed'? What did > you do to try and install? How did you determine that installation had > failed? > > [...] My guess is that he thought that bioperl bundle installed the dependencies *and* bioperl itself. That was my presumption the first time I saw it on CPAN. -- Phillip From bikash_lohia2000 at yahoo.com Mon Nov 20 07:45:38 2006 From: bikash_lohia2000 at yahoo.com (bikash lohia) Date: Mon, 20 Nov 2006 04:45:38 -0800 (PST) Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi Message-ID: <20061120124538.40740.qmail@web54205.mail.yahoo.com> hello group, I am new to this group and want a help.i have list of accesion id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to manually search gene database of NCBI for converting this accession no. of cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i want to do it through perl programming where the program directly takes the list of id ( such as AK105331,Ak070197) from notepad file and searches in gene database of ncbi. to give results in accession id starting with OS****** .i want only the accession id of corresponding Ak***** id. for example - AK070197 of nucleotide databse = Os02g0669100 of gene database. i want to convert all this AK***** ids to OS***** ids through programming in perl/bioperl as manually not possible for long list. please help. i have no idea how can the code be. with thanks in advance from Bikash --------------------------------- Everyone is raving about the all-new Yahoo! Mail beta. From sdavis2 at mail.nih.gov Mon Nov 20 08:31:48 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 08:31:48 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi In-Reply-To: <20061120124538.40740.qmail@web54205.mail.yahoo.com> References: <20061120124538.40740.qmail@web54205.mail.yahoo.com> Message-ID: <200611200831.49098.sdavis2@mail.nih.gov> On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean From sdavis2 at mail.nih.gov Mon Nov 20 08:31:48 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 08:31:48 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi In-Reply-To: <20061120124538.40740.qmail@web54205.mail.yahoo.com> References: <20061120124538.40740.qmail@web54205.mail.yahoo.com> Message-ID: <200611200831.49098.sdavis2@mail.nih.gov> On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean From avilella at gmail.com Mon Nov 20 09:53:08 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 20 Nov 2006 14:53:08 +0000 Subject: [Bioperl-l] mmap perl Message-ID: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> Hi all, A bit of an off-topic: Has anyone ever investigated with libcache-mmap-perl or libcache-fastmmap-perl? Cheers, Albert. From cuiw at ncbi.nlm.nih.gov Mon Nov 20 10:45:13 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 10:45:13 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812330@NIHCESMLBX8.nih.gov> This script only works for 1 ACC to 1 Gene ID. perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 10:45:13 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 10:45:13 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812330@NIHCESMLBX8.nih.gov> This script only works for 1 ACC to 1 Gene ID. perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 11:03:44 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 11:03:44 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812332@NIHCESMLBX8.nih.gov> Correction: perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id")' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 11:03:44 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 11:03:44 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812332@NIHCESMLBX8.nih.gov> Correction: perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id")' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From gwu at molbio.mgh.harvard.edu Mon Nov 20 10:57:48 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 10:57:48 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> Message-ID: <4561D07C.4060800@molbio.mgh.harvard.edu> Hi Hilmar, Thanks for your message. Below are several tests for Oracle and MySQL. MySQL actually also has two tests with failed items which may be related to data in BioSQL database. Could it be my Oracle installation/configuration has some issues? Thanks. Gang Output of 'make test' for Oracle ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....ok 14/19Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. t/01dbadaptor.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-19 Failed 5/19 tests, 73.68% okay t/02species.......ok 5/65Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. t/02species.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-65 Failed 60/65 tests, 7.69% okay t/03simpleseq.....ok 5/59Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/03simpleseq.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-59 Failed 54/59 tests, 8.47% okay t/04swiss.........ok 5/52Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 78. t/04swiss.........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-52 Failed 47/52 tests, 9.62% okay t/05seqfeature....ok 3/48Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/05seqfeature....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 4-48 Failed 45/48 tests, 6.25% okay t/06comment.......ok 2/11Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/06comment.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-11 Failed 9/11 tests, 18.18% okay t/07dblink........ok 2/18Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/07dblink........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/08genbank.......ok 2/18Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/08genbank.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/09fuzzy2........ok 2/21Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 64. t/09fuzzy2........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-21 Failed 19/21 tests, 9.52% okay t/10ensembl.......ok 2/15Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1420. t/10ensembl.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-15 Failed 13/15 tests, 13.33% okay t/11locuslink.....ok 4/110Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/11locuslink.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-110 Failed 106/110 tests, 3.64% okay t/12ontology......ok 4/738Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 98. t/12ontology......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-738 Failed 734/738 tests, 0.54% okay t/13remove........ok 1/59Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. t/13remove........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-59 Failed 58/59 tests, 1.69% okay t/14query.........ok t/15cluster.......ok 5/160Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/15cluster.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-160 Failed 155/160 tests, 3.12% okay t/16obda..........ok 2/12Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/16obda..........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-12 Failed 10/12 tests, 16.67% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 t/02species.t 255 65280 65 120 184.62% 6-65 t/03simpleseq.t 255 65280 59 108 183.05% 6-59 t/04swiss.t 255 65280 52 94 180.77% 6-52 t/05seqfeature.t 255 65280 48 90 187.50% 4-48 t/06comment.t 255 65280 11 18 163.64% 3-11 t/07dblink.t 255 65280 18 32 177.78% 3-18 t/08genbank.t 255 65280 18 32 177.78% 3-18 t/09fuzzy2.t 255 65280 21 38 180.95% 3-21 t/10ensembl.t 255 65280 15 26 173.33% 3-15 t/11locuslink.t 255 65280 110 212 192.73% 5-110 t/12ontology.t 255 65280 738 1468 198.92% 5-738 t/13remove.t 255 65280 59 116 196.61% 2-59 t/15cluster.t 255 65280 160 310 193.75% 6-160 t/16obda.t 255 65280 12 20 166.67% 3-12 Failed 15/16 test scripts, 6.25% okay. 1347/1423 subtests failed, 5.34% okay. make: *** [test_dynamic] Error 255 ======================================================= Output of 'make test TEST_VERBOSE=1' for Oracle ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....1..19 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-19 Failed 5/19 tests, 73.68% okay t/02species.......1..65 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-65 Failed 60/65 tests, 7.69% okay t/03simpleseq.....1..59 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-59 Failed 54/59 tests, 8.47% okay t/04swiss.........1..52 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 78. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-52 Failed 47/52 tests, 9.62% okay t/05seqfeature....1..48 ok 1 ok 2 ok 3 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 4-48 Failed 45/48 tests, 6.25% okay t/06comment.......1..11 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-11 Failed 9/11 tests, 18.18% okay t/07dblink........1..18 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/08genbank.......1..18 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/09fuzzy2........1..21 todo 17; ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 64. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-21 Failed 19/21 tests, 9.52% okay t/10ensembl.......1..15 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1420. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-15 Failed 13/15 tests, 13.33% okay t/11locuslink.....1..110 ok 1 ok 2 ok 3 ok 4 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-110 Failed 106/110 tests, 3.64% okay t/12ontology......1..738 ok 1 ok 2 ok 3 ok 4 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 98. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-738 Failed 734/738 tests, 0.54% okay t/13remove........1..59 ok 1 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-59 Failed 58/59 tests, 1.69% okay t/14query.........1..18 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok t/15cluster.......1..160 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-160 Failed 155/160 tests, 3.12% okay t/16obda..........1..12 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-12 Failed 10/12 tests, 16.67% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 t/02species.t 255 65280 65 120 184.62% 6-65 t/03simpleseq.t 255 65280 59 108 183.05% 6-59 t/04swiss.t 255 65280 52 94 180.77% 6-52 t/05seqfeature.t 255 65280 48 90 187.50% 4-48 t/06comment.t 255 65280 11 18 163.64% 3-11 t/07dblink.t 255 65280 18 32 177.78% 3-18 t/08genbank.t 255 65280 18 32 177.78% 3-18 t/09fuzzy2.t 255 65280 21 38 180.95% 3-21 t/10ensembl.t 255 65280 15 26 173.33% 3-15 t/11locuslink.t 255 65280 110 212 192.73% 5-110 t/12ontology.t 255 65280 738 1468 198.92% 5-738 t/13remove.t 255 65280 59 116 196.61% 2-59 t/15cluster.t 255 65280 160 310 193.75% 6-160 t/16obda.t 255 65280 12 20 166.67% 3-12 Failed 15/16 test scripts, 6.25% okay. 1347/1423 subtests failed, 5.34% okay. make: *** [test_dynamic] Error 255 ======================================================= Output of 'make test' for MySQL =================================================== [root at elegans bioperl-db-1.5.2-RC3]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....ok t/02species.......FAILED tests 11, 14-40, 49-119 Failed 99/65 tests, -52.31% okay t/03simpleseq.....ok t/04swiss.........ok t/05seqfeature....ok t/06comment.......ok t/07dblink........ok t/08genbank.......ok t/09fuzzy2........ok t/10ensembl.......ok t/11locuslink.....ok t/12ontology......ok t/13remove........ok t/14query.........ok t/15cluster.......ok 155/160 -------------------- WARNING --------------------- MSG: failed to store one or more child objects for an instance of class Bio::Cluster::UniGene (PK=168) --------------------------------------------------- t/15cluster.......ok t/16obda..........ok Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/02species.t 65 136 209.23% 11 14-40 49-119 Failed 1/16 test scripts, 93.75% okay. 28/1423 subtests failed, 98.03% okay. make: *** [test_dynamic] Error 255 ====================================================== Output of 'make test_02species TEST_VERBOSE=1' for MySQL ====================================================== [root at elegans bioperl-db-1.5.2-RC3]# make test_02species TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests @ARGV;' t/02species.t t/02species....1..65 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 not ok 11 # Test 11 got: '29' (t/02species.t at line 45) # Expected: '11' ok 12 ok 13 not ok 14 # Test 14 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 49 fail #3) # Expected: 'Hominidae' not ok 15 # Test 15 got: 'Hominidae' (t/02species.t at line 49 fail #4) # Expected: 'Catarrhini' not ok 16 # Test 16 got: 'Hominoidea' (t/02species.t at line 49 fail #5) # Expected: 'Primates' not ok 17 # Test 17 got: 'Catarrhini' (t/02species.t at line 49 fail #6) # Expected: 'Eutheria' not ok 18 # Test 18 got: 'Simiiformes' (t/02species.t at line 49 fail #7) # Expected: 'Mammalia' not ok 19 # Test 19 got: 'Haplorrhini' (t/02species.t at line 49 fail #8) # Expected: 'Vertebrata' not ok 20 # Test 20 got: 'Primates' (t/02species.t at line 49 fail #9) # Expected: 'Chordata' not ok 21 # Test 21 got: 'Euarchontoglires' (t/02species.t at line 49 fail #10) # Expected: 'Metazoa' not ok 22 # Test 22 got: 'Eutheria' (t/02species.t at line 49 fail #11) # Expected: 'Eukaryota' not ok 23 # Failed test 23 in t/02species.t at line 49 fail #12 not ok 24 # Failed test 24 in t/02species.t at line 49 fail #13 not ok 25 # Failed test 25 in t/02species.t at line 49 fail #14 not ok 26 # Failed test 26 in t/02species.t at line 49 fail #15 not ok 27 # Failed test 27 in t/02species.t at line 49 fail #16 not ok 28 # Failed test 28 in t/02species.t at line 49 fail #17 not ok 29 # Failed test 29 in t/02species.t at line 49 fail #18 not ok 30 # Failed test 30 in t/02species.t at line 49 fail #19 not ok 31 # Failed test 31 in t/02species.t at line 49 fail #20 not ok 32 # Failed test 32 in t/02species.t at line 49 fail #21 not ok 33 # Failed test 33 in t/02species.t at line 49 fail #22 not ok 34 # Failed test 34 in t/02species.t at line 49 fail #23 not ok 35 # Failed test 35 in t/02species.t at line 49 fail #24 not ok 36 # Failed test 36 in t/02species.t at line 49 fail #25 not ok 37 # Failed test 37 in t/02species.t at line 49 fail #26 not ok 38 # Failed test 38 in t/02species.t at line 49 fail #27 not ok 39 # Failed test 39 in t/02species.t at line 49 fail #28 not ok 40 # Failed test 40 in t/02species.t at line 49 fail #29 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 not ok 49 # Test 49 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 63 fail #3) # Expected: 'Hominidae' not ok 50 # Test 50 got: 'Hominidae' (t/02species.t at line 63 fail #4) # Expected: 'Catarrhini' not ok 51 # Test 51 got: 'Hominoidea' (t/02species.t at line 63 fail #5) # Expected: 'Primates' not ok 52 # Test 52 got: 'Catarrhini' (t/02species.t at line 63 fail #6) # Expected: 'Eutheria' not ok 53 # Test 53 got: 'Simiiformes' (t/02species.t at line 63 fail #7) # Expected: 'Mammalia' not ok 54 # Test 54 got: 'Haplorrhini' (t/02species.t at line 63 fail #8) # Expected: 'Vertebrata' not ok 55 # Test 55 got: 'Primates' (t/02species.t at line 63 fail #9) # Expected: 'Chordata' not ok 56 # Test 56 got: 'Euarchontoglires' (t/02species.t at line 63 fail #10) # Expected: 'Metazoa' not ok 57 # Test 57 got: 'Eutheria' (t/02species.t at line 63 fail #11) # Expected: 'Eukaryota' not ok 58 # Failed test 58 in t/02species.t at line 63 fail #12 not ok 59 # Failed test 59 in t/02species.t at line 63 fail #13 not ok 60 # Failed test 60 in t/02species.t at line 63 fail #14 not ok 61 # Failed test 61 in t/02species.t at line 63 fail #15 not ok 62 # Failed test 62 in t/02species.t at line 63 fail #16 not ok 63 # Failed test 63 in t/02species.t at line 63 fail #17 not ok 64 # Failed test 64 in t/02species.t at line 63 fail #18 not ok 65 # Failed test 65 in t/02species.t at line 63 fail #19 not ok 66 # Failed test 66 in t/02species.t at line 63 fail #20 not ok 67 # Failed test 67 in t/02species.t at line 63 fail #21 not ok 68 # Failed test 68 in t/02species.t at line 63 fail #22 not ok 69 # Failed test 69 in t/02species.t at line 63 fail #23 not ok 70 # Failed test 70 in t/02species.t at line 63 fail #24 not ok 71 # Failed test 71 in t/02species.t at line 63 fail #25 not ok 72 # Failed test 72 in t/02species.t at line 63 fail #26 not ok 73 # Failed test 73 in t/02species.t at line 63 fail #27 not ok 74 # Failed test 74 in t/02species.t at line 63 fail #28 not ok 75 # Failed test 75 in t/02species.t at line 63 fail #29 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 not ok 90 # Test 90 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 91 fail #3) # Expected: 'Hominidae' not ok 91 # Test 91 got: 'Hominidae' (t/02species.t at line 91 fail #4) # Expected: 'Catarrhini' not ok 92 # Test 92 got: 'Hominoidea' (t/02species.t at line 91 fail #5) # Expected: 'Primates' not ok 93 # Test 93 got: 'Catarrhini' (t/02species.t at line 91 fail #6) # Expected: 'Eutheria' not ok 94 # Test 94 got: 'Simiiformes' (t/02species.t at line 91 fail #7) # Expected: 'Mammalia' not ok 95 # Test 95 got: 'Haplorrhini' (t/02species.t at line 91 fail #8) # Expected: 'Vertebrata' not ok 96 # Test 96 got: 'Primates' (t/02species.t at line 91 fail #9) # Expected: 'Chordata' not ok 97 # Test 97 got: 'Euarchontoglires' (t/02species.t at line 91 fail #10) # Expected: 'Metazoa' not ok 98 # Test 98 got: 'Eutheria' (t/02species.t at line 91 fail #11) # Expected: 'Eukaryota' not ok 99 # Failed test 99 in t/02species.t at line 91 fail #12 not ok 100 # Failed test 100 in t/02species.t at line 91 fail #13 not ok 101 # Failed test 101 in t/02species.t at line 91 fail #14 not ok 102 # Failed test 102 in t/02species.t at line 91 fail #15 not ok 103 # Failed test 103 in t/02species.t at line 91 fail #16 not ok 104 # Failed test 104 in t/02species.t at line 91 fail #17 not ok 105 # Failed test 105 in t/02species.t at line 91 fail #18 not ok 106 # Failed test 106 in t/02species.t at line 91 fail #19 not ok 107 # Failed test 107 in t/02species.t at line 91 fail #20 not ok 108 # Failed test 108 in t/02species.t at line 91 fail #21 not ok 109 # Failed test 109 in t/02species.t at line 91 fail #22 not ok 110 # Failed test 110 in t/02species.t at line 91 fail #23 not ok 111 # Failed test 111 in t/02species.t at line 91 fail #24 not ok 112 # Failed test 112 in t/02species.t at line 91 fail #25 not ok 113 # Failed test 113 in t/02species.t at line 91 fail #26 not ok 114 # Failed test 114 in t/02species.t at line 91 fail #27 not ok 115 # Failed test 115 in t/02species.t at line 91 fail #28 not ok 116 # Failed test 116 in t/02species.t at line 91 fail #29 ok 117 ok 118 ok 119 FAILED tests 11, 14-40, 49-119 Failed 99/65 tests, -52.31% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/02species.t 65 136 209.23% 11 14-40 49-119 Failed 1/1 test scripts, 0.00% okay. 28/65 subtests failed, 56.92% okay. make: *** [test_02species] Error 255 ======================================================= Output of 'make test_15cluster TEST_VERBOSE=1' for MySQL ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test_15cluster TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests @ARGV;' t/15cluster.t t/15cluster....1..160 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 -------------------- WARNING --------------------- MSG: failed to store one or more child objects for an instance of class Bio::Cluster::UniGene (PK=201) --------------------------------------------------- ok 156 ok 157 ok 158 ok 159 ok 160 ok All tests successful. Files=1, Tests=160, 18 wallclock secs ( 4.39 cusr + 0.37 csys = 4.76 CPU) ======================================================= Hilmar Lapp wrote: > This is very odd. I would mean that preparing the statement failed, > i.e., that the generated SQL was not accepted by the server (or the > Oracle client library). > > Which test does this happen with? > > Could you run the test alone in which it happens with TEST_VERBOSE > turned on? E.g., > > $ make test_03simpleseq TEST_VERBOSE=1 > > if it's the simpleseq test that's causing the failure. Capture the > output in a file and send it to me. > > -hilmar > > On Nov 18, 2006, at 3:57 AM, gang wu wrote: > >> Hi everyone, >> >> I used to use MySQL to host the BioSQL schema and load Genbank into it >> with the 'load_seqdatabase.pl' without problem(except extremely slow. It >> took about 12 hours to load Arabidopsis thaliana). I just loaded the >> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database without >> problem. >> >> When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with >> MySQL while always saw an error with Oracle: >> Can't call method "bind_param" on an undefined value at >> /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm >> >> line 939. >> >> , where the code is $sth->bind_param(); >> >> Any idea what the problem is? >> >> Gang >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > --=========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > > From dmessina at wustl.edu Mon Nov 20 11:31:55 2006 From: dmessina at wustl.edu (David Messina) Date: Mon, 20 Nov 2006 10:31:55 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4560FDC2.4000309@purdue.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> Message-ID: On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: > [...] > My guess is that he thought that bioperl bundle installed the > dependencies *and* bioperl itself. That was my presumption the first > time I saw it on CPAN. Me too, actually. Perhaps there could be a big, bold warning displayed when using CPAN to install Bundle::BioPerl, saying something like "you will still need to install BioPerl separately by doing ..." ? Likewise, I think the INSTALL document that comes with the BioPerl distribution (and on the wiki) implies the difference between BioPerl and Bundle::BioPerl but doesn't say so explicitly. I'd be happy to add this to INSTALL if there are no objections... Dave From sdavis2 at mail.nih.gov Mon Nov 20 12:23:33 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 12:23:33 -0500 Subject: [Bioperl-l] mmap perl In-Reply-To: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> References: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> Message-ID: <200611201223.33703.sdavis2@mail.nih.gov> On Monday 20 November 2006 09:53, Albert Vilella wrote: > Hi all, > > A bit of an off-topic: > > Has anyone ever investigated with libcache-mmap-perl or > libcache-fastmmap-perl? Hi, Albert. You will probably need to be more specific here. Yes, there are perl implementations of MANY caching schemes. Sean From cjfields at uiuc.edu Mon Nov 20 12:36:41 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 11:36:41 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: Message-ID: <000301c70cca$70f8d030$15327e82@pyrimidine> > On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: > > [...] > > My guess is that he thought that bioperl bundle installed the > > dependencies *and* bioperl itself. That was my presumption > the first > > time I saw it on CPAN. > > Me too, actually. > > Perhaps there could be a big, bold warning displayed when > using CPAN to install Bundle::BioPerl, saying something like > "you will still need to install BioPerl separately by doing ..." ? > > Likewise, I think the INSTALL document that comes with the > BioPerl distribution (and on the wiki) implies the difference > between BioPerl and Bundle::BioPerl but doesn't say so explicitly. > > I'd be happy to add this to INSTALL if there are no objections... > > Dave Dave, Go ahead. We need to also make the change on the wiki in the relevant pages. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 20 12:46:02 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 20 Nov 2006 17:46:02 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> Message-ID: <4561E9DA.3020002@sendu.me.uk> David Messina wrote: > On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: >> [...] >> My guess is that he thought that bioperl bundle installed the >> dependencies *and* bioperl itself. That was my presumption the first >> time I saw it on CPAN. > > Me too, actually. > > Perhaps there could be a big, bold warning displayed when using CPAN > to install Bundle::BioPerl, saying something like "you will still > need to install BioPerl separately by doing ..." ? > > Likewise, I think the INSTALL document that comes with the BioPerl > distribution (and on the wiki) implies the difference between BioPerl > and Bundle::BioPerl but doesn't say so explicitly. The description for Bundle::BioPerl (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) says: "NOTE: This Bundle does not install BioPerl" > I'd be happy to add this to INSTALL if there are no objections... I'll be changing the INSTALL docs to say not to use Bundle::BioPerl when installing with CPAN (you don't need it). Bundle::BioPerl is only for convenience when installing manually from archives or CVS. From cjfields at uiuc.edu Mon Nov 20 12:52:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 11:52:12 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4561D07C.4060800@molbio.mgh.harvard.edu> Message-ID: <000701c70ccc$9b9c9360$15327e82@pyrimidine> > Hi Hilmar, > > Thanks for your message. Below are several tests for Oracle > and MySQL. > MySQL actually also has two tests with failed items which may > be related to data in BioSQL database. > > Could it be my Oracle installation/configuration has some issues? > > Thanks. > > Gang ... You stated in a previous post that you had preloaded taxonomy; the various species test fails may be from that. Hilmar pointed out in a previous thread that tests require a BioSQL database without NCBI taxonomy loaded (i.e. just the schema). The INSTALL doc should now state that. As for the rest, could it be the DBharness.biosql.conf file setup, which assumes MySQL by default? If you switch to Oracle you have to indicate the proper DBD driver in the conf file: ... # DBD driver to use - mandatory 'driver' => 'oracle', ... Chris > Hilmar Lapp wrote: > > This is very odd. I would mean that preparing the statement failed, > > i.e., that the generated SQL was not accepted by the server (or the > > Oracle client library). > > > > Which test does this happen with? > > > > Could you run the test alone in which it happens with TEST_VERBOSE > > turned on? E.g., > > > > $ make test_03simpleseq TEST_VERBOSE=1 > > > > if it's the simpleseq test that's causing the failure. Capture the > > output in a file and send it to me. > > > > -hilmar > > > > On Nov 18, 2006, at 3:57 AM, gang wu wrote: > > > >> Hi everyone, > >> > >> I used to use MySQL to host the BioSQL schema and load > Genbank into it > >> with the 'load_seqdatabase.pl' without problem(except > extremely slow. It > >> took about 12 hours to load Arabidopsis thaliana). I just > loaded the > >> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy > database without > >> problem. > >> > >> When I 'make test' with bioperl-db-1.5.2.R3, all tests can > pass with > >> MySQL while always saw an error with Oracle: > >> Can't call method "bind_param" on an undefined value at > >> > /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ BasePersistenceAdaptor.pm > >> > >> line 939. > >> > >> , where the code is $sth->bind_param(); > >> > >> Any idea what the problem is? > >> > >> Gang > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > --=========================================================== > > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > > =========================================================== > > > > > > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From dmessina at wustl.edu Mon Nov 20 13:34:27 2006 From: dmessina at wustl.edu (David Messina) Date: Mon, 20 Nov 2006 12:34:27 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4561E9DA.3020002@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> <4561E9DA.3020002@sendu.me.uk> Message-ID: <911B53D4-1E95-4B52-A604-DA3C776EB71A@wustl.edu> On Nov 20, 2006, at 11:46 AM, Sendu Bala wrote: > The description for Bundle::BioPerl > (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) > > says: > "NOTE: This Bundle does not install BioPerl" Right, but if you are in the CPAN shell, you won't see that: cpan[2]> b Bundle::BioPerl CPAN_USERID CRAFFI (Chris Dagdigian ) CPAN_VERSION 2.001008 CPAN_FILE C/CR/CRAFFI/Bundle-BioPerl-2.1.8.tar.gz UPLOAD_DATE 2006-11-18 MANPAGE Bundle::BioPerl - A bundle to install external CPAN modules used by BioPerl 1.5.2 CONTAINS Ace Bio::ASN1::EntrezGene Class::AutoClass Clone Convert::Binary::C Data::Stag::Writer DBD::mysql GD::SVG GD Graph::Directed HTML::Parser HTTP::Request::Common LWP::UserAgent Set::Scalar SOAP::Lite Spreadsheet::ParseExcel Storable SVG SVG::Graph Text::Shellwords XML::DOM::XPath XML::Parser::PerlSAX XML::SAX XML::SAX::Base XML::SAX::Writer XML::Simple XML::Twig XML::Writer INST_FILE /Users/davemessina/.cpan/Bundle/BioPerl.pm INST_VERSION 2.1.8 Nor if you type: cpan[6]> readme Bundle::BioPerl Not to make too much of this (some will miss it no matter how many warnings there are), but I am suggesting that it could be a little more noticeable, that's all. > I'll be changing the INSTALL docs to say not to use Bundle::BioPerl > when installing with CPAN (you don't need it). Bundle::BioPerl is > only for convenience when installing manually from archives or CVS. Ah, okay, great, Sendu. I didn't know that. ;) I'll leave it to you, then. Dave From gwu at molbio.mgh.harvard.edu Mon Nov 20 13:31:34 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:31:34 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <45607D9B.4010703@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> Message-ID: <4561F486.9050601@molbio.mgh.harvard.edu> Hi Sendu, I think the package was not installed at all. The only thing I saw in the Bio folder is ANS1 which was another package(I mistakenly thought it's the only package installed by Bundle-BioPerl 2.1.16). I did not force install with CPAN. So is it possible that the three typos forbid bioperl be installed? Thanks. Gang Sendu Bala wrote: > gang wu wrote: >> It turned out that most of the modules of BioPerl were not installed >> at all. And none of the scripts were installed. I had to download and >> install bioperl-1.5.2-RC3.tar.gz >> again. A similar >> problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually >> copied all stuff under Bio folder to the corresponding Perl library >> folder. Is it Ok to do it in this way? > > It will work, but is hardly good enough from our point of view (you > shouldn't have to do that). > > Can you tell me exactly what you mean by 'were not installed'? What > did you do to try and install? How did you determine that installation > had failed? > > With CPAN, if you were still getting errors during testing, what were > those remaining errors, and did you do a forced install to ignore the > errors? If a forced install didn't actually install anything, what > message did CPAN give you about that, if any? > > With the manual download, after doing "perl Makefile.PL", what is your > output of "make install"? > > > Thank you, > Sendu. From gwu at molbio.mgh.harvard.edu Mon Nov 20 13:39:55 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:39:55 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> <455FCAD4.7050709@molbio.mgh.harvard.edu> <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> Message-ID: <4561F67B.7070401@molbio.mgh.harvard.edu> No gdlib-config was found on my system. The rpm is the newest version from Redhat AS 4 channel for AMD/EM64T. Do you think I need to update the package myself? Thanks Gang Lincoln Stein wrote: > That's very odd. gd.0.28 should install gdlib-config, and the existence of > this executable should inhibit the interactive questions. Could you see if > there's a gdlib-config executable installed on your system? > > Lincoln > > On 11/18/06, gang wu wrote: > >> Lincoln, >> Thanks for your message. I have gd-2.0.28-4.4E.1 and >> gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. >> Attached is the output. >> >> Gang >> >> ================================================== >> [root at elegans GD-2.35]# perl Makefile.PL >> NOTICE: This module requires libgd 2.0.28 or higher. >> >> If you are using Math::Trig 1.01 or lower, it has a bug that >> causes a "prerequisite not found" warning to be issued. You may >> safely ignore this warning. >> >> Type perl Makefile.PL -h for command-line option summary >> >> >> Where is libgd installed? [/usr/lib] >> >> Please choose the features that match how libgd was built: >> Build JPEG support? [y] >> Build PNG support? [y] >> Build FreeType support? [y] >> Build GIF support? [y] >> Build support for animated GIFs? [y] >> Build XPM support? [y] >> >> If you experience compile problems, please check the @INC, @LIBPATH and >> @LIBS >> arrays defined in Makefile.PL and manually adjust, if necessary. >> >> Checking if your kit is complete... >> Looks good >> Writing Makefile for GD >> [root at elegans GD-2.35]# make >> cp GD/Polyline.pm blib/lib/GD/Polyline.pm >> cp qd.pl blib/lib/qd.pl >> cp GD/Image.pm blib/lib/GD/Image.pm >> cp GD.pm blib/lib/GD.pm >> AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) >> cp GD/Simple.pm blib/lib/GD/Simple.pm >> cp GD/Polygon.pm blib/lib/GD/Polygon.pm >> /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap >> /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc >> && mv GD.xsc GD.c >> gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE >> -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include >> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g >> -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC >> "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG >> -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c >> GD.xs: In function `XS_GD__Image_STORABLE_thaw': >> GD.xs:923: warning: cast from pointer to integer of different size >> GD.xs: In function `XS_GD__Image_gifanimbegin': >> GD.xs:990: warning: cast to pointer from integer of different size >> GD.xs: In function `XS_GD__Image_gifanimadd': >> GD.xs:1015: warning: cast to pointer from integer of different size >> GD.xs: In function `XS_GD__Image_gifanimend': >> GD.xs:1034: warning: cast to pointer from integer of different size >> Running Mkbootstrap for GD () >> chmod 644 GD.bs >> rm -f blib/arch/auto/GD/GD.so >> gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 >> -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 >> -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm >> /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz >> /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz >> /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm >> /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when >> searching for -lX11 >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when >> searching for -lX11 >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when >> searching for -lXpm >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when >> searching for -lXpm >> /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc >> /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc >> chmod 755 blib/arch/auto/GD/GD.so >> cp GD.bs blib/arch/auto/GD/GD.bs >> chmod 644 blib/arch/auto/GD/GD.bs >> cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" >> blib/script/bdf2gdfont.pl >> Manifying blib/man1/bdf2gdfont.pl.1 >> Manifying blib/man3/GD::Polyline.3pm >> Manifying blib/man3/GD::Image.3pm >> Manifying blib/man3/GD::Simple.3pm >> Manifying blib/man3/GD.3pm >> Manifying blib/man3/GD::Polygon.3pm >> [root at elegans GD-2.35]# make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: >> ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at >> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. >> at t/GD.t line 14 >> Compilation failed in require at t/GD.t line 14. >> BEGIN failed--compilation aborted at t/GD.t line 14. >> t/GD..........dubious >> >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-12 >> Failed 12/12 tests, 0.00% okay >> t/Polyline....Can't load >> '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: >> /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: >> gdImageGifAnimAddPtr at >> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. >> at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 >> Compilation failed in require at >> /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. >> BEGIN failed--compilation aborted at >> /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. >> Compilation failed in require at t/Polyline.t line 10. >> BEGIN failed--compilation aborted at t/Polyline.t line 10. >> t/Polyline....dubious >> >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED test 1 >> Failed 1/1 tests, 0.00% okay >> Failed Test Stat Wstat Total Fail Failed List of Failed >> >> ------------------------------------------------------------------------------- >> t/GD.t 255 65280 12 23 191.67% 1-12 >> t/Polyline.t 255 65280 1 2 200.00% 1 >> Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. >> make: *** [test_dynamic] Error 255 >> [root at elegans GD-2.35]# >> =========================================================== >> >> Lincoln Stein wrote: >> >>> What version of libgd do you have installed? With recent versions of >>> libgd (more recent than two years old) you will not be given the >>> chance to select whether to compile JPEG, GIF and XPM support, since >>> these options are selected automatically by running libgd-config. >>> >>> Lincoln >>> >>> On 11/18/06, *gang wu* >> > wrote: >>> >>> >>> Sendu Bala wrote: >>> > gang wu wrote: >>> >> Hi everyone, >>> >> >>> >> I saw some problems when installing BioPerl >>> >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>> CPAN could >>> >> not solve all the dependency issues with one shot of 'install >>> >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>> >> installed. >>> > >>> > What problems did you run into specifically with GD? >>> If I enable JPEG, GIFS and XPM, none of the test could pass. Since >>> >> I >> >>> usually use only PNG for output, I can live without them. I am not >>> sure >>> if it's system related problem. All of them work fine with my 32 bit >>> Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with >>> newer >>> libgd runnig Redhat AS4 AMD/EM64T does not work. >>> > >>> >> And it turned out that CPAN refused to install BioPerl with >>> >> some test return value 255. Then I went to /root/.cpan/build to >>> >> configure, test, rebuild those problematic packages. After >>> several more >>> >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>> >> successfully. >>> > >>> > Do you remember what the other problematic packages were, and >>> what you >>> > had to do to get them working? >>> > >>> XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I >>> guess it should be XML::DOM::XPath.pm. I could not recall what other >>> packages had issues, but basically it's special package >>> configuration issue. >>> >> Below attached is the output of CPAN, which stills complains >>> >> three >> >>> >> packages have issues: Data::Stag::writer HTTP::Request::Common- >>> >> Spreadhseet::ParseExcel. I think the first two are typos >>> somewhere in >>> >> the Bundle::BioPerl. And the third module is not on the server >>> and could >>> >> be found on the CPAN site. >>> > >>> > All three are typos. We'll get those fixed. >>> > >>> > >>> >> So my question is : Is this the right way to install BioPerl? >>> > >>> > At the present moment, yes. For 1.5.2 I'll probably be >>> >> recommending >> >>> > not using Bundle::BioPerl once I fix some other things. >>> > >>> See my another message for other issues. >>> > >>> >> It took me two days to figure it out but still not 100% sure all >>> >> packages are >>> >> installed properly. >>> > >>> > I'm sorry for the troubles you ran into. We'll try and do better >>> >> for >> >>> > the final release of 1.5.2. >>> Actually your hard work is benifiting the whole community and we >>> all owe >>> you a Thank You. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 >>> (516) 367-8380 (voice) >>> (516) 367-8389 (fax) >>> FOR URGENT MESSAGES & SCHEDULING, >>> PLEASE CONTACT MY ASSISTANT, >>> SANDRA MICHELSEN, AT michelse at cshl.edu >>> >> > > > From gwu at molbio.mgh.harvard.edu Mon Nov 20 13:54:46 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:54:46 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4561E9DA.3020002@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> <4561E9DA.3020002@sendu.me.uk> Message-ID: <4561F9F6.5020700@molbio.mgh.harvard.edu> Sendu Bala wrote: > David Messina wrote: > >> On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: >> >>> [...] >>> My guess is that he thought that bioperl bundle installed the >>> dependencies *and* bioperl itself. That was my presumption the first >>> time I saw it on CPAN. >>> >> Me too, actually. >> >> Perhaps there could be a big, bold warning displayed when using CPAN >> to install Bundle::BioPerl, saying something like "you will still >> need to install BioPerl separately by doing ..." ? >> >> Likewise, I think the INSTALL document that comes with the BioPerl >> distribution (and on the wiki) implies the difference between BioPerl >> and Bundle::BioPerl but doesn't say so explicitly. >> > > The description for Bundle::BioPerl > (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) > > says: > "NOTE: This Bundle does not install BioPerl" > > > >> I'd be happy to add this to INSTALL if there are no objections... >> > > I'll be changing the INSTALL docs to say not to use Bundle::BioPerl when > installing with CPAN (you don't need it). Bundle::BioPerl is only for > convenience when installing manually from archives or CVS. > This can save a lot of time and confusion. But why can't BioPerl be installed with Bundle::BioPerl when using CPAN? It sounds convenient. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From gwu at molbio.mgh.harvard.edu Mon Nov 20 14:40:56 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 14:40:56 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000701c70ccc$9b9c9360$15327e82@pyrimidine> References: <000701c70ccc$9b9c9360$15327e82@pyrimidine> Message-ID: <456204C8.8000404@molbio.mgh.harvard.edu> Chris Fields wrote: >> Hi Hilmar, >> >> Thanks for your message. Below are several tests for Oracle >> and MySQL. >> MySQL actually also has two tests with failed items which may >> be related to data in BioSQL database. >> >> Could it be my Oracle installation/configuration has some issues? >> >> Thanks. >> >> Gang >> > > ... > > You stated in a previous post that you had preloaded taxonomy; the various > species test fails may be from that. Hilmar pointed out in a previous > thread that tests require a BioSQL database without NCBI taxonomy loaded > (i.e. just the schema). The INSTALL doc should now state that. > You are right, all tests can pass for MySQL after unloading NCBI Taxonomy data. But output for Oracle tests were not affected. Thanks. > As for the rest, could it be the DBharness.biosql.conf file setup, which > assumes MySQL by default? If you switch to Oracle you have to indicate the > proper DBD driver in the conf file: > > ... > > # DBD driver to use - mandatory > 'driver' => 'oracle', > > ... > > I did change the configuration, or it can not pass the DBI connection tests. Below is part of my parameters: 'driver' => 'Oracle', 'host' => 'elegans', 'user' => 'biosqldb_sgowner', 'port' => '1521', 'password' => 'pass', 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], 'dbname' => 'oracle_sid', 'database' => 'biosql', > Chris > > > >> Hilmar Lapp wrote: >> >>> This is very odd. I would mean that preparing the statement failed, >>> i.e., that the generated SQL was not accepted by the server (or the >>> Oracle client library). >>> >>> Which test does this happen with? >>> >>> Could you run the test alone in which it happens with TEST_VERBOSE >>> turned on? E.g., >>> >>> $ make test_03simpleseq TEST_VERBOSE=1 >>> >>> if it's the simpleseq test that's causing the failure. Capture the >>> output in a file and send it to me. >>> >>> -hilmar >>> >>> On Nov 18, 2006, at 3:57 AM, gang wu wrote: >>> >>> >>>> Hi everyone, >>>> >>>> I used to use MySQL to host the BioSQL schema and load >>>> >> Genbank into it >> >>>> with the 'load_seqdatabase.pl' without problem(except >>>> >> extremely slow. It >> >>>> took about 12 hours to load Arabidopsis thaliana). I just >>>> >> loaded the >> >>>> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy >>>> >> database without >> >>>> problem. >>>> >>>> When I 'make test' with bioperl-db-1.5.2.R3, all tests can >>>> >> pass with >> >>>> MySQL while always saw an error with Oracle: >>>> Can't call method "bind_param" on an undefined value at >>>> >>>> >> /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ >> > BasePersistenceAdaptor.pm > >>>> line 939. >>>> >>>> , where the code is $sth->bind_param(); >>>> >>>> Any idea what the problem is? >>>> >>>> Gang >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> --=========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >>> >>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > From cjfields at uiuc.edu Mon Nov 20 15:19:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 14:19:56 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <456204C8.8000404@molbio.mgh.harvard.edu> Message-ID: <000301c70ce1$3ee70190$15327e82@pyrimidine> ... > You are right, all tests can pass for MySQL after unloading > NCBI Taxonomy data. But output for Oracle tests were not > affected. Thanks. Yes, the oracle tests were by far the worst, which suggests something in the driver/configuration. > > As for the rest, could it be the DBharness.biosql.conf file setup, > > which assumes MySQL by default? If you switch to Oracle > you have to > > indicate the proper DBD driver in the conf file: > > > > ... > > > > # DBD driver to use - mandatory > > 'driver' => 'oracle', > > > > ... > > > > > I did change the configuration, or it can not pass the DBI > connection tests. Below is part of my parameters: > 'driver' => 'Oracle', > 'host' => 'elegans', > 'user' => 'biosqldb_sgowner', > 'port' => '1521', > 'password' => 'pass', > 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], > 'dbname' => 'oracle_sid', > 'database' => 'biosql', Try changing the driver to all lower case (i.e. from 'Oracle' to 'oracle'). Also, the schema_sql is still set to the mysql schema (not oracle). That shouldn't make a difference, but you never know. Hopefully that isn't your real password! Chris From gwu at molbio.mgh.harvard.edu Mon Nov 20 15:34:07 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 15:34:07 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000301c70ce1$3ee70190$15327e82@pyrimidine> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> Message-ID: <4562113F.6040306@molbio.mgh.harvard.edu> Chris Fields wrote: > ... > >> You are right, all tests can pass for MySQL after unloading >> NCBI Taxonomy data. But output for Oracle tests were not >> affected. Thanks. >> > > Yes, the oracle tests were by far the worst, which suggests something in the > driver/configuration. > > >>> As for the rest, could it be the DBharness.biosql.conf file setup, >>> which assumes MySQL by default? If you switch to Oracle >>> >> you have to >> >>> indicate the proper DBD driver in the conf file: >>> >>> ... >>> >>> # DBD driver to use - mandatory >>> 'driver' => 'oracle', >>> >>> ... >>> >>> >>> >> I did change the configuration, or it can not pass the DBI >> connection tests. Below is part of my parameters: >> 'driver' => 'Oracle', >> 'host' => 'elegans', >> 'user' => 'biosqldb_sgowner', >> 'port' => '1521', >> 'password' => 'pass', >> 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], >> 'dbname' => 'oracle_sid', >> 'database' => 'biosql', >> > > Try changing the driver to all lower case (i.e. from 'Oracle' to 'oracle'). > Also, the schema_sql is still set to the mysql schema (not oracle). That > shouldn't make a difference, but you never know. > Can not change 'Oracle' to 'oracle', the DBD driver name is DBD::Oracle. It's an odd naming inconsistence. MySQL DBD driver name is DBD::mysql. How about PostgreSQL DBD driver naming? > Hopefully that isn't your real password! > > Chris > > From ryanx07 at hotmail.com Mon Nov 20 15:42:47 2006 From: ryanx07 at hotmail.com (L Xu) Date: Mon, 20 Nov 2006 15:42:47 -0500 Subject: [Bioperl-l] Error message for installation Message-ID: I got an error message when I installed Bioperl through ActivePerl following the online instruction about window installation: ERROR: Installing File-Spec-0.82 would downgrade File::Spec from version 3.12 to 0.82 and File::Spec::Functions from version 1.3 to 1.1 and File::Spec::Mac from version 1.4 to 1.2 and File::Spec::OS2 from version 1.2 to 1.1 and File::Spec::Unix from version 1.5 to 1.2 and File::Spec::VMS from version 1.4 to 1.1 and File::Spec::Win32 from version 1.6 to 1.2 It looks like the Bioperl 1.4 using some old version files compared to ActivePerl. I wonder if these old version files can cause some problems and how to fix them. Thanks and happy thanksgiving. L _________________________________________________________________ Get FREE company branded e-mail accounts and business Web site from Microsoft Office Live http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ From hlapp at gmx.net Mon Nov 20 16:28:29 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:28:29 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4561F0F4.3060106@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> Message-ID: <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> It looks like you are using the MySQL schema under Oracle. There are different DDL scripts for each supported RDBMS. The ones for Oracle are in the sql/biosql-ora subdirectory. Note the INSTALL document in that directory. -hilmar On Nov 20, 2006, at 1:16 PM, gang wu wrote: > Hi Hilmar, > > Below is the output. Thanks. > > Gang > ========================================================== > [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 > [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor > TEST_VERBOSE=1 > PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ > perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e > 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests > @ARGV;' t/01dbadaptor.t > t/01dbadaptor....1..19 > ok 1 > ok 2 > ok 3 > ok 4 > ok 5 > ok 6 > ok 7 > ok 8 > ok 9 > ok 10 > ok 11 > attempting to load adaptor class for BioNamespace > ok 12 > attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor > instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor > ok 13 > ok 14 > attempting to load driver for adaptor class > Bio::DB::BioSQL::BioNamespaceAdaptor > attempting to load driver for adaptor class > Bio::DB::BioSQL::BasePersistenceAdaptor > Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as > driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor > preparing UK select statement: SELECT biodatabase.oid, > biodatabase.name, biodatabase.authority FROM biodatabase WHERE name > = ? > DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": > invalid identifier (DBD ERROR: error possibly near <*> indicator at > char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = :p1') [for > Statement "SELECT biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ > Bio/DB/BioSQL/BaseDriver.pm line 1800. > BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) > Can't call method "bind_param" on an undefined value at blib/lib/ > Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. > dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-19 > Failed 5/19 tests, 73.68% okay > Failed Test Stat Wstat Total Fail Failed List of Failed > ---------------------------------------------------------------------- > --------- > t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 > Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% > okay. > make: *** [test_01dbadaptor] Error 2 > ========================================================= > > > Hilmar Lapp wrote: >> Hi Gang, >> >> what I wanted to get at was the error message from the driver when >> it fails to generate the prepared statement, but this is not in >> the output. >> >> I believe you need set the HARNESS_VERBOSE environment variable to >> 1 before testing to get what I need: >> >> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >> csh/tcsh >> $ make test_01dbadaptor TEST_VERBOSE=1 >> >> This will lead to _a lot_ of debugging output. Do not run this for >> the entire test suite. >> >> The errors for mysql I believe are related to the fact that have >> loaded the NCBI taxonomy before testing? Run the tests on a fresh >> (completely empty) instance of BioSQL. >> >> Let me know what you get for the Oracle test above. >> >> -hilmar >> >> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >> >>> Hi Hilmar, >>> >>> Thanks for your message. Below are several tests for Oracle and >>> MySQL. MySQL actually also has two tests with failed items which >>> may be related to data in BioSQL database. >>> >>> Could it be my Oracle installation/configuration has some issues? >>> >>> Thanks. >>> >>> Gang >> >> --=========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> >> -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Nov 20 16:33:50 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:33:50 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000301c70ce1$3ee70190$15327e82@pyrimidine> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> Message-ID: <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> On Nov 20, 2006, at 3:19 PM, Chris Fields wrote: > Try changing the driver to all lower case (i.e. from 'Oracle' to > 'oracle'). This can in fact be harmful. The driver-specific code is loaded from files or directories named after the driver. On case-sensitive file systems, changing the case will render those files inaccessible. > Also, the schema_sql is still set to the mysql schema (not > oracle). That > shouldn't make a difference, but you never know. It doesn't make a difference if the schema instance exists already (and I wouldn't recommend anything else). -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Nov 20 16:34:30 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:34:30 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4562113F.6040306@molbio.mgh.harvard.edu> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> <4562113F.6040306@molbio.mgh.harvard.edu> Message-ID: <24789A58-9A86-4B83-9CBB-CE2597B1DA60@gmx.net> On Nov 20, 2006, at 3:34 PM, gang wu wrote: > How about PostgreSQL DBD driver naming? DBD::Pg -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From Kevin.M.Brown at asu.edu Mon Nov 20 16:44:22 2006 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Mon, 20 Nov 2006 14:44:22 -0700 Subject: [Bioperl-l] Budle::BioPerl dependency issues Message-ID: <1A4207F8295607498283FE9E93B775B4024C58D3@EX02.asurite.ad.asu.edu> Redhat tends to have two different packages. GD and GD-devel. The first is for runtime applications to use, the other is needed to be able to build code against GD. They do this for almost all the libraries (e.g. glibc & glibc-devel, x11 and x11-devel, etc...). > No gdlib-config was found on my system. The rpm is the newest version > from Redhat AS 4 channel for AMD/EM64T. Do you think I need to update > the package myself? Thanks From n.haigh at sheffield.ac.uk Mon Nov 20 17:45:24 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 20 Nov 2006 22:45:24 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <45623004.1010807@sheffield.ac.uk> Could you answer the following questions, so that we know your setup and are better able to respond: 1) Can you confirm what version of ActivePerl you are running. 2) Can you confirm what PPM repositories you have enabled. 3) Can you confirm what version of Bioperl you tried to install. This issue has cropped up before, but I can't remember off hand exactly what the problem was, or how it was solved. I think it might be a problem with using the new PPM4 GUI to install bioperl 1.4 from the old style PPD. I'll await your response before making further comments. Thanks Nath L Xu wrote: > I got an error message when I installed Bioperl through ActivePerl following > the online instruction about window installation: > > ERROR: Installing File-Spec-0.82 would downgrade File::Spec from version > 3.12 to 0.82 and File::Spec::Functions from version 1.3 to 1.1 and > File::Spec::Mac from version 1.4 to 1.2 and File::Spec::OS2 from version 1.2 > to 1.1 and File::Spec::Unix from version 1.5 to 1.2 and File::Spec::VMS from > version 1.4 to 1.1 and File::Spec::Win32 from version 1.6 to 1.2 > > It looks like the Bioperl 1.4 using some old version files compared to > ActivePerl. I wonder if these old version files can cause some problems and > how to fix them. > > Thanks and happy thanksgiving. > > > L > > _________________________________________________________________ > Get FREE company branded e-mail accounts and business Web site from > Microsoft Office Live > http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From n.haigh at sheffield.ac.uk Mon Nov 20 17:49:51 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 20 Nov 2006 22:49:51 +0000 Subject: [Bioperl-l] Bioperl 1.4 on Windows Message-ID: <4562310F.8080403@sheffield.ac.uk> There have been at least a coupl eof posts recently about users having problems installing bioperl 1.4 using the PPM GUI shipped with ActivePerl 5.8.8.819. I think this is because the Bioperl 1.4 ppd is built for PPM3 and not PPM4. Would it make sense to update the Bioperl 1.4 PPD since it is the official "stable" release? Nath From cjfields at uiuc.edu Mon Nov 20 18:07:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 17:07:12 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> Message-ID: On Nov 20, 2006, at 3:33 PM, Hilmar Lapp wrote: > > On Nov 20, 2006, at 3:19 PM, Chris Fields wrote: > >> Try changing the driver to all lower case (i.e. from 'Oracle' to >> 'oracle'). > > This can in fact be harmful. The driver-specific code is loaded > from files or directories named after the driver. On case-sensitive > file systems, changing the case will render those files inaccessible. Yeah, just noticed that the driver is DBD::Oracle. I thought it might be lowercase, like DBD::mysql. >> Also, the schema_sql is still set to the mysql schema (not >> oracle). That >> shouldn't make a difference, but you never know. > > It doesn't make a difference if the schema instance exists already > (and I wouldn't recommend anything else). > > -hilmar The conf file indicates that as well. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Mon Nov 20 18:33:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 17:33:48 -0600 Subject: [Bioperl-l] Bioperl 1.4 on Windows In-Reply-To: <4562310F.8080403@sheffield.ac.uk> References: <4562310F.8080403@sheffield.ac.uk> Message-ID: On Nov 20, 2006, at 4:49 PM, Nathan S. Haigh wrote: > There have been at least a coupl eof posts recently about users having > problems installing bioperl 1.4 using the PPM GUI shipped with > ActivePerl 5.8.8.819. I think this is because the Bioperl 1.4 ppd is > built for PPM3 and not PPM4. Would it make sense to update the Bioperl > 1.4 PPD since it is the official "stable" release? > > Nath We could change the PPD to remove any versioning requirements. It's possible that PPM4 treats them as explicit version requirements, so instead of installing rel. X or greater, it only tries to install rel. X, which then has version requirements of it's own that PPM4 misreads. Not sure if this is a common problem with PPM4 but it's definitely bad. The best course of action for Windows users will be to update to 1.5.2 when the final version is released. The vast majority will be using it for parsing BLAST reports and retrieving sequences, both of which have undergone major revisions since 1.4 (in fact, I don't think BLAST report parsing will work if they run a BLAST version before 2.2.13). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jcv128 at psu.edu Mon Nov 20 19:52:47 2006 From: jcv128 at psu.edu (Juan Cristobal Vera) Date: Mon, 20 Nov 2006 19:52:47 -0500 Subject: [Bioperl-l] GO terms not present in Swiss annotation object Message-ID: <1164070364l.1106082l.0l@psu.edu> Hi, I'm writing a simple application to extract various fields from swissprot objects and I can't access the GO terms found in "dblink" part of the swiss format flat files. I'm not a professional programmer and I can't figure out why this is occuring. All the other "dblink" keys are being generated as far as I can tell (e.g. embl, pfam, etc). The GO terms are just skipped over and it's driving me crazy. Not sure if this is a bug or a deliberate strategy I'm unfamiliar with. I apologize if this is not the correct forum to ask for this sort of help and would ask to be directed to the proper one. Juan Cristobal Vera Graduate Student Department of Biology Penn State University 208 Mueller Laboratory University Park, PA 16802 (814)863-2957 From cjfields at uiuc.edu Tue Nov 21 01:19:59 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 00:19:59 -0600 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164070364l.1106082l.0l@psu.edu> References: <1164070364l.1106082l.0l@psu.edu> Message-ID: Juan, The DBLink objects should be generated. You'll need to give us a bit more information to go on, though. We need an example sequence, your local version of Bioperl, maybe a test script, etc. This is the right forum for this, yes, if you are using BioPerl. Chris On Nov 20, 2006, at 6:52 PM, Juan Cristobal Vera wrote: > > > Hi, > I'm writing a simple application to extract various fields from > swissprot objects and I can't access the GO terms found in > "dblink" part of the swiss format flat files. I'm not a > professional programmer and I can't figure out why this is > occuring. All the other "dblink" keys are being > generated as far as I can tell (e.g. embl, pfam, etc). The GO > terms are just skipped over and it's driving me crazy. Not sure if > this is a bug or a deliberate strategy I'm unfamiliar with. I > apologize if this is not the correct forum to ask for this sort of > help and would ask to be directed to the proper one. > > > > Juan Cristobal Vera > > Graduate Student > > Department of Biology > > Penn State University > > 208 Mueller Laboratory > > University Park, PA 16802 > > (814)863-2957 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From gwu at molbio.mgh.harvard.edu Tue Nov 21 03:11:03 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 03:11:03 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> Message-ID: <4562B497.6080805@molbio.mgh.harvard.edu> Can you show me where it indicates I am actually using the MySQL schema. I am pretty sure that I used the sql script files from sql/biosql-ora(Has anyone actually tried to install MySQL schema on Oracle?). I can reinstall the schema if you think that's the way to solve the problem. Thanks very much. Gang Hilmar Lapp wrote: > It looks like you are using the MySQL schema under Oracle. There are > different DDL scripts for each supported RDBMS. The ones for Oracle > are in the sql/biosql-ora subdirectory. Note the INSTALL document in > that directory. > > -hilmar > > > On Nov 20, 2006, at 1:16 PM, gang wu wrote: > > >> Hi Hilmar, >> >> Below is the output. Thanks. >> >> Gang >> ========================================================== >> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >> TEST_VERBOSE=1 >> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >> @ARGV;' t/01dbadaptor.t >> t/01dbadaptor....1..19 >> ok 1 >> ok 2 >> ok 3 >> ok 4 >> ok 5 >> ok 6 >> ok 7 >> ok 8 >> ok 9 >> ok 10 >> ok 11 >> attempting to load adaptor class for BioNamespace >> ok 12 >> attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor >> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >> ok 13 >> ok 14 >> attempting to load driver for adaptor class >> Bio::DB::BioSQL::BioNamespaceAdaptor >> attempting to load driver for adaptor class >> Bio::DB::BioSQL::BasePersistenceAdaptor >> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >> preparing UK select statement: SELECT biodatabase.oid, >> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >> = ? >> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >> invalid identifier (DBD ERROR: error possibly near <*> indicator at >> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >> Statement "SELECT biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >> Bio/DB/BioSQL/BaseDriver.pm line 1800. >> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >> Can't call method "bind_param" on an undefined value at blib/lib/ >> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >> dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 15-19 >> Failed 5/19 tests, 73.68% okay >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ---------------------------------------------------------------------- >> --------- >> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >> okay. >> make: *** [test_01dbadaptor] Error 2 >> ========================================================= >> >> >> Hilmar Lapp wrote: >> >>> Hi Gang, >>> >>> what I wanted to get at was the error message from the driver when >>> it fails to generate the prepared statement, but this is not in >>> the output. >>> >>> I believe you need set the HARNESS_VERBOSE environment variable to >>> 1 before testing to get what I need: >>> >>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>> csh/tcsh >>> $ make test_01dbadaptor TEST_VERBOSE=1 >>> >>> This will lead to _a lot_ of debugging output. Do not run this for >>> the entire test suite. >>> >>> The errors for mysql I believe are related to the fact that have >>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>> (completely empty) instance of BioSQL. >>> >>> Let me know what you get for the Oracle test above. >>> >>> -hilmar >>> >>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>> >>> >>>> Hi Hilmar, >>>> >>>> Thanks for your message. Below are several tests for Oracle and >>>> MySQL. MySQL actually also has two tests with failed items which >>>> may be related to data in BioSQL database. >>>> >>>> Could it be my Oracle installation/configuration has some issues? >>>> >>>> Thanks. >>>> >>>> Gang >>>> >>> --=========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >>> >>> >>> > > From n.haigh at sheffield.ac.uk Tue Nov 21 03:47:40 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 21 Nov 2006 08:47:40 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <4562BD2C.4000906@sheffield.ac.uk> L Xu wrote: > Thank you for the prompt response. Here is the information you needed: > (1)ActivePerl version 5.8.8.819 and PPM version 4.00 > (2)http://ppm4.activestate.com/MsWin32-x86/5.8/819/package.xml > http://bioperl.org/DIST/RC > http://bioperl.org/DIST > http://theoryx5.uwinnipeg.ca/ppms > http://www.Bribes.org/perl/ppm > (3)bioperl-1.4 > > Once again, thank you very much. > > L When you do a search for Bioperl, do you also get listing for Bioperl 1.5.2 RC2. If you do, try to install that and let us know how you get on. If you don't see a 1.5.2 RC2 let me know and I'll try to find out what the problem is. The PPM package is a little behind since there is an RC4 - I'll try to get the RC4 packaged today if I have time. We are hoping that RC4 is the last release candidate before the official 1.5.2 release, so if you do install the RC2 remember to upgrade the package in a week or two. Cheers Nath From er at xs4all.nl Tue Nov 21 07:16:53 2006 From: er at xs4all.nl (Erik) Date: Tue, 21 Nov 2006 13:16:53 +0100 (CET) Subject: [Bioperl-l] double-colon bug Message-ID: <6661.156.83.1.251.1164111413.squirrel@webmail.xs4all.nl> Hi all, Could one of the committers apply the fix as proposed for bug 2146 ? It's a small change: added a ':' to the regex at line 507. I did add a 'show the bug' snippet, albeit somewhat belatedly. It passes all 135 genbank tests with that change. Also, it fixes my application :) Thanks, Erik http://bugzilla.open-bio.org/show_bug.cgi?id=2146 From cjfields at uiuc.edu Tue Nov 21 08:21:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 07:21:35 -0600 Subject: [Bioperl-l] Error message for installation In-Reply-To: <4562BD2C.4000906@sheffield.ac.uk> References: <4562BD2C.4000906@sheffield.ac.uk> Message-ID: <67BD6F52-A994-4FC7-8E4F-375F21D1E1F9@uiuc.edu> All of the RCs are in their own directory; http://www.bioperl.org/DIST/RC I couldn't install 1.5.2 myself unless I set the repository to that directory. I think that's fine as long as we set the final release to the regular installation directory (http://www.bioperl.org/DIST) and use package.xml to point to the other required packages in the RC directory. Chris On Nov 21, 2006, at 2:47 AM, Nathan S. Haigh wrote: > L Xu wrote: >> Thank you for the prompt response. Here is the information you >> needed: >> (1)ActivePerl version 5.8.8.819 and PPM version 4.00 >> (2)http://ppm4.activestate.com/MsWin32-x86/5.8/819/package.xml >> http://bioperl.org/DIST/RC >> http://bioperl.org/DIST >> http://theoryx5.uwinnipeg.ca/ppms >> http://www.Bribes.org/perl/ppm >> (3)bioperl-1.4 >> >> Once again, thank you very much. >> >> L > > When you do a search for Bioperl, do you also get listing for Bioperl > 1.5.2 RC2. If you do, try to install that and let us know how you get > on. If you don't see a 1.5.2 RC2 let me know and I'll try to find out > what the problem is. > > The PPM package is a little behind since there is an RC4 - I'll try to > get the RC4 packaged today if I have time. We are hoping that RC4 > is the > last release candidate before the official 1.5.2 release, so if you do > install the RC2 remember to upgrade the package in a week or two. > > Cheers > Nath > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Tue Nov 21 09:56:29 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 21 Nov 2006 14:56:29 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <4563139D.2040108@sheffield.ac.uk> L Xu wrote: > I tried to install 1,5,2RC2, but got the following error message: > ################### > ...... > Generating HTML for Heap-0.71 ... DONE > Generating HTML for Error-0.17008 ... DONE > Generating HTML for XML-RegExp-0.03 ... DONE > Installing to site area ... failed > > ERROR: File conflict; package Bioperl-1.4 already provide > C:/Perl/html/bin/bp_aacomp.html > ########################## > Should I first uninstall Bioperl-1.4, if so how to do it? Thanks. > > > L > I'll have a look at this a bit later this afternoon. If you are using the PPM4 GUI, you should be able to right click an installed package and click remove (or something to that effect) and you will then have to apply the changes (like when you install a package). Once it's uninstalled, try installing 1.5.2 RC2 and let me know how you go. Cheers Nath From akarger at CGR.Harvard.edu Tue Nov 21 10:21:18 2006 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 21 Nov 2006 10:21:18 -0500 Subject: [Bioperl-l] Translating alternate start codons Message-ID: I think this is more a Bio question than a Bioperl question. I did this: ######### #!/usr/local/bin/perl use strict; use warnings; use Bio::Seq; use Bio::Tools::CodonTable; my $seqobj = Bio::PrimarySeq->new ( -seq => 'ATATGATAA', -id => 'GeneFragment-12', -accession_number => 'X78121', -alphabet => 'dna', ); $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; print "ATA $is a valid start codon\n"; print "Table 4: ", $seqobj->translate("-codontable_id" => 4)->seq,"\n"; print "Table 1: ", $seqobj->translate("-codontable_id" => 1)->seq,"\n"; ########### I got this: ATA is a valid start codon Table 4: IW* Table 1: I** But EMBL tells me that EMBLCDS:AAT64955 starts with an M: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[EMBLCDS:'A AT64955']+-qnum+1+-enum+3 So, does Bioperl purposely not translate start codons to M, while EMBL does? Am I supposed to just change the I to M explicitly in my code? I didn't see an obvious option to translate() to do it. Thanks, - Amir Karger Research Computing Life Sciences Division Harvard University 617-496-0626 From bix at sendu.me.uk Tue Nov 21 10:21:34 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 15:21:34 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Message-ID: <4563197E.7010909@sendu.me.uk> Nathan Haigh wrote: > > If anyone is aware of a way to force CPAN to install modules in a > specific order, please let Sendu know - we may be able to make the > install process much easier to the users. As regards the Bundle, you just have to specify the modules in the desired order. The question is, what order of installation, if any, results in no first-time failures? From akarger at CGR.Harvard.edu Tue Nov 21 11:16:01 2006 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 21 Nov 2006 11:16:01 -0500 Subject: [Bioperl-l] Translating alternate start codons Message-ID: > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > Amir, > > The best documentation for translate() is in the online > Bioperl Tutorial, > have you checked that? > > Brian O. Thanks for the quick response. The tutorial is quite informative. It seems to me that the POD needs to document -complete more thoroughly, though: Or if you expect a complete coding sequence (CDS) translation, with inititator at the beginning and terminator at the end: $protein_seq_obj = $cds_seq_obj->translate(-complete => 1); This doesn't really explain what it does. I guess -complete was chosen as a compromise between having too many options and having lots of functionality. In my case, I want to keep the *, and I don't want warnings about terminators in the middle, because I've got a bunch of pseudogenes. So I'll just translate the M myself. I'm sure you've had many "the documentation is spread out in too many places" discussions before, and I know keeping docs up to date is Hard. Oh well. -Amir > > > On 11/21/06 10:21 AM, "Amir Karger" wrote: > > > I think this is more a Bio question than a Bioperl question. > > > > I did this: > > > > ######### > > #!/usr/local/bin/perl > > > > use strict; > > use warnings; > > > > use Bio::Seq; > > use Bio::Tools::CodonTable; > > > > my $seqobj = Bio::PrimarySeq->new ( > > -seq => 'ATATGATAA', > > -id => 'GeneFragment-12', > > -accession_number => 'X78121', > > -alphabet => 'dna', > > ); > > > > $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); > > my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; > > print "ATA $is a valid start codon\n"; > > print "Table 4: ", $seqobj->translate("-codontable_id" => > 4)->seq,"\n"; > > print "Table 1: ", $seqobj->translate("-codontable_id" => > 1)->seq,"\n"; > > ########### > > > > I got this: > > ATA is a valid start codon > > Table 4: IW* > > Table 1: I** > > > > But EMBL tells me that EMBLCDS:AAT64955 starts with an M: > > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ > EMBLCDS:'A > > AT64955']+-qnum+1+-enum+3 > > > > So, does Bioperl purposely not translate start codons to M, > while EMBL > > does? Am I supposed to just change the I to M explicitly in > my code? I > > didn't see an obvious option to translate() to do it. > > > > Thanks, > > > > - Amir Karger > > Research Computing > > Life Sciences Division > > Harvard University > > 617-496-0626 > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From gwu at molbio.mgh.harvard.edu Tue Nov 21 12:00:55 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 12:00:55 -0500 Subject: [Bioperl-l] Two BioPerl-1.5.2-RC3 installation issues Message-ID: <456330C7.1020801@molbio.mgh.harvard.edu> When installing bioperl-1.5.2RC3, I chose to run the BioDBGFF tests with MySQL database. Below is the warning message. =============================================== Checking if your kit is complete... Warning: the following files are missing in your kit: t/BioDBSeqFeature_mysql.t Please inform the author. Writing Makefile for Bio =============================================== Another thins is the installation of Bio-ASN1-EntrezGene-1.09, the 'make test' requires bioperl be preinstalled(Bio::Index::...) while bioperl requires it be preinstalled. Is this a circle reference issue? Gang Gang From bix at sendu.me.uk Tue Nov 21 12:31:37 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:31:37 +0000 Subject: [Bioperl-l] Two BioPerl-1.5.2-RC3 installation issues In-Reply-To: <456330C7.1020801@molbio.mgh.harvard.edu> References: <456330C7.1020801@molbio.mgh.harvard.edu> Message-ID: <456337F9.6090001@sendu.me.uk> gang wu wrote: > When installing bioperl-1.5.2RC3, I chose to run the BioDBGFF tests with > MySQL database. Below is the warning message. > =============================================== > Checking if your kit is complete... > Warning: the following files are missing in your kit: > t/BioDBSeqFeature_mysql.t > Please inform the author. > Writing Makefile for Bio > =============================================== That should get resolved in RC4. > Another thins is the installation of Bio-ASN1-EntrezGene-1.09, the 'make > test' requires bioperl be preinstalled(Bio::Index::...) while bioperl > requires it be preinstalled. Is this a circle reference issue? Yes it is. You'll have to force install one of them. Again, it should get resolved in RC4 (Bio::ASN1::EntrezGene won't be a requirement). Thank you for your feedback, Sendu. From bix at sendu.me.uk Tue Nov 21 12:41:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:41:04 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read Message-ID: <45633A30.7060009@sendu.me.uk> With the new Build.PL, when it does its check to see if optional external modules are installed or not, for each module that isn't installed I can print out details of what Bioperl modules need it and why and then ask if you'd like to install that module before proceeding. This is obviously very useful for people doing one-off installations from CPAN, giving them informed choices and letting them avoid any problems with particular external modules (vs. having all or nothing by installing Bundle::BioPerl). But for developers, if you choose not to install a module, you'll keep getting asked if you want to install it every time you run Build.PL. So the question is, would this be too annoying? How often do you run Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I run it all the time because I'm developing the thing and trying to sort out installation issues, but would it bother anyone else? Cheers, Sendu. From bix at sendu.me.uk Tue Nov 21 12:45:46 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:45:46 +0000 Subject: [Bioperl-l] Changing default reply-to on this list Message-ID: <45633B4A.6060804@sendu.me.uk> Hi, I'd like to propose changing the default reply-to for posts on this list from the current 'reply to the poster' to 'reply to the mailing list'. That way people can just hit 'reply' instead of 'reply to all' in order to get a reply back to the list. If people then changed the current habit of 'reply to all' to just 'reply' it would avoid people being replied to getting multiple copies of the reply - one direct, a second from the mailing list. Cheers, Sendu. From stefan.kirov at bms.com Tue Nov 21 13:08:02 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 13:08:02 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: <45634082.6040001@bms.com> Sendu, This is not a problem - see prerequisites_policy ask/follow options for CPAN config. Hope this helps. Stefan Sendu Bala wrote: > With the new Build.PL, when it does its check to see if optional > external modules are installed or not, for each module that isn't > installed I can print out details of what Bioperl modules need it and > why and then ask if you'd like to install that module before proceeding. > > This is obviously very useful for people doing one-off installations > from CPAN, giving them informed choices and letting them avoid any > problems with particular external modules (vs. having all or nothing by > installing Bundle::BioPerl). > > But for developers, if you choose not to install a module, you'll keep > getting asked if you want to install it every time you run Build.PL. > > So the question is, would this be too annoying? How often do you run > Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I > run it all the time because I'm developing the thing and trying to sort > out installation issues, but would it bother anyone else? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bix at sendu.me.uk Tue Nov 21 13:17:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 18:17:10 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45634082.6040001@bms.com> References: <45633A30.7060009@sendu.me.uk> <45634082.6040001@bms.com> Message-ID: <456342A6.4060000@sendu.me.uk> Stefan Kirov wrote: > Sendu, > This is not a problem - see > prerequisites_policy ask/follow > options for CPAN config. That does not apply to the situation I describe. The follow policy applies to required modules when installing with CPAN. I am talking about installing modules that are /not/ required when using CPAN and even when /not/ using CPAN to do an installation. From n.haigh at sheffield.ac.uk Tue Nov 21 13:20:15 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 21 Nov 2006 18:20:15 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <4563435F.5010400@sheffield.ac.uk> Sendu Bala wrote: > Hi, > > I'd like to propose changing the default reply-to for posts on this list > from the current 'reply to the poster' to 'reply to the mailing list'. > That way people can just hit 'reply' instead of 'reply to all' in order > to get a reply back to the list. > > If people then changed the current habit of 'reply to all' to just > 'reply' it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > I don't seem to get multiple copies! However, the first reason (to just hit replay) is reason enough to change the default behaviour! :-) Nath From stefan.kirov at bms.com Tue Nov 21 13:24:39 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 13:24:39 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <456342A6.4060000@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> <45634082.6040001@bms.com> <456342A6.4060000@sendu.me.uk> Message-ID: <45634467.5010300@bms.com> Sendu Bala wrote: > Stefan Kirov wrote: >> Sendu, >> This is not a problem - see >> prerequisites_policy ask/follow >> options for CPAN config. > > That does not apply to the situation I describe. The follow policy > applies to required modules when installing with CPAN. I am talking > about installing modules that are /not/ required when using CPAN and > even when /not/ using CPAN to do an installation. > Sorry, I did not get that.... I personally do not run make often and would guess this to be case for most people as well. Stefan From stefan.kirov at bms.com Tue Nov 21 12:20:34 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 12:20:34 -0500 Subject: [Bioperl-l] Performance of Bio::Species Message-ID: <45633562.2030107@bms.com> New Bio::Species implementation seems to degrade significantly performance. It seems this happens when the Bio::Tree::Tree is constructed. See the stats bellow (based on simple Bio::Species object construction, script and test sequence file attached): 10000 iterrations new implementation: Constructor: 115 wallclock secs (113.50 usr + 0.67 sys = 114.17 CPU) Accessor: 0 wallclock secs ( 0.17 usr + 0.00 sys = 0.17 CPU) old implementation (bioperl-1.4 Constructor: 1 wallclock secs ( 0.84 usr + 0.10 sys = 0.94 CPU) Accessor: 0 wallclock secs ( 0.13 usr + 0.01 sys = 0.14 CPU) You can see that when reading a genbank file you would double the time necessary to construct the Bio::Seq object (100 iterations): old implementation (bioperl-1.4 Constructor: 0 wallclock secs ( 0.01 usr + 0.00 sys = 0.01 CPU) Accessor: 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU) Constructor(seqio)/reading seq: 3 wallclock secs ( 2.51 usr + 0.31 sys = 2.83 CPU) new implementation: Constructor: 2 wallclock secs ( 1.14 usr + 0.01 sys = 1.15 CPU) Accessor: 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU) Constructor(seqio)/reading seq: 5 wallclock secs ( 5.10 usr + 0.20 sys = 5.30 CPU) This may not pose a problem to people who read few sequences or files with no lineage data, but it could be a significant headache otherwise. I saw from CVS that Sendu knows there are memory leaks (I find cycles). If the classification is supplied incorrectly (includes a reference to an array in the classification array) things get really messy (~17 GB of RAM for a Bio::Species object), though weird enough the cycle is not indefinite. If I have more time I will try to debug this further and submit a formal bug report/patch, but I am not sure if I will anytime soon. I am sure there are people who understand Bio::Taxon/Bio::Tree::Tree better than me and might have better idea how to fix this. Stefan /// use Bio::Species; use Benchmark; use Bio::SeqIO; my @classification=qw( sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota ); my $species; my $t1 = new Benchmark; for my $i (1..100) { $species = Bio::Species->new(-classification => [@classification]); } my $t2 = new Benchmark; for my $i (1..100) { my $bin = $species->binomial; } my $t3 = new Benchmark; print "Constructor: ", timestr(timediff($t2, $t1)),"\n"; print "Accessor: ", timestr(timediff($t3, $t2)),"\n"; my $f=shift; my $t4= new Benchmark; for my $i (1..100) { my $sio=new Bio::SeqIO(-file=>$f,-format=>'genbank'); my $seq=$sio->next_seq; } my $t5= new Benchmark; print "Constructor(seqio)/reading seq: ", timestr(timediff($t5, $t4)),"\n"; -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: NM_000161.genbank URL: From dmessina at wustl.edu Tue Nov 21 14:06:38 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:06:38 -0600 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> > it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. This behavior can be changed by going to http://lists.open-bio.org/mailman/listinfo/bioperl-l entering your subscribed email address in the last field on the page, clicking the "unsubscribe or edit options" button to the right of that field. On the next page, enter your password in the password field and click "Log in". On the options page that you see next, the last option, called "Avoid duplicate copies of messages?", should be set to "Yes" if you don't want multiple copies. Dave From dmessina at wustl.edu Tue Nov 21 14:11:06 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:11:06 -0600 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> Would it be possible to set it up such that when the user is asked whether to install an unrequired module, the possible answers are "yes", "no", "skip all"? The latter being to skip all subsequent questions about unrequired modules. Dave From bix at sendu.me.uk Tue Nov 21 14:30:52 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:30:52 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> References: <45633A30.7060009@sendu.me.uk> <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> Message-ID: <456353EC.9030304@sendu.me.uk> David Messina wrote: > Would it be possible to set it up such that when the user is asked > whether to install an unrequired module, the possible answers are "yes", > "no", "skip all"? The latter being to skip all subsequent questions > about unrequired modules. Yes, thanks, that's a good idea. I currently (in my private copy) have the default as 'no', but if changed as above, should the default be to 'skip all'? Or, perhaps have an initial question 'do you want to be asked to install optional modules you don't have' would be better? From hlapp at gmx.net Tue Nov 21 14:33:11 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:33:11 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4562B497.6080805@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> Message-ID: The Oracle error is ORA-00904: "BIODATABASE"."OID": invalid identifier and if you look at the accompanying statement, it's the UK select statement: SELECT <*>biodatabase.oid, biodatabase.name, biodatabase.authority FROM biodatabase WHERE name = :p1 The column OID must exist in the Biodatabase table (which actually is a synonym to the SG_BIODATABASE table), if it is the Oracle schema. This actually prompts another suggestion, sorry for not asking that first: did you actually install the BioSQL-API on top of the schema by running the script BS-create-Biosql-API.sql? (It seems that the statement it chokes on is also the first statement being prepared, so this may well be the reason) -hilmar On Nov 21, 2006, at 3:11 AM, gang wu wrote: > Can you show me where it indicates I am actually using the MySQL > schema. > I am pretty sure that I used the sql script files from > sql/biosql-ora(Has anyone actually tried to install MySQL schema on > Oracle?). I can reinstall the schema if you think that's the way to > solve the problem. Thanks very much. > > Gang > > Hilmar Lapp wrote: >> It looks like you are using the MySQL schema under Oracle. There are >> different DDL scripts for each supported RDBMS. The ones for Oracle >> are in the sql/biosql-ora subdirectory. Note the INSTALL document in >> that directory. >> >> -hilmar >> >> >> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >> >> >>> Hi Hilmar, >>> >>> Below is the output. Thanks. >>> >>> Gang >>> ========================================================== >>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>> TEST_VERBOSE=1 >>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>> @ARGV;' t/01dbadaptor.t >>> t/01dbadaptor....1..19 >>> ok 1 >>> ok 2 >>> ok 3 >>> ok 4 >>> ok 5 >>> ok 6 >>> ok 7 >>> ok 8 >>> ok 9 >>> ok 10 >>> ok 11 >>> attempting to load adaptor class for BioNamespace >>> ok 12 >>> attempting to load module >>> Bio::DB::BioSQL::BioNamespaceAdaptor >>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>> ok 13 >>> ok 14 >>> attempting to load driver for adaptor class >>> Bio::DB::BioSQL::BioNamespaceAdaptor >>> attempting to load driver for adaptor class >>> Bio::DB::BioSQL::BasePersistenceAdaptor >>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>> preparing UK select statement: SELECT biodatabase.oid, >>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >>> = ? >>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>> invalid identifier (DBD ERROR: error possibly near <*> indicator at >>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>> Statement "SELECT biodatabase.oid, biodatabase.name, >>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >>> Can't call method "bind_param" on an undefined value at blib/lib/ >>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>> dubious >>> Test returned status 255 (wstat 65280, 0xff00) >>> DIED. FAILED tests 15-19 >>> Failed 5/19 tests, 73.68% okay >>> Failed Test Stat Wstat Total Fail Failed List of Failed >>> -------------------------------------------------------------------- >>> -- >>> --------- >>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>> okay. >>> make: *** [test_01dbadaptor] Error 2 >>> ========================================================= >>> >>> >>> Hilmar Lapp wrote: >>> >>>> Hi Gang, >>>> >>>> what I wanted to get at was the error message from the driver when >>>> it fails to generate the prepared statement, but this is not in >>>> the output. >>>> >>>> I believe you need set the HARNESS_VERBOSE environment variable to >>>> 1 before testing to get what I need: >>>> >>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>> csh/tcsh >>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>> >>>> This will lead to _a lot_ of debugging output. Do not run this for >>>> the entire test suite. >>>> >>>> The errors for mysql I believe are related to the fact that have >>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>> (completely empty) instance of BioSQL. >>>> >>>> Let me know what you get for the Oracle test above. >>>> >>>> -hilmar >>>> >>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>> >>>> >>>>> Hi Hilmar, >>>>> >>>>> Thanks for your message. Below are several tests for Oracle and >>>>> MySQL. MySQL actually also has two tests with failed items which >>>>> may be related to data in BioSQL database. >>>>> >>>>> Could it be my Oracle installation/configuration has some issues? >>>>> >>>>> Thanks. >>>>> >>>>> Gang >>>>> >>>> --=========================================================== >>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>> =========================================================== >>>> >>>> >>>> >>>> >>>> >>>> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From dmessina at wustl.edu Tue Nov 21 14:36:10 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:36:10 -0600 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <456353EC.9030304@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> <456353EC.9030304@sendu.me.uk> Message-ID: <5DF4D1D9-754F-443F-ADDE-4127C579BF82@wustl.edu> On Nov 21, 2006, at 1:30 PM, Sendu Bala wrote: > Yes, thanks, that's a good idea. I currently (in my private copy) > have the default as 'no', but if changed as above, should the > default be to 'skip all'? Yeah, that makes sense to me. > Or, perhaps have an initial question 'do you want to be asked to > install optional modules you don't have' would be better? I think that would work fine, too -- whichever is easiest for you... Dave From bix at sendu.me.uk Tue Nov 21 14:37:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:37:14 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45633562.2030107@bms.com> References: <45633562.2030107@bms.com> Message-ID: <4563556A.1050101@sendu.me.uk> Stefan Kirov wrote: > New Bio::Species implementation seems to degrade significantly > performance. It seems this happens when the Bio::Tree::Tree is constructed. > See the stats bellow (based on simple Bio::Species object construction, > script and test sequence file attached): [snip] Thanks. If you come up with anything, please file that bug report. I certainly regard this as an important thing that must be fixed, though I don't know if I should hold up release of 1.5.2 for it. Now that you've reported on it I'm leaning toward yes, since the new Bio::Species implementation is one of the major new features of 1.5.2 and it ought to work well. Anyway, for the memory leak I have some ideas I haven't tried yet; I don't know if my efforts will solve the speed issue though. If anyone can spare the time to look at the problem, please do. Cheers, Sendu. From hlapp at gmx.net Tue Nov 21 14:46:45 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:46:45 -0500 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <93D5ABA0-290A-4087-8999-4FFBA6CFD918@gmx.net> I don't think that's a good idea. First, it is really hard to reply to someone off-list that way. Second, it is especially annoying given that reply-to-poster is generally considered best-practice and so therefore almost all lists reply off-list if you just hit reply. In fact I had this set to reply-to-list on one of our (NESCent's) own listserves to help the less computer-savvy but it was so annoying that I set it back to reply-to-sender within days. Compared to that, hitting the delete key on the duplicate takes about 0.2 seconds for me and hasn't bothered me much ever. Bottom line is, if you suggest people to change their habits then it is close impossible if it is only a single place that likes to do it the other way. -hilmar On Nov 21, 2006, at 12:45 PM, Sendu Bala wrote: > Hi, > > I'd like to propose changing the default reply-to for posts on this > list >> from the current 'reply to the poster' to 'reply to the mailing >> list'. > That way people can just hit 'reply' instead of 'reply to all' in > order > to get a reply back to the list. > > If people then changed the current habit of 'reply to all' to just > 'reply' it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Nov 21 14:41:25 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:41:25 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: I typically run (ran) perl Makefile.PL when I'm forced to, i.e., if someone changed Makefile.PL in the repository and I cvs update. Or if something is just going weird, as a last resort before rebooting ;) On Nov 21, 2006, at 12:41 PM, Sendu Bala wrote: > With the new Build.PL, when it does its check to see if optional > external modules are installed or not, for each module that isn't > installed I can print out details of what Bioperl modules need it and > why and then ask if you'd like to install that module before > proceeding. > > This is obviously very useful for people doing one-off installations >> from CPAN, giving them informed choices and letting them avoid any > problems with particular external modules (vs. having all or > nothing by > installing Bundle::BioPerl). > > But for developers, if you choose not to install a module, you'll keep > getting asked if you want to install it every time you run Build.PL. > > So the question is, would this be too annoying? How often do you run > Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I > run it all the time because I'm developing the thing and trying to > sort > out installation issues, but would it bother anyone else? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Nov 21 14:56:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:56:18 -0500 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4563556A.1050101@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > I don't know if I should hold up release of 1.5.2 for it. Now that > you've > reported on it I'm leaning toward yes, since the new Bio::Species > implementation is one of the major new features of 1.5.2 and it > ought to > work well. I disagree to some extent. This is a developer release, so not everything is expected to work perfectly. What's not desirable is if fixing this required another entire redesign of the API, so that every dev release introduces different API. The thing is, you'll really only get trouble reports once you put it out and people start using it in anger. Don't expect to make it perfect before. > > Anyway, for the memory leak I have some ideas I haven't tried yet; I > don't know if my efforts will solve the speed issue though. The memory leak sounds more concerning to me. Under which circumstances would it crash a script or blow throuhg all of say 1-2GB when it should have taken only a tenth of that. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Tue Nov 21 14:58:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:58:58 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> References: <45633B4A.6060804@sendu.me.uk> <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> Message-ID: <45635A82.6070209@sendu.me.uk> David Messina wrote: >> it would avoid people being replied to getting multiple copies >> of the reply - one direct, a second from the mailing list. > > This behavior can be changed by going to > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > entering your subscribed email address in the last field on the page, > clicking the "unsubscribe or edit options" button to the right of > that field. > > On the next page, enter your password in the password field and click > "Log in". On the options page that you see next, the last option, > called "Avoid duplicate copies of messages?", should be set to "Yes" > if you don't want multiple copies. Ah, thanks for that. Given Hilmar's reply, forget the proposal. I'll just live in misery :( From bosborne11 at verizon.net Tue Nov 21 14:58:00 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 21 Nov 2006 14:58:00 -0500 Subject: [Bioperl-l] Translating alternate start codons In-Reply-To: Message-ID: Amir, I think I understand your question, perhaps not, and I think the recommended solution is to create your own "custom" codon table. See t/CodonTable.t for an example. Brian O. On 11/21/06 11:16 AM, "Amir Karger" wrote: >> From: Brian Osborne [mailto:bosborne11 at verizon.net] >> >> Amir, >> >> The best documentation for translate() is in the online >> Bioperl Tutorial, >> have you checked that? >> >> Brian O. > > Thanks for the quick response. The tutorial is quite informative. > It seems to me that the POD needs to document -complete more thoroughly, > though: > > Or if you expect a complete coding sequence (CDS) > translation, > with inititator at the beginning and terminator at the > end: > > $protein_seq_obj = $cds_seq_obj->translate(-complete > => 1); > > This doesn't really explain what it does. > > I guess -complete was chosen as a compromise between having too many > options and having lots of functionality. In my case, I want to keep the > *, and I don't want warnings about terminators in the middle, because > I've got a bunch of pseudogenes. So I'll just translate the M myself. > > I'm sure you've had many "the documentation is spread out in too many > places" discussions before, and I know keeping docs up to date is Hard. > Oh well. > > -Amir > >> >> >> On 11/21/06 10:21 AM, "Amir Karger" wrote: >> >>> I think this is more a Bio question than a Bioperl question. >>> >>> I did this: >>> >>> ######### >>> #!/usr/local/bin/perl >>> >>> use strict; >>> use warnings; >>> >>> use Bio::Seq; >>> use Bio::Tools::CodonTable; >>> >>> my $seqobj = Bio::PrimarySeq->new ( >>> -seq => 'ATATGATAA', >>> -id => 'GeneFragment-12', >>> -accession_number => 'X78121', >>> -alphabet => 'dna', >>> ); >>> >>> $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); >>> my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; >>> print "ATA $is a valid start codon\n"; >>> print "Table 4: ", $seqobj->translate("-codontable_id" => >> 4)->seq,"\n"; >>> print "Table 1: ", $seqobj->translate("-codontable_id" => >> 1)->seq,"\n"; >>> ########### >>> >>> I got this: >>> ATA is a valid start codon >>> Table 4: IW* >>> Table 1: I** >>> >>> But EMBL tells me that EMBLCDS:AAT64955 starts with an M: >>> >> http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ >> EMBLCDS:'A >>> AT64955']+-qnum+1+-enum+3 >>> >>> So, does Bioperl purposely not translate start codons to M, >> while EMBL >>> does? Am I supposed to just change the I to M explicitly in >> my code? I >>> didn't see an obvious option to translate() to do it. >>> >>> Thanks, >>> >>> - Amir Karger >>> Research Computing >>> Life Sciences Division >>> Harvard University >>> 617-496-0626 >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Tue Nov 21 15:16:18 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 20:16:18 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: <45635E92.7080000@sendu.me.uk> Hilmar Lapp wrote: > > On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > >> Anyway, for the memory leak I have some ideas I haven't tried yet; I >> don't know if my efforts will solve the speed issue though. > > The memory leak sounds more concerning to me. Under which circumstances > would it crash a script or blow throuhg all of say 1-2GB when it should > have taken only a tenth of that. Its been reported as causing problems if you do something like parse a large embl file with many (10s of thousands) sequences in it. So basically any situation that you make lots of Bio::Species objects. IIRC the reporter ran out of memory on a ~40000 sequence embl file. Neither the memory leak fix or speed fix ought to require any API change. I'm fairly certain that the memory leak, at least, is confined to a problem with (as suggested) Bio::Tree* stuff failing to clean up on destruction. There was in fact already an unnoticed problem with Bio::Tree::Node not getting cleaned up (see my #*** comment in the code), but my Bio::Species-related changes exacerbated the problem and also made them noticeable, since you're more likely to create thousands of Bio::Species than you were Bio::Tree::Node. From jason at bioperl.org Tue Nov 21 00:57:54 2006 From: jason at bioperl.org (Jason Stajich) Date: Mon, 20 Nov 2006 21:57:54 -0800 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164070364l.1106082l.0l@psu.edu> References: <1164070364l.1106082l.0l@psu.edu> Message-ID: a specific accession and example code will make it easier for someone to reproduce (and debug) your problem. On Nov 20, 2006, at 4:52 PM, Juan Cristobal Vera wrote: > > > Hi, > I'm writing a simple application to extract various fields from > swissprot objects and I can't access the GO terms found in > "dblink" part of the swiss format flat files. I'm not a > professional programmer and I can't figure out why this is > occuring. All the other "dblink" keys are being > generated as far as I can tell (e.g. embl, pfam, etc). The GO > terms are just skipped over and it's driving me crazy. Not sure if > this is a bug or a deliberate strategy I'm unfamiliar with. I > apologize if this is not the correct forum to ask for this sort of > help and would ask to be directed to the proper one. > > > > Juan Cristobal Vera > > Graduate Student > > Department of Biology > > Penn State University > > 208 Mueller Laboratory > > University Park, PA 16802 > > (814)863-2957 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason at bioperl.org http://jason.open-bio.org/ From stefan.kirov at bms.com Tue Nov 21 15:20:40 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 15:20:40 -0500 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: <45635F98.8030901@bms.com> Hilmar Lapp wrote: > On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > > >> I don't know if I should hold up release of 1.5.2 for it. Now that >> you've >> reported on it I'm leaning toward yes, since the new Bio::Species >> implementation is one of the major new features of 1.5.2 and it >> ought to >> work well. >> > > I disagree to some extent. This is a developer release, so not > everything is expected to work perfectly. > > What's not desirable is if fixing this required another entire > redesign of the API, so that every dev release introduces different API. > > The thing is, you'll really only get trouble reports once you put it > out and people start using it in anger. Don't expect to make it > perfect before. > > >> Anyway, for the memory leak I have some ideas I haven't tried yet; I >> don't know if my efforts will solve the speed issue though. >> > > The memory leak sounds more concerning to me. Under which > circumstances would it crash a script or blow throuhg all of say > 1-2GB when it should have taken only a tenth of that. > > As I was saying, I did pass ref to an array in the classification (wrong parsing): push @classification,'sapiens', 'Homo', 'Hominidae', $arrayref; and my script took 17-18 GB. I am really surprised it stopped getting more RAM and finished successfully. I did not explore further. Stefan > -hilmar > > From gwu at molbio.mgh.harvard.edu Tue Nov 21 15:33:10 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 15:33:10 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> Message-ID: <45636286.6040504@molbio.mgh.harvard.edu> Hi Hilmar, I just rebuilt the Oracle BioSQL database by strictly following the INSTALL doc. You are right that BS-create-Biosql-API.sql must be run to make bioperl-db work with it(the oid columns). But my installation problem was caused by running BS-create-Biosql-API2.sql after it, which rendered the database not compatible with bioperl-db. If I ran only BS-create-Biosql-API.sql, ll bioperl-db tests could pass. Does this mean that the Oracle version is not interoperable between the Bio- projects at this point? Did I miss anything in the INSTALL or README? I only saw a line "-- all others (Biojava, etc)" but did not realize I could not run both BS-create-Biosql-API.sql and BS-create-Biosql-API2.sql. I this is the case, can you please add it to the docs? Thanks very much for your help. Gang Hilmar Lapp wrote: > The Oracle error is > > ORA-00904: "BIODATABASE"."OID": invalid identifier > > and if you look at the accompanying statement, it's the UK select > statement: > > SELECT <*>biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = :p1 > > The column OID must exist in the Biodatabase table (which actually is > a synonym to the SG_BIODATABASE table), if it is the Oracle schema. > > This actually prompts another suggestion, sorry for not asking that > first: did you actually install the BioSQL-API on top of the schema by > running the script BS-create-Biosql-API.sql? (It seems that the > statement it chokes on is also the first statement being prepared, so > this may well be the reason) > > -hilmar > > On Nov 21, 2006, at 3:11 AM, gang wu wrote: > >> Can you show me where it indicates I am actually using the MySQL schema. >> I am pretty sure that I used the sql script files from >> sql/biosql-ora(Has anyone actually tried to install MySQL schema on >> Oracle?). I can reinstall the schema if you think that's the way to >> solve the problem. Thanks very much. >> >> Gang >> >> Hilmar Lapp wrote: >>> It looks like you are using the MySQL schema under Oracle. There are >>> different DDL scripts for each supported RDBMS. The ones for Oracle >>> are in the sql/biosql-ora subdirectory. Note the INSTALL document in >>> that directory. >>> >>> -hilmar >>> >>> >>> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >>> >>> >>>> Hi Hilmar, >>>> >>>> Below is the output. Thanks. >>>> >>>> Gang >>>> ========================================================== >>>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>>> TEST_VERBOSE=1 >>>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >>>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>>> @ARGV;' t/01dbadaptor.t >>>> t/01dbadaptor....1..19 >>>> ok 1 >>>> ok 2 >>>> ok 3 >>>> ok 4 >>>> ok 5 >>>> ok 6 >>>> ok 7 >>>> ok 8 >>>> ok 9 >>>> ok 10 >>>> ok 11 >>>> attempting to load adaptor class for BioNamespace >>>> ok 12 >>>> attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor >>>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>>> ok 13 >>>> ok 14 >>>> attempting to load driver for adaptor class >>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>> attempting to load driver for adaptor class >>>> Bio::DB::BioSQL::BasePersistenceAdaptor >>>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>>> preparing UK select statement: SELECT biodatabase.oid, >>>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >>>> = ? >>>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>>> invalid identifier (DBD ERROR: error possibly near <*> indicator at >>>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>>> Statement "SELECT biodatabase.oid, biodatabase.name, >>>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >>>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>>> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >>>> Can't call method "bind_param" on an undefined value at blib/lib/ >>>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>>> dubious >>>> Test returned status 255 (wstat 65280, 0xff00) >>>> DIED. FAILED tests 15-19 >>>> Failed 5/19 tests, 73.68% okay >>>> Failed Test Stat Wstat Total Fail Failed List of Failed >>>> ---------------------------------------------------------------------- >>>> --------- >>>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>>> okay. >>>> make: *** [test_01dbadaptor] Error 2 >>>> ========================================================= >>>> >>>> >>>> Hilmar Lapp wrote: >>>> >>>>> Hi Gang, >>>>> >>>>> what I wanted to get at was the error message from the driver when >>>>> it fails to generate the prepared statement, but this is not in >>>>> the output. >>>>> >>>>> I believe you need set the HARNESS_VERBOSE environment variable to >>>>> 1 before testing to get what I need: >>>>> >>>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>>> csh/tcsh >>>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>>> >>>>> This will lead to _a lot_ of debugging output. Do not run this for >>>>> the entire test suite. >>>>> >>>>> The errors for mysql I believe are related to the fact that have >>>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>>> (completely empty) instance of BioSQL. >>>>> >>>>> Let me know what you get for the Oracle test above. >>>>> >>>>> -hilmar >>>>> >>>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>>> >>>>> >>>>>> Hi Hilmar, >>>>>> >>>>>> Thanks for your message. Below are several tests for Oracle and >>>>>> MySQL. MySQL actually also has two tests with failed items which >>>>>> may be related to data in BioSQL database. >>>>>> >>>>>> Could it be my Oracle installation/configuration has some issues? >>>>>> >>>>>> Thanks. >>>>>> >>>>>> Gang >>>>>> >>>>> --=========================================================== >>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>>> =========================================================== >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > --=========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > > From jason at bioperl.org Tue Nov 21 11:47:37 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 21 Nov 2006 08:47:37 -0800 Subject: [Bioperl-l] Translating alternate start codons In-Reply-To: References: Message-ID: <8273f6c20611210847q7178025bm8e5367a5ae2138d4@mail.gmail.com> It seem then you don't want to use 'complete' since you don't always expect complete CDSes. Shouldn't you just translate to generate the peptide and then operate on the initial and terminal residues to achieve what you want. substr($peptide,0,1,'M'); chop($peptide) if substr($peptide,-1,1) eq $TERMINATOR; This is a community project so any help in improving apparent deficiencies in documentation are gladly welcomed - the wiki is designed to let everyone contribute. I think that clarifications and better descriptions for modules should reside there so please add your input on the webpages. A dev with write access can migrate updated documentation to the module's POD where appropriate. -jason On 11/21/06, Amir Karger wrote: > > > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > > > Amir, > > > > The best documentation for translate() is in the online > > Bioperl Tutorial, > > have you checked that? > > > > Brian O. > > Thanks for the quick response. The tutorial is quite informative. > It seems to me that the POD needs to document -complete more thoroughly, > though: > > Or if you expect a complete coding sequence (CDS) > translation, > with inititator at the beginning and terminator at the > end: > > $protein_seq_obj = $cds_seq_obj->translate(-complete > => 1); > > This doesn't really explain what it does. > > I guess -complete was chosen as a compromise between having too many > options and having lots of functionality. In my case, I want to keep the > *, and I don't want warnings about terminators in the middle, because > I've got a bunch of pseudogenes. So I'll just translate the M myself. > > I'm sure you've had many "the documentation is spread out in too many > places" discussions before, and I know keeping docs up to date is Hard. > Oh well. > > -Amir > > > > > > > On 11/21/06 10:21 AM, "Amir Karger" wrote: > > > > > I think this is more a Bio question than a Bioperl question. > > > > > > I did this: > > > > > > ######### > > > #!/usr/local/bin/perl > > > > > > use strict; > > > use warnings; > > > > > > use Bio::Seq; > > > use Bio::Tools::CodonTable; > > > > > > my $seqobj = Bio::PrimarySeq->new ( > > > -seq => 'ATATGATAA', > > > -id => 'GeneFragment-12', > > > -accession_number => 'X78121', > > > -alphabet => 'dna', > > > ); > > > > > > $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); > > > my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; > > > print "ATA $is a valid start codon\n"; > > > print "Table 4: ", $seqobj->translate("-codontable_id" => > > 4)->seq,"\n"; > > > print "Table 1: ", $seqobj->translate("-codontable_id" => > > 1)->seq,"\n"; > > > ########### > > > > > > I got this: > > > ATA is a valid start codon > > > Table 4: IW* > > > Table 1: I** > > > > > > But EMBL tells me that EMBLCDS:AAT64955 starts with an M: > > > > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ > > EMBLCDS:'A > > > AT64955']+-qnum+1+-enum+3 > > > > > > So, does Bioperl purposely not translate start codons to M, > > while EMBL > > > does? Am I supposed to just change the I to M explicitly in > > my code? I > > > didn't see an obvious option to translate() to do it. > > > > > > Thanks, > > > > > > - Amir Karger > > > Research Computing > > > Life Sciences Division > > > Harvard University > > > 617-496-0626 > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich jason at bioperl.org http://www.duke.edu/~jes12/ From bosborne11 at verizon.net Tue Nov 21 15:53:39 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 21 Nov 2006 15:53:39 -0500 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: <200611211032.kALAWahR014137@dev.open-bio.org> Message-ID: Bioperl-l, INSTALL has changed in CVS but the Wiki's version has not - you always have to change both versions of the INSTALL instructions, this is how Chris has elected to do it. Brian O. Date: Tue, 21 Nov 2006 10:32:36 +0000 To: Subject: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 Update of /home/repository/bioperl/bioperl-live In directory dev.open-bio.org:/tmp/cvs-serv14112 Modified Files: DEPENDENCIES INSTALL INSTALL.WIN Log Message: clarification for Bundle::BioPerl, updates for Build.PL Index: DEPENDENCIES =================================================================== RCS file: /home/repository/bioperl/bioperl-live/DEPENDENCIES,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** DEPENDENCIES 14 Nov 2006 15:13:24 -0000 1.1 --- DEPENDENCIES 21 Nov 2006 10:32:34 -0000 1.2 *************** *** 5,10 **** The following packages are used by Bioperl. Not all are required for Bioperl to operate properly, however some functionality will be missing ! without them. You can easily install all of these, except srsperl.pm, ! using the Bundle::BioPerl CPAN bundle. The DBD::mysql, DB_File and XML::Parser modules require other applications --- 5,11 ---- The following packages are used by Bioperl. Not all are required for Bioperl to operate properly, however some functionality will be missing ! without them. You can easily install all of these by using CPAN to install ! Bioperl, or if you have installed Bioperl manually (from archive or CVS), ! by using the Bundle::BioPerl CPAN bundle. The DBD::mysql, DB_File and XML::Parser modules require other applications Index: INSTALL =================================================================== RCS file: /home/repository/bioperl/bioperl-live/INSTALL,v retrieving revision 1.57 retrieving revision 1.58 diff -C2 -d -r1.57 -r1.58 *** INSTALL 16 Nov 2006 16:27:49 -0000 1.57 --- INSTALL 21 Nov 2006 10:32:34 -0000 1.58 *************** *** 1,24 **** # $Id$ ! Installing Bioperl for Unix ! * BIOPERL INSTALLATION ! * SYSTEM REQUIREMENTS ! * OPTIONAL ! * ADDITIONAL INSTALLATION INFORMATION ! * THE BIOPERL BUNDLE ! * INSTALLING BIOPERL THE EASY WAY USING CPAN ! * INSTALLING BIOPERL THE EASY WAY USING GNU 'make' ! * WHERE ARE THE MAN PAGES? ! * EXTERNAL PROGRAMS ! * Environment Variables ! * INSTALLING BIOPERL SCRIPTS ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA ! * INSTALLING BIOPERL MODULES THE HARD WAY ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION ! * THE TEST SYSTEM ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE ! * CONFIGURING for BSD and Solaris boxes ! * INSTALLATION BIOPERL INSTALLATION --- 1,24 ---- # $Id$ ! Installing Bioperl for Unix ! * BIOPERL INSTALLATION ! * SYSTEM REQUIREMENTS ! * OPTIONAL ! * ADDITIONAL INSTALLATION INFORMATION ! * THE BIOPERL BUNDLE ! * INSTALLING BIOPERL THE EASY WAY USING CPAN ! * INSTALLING BIOPERL THE EASY WAY USING Build.PL ! * WHERE ARE THE MAN PAGES? ! * EXTERNAL PROGRAMS ! * Environment Variables ! * INSTALLING BIOPERL SCRIPTS ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA ! * INSTALLING BIOPERL MODULES THE HARD WAY ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION ! * THE TEST SYSTEM ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE ! * CONFIGURING for BSD and Solaris boxes ! * INSTALLATION BIOPERL INSTALLATION *************** *** 41,48 **** modules is included in the DEPENDENCIES file. ! The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation of these ! external modules easy. Simply install the bundle using your CPAN shell and ! all necessary modules will be installed. See THE BIOPERL BUNDLE, ! below. OPTIONAL --- 41,49 ---- modules is included in the DEPENDENCIES file. ! When not using CPAN to install Bioperl itself, the CPAN Bioperl Bundle ! (Bundle::BioPerl) makes installation of these external modules easy. Simply ! install the bundle using your CPAN shell and many optional modules will be ! installed. See THE BIOPERL BUNDLE, below. However, it is recommended you use ! CPAN to install Bioperl and not use Bundle::BioPerl. OPTIONAL *************** *** 61,64 **** --- 62,72 ---- THE BIOPERL BUNDLE + You do not need to install Bundle::BioPerl if you will install Bioperl + using CPAN. This is for users manually installing Bioperl from archives + or CVS, who also want an easy way to install the optional external + modules that Bioperl makes use of. + + Bundle::BioPerl does *not* install Bioperl. + You typically need root privileges to install using CPAN. If you don't have these privileges please see INSTALLING BIOPERL IN A PERSONAL *************** *** 86,96 **** CPAN: Storable loaded ok Going to read /home/bosborne/.cpan/Metadata ! Database was generated on Tue, 24 Feb 2004 23:55:23 GMT ! DistributionB/BI/BIRNEY/bioperl-1.2.tar.gz ! DistributionB/BI/BIRNEY/bioperl-1.4.tar.gz Now install: ! cpan>install B/BI/BIRNEY/bioperl-1.4.tar.gz If you've installed everything perfectly and all the network connections --- 94,105 ---- CPAN: Storable loaded ok Going to read /home/bosborne/.cpan/Metadata ! Database was generated on Mon, 20 Nov 2006 05:24:36 GMT ! Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz ! Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz ! Distribution S/SE/SENDU/bioperl-1.5.2_100.tar.gz Now install: ! cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz If you've installed everything perfectly and all the network connections *************** *** 100,105 **** undetected bug in Bioperl, flawed test script, problems with CGI script used for sequence retrieval at public database, and so on. Remember ! that there are over 700 modules in Bioperl and the test suite is running ! more than 9000 individual tests, a few failed tests may not affect your usage of Bioperl. --- 109,114 ---- undetected bug in Bioperl, flawed test script, problems with CGI script used for sequence retrieval at public database, and so on. Remember ! that there are over 800 modules in Bioperl and the test suite is running ! more than 12000 individual tests, a few failed tests may not affect your usage of Bioperl. *************** *** 107,111 **** Bioperl and you'd like to install anyway do: ! cpan>force install B/BI/BIRNEY/bioperl-1.4.tar.gz This is what most experienced Bioperl users would do. However, if you're --- 116,120 ---- Bioperl and you'd like to install anyway do: ! cpan>force install S/SE/SENDU/bioperl-1.5.2_100.tar.gz This is what most experienced Bioperl users would do. However, if you're *************** *** 113,117 **** bioperl-l at bioperl.org. ! INSTALLING BIOPERL THE EASY WAY USING GNU 'make' The advantage of this approach is it's stepwise, so it's easy to stop and --- 122,126 ---- bioperl-l at bioperl.org. ! INSTALLING BIOPERL THE EASY WAY USING Build.PL The advantage of this approach is it's stepwise, so it's easy to stop and *************** *** 120,126 **** Download, then unpack the tar file. For example: ! >gunzip bioperl-1.5.2.tar.gz ! >tar xvf bioperl-1.5.2.tar ! >cd bioperl-1.5.2 Now issue the make commands: --- 129,135 ---- Download, then unpack the tar file. For example: ! >gunzip bioperl-1.5.2_100.tar.gz ! >tar xvf bioperl-1.5.2_100.tar ! >cd bioperl-1.5.2_100 Now issue the make commands: *************** *** 135,141 **** undetected bug in Bioperl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that ! there are over 700 modules in Bioperl and the test suite is running almost ! 9000 individual tests, a few failed tests may not affect your usage of ! Bioperl. If you decide that the failed tests will not affect how you intend to use --- 144,150 ---- undetected bug in Bioperl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that ! there are over 800 modules in Bioperl and the test suite is running more ! than 12000 individual tests, a few failed tests may not affect your usage ! of Bioperl. If you decide that the failed tests will not affect how you intend to use *************** *** 148,154 **** bioperl-l at bioperl.org. ! To 'make install' you need write permission in the perl5/site_perl/source ! area. Usually this will require you becoming root, so you will want to ! talk to your systems manager if you don't have the necessary privileges. It is also straightforward to install the package outside of the this --- 157,164 ---- bioperl-l at bioperl.org. ! To './Build install' you need write permission in the perl5/site_perl/source ! area (or similar, depending on your environment). Usually this will require ! you becoming root, so you will want to talk to your systems manager if you ! don't have the necessary privileges. It is also straightforward to install the package outside of the this *************** *** 158,165 **** WHERE ARE THE MAN PAGES? ! When using Makefile.PL, we had to disable the automatic creation of man ! pages because this step was triggering a "line too long" error on some ! OSs due to shell constraints. If you want man pages installed use the ! Build.PL installation process. EXTERNAL PROGRAMS --- 168,176 ---- WHERE ARE THE MAN PAGES? ! When using Makefile.PL (no longer covered in this documentation), we had ! to disable the automatic creation of man pages because this step was ! triggering a "line too long" error on some OSs due to shell constraints. ! If you want man pages installed use the Build.PL installation process ! discussed above. EXTERNAL PROGRAMS *************** *** 229,234 **** like, simply answer the questions on 'perl Build.PL'. The installation directory can be specified by ! perl Build.PL ! ./Build install --install_path script=/foo/scripts By default they install to /usr/bin or similar, depending on platform. --- 240,245 ---- like, simply answer the questions on 'perl Build.PL'. The installation directory can be specified by ! perl Build.PL ! ./Build install --install_path script=/foo/scripts By default they install to /usr/bin or similar, depending on platform. *************** *** 297,301 **** execute the make commands from the Compile/SW directory. ! If all else fails or are unable to access the perl distribution directories, ask your system administrator to place the files there for you. You can always execute perl scripts in the same directory as the --- 308,312 ---- execute the make commands from the Compile/SW directory. ! If all else fails and you are unable to access the perl distribution directories, ask your system administrator to place the files there for you. You can always execute perl scripts in the same directory as the *************** *** 312,316 **** #!/usr/bin/perl use lib "/home/users/dag/lib/perl5/"; ! use Bio::Seq; #<...insert whizzy perl code here...> --- 323,327 ---- #!/usr/bin/perl use lib "/home/users/dag/lib/perl5/"; ! use Bio::Perl; #<...insert whizzy perl code here...> *************** *** 319,341 **** csh or tcsh: ! setenv PERL5LIB /home/users/dag/lib/perl5// bash or sh: ! export PERL5LIB=/home/users/dag/lib/perl5// THE TEST SYSTEM The Bioperl test system is located in the t/ directory and is ! automatically run whenever you execute the 'make test' command. Alternatively if you want to investigate the behavior of a specific test ! such as the SeqIO test you would type: ! >perl -I. -w t/SeqIO.t ! The -I. tells Perl to use the current directory as the include path - this ! makes sure you are testing the modules in this directory not ones ! installed elsewhere in your PERL5LIB path. The -w tells Perl to print all ! warnings. If you are trying to learn how to use a module, often the test suite is a --- 330,357 ---- csh or tcsh: ! setenv PERL5LIB /home/users/dag/lib/perl5/ bash or sh: ! export PERL5LIB=/home/users/dag/lib/perl5/ THE TEST SYSTEM The Bioperl test system is located in the t/ directory and is ! automatically run whenever you execute the './Build test' command ! (having previously run 'Perl Build.PL'; if you have already installed ! Bioperl answer 'no' to script installation to get nicer test output ! later). Alternatively if you want to investigate the behavior of a specific test ! such as the Seq test you would type: ! >./Build test --test_files t/Seq.t --verbose ! The ./ ensures you are using the Build script in the current directory to ! make sure you are testing the modules in this directory not ones ! installed elsewhere. The --test_files arguement can be used multiple times ! to try a set of test scripts in one go. The --verbose arguement outputs ! the detailed test results, instead of just the summary you see during ! './Build test'. If you are trying to learn how to use a module, often the test suite is a *************** *** 385,388 **** This should install the compiled extension. The Bio::Tools::pSW module will work cleanly now. - - \ No newline at end of file --- 401,402 ---- Index: INSTALL.WIN =================================================================== RCS file: /home/repository/bioperl/bioperl-live/INSTALL.WIN,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -d -r1.23 -r1.24 *** INSTALL.WIN 14 Nov 2006 15:13:24 -0000 1.23 --- INSTALL.WIN 21 Nov 2006 10:32:34 -0000 1.24 *************** *** 80,89 **** 7) Right click the latest version of Bioperl available and choose ! install. ! ! 7a) This package will be sufficient for the main ! functionality of Bioperl. However, if you require ! full functionality, you should also install the ! latest Bundle-BioPerl package. 8) Click the green arrow (Run marked actions) to complete the --- 80,85 ---- 7) Right click the latest version of Bioperl available and choose ! install. (Note for users of previous Bioperl releases: you should ! not have to use the Bundle-BioPerl package anymore.) 8) Click the green arrow (Run marked actions) to complete the _______________________________________________ Bioperl-guts-l mailing list Bioperl-guts-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l ------ End of Forwarded Message From bix at sendu.me.uk Tue Nov 21 16:32:02 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 21:32:02 +0000 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: References: Message-ID: <45637052.4040003@sendu.me.uk> Brian Osborne wrote: > Bioperl-l, > > INSTALL has changed in CVS but the Wiki's version has not - you always have > to change both versions of the INSTALL instructions, this is how Chris has > elected to do it. Yes, I will edit the wiki when I've finished with the INSTALL docs. (I may be changing them further, please don't consider the current information gospel.) From hlapp at gmx.net Tue Nov 21 16:44:50 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 16:44:50 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <45636286.6040504@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> <45636286.6040504@molbio.mgh.harvard.edu> Message-ID: <064D0938-C753-40BD-8A0D-C900985193B8@gmx.net> Yes this needs to be better documented. Note that you can use both APIs if you install them under different users (= schema in Oracle). I'm not 100% sure whether both variants are fully prepared for this; you may have to create synonyms for the schema-owner tables first, i.e., SQL> CREATE SYNONYM sg_biodatabase FOR biosqlowner.sg_biodatabase; etc, assuming that are logged on as the user under which you want to create the API, and biosqlowner is the schema-owner of the BioSQL instance. Did you want to use BioSQL with both bioperl and biojava? -hilmar On Nov 21, 2006, at 3:33 PM, gang wu wrote: > Hi Hilmar, > > I just rebuilt the Oracle BioSQL database by strictly following the > INSTALL doc. You are right that BS-create-Biosql-API.sql must be > run to make bioperl-db work with it(the oid columns). But my > installation problem was caused by running BS-create-Biosql- > API2.sql after it, which rendered the database not compatible with > bioperl-db. If I ran only BS-create-Biosql-API.sql, ll bioperl-db > tests could pass. Does this mean that the Oracle version is not > interoperable between the Bio- projects at this point? > > Did I miss anything in the INSTALL or README? I only saw a line "-- > all others (Biojava, etc)" but did not realize I could not run both > BS-create-Biosql-API.sql and BS-create-Biosql-API2.sql. I this is > the case, can you please add it to the docs? > > Thanks very much for your help. > > Gang > > Hilmar Lapp wrote: >> The Oracle error is >> >> ORA-00904: "BIODATABASE"."OID": invalid identifier >> >> and if you look at the accompanying statement, it's the UK select >> statement: >> >> SELECT <*>biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = :p1 >> >> The column OID must exist in the Biodatabase table (which actually >> is a synonym to the SG_BIODATABASE table), if it is the Oracle >> schema. >> >> This actually prompts another suggestion, sorry for not asking >> that first: did you actually install the BioSQL-API on top of the >> schema by running the script BS-create-Biosql-API.sql? (It seems >> that the statement it chokes on is also the first statement being >> prepared, so this may well be the reason) >> >> -hilmar >> >> On Nov 21, 2006, at 3:11 AM, gang wu wrote: >> >>> Can you show me where it indicates I am actually using the MySQL >>> schema. >>> I am pretty sure that I used the sql script files from >>> sql/biosql-ora(Has anyone actually tried to install MySQL schema on >>> Oracle?). I can reinstall the schema if you think that's the way to >>> solve the problem. Thanks very much. >>> >>> Gang >>> >>> Hilmar Lapp wrote: >>>> It looks like you are using the MySQL schema under Oracle. There >>>> are >>>> different DDL scripts for each supported RDBMS. The ones for Oracle >>>> are in the sql/biosql-ora subdirectory. Note the INSTALL >>>> document in >>>> that directory. >>>> >>>> -hilmar >>>> >>>> >>>> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >>>> >>>> >>>>> Hi Hilmar, >>>>> >>>>> Below is the output. Thanks. >>>>> >>>>> Gang >>>>> ========================================================== >>>>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>>>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>>>> TEST_VERBOSE=1 >>>>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/ >>>>> lib64/ >>>>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>>>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>>>> @ARGV;' t/01dbadaptor.t >>>>> t/01dbadaptor....1..19 >>>>> ok 1 >>>>> ok 2 >>>>> ok 3 >>>>> ok 4 >>>>> ok 5 >>>>> ok 6 >>>>> ok 7 >>>>> ok 8 >>>>> ok 9 >>>>> ok 10 >>>>> ok 11 >>>>> attempting to load adaptor class for BioNamespace >>>>> ok 12 >>>>> attempting to load module >>>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> ok 13 >>>>> ok 14 >>>>> attempting to load driver for adaptor class >>>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> attempting to load driver for adaptor class >>>>> Bio::DB::BioSQL::BasePersistenceAdaptor >>>>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>>>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> preparing UK select statement: SELECT biodatabase.oid, >>>>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE >>>>> name >>>>> = ? >>>>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>>>> invalid identifier (DBD ERROR: error possibly near <*> >>>>> indicator at >>>>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>>>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>>>> Statement "SELECT biodatabase.oid, biodatabase.name, >>>>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/ >>>>> lib/ >>>>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>>>> BioNamespaceAdaptor: binding UK column 1 to >>>>> "__dummy__" (namespace) >>>>> Can't call method "bind_param" on an undefined value at blib/lib/ >>>>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>>>> dubious >>>>> Test returned status 255 (wstat 65280, 0xff00) >>>>> DIED. FAILED tests 15-19 >>>>> Failed 5/19 tests, 73.68% okay >>>>> Failed Test Stat Wstat Total Fail Failed List of Failed >>>>> ------------------------------------------------------------------ >>>>> ---- >>>>> --------- >>>>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>>>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>>>> okay. >>>>> make: *** [test_01dbadaptor] Error 2 >>>>> ========================================================= >>>>> >>>>> >>>>> Hilmar Lapp wrote: >>>>> >>>>>> Hi Gang, >>>>>> >>>>>> what I wanted to get at was the error message from the driver >>>>>> when >>>>>> it fails to generate the prepared statement, but this is not in >>>>>> the output. >>>>>> >>>>>> I believe you need set the HARNESS_VERBOSE environment >>>>>> variable to >>>>>> 1 before testing to get what I need: >>>>>> >>>>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>>>> csh/tcsh >>>>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>>>> >>>>>> This will lead to _a lot_ of debugging output. Do not run this >>>>>> for >>>>>> the entire test suite. >>>>>> >>>>>> The errors for mysql I believe are related to the fact that have >>>>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>>>> (completely empty) instance of BioSQL. >>>>>> >>>>>> Let me know what you get for the Oracle test above. >>>>>> >>>>>> -hilmar >>>>>> >>>>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>>>> >>>>>> >>>>>>> Hi Hilmar, >>>>>>> >>>>>>> Thanks for your message. Below are several tests for Oracle and >>>>>>> MySQL. MySQL actually also has two tests with failed items which >>>>>>> may be related to data in BioSQL database. >>>>>>> >>>>>>> Could it be my Oracle installation/configuration has some >>>>>>> issues? >>>>>>> >>>>>>> Thanks. >>>>>>> >>>>>>> Gang >>>>>>> >>>>>> --=========================================================== >>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>>>> =========================================================== >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> --=========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> >> -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Tue Nov 21 18:54:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 17:54:32 -0600 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164141156l.712786l.0l@psu.edu> References: <1164141156l.712786l.0l@psu.edu> Message-ID: <101BBBA4-391D-4F87-8181-F754A2357DA8@uiuc.edu> You'll want to always reply to the list as well. I would say update to a newer version; many changes have been made to parsing GenBank/ SwissProt/EMBL since rel 1.4, including dblinks. If you're using windows you'll need to follow the instructions on the website for the latest release candidate: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Note that the release candidates are located in a different repository, so you'll need to set that up to find them. chris On Nov 21, 2006, at 2:32 PM, Juan Cristobal Vera wrote: > ok, thanks for responding! > I'm using ActivePerl 5.8.8 build 819 on a windows machine (sorry) > and the bioperl 1.4 PPM3 package. Perhaps this is too old? > Here's part of my code (mostly derived from bioperl docs): > ......................... > #cut > > $seqInObj = $indexObj->get_Seq_by_id($line); #get sequence and > create seq object > > #cut > > if (defined $seqInObj->annotation){ > $annotObj = $seqInObj->annotation; #create annotation object > foreach $key ($annotObj->get_all_annotation_keys){ > @values = $annotObj->get_Annotations($key); > foreach $value (@values){ > if (lc($key) eq "dblink"){ > print $outfh "Annotation: $key\n"; > print $outfh $value->as_text,"\n"; > $dbhash_ref = $value->hash_tree; > for $dbKey (keys %{$dbhash_ref}) { > print $outfh $dbKey,": ",$dbhash_ref-> > {$dbKey},"\n"; #none of these prints produce GO terms > } > } > } > } > } > ......................... > My program searches an indexed database on my machine, creates the > objects, and prints out relevant annotations. > Here are some of the accessions I used for testing: > P19351 TNNT_DROME > P36188 TNNI_DROME > P11147 HSP7D_DROME > .......................................... > the relevant output looks something like this (for debugging) for > P19351: > ...................................................................... > Direct database link to X58188 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: X58188 > optional_id: CAA41171.1 > Annotation: dblink > Direct database link to X59376 in database EMBL > database: EMBL > comment: -; mRNA. > primary_id: X59376 > optional_id: CAA42020.1 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48802.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48803.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48804.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48805.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAN09458.1 > Annotation: dblink > Direct database link to AY122145 in database EMBL > database: EMBL > comment: -; mRNA. > primary_id: AY122145 > optional_id: AAM52657.1 > Annotation: dblink > Direct database link to A40547 in database PIR > database: PIR > primary_id: A40547 > optional_id: A40547 > Annotation: dblink > Direct database link to B38594 in database PIR > database: PIR > primary_id: B38594 > optional_id: B38594 > Annotation: dblink > Direct database link to Dm.1717 in database UniGene > database: UniGene > primary_id: Dm.1717 > optional_id: - > Annotation: dblink > Direct database link to P45379 in database HSSP > database: HSSP > primary_id: P45379 > optional_id: 1J1E > Annotation: dblink > Direct database link to P36188 in database IntAct > database: IntAct > primary_id: P36188 > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PA in database KEGG > database: KEGG > primary_id: dme:CG7178-PA > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PB in database KEGG > database: KEGG > primary_id: dme:CG7178-PB > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PC in database KEGG > database: KEGG > primary_id: dme:CG7178-PC > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PD in database KEGG > database: KEGG > primary_id: dme:CG7178-PD > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PG in database KEGG > database: KEGG > primary_id: dme:CG7178-PG > optional_id: - > Annotation: dblink > Direct database link to FBgn0004028 in database FlyBase > database: FlyBase > primary_id: FBgn0004028 > optional_id: wupA > Annotation: dblink > Direct database link to IPR001978 in database InterPro > database: InterPro > primary_id: IPR001978 > optional_id: Troponin > Annotation: dblink > Direct database link to PF00992 in database Pfam > database: Pfam > comment: 1 > primary_id: PF00992 > optional_id: Troponin > .............................................. > as you can see, no GO terms above > ...................................................... > Vs. the actual content of the flat file from for the dblinks from > P19351: > DR EMBL; X54504; CAA38366.1; -; mRNA. > DR EMBL; AY439172; AAR24583.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24584.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24585.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24586.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24587.1; -; Genomic_DNA. > DR EMBL; AY665838; AAU09446.1; -; mRNA. > DR EMBL; AE014298; AAF48288.2; -; Genomic_DNA. > DR EMBL; AE014298; AAF48289.2; -; Genomic_DNA. > DR EMBL; AE014298; AAF48290.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52491.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52492.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52493.1; -; Genomic_DNA. > DR EMBL; AY051989; AAK93413.1; -; mRNA. > DR EMBL; AY070875; AAL48497.1; ALT_SEQ; mRNA. > DR PIR; S13251; S13251. > DR UniGene; Dm.20472; -. > DR HSSP; P45379; 1J1E. > DR Ensembl; CG7107; Drosophila melanogaster. > DR KEGG; dme:CG7107-PE; -. > DR KEGG; dme:CG7107-PF; -. > DR KEGG; dme:CG7107-PG; -. > DR FlyBase; FBgn0004169; up. > DR GO; GO:0007498; P:mesoderm development; IEP:FlyBase. ...... > where the GO term is last entry in dblink section above. > Any help you could provide would be most welcome. Let me know if > this is insufficient information or if you need a working script. > > > On Tue, 21 Nov 2006 00:19:59 -0600 Chris Fields wrote: > Juan, The DBLink objects should be generated. You'll need to give > us a bit more information to go on, though. We need an example > sequence, your local version of Bioperl, maybe a test script, etc. > This is the right forum for this, yes, if you are using BioPerl. > Chris On Nov 20, 2006, at 6:52 PM, Juan Cristobal Vera wrote: > > > > Hi, > I'm writing a simple application to extract various fields > from > swissprot objects and I can't access the GO terms found in > > "dblink" part of the swiss format flat files. I'm not a > > professional programmer and I can't figure out why this is > > occuring. All the other "dblink" keys are being > > generated as far as I can tell (e.g. embl, pfam, etc). The GO > > terms are just skipped over and it's driving me crazy. Not sure if > > this is a bug or a deliberate strategy I'm unfamiliar with. I > > apologize if this is not the correct forum to ask for this sort of > > help and would ask to be directed to the proper one. > > > > Juan > Cristobal Vera > > Graduate Student > > Department of Biology > > > Penn State University > > 208 Mueller Laboratory > > University > Park, PA 16802 > > (814)863-2957 > > > _______________________________________________ > Bioperl-l mailing > list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/ > mailman/listinfo/bioperl-l Christopher Fields Postdoctoral > Researcher Lab of Dr. Robert Switzer Dept of Biochemistry > University of Illinois Urbana-Champaign > > Juan Cristobal Vera > Graduate Student > Department of Biology > Penn State University > 208 Mueller Laboratory > University Park, PA 16802 > (814)863-2957 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Nov 21 18:56:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 17:56:48 -0600 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: References: Message-ID: On Nov 21, 2006, at 2:53 PM, Brian Osborne wrote: > Bioperl-l, > > INSTALL has changed in CVS but the Wiki's version has not - you > always have > to change both versions of the INSTALL instructions, this is how > Chris has > elected to do it. > > Brian O. Agreed (thanks Brian for pointing that out). I have to update these by hand until I can find a more automated way (which will be hard considering the meta content in the wiki). Chris > > > > Date: Tue, 21 Nov 2006 10:32:36 +0000 > To: > Subject: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 > INSTALL, 1.57, > 1.58 INSTALL.WIN, 1.23, 1.24 > > Update of /home/repository/bioperl/bioperl-live > In directory dev.open-bio.org:/tmp/cvs-serv14112 > > Modified Files: > DEPENDENCIES INSTALL INSTALL.WIN > Log Message: > clarification for Bundle::BioPerl, updates for Build.PL > > Index: DEPENDENCIES > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/DEPENDENCIES,v > retrieving revision 1.1 > retrieving revision 1.2 > diff -C2 -d -r1.1 -r1.2 > *** DEPENDENCIES 14 Nov 2006 15:13:24 -0000 1.1 > --- DEPENDENCIES 21 Nov 2006 10:32:34 -0000 1.2 > *************** > *** 5,10 **** > The following packages are used by Bioperl. Not all are required for > Bioperl to operate properly, however some functionality will be > missing > ! without them. You can easily install all of these, except > srsperl.pm, > ! using the Bundle::BioPerl CPAN bundle. > > The DBD::mysql, DB_File and XML::Parser modules require other > applications > --- 5,11 ---- > The following packages are used by Bioperl. Not all are required for > Bioperl to operate properly, however some functionality will be > missing > ! without them. You can easily install all of these by using CPAN > to install > ! Bioperl, or if you have installed Bioperl manually (from archive > or CVS), > ! by using the Bundle::BioPerl CPAN bundle. > > The DBD::mysql, DB_File and XML::Parser modules require other > applications > > Index: INSTALL > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/INSTALL,v > retrieving revision 1.57 > retrieving revision 1.58 > diff -C2 -d -r1.57 -r1.58 > *** INSTALL 16 Nov 2006 16:27:49 -0000 1.57 > --- INSTALL 21 Nov 2006 10:32:34 -0000 1.58 > *************** > *** 1,24 **** > # $Id$ > > ! Installing Bioperl for Unix > > ! * BIOPERL INSTALLATION > ! * SYSTEM REQUIREMENTS > ! * OPTIONAL > ! * ADDITIONAL INSTALLATION INFORMATION > ! * THE BIOPERL BUNDLE > ! * INSTALLING BIOPERL THE EASY WAY USING CPAN > ! * INSTALLING BIOPERL THE EASY WAY USING GNU 'make' > ! * WHERE ARE THE MAN PAGES? > ! * EXTERNAL PROGRAMS > ! * Environment Variables > ! * INSTALLING BIOPERL SCRIPTS > ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA > ! * INSTALLING BIOPERL MODULES THE HARD WAY > ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION > ! * THE TEST SYSTEM > ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE > ! * CONFIGURING for BSD and Solaris boxes > ! * INSTALLATION > > BIOPERL INSTALLATION > --- 1,24 ---- > # $Id$ > > ! Installing Bioperl for Unix > > ! * BIOPERL INSTALLATION > ! * SYSTEM REQUIREMENTS > ! * OPTIONAL > ! * ADDITIONAL INSTALLATION INFORMATION > ! * THE BIOPERL BUNDLE > ! * INSTALLING BIOPERL THE EASY WAY USING CPAN > ! * INSTALLING BIOPERL THE EASY WAY USING Build.PL > ! * WHERE ARE THE MAN PAGES? > ! * EXTERNAL PROGRAMS > ! * Environment Variables > ! * INSTALLING BIOPERL SCRIPTS > ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA > ! * INSTALLING BIOPERL MODULES THE HARD WAY > ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION > ! * THE TEST SYSTEM > ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE > ! * CONFIGURING for BSD and Solaris boxes > ! * INSTALLATION > > BIOPERL INSTALLATION > *************** > *** 41,48 **** > modules is included in the DEPENDENCIES file. > > ! The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation of > these > ! external modules easy. Simply install the bundle using your CPAN > shell and > ! all necessary modules will be installed. See THE BIOPERL BUNDLE, > ! below. > > OPTIONAL > --- 41,49 ---- > modules is included in the DEPENDENCIES file. > > ! When not using CPAN to install Bioperl itself, the CPAN Bioperl > Bundle > ! (Bundle::BioPerl) makes installation of these external modules easy. > Simply > ! install the bundle using your CPAN shell and many optional > modules will be > ! installed. See THE BIOPERL BUNDLE, below. However, it is > recommended you > use > ! CPAN to install Bioperl and not use Bundle::BioPerl. > > OPTIONAL > *************** > *** 61,64 **** > --- 62,72 ---- > THE BIOPERL BUNDLE > > + You do not need to install Bundle::BioPerl if you will install > Bioperl > + using CPAN. This is for users manually installing Bioperl from > archives > + or CVS, who also want an easy way to install the optional external > + modules that Bioperl makes use of. > + > + Bundle::BioPerl does *not* install Bioperl. > + > You typically need root privileges to install using CPAN. If you > don't > have these privileges please see INSTALLING BIOPERL IN A PERSONAL > *************** > *** 86,96 **** > CPAN: Storable loaded ok > Going to read /home/bosborne/.cpan/Metadata > ! Database was generated on Tue, 24 Feb 2004 23:55:23 GMT > ! DistributionB/BI/BIRNEY/bioperl-1.2.tar.gz > ! DistributionB/BI/BIRNEY/bioperl-1.4.tar.gz > > Now install: > > ! cpan>install B/BI/BIRNEY/bioperl-1.4.tar.gz > > If you've installed everything perfectly and all the network > connections > --- 94,105 ---- > CPAN: Storable loaded ok > Going to read /home/bosborne/.cpan/Metadata > ! Database was generated on Mon, 20 Nov 2006 05:24:36 GMT > ! Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz > ! Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz > ! Distribution S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > Now install: > > ! cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > If you've installed everything perfectly and all the network > connections > *************** > *** 100,105 **** > undetected bug in Bioperl, flawed test script, problems with CGI > script used for sequence retrieval at public database, and so on. > Remember > ! that there are over 700 modules in Bioperl and the test suite is > running > ! more than 9000 individual tests, a few failed tests may not > affect your > usage of Bioperl. > > --- 109,114 ---- > undetected bug in Bioperl, flawed test script, problems with CGI > script used for sequence retrieval at public database, and so on. > Remember > ! that there are over 800 modules in Bioperl and the test suite is > running > ! more than 12000 individual tests, a few failed tests may not > affect your > usage of Bioperl. > > *************** > *** 107,111 **** > Bioperl and you'd like to install anyway do: > > ! cpan>force install B/BI/BIRNEY/bioperl-1.4.tar.gz > > This is what most experienced Bioperl users would do. However, if > you're > --- 116,120 ---- > Bioperl and you'd like to install anyway do: > > ! cpan>force install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > This is what most experienced Bioperl users would do. However, if > you're > *************** > *** 113,117 **** > bioperl-l at bioperl.org. > > ! INSTALLING BIOPERL THE EASY WAY USING GNU 'make' > > The advantage of this approach is it's stepwise, so it's easy to > stop and > --- 122,126 ---- > bioperl-l at bioperl.org. > > ! INSTALLING BIOPERL THE EASY WAY USING Build.PL > > The advantage of this approach is it's stepwise, so it's easy to > stop and > *************** > *** 120,126 **** > Download, then unpack the tar file. For example: > > ! >gunzip bioperl-1.5.2.tar.gz > ! >tar xvf bioperl-1.5.2.tar > ! >cd bioperl-1.5.2 > > Now issue the make commands: > --- 129,135 ---- > Download, then unpack the tar file. For example: > > ! >gunzip bioperl-1.5.2_100.tar.gz > ! >tar xvf bioperl-1.5.2_100.tar > ! >cd bioperl-1.5.2_100 > > Now issue the make commands: > *************** > *** 135,141 **** > undetected bug in Bioperl, flawed test script, problems with CGI > script > using for sequence retrieval at public database, and so on. > Remember that > ! there are over 700 modules in Bioperl and the test suite is > running almost > ! 9000 individual tests, a few failed tests may not affect your > usage of > ! Bioperl. > > If you decide that the failed tests will not affect how you > intend to use > --- 144,150 ---- > undetected bug in Bioperl, flawed test script, problems with CGI > script > using for sequence retrieval at public database, and so on. > Remember that > ! there are over 800 modules in Bioperl and the test suite is > running more > ! than 12000 individual tests, a few failed tests may not affect > your usage > ! of Bioperl. > > If you decide that the failed tests will not affect how you > intend to use > *************** > *** 148,154 **** > bioperl-l at bioperl.org. > > ! To 'make install' you need write permission in the perl5/ > site_perl/source > ! area. Usually this will require you becoming root, so you will > want to > ! talk to your systems manager if you don't have the necessary > privileges. > > It is also straightforward to install the package outside of the > this > --- 157,164 ---- > bioperl-l at bioperl.org. > > ! To './Build install' you need write permission in the > perl5/site_perl/source > ! area (or similar, depending on your environment). Usually this will > require > ! you becoming root, so you will want to talk to your systems > manager if you > ! don't have the necessary privileges. > > It is also straightforward to install the package outside of the > this > *************** > *** 158,165 **** > WHERE ARE THE MAN PAGES? > > ! When using Makefile.PL, we had to disable the automatic creation > of man > ! pages because this step was triggering a "line too long" error on > some > ! OSs due to shell constraints. If you want man pages installed use > the > ! Build.PL installation process. > > EXTERNAL PROGRAMS > --- 168,176 ---- > WHERE ARE THE MAN PAGES? > > ! When using Makefile.PL (no longer covered in this documentation), > we had > ! to disable the automatic creation of man pages because this step was > ! triggering a "line too long" error on some OSs due to shell > constraints. > ! If you want man pages installed use the Build.PL installation > process > ! discussed above. > > EXTERNAL PROGRAMS > *************** > *** 229,234 **** > like, simply answer the questions on 'perl Build.PL'. > The installation directory can be specified by > ! perl Build.PL > ! ./Build install --install_path script=/foo/scripts > By default they install to /usr/bin or similar, depending on > platform. > > --- 240,245 ---- > like, simply answer the questions on 'perl Build.PL'. > The installation directory can be specified by > ! perl Build.PL > ! ./Build install --install_path script=/foo/scripts > By default they install to /usr/bin or similar, depending on > platform. > > *************** > *** 297,301 **** > execute the make commands from the Compile/SW directory. > > ! If all else fails or are unable to access the perl distribution > directories, ask your system administrator to place the files > there for > you. You can always execute perl scripts in the same directory as > the > --- 308,312 ---- > execute the make commands from the Compile/SW directory. > > ! If all else fails and you are unable to access the perl distribution > directories, ask your system administrator to place the files > there for > you. You can always execute perl scripts in the same directory as > the > *************** > *** 312,316 **** > #!/usr/bin/perl > use lib "/home/users/dag/lib/perl5/"; > ! use Bio::Seq; > #<...insert whizzy perl code here...> > > --- 323,327 ---- > #!/usr/bin/perl > use lib "/home/users/dag/lib/perl5/"; > ! use Bio::Perl; > #<...insert whizzy perl code here...> > > *************** > *** 319,341 **** > csh or tcsh: > > ! setenv PERL5LIB /home/users/dag/lib/perl5// > > bash or sh: > > ! export PERL5LIB=/home/users/dag/lib/perl5// > > THE TEST SYSTEM > > The Bioperl test system is located in the t/ directory and is > ! automatically run whenever you execute the 'make test' command. > Alternatively if you want to investigate the behavior of a > specific test > ! such as the SeqIO test you would type: > > ! >perl -I. -w t/SeqIO.t > > ! The -I. tells Perl to use the current directory as the include > path - this > ! makes sure you are testing the modules in this directory not ones > ! installed elsewhere in your PERL5LIB path. The -w tells Perl to > print all > ! warnings. > > If you are trying to learn how to use a module, often the test > suite is a > --- 330,357 ---- > csh or tcsh: > > ! setenv PERL5LIB /home/users/dag/lib/perl5/ > > bash or sh: > > ! export PERL5LIB=/home/users/dag/lib/perl5/ > > THE TEST SYSTEM > > The Bioperl test system is located in the t/ directory and is > ! automatically run whenever you execute the './Build test' command > ! (having previously run 'Perl Build.PL'; if you have already > installed > ! Bioperl answer 'no' to script installation to get nicer test output > ! later). > Alternatively if you want to investigate the behavior of a > specific test > ! such as the Seq test you would type: > > ! >./Build test --test_files t/Seq.t --verbose > > ! The ./ ensures you are using the Build script in the current > directory to > ! make sure you are testing the modules in this directory not ones > ! installed elsewhere. The --test_files arguement can be used > multiple times > ! to try a set of test scripts in one go. The --verbose arguement > outputs > ! the detailed test results, instead of just the summary you see > during > ! './Build test'. > > If you are trying to learn how to use a module, often the test > suite is a > *************** > *** 385,388 **** > This should install the compiled extension. The Bio::Tools::pSW > module will work cleanly now. > - > - > \ No newline at end of file > --- 401,402 ---- > > Index: INSTALL.WIN > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/INSTALL.WIN,v > retrieving revision 1.23 > retrieving revision 1.24 > diff -C2 -d -r1.23 -r1.24 > *** INSTALL.WIN 14 Nov 2006 15:13:24 -0000 1.23 > --- INSTALL.WIN 21 Nov 2006 10:32:34 -0000 1.24 > *************** > *** 80,89 **** > > 7) Right click the latest version of Bioperl available > and > choose > ! install. > ! > ! 7a) This package will be sufficient for > the main > ! functionality of Bioperl. However, if you > require > ! full functionality, you should also > install the > ! latest Bundle-BioPerl package. > > 8) Click the green arrow (Run marked actions) to > complete the > --- 80,85 ---- > > 7) Right click the latest version of Bioperl available > and > choose > ! install. (Note for users of previous Bioperl releases: > you > should > ! not have to use the Bundle-BioPerl package anymore.) > > 8) Click the green arrow (Run marked actions) to > complete the > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l > > ------ End of Forwarded Message > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jcv128 at psu.edu Tue Nov 21 15:53:07 2006 From: jcv128 at psu.edu (Juan Cristobal Vera) Date: Tue, 21 Nov 2006 15:53:07 -0500 Subject: [Bioperl-l] GO terms not present in Swiss annotation object-more details Message-ID: <1164142374l.1118292l.0l@psu.edu> Hi, I'm writing a simple application to extract various fields from swissprot objects and I can't access the GO terms found in dblink part of the swiss format flat files. I'm not a professional programmer and I can't figure out why this is occuring. All the other dblink keys are being generated as far as I can tell (e.g. embl, pfam, etc). The GO terms are just skipped over and it's driving me crazy. Not sure if this is a bug or a deliberate strategy I'm unfamiliar with. I'm using ActivePerl 5.8.8 build 819 on a windows machine (sorry) and the bioperl 1.4 PPM3 package. Perhaps this is too old? Here's part of my code (mostly derived from bioperl docs): ......................... #cut $seqInObj = $indexObj->get_Seq_by_id($line); #get sequence and create seq object #cut if (defined $seqInObj->annotation){ $annotObj = $seqInObj->annotation; #create annotation object foreach $key ($annotObj->get_all_annotation_keys){ @values =$annotObj->get_Annotations($key); foreach $value (@values){ if (lc($key) eq "dblink"){ print $outfh "Annotation: $key\n"; print $outfh $value->as_text,"\n"; $dbhash_ref = $value->hash_tree; for $dbKey (keys %{$dbhash_ref}) { print $outfh $dbKey,":",$dbhash_ref->{$dbKey},"\n"; #none of these prints produce GO terms } } } } } ......................... My program searches an indexed database on my machine, creates the objects, and prints out relevant annotations. Here are some of the accessions I used for testing: P19351 TNNT_DROME P36188 TNNI_DROME P11147 HSP7D_DROME .......................................... the relevant output looks something like this (for debugging) for P19351: ...................................................................... Direct database link to X58188 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: X58188 optional_id: CAA41171.1 Annotation: dblink Direct database link to X59376 in database EMBL database: EMBL comment: -; mRNA. primary_id: X59376 optional_id: CAA42020.1 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48802.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48803.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48804.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48805.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAN09458.1 Annotation: dblink Direct database link to AY122145 in database EMBL database: EMBL comment: -; mRNA. primary_id: AY122145 optional_id: AAM52657.1 Annotation: dblink Direct database link to A40547 in database PIR database: PIR primary_id: A40547 optional_id: A40547 Annotation: dblink Direct database link to B38594 in database PIR database: PIR primary_id: B38594 optional_id: B38594 Annotation: dblink Direct database link to Dm.1717 in database UniGene database: UniGene primary_id: Dm.1717 optional_id: - Annotation: dblink Direct database link to P45379 in database HSSP database: HSSP primary_id: P45379 optional_id: 1J1E Annotation: dblink Direct database link to P36188 in database IntAct database: IntAct primary_id: P36188 optional_id: - Annotation: dblink Direct database link to dme:CG7178-PA in database KEGG database: KEGG primary_id: dme:CG7178-PA optional_id: - Annotation: dblink Direct database link to dme:CG7178-PB in database KEGG database: KEGG primary_id: dme:CG7178-PB optional_id: - Annotation: dblink Direct database link to dme:CG7178-PC in database KEGG database: KEGG primary_id: dme:CG7178-PC optional_id: - Annotation: dblink Direct database link to dme:CG7178-PD in database KEGG database: KEGG primary_id: dme:CG7178-PD optional_id: - Annotation: dblink Direct database link to dme:CG7178-PG in database KEGG database: KEGG primary_id: dme:CG7178-PG optional_id: - Annotation: dblink Direct database link to FBgn0004028 in database FlyBase database: FlyBase primary_id: FBgn0004028 optional_id: wupA Annotation: dblink Direct database link to IPR001978 in database InterPro database: InterPro primary_id: IPR001978 optional_id: Troponin Annotation: dblink Direct database link to PF00992 in database Pfam database: Pfam comment: 1 primary_id: PF00992 optional_id: Troponin .............................................. as you can see, no GO terms above ...................................................... Vs. the actual content of the flat file from for the dblinks from P19351: DR EMBL; X54504; CAA38366.1; -; mRNA. DR EMBL; AY439172; AAR24583.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24584.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24585.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24586.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24587.1; -; Genomic_DNA. DR EMBL; AY665838; AAU09446.1; -; mRNA. DR EMBL; AE014298; AAF48288.2; -; Genomic_DNA. DR EMBL; AE014298; AAF48289.2; -; Genomic_DNA. DR EMBL; AE014298; AAF48290.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52491.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52492.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52493.1; -; Genomic_DNA. DR EMBL; AY051989; AAK93413.1; -; mRNA. DR EMBL; AY070875; AAL48497.1; ALT_SEQ; mRNA. DR PIR; S13251; S13251. DR UniGene; Dm.20472; -. DR HSSP; P45379; 1J1E. DR Ensembl; CG7107; Drosophila melanogaster. DR KEGG; dme:CG7107-PE; -. DR KEGG; dme:CG7107-PF; -. DR KEGG; dme:CG7107-PG; -. DR FlyBase; FBgn0004169; up. DR GO; GO:0007498; P:mesoderm development; IEP:FlyBase. ...... where the GO term is last entry in dblink section above. Any help you could provide would be most welcome. Let me know if this is insufficient information or if you need a working script. Juan Cristobal Vera Graduate Student Department of Biology Penn State University 208 Mueller Laboratory University Park, PA 16802 (814)863-2957 From s.bulashevska at dkfz-heidelberg.de Wed Nov 22 06:20:32 2006 From: s.bulashevska at dkfz-heidelberg.de (Svetlana Bulashevska) Date: Wed, 22 Nov 2006 12:20:32 +0100 Subject: [Bioperl-l] a question on gene retrieval Message-ID: <45643280.3000001@dkfz.de> Dear Sirs, I am very new to bioperl and I would highly appreciate if you could advise me on the following. I have the locations of the sequences (like chr5|-1|102826728|102828399) in the human genome and I would like to retrieve what known genes lay in the close proximity to the sequences (they can also overlap with the sequence). What bioperl modules and classes should I use? Thank you very much, Svetlana Bulashevska. From bosborne11 at verizon.net Wed Nov 22 09:04:35 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 22 Nov 2006 09:04:35 -0500 Subject: [Bioperl-l] a question on gene retrieval In-Reply-To: <45643280.3000001@dkfz.de> Message-ID: Svetlana, There's a page discussing these sorts of questions at the Bioperl Wiki: http://www.bioperl.org/wiki/Getting_Genomic_Sequences It sounds like you just want to compare pairs of coordinates initially, not retrieve sequence, yes? Brian O. On 11/22/06 6:20 AM, "Svetlana Bulashevska" wrote: > Dear Sirs, > I am very new to bioperl and I would highly appreciate if you could > advise me on the following. > I have the locations of the sequences (like chr5|-1|102826728|102828399) > in the human genome > and I would like to retrieve what known genes lay in the close proximity > to the sequences (they can also overlap with the sequence). What bioperl > modules and classes should I use? > Thank you very much, > Svetlana Bulashevska. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Wed Nov 22 11:50:07 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Wed, 22 Nov 2006 11:50:07 -0500 Subject: [Bioperl-l] a question on gene retrieval In-Reply-To: <45643280.3000001@dkfz.de> Message-ID: <18C407FD4FFB424292D769FBD68C1987018123A1@NIHCESMLBX8.nih.gov> You can use LWP to retrieve the following URL http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=5&maps=genes [102826728:104828399]-r&cmd=txt and then parse the HTML. Good luck! Wenwu Cui -----Original Message----- From: Svetlana Bulashevska [mailto:s.bulashevska at dkfz-heidelberg.de] Sent: Wednesday, November 22, 2006 6:21 AM To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] a question on gene retrieval Dear Sirs, I am very new to bioperl and I would highly appreciate if you could advise me on the following. I have the locations of the sequences (like chr5|-1|102826728|102828399) in the human genome and I would like to retrieve what known genes lay in the close proximity to the sequences (they can also overlap with the sequence). What bioperl modules and classes should I use? Thank you very much, Svetlana Bulashevska. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cain at cshl.edu Wed Nov 22 14:09:13 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 14:09:13 -0500 (EST) Subject: [Bioperl-l] Unable to build Module::Build on CentOS Message-ID: Hello, I don't want to throw too much fuel on the Module::Build fire, but I have just discovered that I can't get Module::Build to install on CentOS 4.4. It appears that the developers of MB are aware of the problem, but the currently release ---------------------------------------------------------------------- Scott Cain, Ph. D. cain at cshl.org GMOD Coordinator, http://www.gmod.org/ (216)392-3087 ---------------------------------------------------------------------- From cain at cshl.edu Wed Nov 22 14:59:53 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 14:59:53 -0500 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: References: Message-ID: <1164225594.2639.2.camel@localhost.localdomain> Whoops! That was a half composed message that I thought I canceled. \me blushes Oh well, I was going to write a short note to indicate that in fact, I could not get Module::Build to pass tests on CentOS 4.4 and the authors appear to be aware of the problem, but I have no idea if it is likely to be fixed any time soon. So, if anyone wants to install BioPerl 1.5.2 on any CentOS boxes, they have to force install Module::Build. :-/ Scott On Wed, 2006-11-22 at 14:09 -0500, Scott Cain wrote: > Hello, > > I don't want to throw too much fuel on the Module::Build fire, but I have > just discovered that I can't get Module::Build to install on CentOS 4.4. > It appears that the developers of MB are aware of the problem, but the > currently release > > ---------------------------------------------------------------------- > Scott Cain, Ph. D. cain at cshl.org > GMOD Coordinator, http://www.gmod.org/ (216)392-3087 > ---------------------------------------------------------------------- > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From cain at cshl.edu Wed Nov 22 15:04:25 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 15:04:25 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows Message-ID: <1164225865.2639.8.camel@localhost.localdomain> Hello, I just wanted to mention that I made a few minor changes to Build.PL so that I could get `perl Build.PL` to complete successfully. I am using ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't present either. The main thing I did was to have the BioDBGFF test subroutine quit without asking any questions if Build.PL detected that it was running on Windows. There may be a more elegant way of fixing the problem, but I just wanted it to work (as I am also working a release candidate of GBrowse that depends on the release candidate of bioperl). Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From bix at sendu.me.uk Wed Nov 22 18:16:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 22 Nov 2006 23:16:10 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <1164225594.2639.2.camel@localhost.localdomain> References: <1164225594.2639.2.camel@localhost.localdomain> Message-ID: <4564DA3A.1000601@sendu.me.uk> Scott Cain wrote: > Whoops! That was a half composed message that I thought I canceled. > > \me blushes > > Oh well, I was going to write a short note to indicate that in fact, I > could not get Module::Build to pass tests on CentOS 4.4 and the authors > appear to be aware of the problem, but I have no idea if it is likely to > be fixed any time soon. So, if anyone wants to install BioPerl 1.5.2 on > any CentOS boxes, they have to force install Module::Build. :-/ Thanks for the info. 1.5.2 will come with the old ExtUtils::MakeMaker-based Makefile.PL so it should still be possible to install without a force. From bix at sendu.me.uk Wed Nov 22 18:30:07 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 22 Nov 2006 23:30:07 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164225865.2639.8.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> Message-ID: <4564DD7F.8090301@sendu.me.uk> Scott Cain wrote: > Hello, > > I just wanted to mention that I made a few minor changes to Build.PL so > that I could get `perl Build.PL` to complete successfully. I am using > ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > present either. The main thing I did was to have the BioDBGFF test > subroutine quit without asking any questions if Build.PL detected that > it was running on Windows. Is it completely impossible for it to pass under Windows? I find that quite a shame! I'm surprised it was necessary to make your changes, because it already had to return true from: DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0}) Can Windows pass that test without DBD::mysql installed, and having passed it why does it then fail the actual BioDBSeqFeature_mysql.t script? The cleanest way to do your change would be to make some change to the test_db() sub, eg: sub test_db { eval {require DBI;}; if ($^O =~ /mswin/i) { return "Windows isn't supported"; } unless (DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0})) { return "Could not connect to test database"; } return; } From cjfields at uiuc.edu Wed Nov 22 22:32:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 22 Nov 2006 21:32:34 -0600 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <4564DD7F.8090301@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> Message-ID: On Nov 22, 2006, at 5:30 PM, Sendu Bala wrote: > Scott Cain wrote: >> Hello, >> >> I just wanted to mention that I made a few minor changes to >> Build.PL so >> that I could get `perl Build.PL` to complete successfully. I am >> using >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't >> present either. The main thing I did was to have the BioDBGFF test >> subroutine quit without asking any questions if Build.PL detected >> that >> it was running on Windows. > > Is it completely impossible for it to pass under Windows? I find that > quite a shame! > > I'm surprised it was necessary to make your changes, because it > already > had to return true from: > > DBI->connect('dbi:mysql:test',undef,undef, > {RaiseError=>0,PrintError=>0}) > > Can Windows pass that test without DBD::mysql installed, and having > passed it why does it then fail the actual BioDBSeqFeature_mysql.t > script? I think he means the BioDBGFF.t tests, not BioDBSeqFeature_mysql.t. Myself, I can't get the Build script to detect my local MySQL on WinXP, though the BioDBGFF.t tests passed. I haven't been back to work since last Friday so I can't run updated WinXP tests myself. ... chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From roy at colibase.bham.ac.uk Tue Nov 21 13:51:30 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Tue, 21 Nov 2006 18:51:30 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <45634AB2.1020701@colibase.bham.ac.uk> > I'd like to propose changing the default reply-to for posts on this list > from the current 'reply to the poster' to 'reply to the mailing list'. > That way people can just hit 'reply' instead of 'reply to all' in order > to get a reply back to the list. We did this on our mailing list, and found it to be problematic if the messages still appear to come from an individual rather than the list- people may not realise they are replying to the whole list. This can lead to all sorts of issues- my boss and a collaborator once had a discussion (fortunately nothing too sensitive) that was accidentally copied to everyone in their field. The alternative is to overwrite the from: field as well as reply-to:, but then you rely on people having suitably informative signatures should anyone want to contact them off-list, and it makes the archives less useful. See also this: http://www.unicom.com/pw/reply-to-harmful.html Maybe you could tag a reminder to reply-all on every list message? Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From torsten.seemann at infotech.monash.edu.au Wed Nov 22 21:09:42 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Thu, 23 Nov 2006 13:09:42 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: References: Message-ID: <456502E6.8030409@infotech.monash.edu.au> > I don't want to throw too much fuel on the Module::Build fire, but I have > just discovered that I can't get Module::Build to install on CentOS 4.4. I concur with this problem :-( Most of the errors seem to be due to the large number of environmental variables I have set: "Couldn't run Build.PL: Argument list too long at /root/.cpan/build/Module-Build-0.2805/blib/lib/Module/Build/Compat.pm line 200." I had to "force install" the latest Module::Build to get bioperl-live tested and installed via Build.PL. -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From bix at sendu.me.uk Thu Nov 23 02:44:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 07:44:16 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <456502E6.8030409@infotech.monash.edu.au> References: <456502E6.8030409@infotech.monash.edu.au> Message-ID: <45655150.7090300@sendu.me.uk> Torsten Seemann wrote: >> I don't want to throw too much fuel on the Module::Build fire, but I have >> just discovered that I can't get Module::Build to install on CentOS 4.4. > > I concur with this problem :-( > > Most of the errors seem to be due to the large number of environmental > variables I have set: > > "Couldn't run Build.PL: Argument list too long at > /root/.cpan/build/Module-Build-0.2805/blib/lib/Module/Build/Compat.pm > line 200." > > I had to "force install" the latest Module::Build to get bioperl-live > tested and installed via Build.PL. Did everything with the Bioperl Build.PL script work fine after that? From bix at sendu.me.uk Thu Nov 23 05:48:05 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 10:48:05 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <4564DD7F.8090301@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> Message-ID: <45657C65.50200@sendu.me.uk> Sendu Bala wrote: > Scott Cain wrote: >> Hello, >> >> I just wanted to mention that I made a few minor changes to Build.PL so >> that I could get `perl Build.PL` to complete successfully. I am using >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't >> present either. The main thing I did was to have the BioDBGFF test >> subroutine quit without asking any questions if Build.PL detected that >> it was running on Windows. > > Is it completely impossible for it to pass under Windows? I find that > quite a shame! > > I'm surprised it was necessary to make your changes, because it already > had to return true from: [snip] Sorry, that all made no sense because I didn't pay attention to what changes you actually made. Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if being on mswin still causes a problem, or can the excludes_os restriction on line 78 of Build.PL be lifted now? Cheers, Sendu. From Squig at web.de Thu Nov 23 05:46:30 2006 From: Squig at web.de (Squig at web.de) Date: Thu, 23 Nov 2006 11:46:30 +0100 Subject: [Bioperl-l] Bioperl-ext and Staden Package Message-ID: <914558313@web.de> Hello, I have a short question concerning bioperl-ext and the io_lib from the staden package. Are there plans to fix bioperl-ext so it could be used with the actual version of io_lib (at the moment 1.10.1)? Myself has no experience in evoking externally written c - code from perl. But I think the changes to the io_lib - api are very well documented so a fix shouldn't be to hard for somebody with experience in this field. Please correct me if I'm totally wrong. Here you find the changes, you have to scroll a little bit down to "Changes". https://sourceforge.net/project/shownotes.php?release_id=340318&group_id=100316 If you think I could give a helping hand, please let me know. With kind regards, Stefan _______________________________________________________________________ Viren-Scan f?r Ihren PC! Jetzt f?r jeden. Sofort, online und kostenlos. Gleich testen! http://www.pc-sicherheit.web.de/freescan/?mc=022222 From cjfields at uiuc.edu Thu Nov 23 09:12:20 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 08:12:20 -0600 Subject: [Bioperl-l] Bioperl-ext and Staden Package In-Reply-To: <914558313@web.de> References: <914558313@web.de> Message-ID: On Nov 23, 2006, at 4:46 AM, Squig at web.de wrote: > Hello, > > I have a short question concerning bioperl-ext and the io_lib from > the staden package. > > Are there plans to fix bioperl-ext so it could be used with the > actual version of io_lib (at the moment 1.10.1)? This is one of the things tentatively planned but there have been no volunteers for it. > Myself has no experience in evoking externally written c - code > from perl. But I think the changes to the io_lib - api are very > well documented so a fix shouldn't be to hard for somebody with > experience in this field. Please correct me if I'm totally wrong. > > Here you find the changes, you have to scroll a little bit down to > "Changes". > https://sourceforge.net/project/shownotes.php? > release_id=340318&group_id=100316 > > If you think I could give a helping hand, please let me know. > > > With kind regards, > > Stefan > Any help would be greatly appreciated! There are tests included with bioperl-ext which you can add to or modify if needed. You can post patches for any changed code to bugzilla. Here's a HOWTO: http://www.bioperl.org/wiki/HOWTO:SubmitPatch Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sdavis2 at mail.nih.gov Thu Nov 23 10:43:37 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu, 23 Nov 2006 10:43:37 -0500 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45634AB2.1020701@colibase.bham.ac.uk> References: <45633B4A.6060804@sendu.me.uk> <45634AB2.1020701@colibase.bham.ac.uk> Message-ID: <4565C1A9.4080605@mail.nih.gov> Roy Chaudhuri wrote: >> I'd like to propose changing the default reply-to for posts on this list >> from the current 'reply to the poster' to 'reply to the mailing list'. >> That way people can just hit 'reply' instead of 'reply to all' in order >> to get a reply back to the list. >> > > We did this on our mailing list, and found it to be problematic if the > messages still appear to come from an individual rather than the list- > people may not realise they are replying to the whole list. This can > lead to all sorts of issues- my boss and a collaborator once had a > discussion (fortunately nothing too sensitive) that was accidentally > copied to everyone in their field. The alternative is to overwrite the > from: field as well as reply-to:, but then you rely on people having > suitably informative signatures should anyone want to contact them > off-list, and it makes the archives less useful. > > See also this: > http://www.unicom.com/pw/reply-to-harmful.html > I tend to agree here. I have seen some pretty significant accidents due to this feature. I think less harm is done by simply putting the thread back on list, if appropriate, if the sender happens to send to the original sender and not the entire list. Sean From bix at sendu.me.uk Thu Nov 23 16:18:01 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 21:18:01 +0000 Subject: [Bioperl-l] Please do not commit without testing Message-ID: <45661009.8040303@sendu.me.uk> Developers, Please do not commit changes without testing the test suite first, especially to branches! Note that: perl -I. -w t/test.t is NOT a good enough test, especially for test scripts that still use Test and not Test::More. (The above doesn't capture an incorrect number of tests in the plan.) Always initially do: ./Build test --test_files t/test.t --verbose Then run the entire test suite: ./Build test Thank you, Sendu. From The_Polymorph at rocketmail.com Thu Nov 23 16:30:42 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 23 Nov 2006 13:30:42 -0800 (PST) Subject: [Bioperl-l] Bioperl install question. Message-ID: <541373.13923.qm@web50815.mail.yahoo.com> Hi all. My set-up: WinXP (SP2) ActiveState Perl 5.8.8 I used the perl package manager to download BioPerl 1.2.3 but since that is rather old, I downloaded BioPerl-1.4.zip. Can anyone help me from this point? Where should I unzip the file to? Thanks, ~Katie ____________________________________________________________________________________ Want to start your own business? Learn how on Yahoo! Small Business. http://smallbusiness.yahoo.com/r-index From cjfields at uiuc.edu Thu Nov 23 16:43:30 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 15:43:30 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661009.8040303@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> Message-ID: On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: > Developers, > > Please do not commit changes without testing the test suite first, > especially to branches! > > Note that: > > perl -I. -w t/test.t > > is NOT a good enough test, especially for test scripts that still use > Test and not Test::More. (The above doesn't capture an incorrect > number > of tests in the plan.) > > Always initially do: > > ./Build test --test_files t/test.t --verbose > > Then run the entire test suite: > > ./Build test My bad. As a lousy excuse I have been extremely busy with family this holiday. However, the various changes using Module::Build need to be well-documented both in CVS docs and on the wiki. Your latter example ('./Build test --test_files t/test.t --verbose') is nowhere to be found. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 23 17:07:06 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 22:07:06 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> Message-ID: <45661B8A.9060405@sendu.me.uk> Chris Fields wrote: > > On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: > >> Developers, >> >> Please do not commit changes without testing the test suite first, >> especially to branches! >> >> Note that: >> >> perl -I. -w t/test.t >> >> is NOT a good enough test, especially for test scripts that still use >> Test and not Test::More. (The above doesn't capture an incorrect number >> of tests in the plan.) >> >> Always initially do: >> >> ./Build test --test_files t/test.t --verbose >> >> Then run the entire test suite: >> >> ./Build test [snip] > However, the various changes using Module::Build need to be > well-documented both in CVS docs and on the wiki. Your latter example > ('./Build test --test_files t/test.t --verbose') is nowhere to be found. I posted to the list about it on the 17th in thread 'Testing with Build.PL'. Where would you suggest a good place on the wiki would be to mention something like that? From cjfields at uiuc.edu Thu Nov 23 17:23:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 16:23:12 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> On Nov 23, 2006, at 4:07 PM, Sendu Bala wrote: > Chris Fields wrote: >> ... > [snip] >> However, the various changes using Module::Build need to be well- >> documented both in CVS docs and on the wiki. Your latter example >> ('./Build test --test_files t/test.t --verbose') is nowhere to be >> found. > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would > be to mention something like that? The mail list isn't the best place to document this; very few people (including developers) will take the time to go back digging through old posts except as a last resort. Hence these need to be well- documented AND easily accessible. Relevant changes need to be made everywhere that testing or using make/nmake is mentioned in CVS or the wiki. For the testing case I raised, maybe adding something to the various INSTALL docs and the FAQ would be a good start. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 23 17:36:47 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 22:36:47 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> Message-ID: <4566227F.4060102@sendu.me.uk> Chris Fields wrote: > On Nov 23, 2006, at 4:07 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> ... >> [snip] >>> However, the various changes using Module::Build need to be >>> well-documented both in CVS docs and on the wiki. Your latter >>> example ('./Build test --test_files t/test.t --verbose') is nowhere >>> to be found. >> >> I posted to the list about it on the 17th in thread 'Testing with >> Build.PL'. Where would you suggest a good place on the wiki would be >> to mention something like that? > > The mail list isn't the best place to document this; very few people > (including developers) will take the time to go back digging through old > posts except as a last resort. Hence these need to be well-documented > AND easily accessible. Relevant changes need to be made everywhere that > testing or using make/nmake is mentioned in CVS or the wiki. For the > testing case I raised, maybe adding something to the various INSTALL > docs and the FAQ would be a good start. It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's also on the wiki version of same.) I'm not sure that a developer would think to look in the installation documentation for that kind of information, so I've added the info to http://www.bioperl.org/wiki/Bioperl_Best_Practices#Testing as well. From n.haigh at sheffield.ac.uk Thu Nov 23 17:39:17 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 23 Nov 2006 22:39:17 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <45662315.5090600@sheffield.ac.uk> Sendu Bala wrote: > Chris Fields wrote: > >> On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: >> >> >>> Developers, >>> >>> Please do not commit changes without testing the test suite first, >>> especially to branches! >>> >>> Note that: >>> >>> perl -I. -w t/test.t >>> >>> is NOT a good enough test, especially for test scripts that still use >>> Test and not Test::More. (The above doesn't capture an incorrect number >>> of tests in the plan.) >>> >>> Always initially do: >>> >>> ./Build test --test_files t/test.t --verbose >>> >>> Then run the entire test suite: >>> >>> ./Build test >>> > [snip] > >> However, the various changes using Module::Build need to be >> well-documented both in CVS docs and on the wiki. Your latter example >> ('./Build test --test_files t/test.t --verbose') is nowhere to be found. >> > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would be to > mention something like that? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > I'd possibly put it somewhere like: http://www.bioperl.org/wiki/Developer_Information If there's enough stuff to create a new page? If so, how about a page called "testing" or "test suite" or "running tests"?? Just ensure it's given the "Developer resources" Category to make it that bit easier to locate. Nath From n.haigh at sheffield.ac.uk Thu Nov 23 17:31:58 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 23 Nov 2006 22:31:58 +0000 Subject: [Bioperl-l] Bioperl install question. In-Reply-To: <541373.13923.qm@web50815.mail.yahoo.com> References: <541373.13923.qm@web50815.mail.yahoo.com> Message-ID: <4566215E.9090409@sheffield.ac.uk> Caitlin wrote: > Hi all. > > My set-up: > > WinXP (SP2) > ActiveState Perl 5.8.8 > > > I used the perl package manager to download BioPerl 1.2.3 but since > that is rather old, I downloaded BioPerl-1.4.zip. Can anyone help me > from this point? Where should I unzip the file to? > > Thanks, > > ~Katie > > > Hi Katie, First of all try installing Bioperl 1.5.2 RC2 by following the installation instructions for windows at: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows#Installation_Guide See how you get on with that and let us know if you have troubles, or indeed if you manage to install successfully! Thanks Nathan From bix at sendu.me.uk Thu Nov 23 18:31:59 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 23:31:59 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45662909.3010101@infotech.monash.edu.au> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> <45662909.3010101@infotech.monash.edu.au> Message-ID: <45662F6F.2090700@sendu.me.uk> Torsten Seemann wrote: >>> I had to "force install" the latest Module::Build to get bioperl-live >>> tested and installed via Build.PL. >> >> Did everything with the Bioperl Build.PL script work fine after that? > > Yes. > > However it was much "slower" to install, it initially pauses for a long > time, then eventually does the install. I'm guessing you're describing the period of time that it manifies the documentation? Don't you see lots of output detailing what is going on at each moment in time? From torsten.seemann at infotech.monash.edu.au Thu Nov 23 18:50:30 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 24 Nov 2006 10:50:30 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45662F6F.2090700@sendu.me.uk> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> <45662909.3010101@infotech.monash.edu.au> <45662F6F.2090700@sendu.me.uk> Message-ID: <456633C6.5080109@infotech.monash.edu.au> >>>> I had to "force install" the latest Module::Build to get >>>> bioperl-live tested and installed via Build.PL. >>> >>> Did everything with the Bioperl Build.PL script work fine after that? >> >> Yes. >> >> However it was much "slower" to install, it initially pauses for a >> long time, then eventually does the install. > > I'm guessing you're describing the period of time that it manifies the > documentation? Don't you see lots of output detailing what is going on > at each moment in time? Yes I see all the usual output. The pause is between the following two events:. ... ... Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 . # (no output for 15+ seconds on unloaded server) . Installing /usr/share/man/man1/bp_chaos_plot.pl.1" ... ... -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From torsten.seemann at infotech.monash.edu.au Thu Nov 23 18:04:41 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 24 Nov 2006 10:04:41 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45655150.7090300@sendu.me.uk> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> Message-ID: <45662909.3010101@infotech.monash.edu.au> >> I had to "force install" the latest Module::Build to get bioperl-live >> tested and installed via Build.PL. > > Did everything with the Bioperl Build.PL script work fine after that? Yes. However it was much "slower" to install, it initially pauses for a long time, then eventually does the install. -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From cjfields at uiuc.edu Thu Nov 23 23:04:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 22:04:58 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <4566227F.4060102@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> Message-ID: On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: ... > It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's > also on the wiki version of same.) Okay, but I find the Windows page hasn't been updated (still shows nmake). Everything needs to be changed, not just the UNIX pages > I'm not sure that a developer would think to look in the installation > documentation for that kind of information, so I've added the info to > http://www.bioperl.org/wiki/Bioperl_Best_Practices#Testing as well. Sounds good. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 23 23:09:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 22:09:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45662315.5090600@sheffield.ac.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45662315.5090600@sheffield.ac.uk> Message-ID: On Nov 23, 2006, at 4:39 PM, Nathan S. Haigh wrote: > Sendu Bala wrote: >> >> I posted to the list about it on the 17th in thread 'Testing with >> Build.PL'. Where would you suggest a good place on the wiki would >> be to >> mention something like that? >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > I'd possibly put it somewhere like: > http://www.bioperl.org/wiki/Developer_Information > > If there's enough stuff to create a new page? If so, how about a page > called "testing" or "test suite" or "running tests"?? > > Just ensure it's given the "Developer resources" Category to make it > that bit easier to locate. > > Nath ... I think we need to gear some docs not just towards users but also towards potential developers, so maybe a HOWTO for writing and running tests might be the best way to go. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From The_Polymorph at rocketmail.com Thu Nov 23 23:29:18 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 23 Nov 2006 20:29:18 -0800 (PST) Subject: [Bioperl-l] BioPerl install question (update). Message-ID: <20061124042918.5392.qmail@web50801.mail.yahoo.com> Hi all. Ok. I upgraded my ActiveState perl install from build 817 to build 819 and followed the directions located at the site below to install BioPerl 1.5.2 RC2: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Thanks for the help Nathan! ~Katie ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited From bix at sendu.me.uk Fri Nov 24 02:54:19 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 07:54:19 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> Message-ID: <4566A52B.80304@sendu.me.uk> Chris Fields wrote: > On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: > ... > >> It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's >> also on the wiki version of same.) > > Okay, but I find the Windows page hasn't been updated (still shows > nmake). Everything needs to be changed, not just the UNIX pages I don't know what to say for the windows docs. I can't even get perl -V to work on my Windows machine: &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. The Build.PL scripts fails similarly: &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. Can't locate the perl binary used to run this script in (C:\Perl\bin C:\Perl\bin C:\Perl\bin . C:\Program Files\ActiveState Komodo 3.5 C:\Perl\bin C:\WINDOWS\sy stem32 C:\WINDOWS C:\WINDOWS\System32\Wbem C:\Program Files\ATI Technologies\ATI .ACE) I took it that you had no problems? Should I just make the Windows docs similar to the Unix ones? (Or can you do the appropriate update?) From bix at sendu.me.uk Fri Nov 24 03:56:15 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 08:56:15 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 Message-ID: <4566B3AF.2050305@sendu.me.uk> Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. See http://www.bioperl.org/wiki/Release_1.5.2 for instructions on getting and testing this RC. Everyone: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into. Please try the new Build.PL installation script and report back how you get on. Also try installing using CPAN. Your CPAN mirrors may not be current enough, so you may have delete all entries in your urllist first. Developers: Please experiment with installation, especially via CPAN. If you already have all/most prerequisite external modules installed, try uninstalling some and report how effective the system is at reinstalling them for you. RC5 may form the final release for some of the packages (probably all except for bioperl-run), so any further commits made, even to branch-1-5-2, may not make final release. If you think you've committed an important bug fix that should be part of final release, let me know. Thank you, Sendu. PS. What happened to RC4? I didn't announce it, but it was available on CPAN where I did some testing on it. From n.haigh at sheffield.ac.uk Fri Nov 24 04:35:01 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Fri, 24 Nov 2006 09:35:01 +0000 Subject: [Bioperl-l] Bioperl install question. In-Reply-To: <20061124012953.66815.qmail@web50812.mail.yahoo.com> References: <20061124012953.66815.qmail@web50812.mail.yahoo.com> Message-ID: <4566BCC5.7050003@sheffield.ac.uk> Caitlin wrote: > Hi Nathan, > > Thanks for the quick reply. I wasn't able to locate a Perl Package > Manager GUI from the Start menu. The only options displayed are: > > Documentation > OLE Browser > Perl Package Manager > > Clicking on 'Perl Package Manager' loads ppm in a console window (i.e. > non-GUI environment). Should I re-install ActivePerl? If so, that would > eliminate my installed modules wouldn't it? > > Thanks, > > ~Katie > > It sounds like you probably have a version of ActivePerl < 5.8.8.819. If this is the case, download and install the latest ActivePerl version >= 5.8.8.819. If you do a reinstall into the same location as your current ActivePerl installation you will probably maintain all the currently installed modules - but I can't say for definate. Once you have ActivePerl >= 5.8.8.819 installed, you should be able to follow the instructions in the link I provided previously. Nath From n.haigh at sheffield.ac.uk Fri Nov 24 04:38:54 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Fri, 24 Nov 2006 09:38:54 +0000 Subject: [Bioperl-l] BioPerl install question (update). In-Reply-To: <20061124042918.5392.qmail@web50801.mail.yahoo.com> References: <20061124042918.5392.qmail@web50801.mail.yahoo.com> Message-ID: <4566BDAE.50105@sheffield.ac.uk> Caitlin wrote: > Hi all. > > Ok. I upgraded my ActiveState perl install from build 817 to build 819 > and followed the directions located at the site below to install > BioPerl 1.5.2 RC2: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Thanks for the help Nathan! > > ~Katie > > Ah - have just sent an e-mail to say update to build 819! We should be releasing the proper 1.5.2 release quite soon (hopefully in a week or two) At that stage, you should update the bioperl package. It nice to hear it when things work! Nath From cjfields at uiuc.edu Fri Nov 24 07:15:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 24 Nov 2006 06:15:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <4566A52B.80304@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> <4566A52B.80304@sendu.me.uk> Message-ID: On Nov 24, 2006, at 1:54 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: >> ... >>> It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. >>> (It's >>> also on the wiki version of same.) >> Okay, but I find the Windows page hasn't been updated (still shows >> nmake). Everything needs to be changed, not just the UNIX pages > > I don't know what to say for the windows docs. I can't even get > > perl -V > > to work on my Windows machine: > > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > > The Build.PL scripts fails similarly: > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > Can't locate the perl binary used to run this script in (C:\Perl > \bin C:\Perl\bin > C:\Perl\bin . C:\Program Files\ActiveState Komodo 3.5 C:\Perl\bin > C:\WINDOWS\sy > stem32 C:\WINDOWS C:\WINDOWS\System32\Wbem C:\Program Files\ATI > Technologies\ATI > .ACE) > > I took it that you had no problems? Should I just make the Windows > docs similar to the Unix ones? (Or can you do the appropriate update?) No, everything worked on my machine. I'll try making the necessary changes as soon as I can, but it won't be today. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Fri Nov 24 16:38:07 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 16:38:07 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: Is it possible to add a file to the repository (at least temporarily) called README.Build or something that would contain those examples? I find myself saving your emails which I don't think is the most efficient way for me to have those bits handy when I'll need them. -hilmar On Nov 23, 2006, at 5:07 PM, Sendu Bala wrote: > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would > be to > mention something like that? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Fri Nov 24 17:08:37 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 22:08:37 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <45676D65.6000409@sendu.me.uk> Hilmar Lapp wrote: > Is it possible to add a file to the repository (at least temporarily) > called README.Build or something that would contain those examples? > > I find myself saving your emails which I don't think is the most > efficient way for me to have those bits handy when I'll need them. Given that Makefile.PL is just a stub that prints a message about Build.PL, I can just extend the message to include more tips? From hlapp at gmx.net Fri Nov 24 17:27:43 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 17:27:43 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45676D65.6000409@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> Message-ID: On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: > Hilmar Lapp wrote: >> Is it possible to add a file to the repository (at least temporarily) >> called README.Build or something that would contain those examples? >> >> I find myself saving your emails which I don't think is the most >> efficient way for me to have those bits handy when I'll need them. > > Given that Makefile.PL is just a stub that prints a message about > Build.PL, I can just extend the message to include more tips? You could but that wouldn't substitute. Typing ./Build instead of make is not too hard of a change to make; however, you don't want me to go back and run perl Makefile.PL to get a quick refresher every time I want to use a more advanced feature of the generated Build file, do you? -hilmar > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Fri Nov 24 17:46:49 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 22:46:49 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> Message-ID: <45677659.404@sendu.me.uk> Hilmar Lapp wrote: > > On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: > >> Hilmar Lapp wrote: >>> Is it possible to add a file to the repository (at least temporarily) >>> called README.Build or something that would contain those examples? >>> >>> I find myself saving your emails which I don't think is the most >>> efficient way for me to have those bits handy when I'll need them. >> >> Given that Makefile.PL is just a stub that prints a message about >> Build.PL, I can just extend the message to include more tips? > > You could but that wouldn't substitute. Typing ./Build instead of make > is not too hard of a change to make; however, you don't want me to go > back and run perl Makefile.PL to get a quick refresher every time I want > to use a more advanced feature of the generated Build file, do you? If you can remember at least that it is ./Build you need to do something with, it has lovely in-built help. It's entirely standard stuff so nothing to learn - just remember its there! > ./Build -h No action '-h' defined, try running the 'help' action. ./Build help ./Build help test From hlapp at gmx.net Fri Nov 24 19:08:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 19:08:18 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45677659.404@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> <45677659.404@sendu.me.uk> Message-ID: <965EC1D8-AC7D-491A-BCFE-82776D724161@gmx.net> On Nov 24, 2006, at 5:46 PM, Sendu Bala wrote: > If you can remember at least that it is ./Build you need to do > something > with, it has lovely in-built help. It's entirely standard stuff so > nothing to learn - just remember its there! > >> ./Build -h > No action '-h' defined, try running the 'help' action. > > > > ./Build help > > > > ./Build help test > > Sounds nice & will surely be helpful. I guess what I was trying to say is that you could make the value of the examples you typed up in emails already (including the above) much more lasting by copy&pasting them into a document that's within easy reach of a developer who is losing his/her nerves because somebody from the extended family spilled cranberry sauce across his/her new laptop over Thanksgiving. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Fri Nov 24 19:13:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 24 Nov 2006 18:13:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45677659.404@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> <45677659.404@sendu.me.uk> Message-ID: <9AF9038D-71FD-46AD-A486-5B9472BC29AA@uiuc.edu> On Nov 24, 2006, at 4:46 PM, Sendu Bala wrote: > Hilmar Lapp wrote: >> >> On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: >> >>> Hilmar Lapp wrote: >>>> Is it possible to add a file to the repository (at least >>>> temporarily) >>>> called README.Build or something that would contain those examples? >>>> >>>> I find myself saving your emails which I don't think is the most >>>> efficient way for me to have those bits handy when I'll need them. >>> >>> Given that Makefile.PL is just a stub that prints a message about >>> Build.PL, I can just extend the message to include more tips? >> >> You could but that wouldn't substitute. Typing ./Build instead of >> make >> is not too hard of a change to make; however, you don't want me to go >> back and run perl Makefile.PL to get a quick refresher every time >> I want >> to use a more advanced feature of the generated Build file, do you? > > If you can remember at least that it is ./Build you need to do > something > with, it has lovely in-built help. It's entirely standard stuff so > nothing to learn - just remember its there! > >> ./Build -h > No action '-h' defined, try running the 'help' action. > > > > ./Build help > > > > ./Build help test > > Hilmar's suggestion of collecting these snippets of Build-related commands in a single place seems like a good start, since it doesn't really pertain to installation but is of use for developers and future release pumpkins. As for the help example above, as helpful as it is, I don't think most would know it was even there unless it was pointed out. A few blurbs in the FAQ, maybe in the 'BioPerl in General' or a new developer section, might also help. 'How do I run tests using Module::Build?' or 'Where can I find out more about Module::Build?', for instance. It's also much easier (at least to me) to point out to new users or developers that any relevant information is found in 'document x' vs. 'this post on the mail list, found in the mail archives at this link, just follow the thread...'. chris (still recovering after being dragged out on Black Friday). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Fri Nov 24 18:16:47 2006 From: jason at bioperl.org (Jason Stajich) Date: Fri, 24 Nov 2006 15:16:47 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45635F98.8030901@bms.com> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> Message-ID: <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> Can we just weaken the references with Scalar::Util? This should solve the problem for circular refs. Is Scalar::Util part of the core distro in the min perl we are supporting? I can add this in Bio::Tree::Node and look around to see where else it is a problem. We just need a simple script to verify it is having an effect (i.e. a bug report with this). -jason On Nov 21, 2006, at 12:20 PM, Stefan Kirov wrote: > Hilmar Lapp wrote: >> On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: >> >> >>> I don't know if I should hold up release of 1.5.2 for it. Now that >>> you've >>> reported on it I'm leaning toward yes, since the new Bio::Species >>> implementation is one of the major new features of 1.5.2 and it >>> ought to >>> work well. >>> >> >> I disagree to some extent. This is a developer release, so not >> everything is expected to work perfectly. >> >> What's not desirable is if fixing this required another entire >> redesign of the API, so that every dev release introduces >> different API. >> >> The thing is, you'll really only get trouble reports once you put it >> out and people start using it in anger. Don't expect to make it >> perfect before. >> >> >>> Anyway, for the memory leak I have some ideas I haven't tried yet; I >>> don't know if my efforts will solve the speed issue though. >>> >> >> The memory leak sounds more concerning to me. Under which >> circumstances would it crash a script or blow throuhg all of say >> 1-2GB when it should have taken only a tenth of that. >> >> > As I was saying, I did pass ref to an array in the classification > (wrong > parsing): > push @classification,'sapiens', 'Homo', 'Hominidae', $arrayref; > and my script took 17-18 GB. I am really surprised it stopped getting > more RAM and finished successfully. I did not explore further. > Stefan >> -hilmar >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Sat Nov 25 07:47:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 12:47:28 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> Message-ID: <45683B60.9090402@sendu.me.uk> Jason Stajich wrote: > Can we just weaken the references with Scalar::Util? This should solve > the problem for circular refs. I don't know about Stefan's problem, but I tried weakening refs - it fixed the memory leak I was seeing, but caused other problems. > Is Scalar::Util part of the core distro in the min perl we are supporting? Yes. > I can add this in Bio::Tree::Node and look around to see where else it > is a problem. We just need a simple script to verify it is having an > effect (i.e. a bug report with this). perl -w -MBio::SeqIO -e '$si = new Bio::SeqIO(-file => "5UTR.Pln_nr.dat", -format => "embl"); while ($seq = $si->next_seq) { $seq->id; }' Where 5UTR.Pln_nr.dat is a large embl file with ~50000 sequences. For me this takes ~11mins to parse and ~2GB memory. Once I weakened refs in all the places I could find in Bio::Tree::Node and Bio::Tree::Tree it used a constant 0.3% of memory but still took around 11mins. However lots of the tests in the test suite then fail, because Nodes are often made purely to add into a Tree, with the requirement that the Tree keeps hard refs to them all (else the Tree would fall apart). I think the Tree actually only keeps a ref to its root Node, which means Nodes in general must keep hard refs to their Descendants. With that constraint, I haven't been able to break the deadlock and get these things to clean up. Hopefully I'm missing something obvious; please look into it. From cjfields at uiuc.edu Sat Nov 25 08:32:43 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 25 Nov 2006 07:32:43 -0600 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45683B60.9090402@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> Message-ID: <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: ... > I think the Tree actually only keeps a ref to its root Node, which > means > Nodes in general must keep hard refs to their Descendants. With that > constraint, I haven't been able to break the deadlock and get these > things to clean up. > > Hopefully I'm missing something obvious; please look into it. I'm curious to see if this affects sequence parsing (i.e. SwissProt DB parsing). Does anyone know? It sounds pretty serious. Sendu, could you commit a bug report for this? I don't think this should hold up rel 1.5.2 (it's a dev release) but it would be nice to get it fixed. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Sat Nov 25 08:57:53 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 13:57:53 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> Message-ID: <45684BE1.8010902@sendu.me.uk> Chris Fields wrote: > > On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: > ... > >> I think the Tree actually only keeps a ref to its root Node, which means >> Nodes in general must keep hard refs to their Descendants. With that >> constraint, I haven't been able to break the deadlock and get these >> things to clean up. >> >> Hopefully I'm missing something obvious; please look into it. > > I'm curious to see if this affects sequence parsing (i.e. SwissProt DB > parsing). Does anyone know? It sounds pretty serious. Any time you create lots of Bio::Species objects the memory leak ought to arise. > Sendu, could you commit a bug report for this? I don't think this > should hold up rel 1.5.2 (it's a dev release) but it would be nice to > get it fixed. http://bugzilla.open-bio.org/show_bug.cgi?id=2149 From bix at sendu.me.uk Sat Nov 25 17:08:59 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 22:08:59 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> Message-ID: <4568BEFB.4070201@sendu.me.uk> Jason Stajich wrote: > > The circular ref is from Bio::Species when you have > $self->{tree} = Bio::Tree::Tree->new(-root => $self); > > I added a weaken call in Bio::Species code explicitly -- we can't > generally weaken the ref to the root node in Bio::Tree::Tree as that > breaks some other things as you saw. Thanks. Though there's still the issue with Bio::Tree::Node::node_cleanup not doing anything. > I'm not sure I am digging what you've done with Bio::Tree::Tree. Why > didn't you make a specialized Tree object for Taxonomy stuff so that you > can add methods like lineage_node, etc? http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because it's a Tree function. It goes hand in hand with get_lca(), which was already there. I suppose you're saying it would have been more appropriate to have a new Tree-based object that only differed in its new() instead of adding an option to Tree's new()? My thinking was that both the -node option and get_lineage_nodes() are useful for trees in general, not just Bio::Taxon. From jason at bioperl.org Sat Nov 25 16:20:41 2006 From: jason at bioperl.org (Jason Stajich) Date: Sat, 25 Nov 2006 13:20:41 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45684BE1.8010902@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> Message-ID: The circular ref is from Bio::Species when you have $self->{tree} = Bio::Tree::Tree->new(-root => $self); I added a weaken call in Bio::Species code explicitly -- we can't generally weaken the ref to the root node in Bio::Tree::Tree as that breaks some other things as you saw. I'm not sure I am digging what you've done with Bio::Tree::Tree. Why didn't you make a specialized Tree object for Taxonomy stuff so that you can add methods like lineage_node, etc? We'll talk about it in more detail in Dec I guess to see if we can clean up some of the things here. -jason On Nov 25, 2006, at 5:57 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: >> ... >>> I think the Tree actually only keeps a ref to its root Node, >>> which means >>> Nodes in general must keep hard refs to their Descendants. With that >>> constraint, I haven't been able to break the deadlock and get these >>> things to clean up. >>> >>> Hopefully I'm missing something obvious; please look into it. >> I'm curious to see if this affects sequence parsing (i.e. >> SwissProt DB parsing). Does anyone know? It sounds pretty serious. > > Any time you create lots of Bio::Species objects the memory leak > ought to arise. > > >> Sendu, could you commit a bug report for this? I don't think this >> should hold up rel 1.5.2 (it's a dev release) but it would be nice >> to get it fixed. > > http://bugzilla.open-bio.org/show_bug.cgi?id=2149 -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From biology0046 at hotmail.com Sun Nov 26 08:19:45 2006 From: biology0046 at hotmail.com (=?gb2312?B?va0gzsTi/Q==?=) Date: Sun, 26 Nov 2006 13:19:45 +0000 Subject: [Bioperl-l] PAML problem Message-ID: I use scripts at PAML Howto page to caculate M7 or M8 model. but it always report errors: ------------------------------------------------- Error: err: incorrect model for pairwise comparison.check NSsites, alpha, aaDist.. ------------------------------------------------- Can't call method "next_result" on an undefined value at pamtest.txt line 65. ---------------------------------------------------------- use Bio::Tools::Run::Phylo::PAML::Codeml; use Bio::Tools::Run::Alignment::Clustalw; # for projecting alignments from protein to R/DNA space use Bio::Align::Utilities qw(aa_to_dna_aln); # for input of the sequence data use Bio::SeqIO; use Bio::AlignIO; my $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new; #my $seqdata = shift || 'cds.fa'; my $seqio = new Bio::SeqIO(-file =>"CG4686.cds", -format => 'fasta'); my %seqs; my @prots; # process each sequence while ( my $seq = $seqio->next_seq ) { $seqs{$seq->display_id} = $seq; # translate them into protein my $protein = $seq->translate(); my $pseq = $protein->seq(); if( $pseq =~ /\*/ && $pseq !~ /\*$/ ) { warn("provided a CDS sequence with a stop codon, PAML will choke!"); #exit(0); } # Tcoffee can't handle '*' even if it is trailing $pseq =~ s/\*//g; $protein->seq($pseq); push @prots, $protein; } if( @prots < 2 ) { warn("Need at least 2 CDS sequences to proceed"); exit(0); } open(OUT, ">align_output.txt") || die("cannot open output align_output for writing"); # Align the sequences with clustalw my $aa_aln = $aln_factory->align(\@prots); # project the protein alignment back to CDS coordinates my $dna_aln = aa_to_dna_aln($aa_aln, \%seqs); my @each = $dna_aln->each_seq(); my $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new ( -params => { 'NSsites' => 7, 'ncatG'=>10, 'seqtype' => 1, } ); #I change the parameters here # set the alignment object $kaks_factory->alignment($dna_aln); # run the KaKs analysis my ($rc,$parser) = $kaks_factory->run(); my $result = $parser->next_result; Seqfile:>D_pseudoobscuraATGATGGACACATTGGACTACATCACCCTCAGCAATCCCGTGAGCAAGGCGGTTATATATTCGGGATCGGCTATCTTCCGAGCCCTTGGGCTGCGTCCGAAACAGTTGGTTCCGAAGGAGACCCAGACAGTGCGTCCGGTAATGACTCAGTACATGTCGCCGGGTGCTGGCTCGCTGCATAATTTGGCCGGCCGGTACTATCATTTCGTGCGACTGGCTGGCCTAGGCGGCGCTTCGGCTATTTTCATGGGAGCCTACTGCAAATACGTCCTGAAGGAGATCAAGAACGAAAAGGAGCAGCTGGACTCGCAGGCCTTTGCCGATGTCGCCAATCGCATACACTTTTTGCATTCGTTTGCACTGATGGCCATGCCACTGGCCCACTATCCCATAATCACGGGCTCTTTGATGACCACTGGCACACTGCTCTTCAGCGGCTGCATGTACTATCGTGCATTGACGGGCGAGAAGCGCTTCCAGCCGTTTGCCACCGTTGGAGGCTTCTGTCTGATAGCCGCTTGGCTGACGCTGATATTT >D_willistoniATGTCAATAGTTGATACATTGGACTATATAACCCTGGGTAATCCAGTGAGTCGCTTGGTCATATCTTCAACATCGGCATTAATGCGTACAATTGGTCTGCGCCCCAAGCAGGTGCCTATAAAGGATACAGAAATAGCTGGATTGCCACAGCAGGTCCATCATTTCGGAAATCCAAATGGCCCATCCTTATATACAATTGCCGGCTCTCATTATAACTTTATTCGTCTAGCTGGAATTGGCGGAGCATCGGCTATATTTATGGGAGCGTATTGTAAATATTTTCTTAAGGATATCAATGATCCCAAGGAACAGTTGGATTCACAAGCCTTTGCCGATGTGGCCAATCGTATACATTTTCTCCACTCATTTGCATTAATGGCGATGCCCTTGGCTCATTATCCAGTTTTTACTGGCGCCCTTATGACCACCGGCACATTACTTTTCAGTGGGTGTATGTACTATCGCGCTTTAACCGGTGATAAGAGACTTCAACATTATGCCACAATTGGTGGCTTCTGTCTAATGGCTGCTTGGTTATCCTTGGTTTTG >D_melanogasterATGTCAGTCGCTGACACCATTGAATACGTGACCCTGGGCAATCCTGTCAGCAAGATGGTAGCCTCGTCCGCATCCGCCCTGCTCCGCACGCTTGGTCTGCGTCCCAAGAAGGTGCCGGTGCAGGAGACGAGTATGGCGGTGCTCCCTGCCGCCCACAGCTACGCGCATTCACACGGATCACTCTATCGACTGGCCGGCTGCCATTACCACTTCATTCGGCTGGCCGGGATCGTCGGCGCGTCGGCCATCTTTATGGGCGCCTACTGCAAGTACGTCCTGAAGGACGTCAGCGATCCCAAGGAGCAGGTGGACTCGCAGGCCTTTGCTGATGTGGCCAATCGCATCCACTTTCTGCACTCCTTTGCCATGATGGCCATGCCTCTGGCCCACTATCCCGTATTCACTGGCACTTTGATGATTACGGGCATGATGCTTTTCAGCGGCTGCATGTACTACCGCGCTTTGACTGGCGAGAAGCGTCTGCAACCGTACGCGACCGTCGGAGGATTCTGCCTGATGGCCGCGTGGCTGTCGCTGGTCCTG _________________________________________________________________ ???????????????????????????? MSN Messenger: http://messenger.msn.com/cn From chhalling at verizon.net Sun Nov 26 16:00:18 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 26 Nov 2006 16:00:18 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456A0062.6080103@verizon.net> I attempted to use CPAN to install BioPerl 1.5.2 RC5 into a fresh installation of Perl 5.8.8 under Mac OS X 10.4.8 with all dependencies installed. The tests fail for t/SearchIO. An edited record of the output is shown below. cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz [*snip*] *** Optional dependencies section *** All dependencies are installed [*snip*] Running make test PERL_DL_NONLAZY=1 /test/perl/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t [*snip*] t/SearchIO...................ok 1/1340 -------------------- WARNING --------------------- MSG: XML::SAX::Expat not currently supported; must have local copies of NCBI DTD docs! --------------------------------------------------- -------------------- WARNING --------------------- MSG: error in parsing a report: 404 File `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/NCBI_BlastOutput.dtd' does not exist file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/NCBI_BlastOutput.dtd Handler couldn't resolve external entity at line 2, column 82, byte 104 error in processing external entity reference at line 2, column 82, byte 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm line 187 --------------------------------------------------- t/SearchIO...................NOK 5/1340 # Failed test 'The object isa Bio::Search::Result::ResultI' # in t/SearchIO.t at line 65. # The object isn't defined Can't call method "database_name" on an undefined value at t/SearchIO.t line 66. # Looks like you planned 1340 tests but only ran 5. # Looks like you failed 1 test of 5 run. # Looks like your test died just after 5. t/SearchIO...................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-1340 Failed 1336/1340 tests, 0.30% okay [*snip*] Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/SearchIO.t 255 65280 1340 2671 5-1340 2 tests and 126 subtests skipped. Failed 1/235 test scripts. 1336/11940 subtests failed. Files=235, Tests=11940, 321 wallclock secs (154.44 cusr + 24.28 csys = 178.72 CPU) Failed 1/235 test programs. 1336/11940 subtests failed. make: *** [test_dynamic] Error 255 /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Everyone: > Even though 1.5.2 is a 'developer' release, we consider it the most > stable and capable version of Bioperl, and recommend that you use > it in all but the most critical production environments. Please > try it out and let us know of any problems or difficulties you run > into. > > Please try the new Build.PL installation script and report back how > you get on. Also try installing using CPAN. Your CPAN mirrors may > not be current enough, so you may have delete all entries in your > urllist first. > > > Developers: > Please experiment with installation, especially via CPAN. If you > already have all/most prerequisite external modules installed, > try uninstalling some and report how effective the system is at > reinstalling them for you. > > RC5 may form the final release for some of the packages (probably > all except for bioperl-run), so any further commits made, even to > branch-1-5-2, may not make final release. If you think you've > committed an important bug fix that should be part of final release, > let me know. > > > Thank you, > Sendu. > > > PS. What happened to RC4? I didn't announce it, but it was available on > CPAN where I did some testing on it. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Conrad Halling chhalling at verizon.net From cjfields at uiuc.edu Sun Nov 26 17:04:59 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 16:04:59 -0600 Subject: [Bioperl-l] EntrezGene test failures Message-ID: I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ Build test --test_files t/entrezgene.t --verbose': .. ok 1367 ok 1368 - correct number of loops for T18 # Looks like you planned 1417 tests but only ran 1368. # Looks like you failed 22 tests of 1368 run. dubious Test returned status 22 (wstat 5632, 0x1600) DIED. FAILED tests 56, 162, 182, 184, 367, 512, 603, 631, 667, 711, 766, 920, 998, 1107, 1140, 1192, 1225, 1248, 1270, 1297, 1320, 1345, 1369-1417 Failed 71/1417 tests, 94.99% okay Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------ ------- t/entrezgene.t 22 5632 1417 120 56 162 182 184 367 512 603 631 667 711 766 920 998 1107 1140 1192 1225 1248 1270 1297 1320 1345 1369-1417 Failed 1/1 test scripts. 71/1417 subtests failed. Files=1, Tests=1417, 3 wallclock secs ( 3.06 cusr + 0.09 csys = 3.15 CPU) Failed 1/1 test programs. 71/1417 subtests failed. Looks like not all tests are run. Of the tests that fail, all are from unmatched values. A few examples: # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '14' # expected: '16' not ok 56 - correct number of loops for T15 ... # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '28' # expected: '30' ... not ok 162 - correct number of loops for T15 # Failed test in t/entrezgene.t at line 456. # got: '0' # expected: '1' # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '6' # expected: '5' chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Sun Nov 26 17:17:30 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 16:17:30 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456A0062.6080103@verizon.net> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> Message-ID: <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: > I attempted to use CPAN to install BioPerl 1.5.2 RC5 into a fresh > installation of Perl 5.8.8 under Mac OS X 10.4.8 with all dependencies > installed. > > The tests fail for t/SearchIO. An edited record of the output is shown > below. > > > cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz > > [*snip*] > > *** Optional dependencies section *** > All dependencies are installed > > [*snip*] > > Running make test > PERL_DL_NONLAZY=1 /test/perl/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > > [*snip*] > > t/SearchIO...................ok > 1/1340 > -------------------- WARNING --------------------- > MSG: XML::SAX::Expat not currently supported; must have local > copies of > NCBI DTD docs! > --------------------------------------------------- > > -------------------- WARNING --------------------- > MSG: error in parsing a report: > > 404 File > `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ > NCBI_BlastOutput.dtd' > does not exist > file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ > NCBI_BlastOutput.dtd > Handler couldn't resolve external entity at line 2, column 82, byte > 104 > error in processing external entity reference at line 2, column 82, > byte > 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm > line 187 > > --------------------------------------------------- > t/SearchIO...................NOK > 5/1340 > # Failed test 'The object isa Bio::Search::Result::ResultI' > # in t/SearchIO.t at line 65. > # The object isn't defined > Can't call method "database_name" on an undefined value at t/ > SearchIO.t > line 66. > # Looks like you planned 1340 tests but only ran 5. > # Looks like you failed 1 test of 5 run. > # Looks like your test died just after 5. > t/SearchIO...................dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-1340 > Failed 1336/1340 tests, 0.30% okay > > [*snip*] > > Failed Test Stat Wstat Total Fail List of Failed > ---------------------------------------------------------------------- > --------- > t/SearchIO.t 255 65280 1340 2671 5-1340 > 2 tests and 126 subtests skipped. > Failed 1/235 test scripts. 1336/11940 subtests failed. > Files=235, Tests=11940, 321 wallclock secs (154.44 cusr + 24.28 csys = > 178.72 CPU) > Failed 1/235 test programs. 1336/11940 subtests failed. > make: *** [test_dynamic] Error 255 > /usr/bin/make test -- NOT OK > Running make install > make test had returned bad status, won't install without force > ... There is an eval{} block set up to catch that error but apparently it doesn't work. I'll have a look at it. Like the warning states, XML::SAX::Expat is not supported for BLASTXML parsing unless you have the NCBI DTDs installed as well (blame this on NCBI since their BLAST DTDs don't have the explicit web address). Saying that I don't recommend using XML::SAX::Expat at all (it is no longer actively maintained). Pretty much any other XML::SAX backend works; I recommend using XML::SAX::ExpatXS or XML::LibXML for speedier parsing, though XML::SAX::PurePerl also works. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Sun Nov 26 17:56:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 26 Nov 2006 22:56:28 +0000 Subject: [Bioperl-l] EntrezGene test failures In-Reply-To: References: Message-ID: <456A1B9C.5000105@sendu.me.uk> Chris Fields wrote: > I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ > Build test --test_files t/entrezgene.t --verbose': Yes, Stefan is in the middle of bug fixing/ improvements. I changed the test script recently to highlight the problems. From cjfields at uiuc.edu Sun Nov 26 18:48:23 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 17:48:23 -0600 Subject: [Bioperl-l] EntrezGene test failures In-Reply-To: <2ac232dd4a.2dd4a2ac23@bms.com> References: <2ac232dd4a.2dd4a2ac23@bms.com> Message-ID: On Nov 26, 2006, at 5:44 PM, Stefan Kirov wrote: > I thought Sendu rolled back some changes I've made. I was planning to > commit changes both to the module and the tests, but I am not done > yet. > Stefan Not a problem, just wanted to check. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Sun Nov 26 18:44:29 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Sun, 26 Nov 2006 18:44:29 -0500 Subject: [Bioperl-l] EntrezGene test failures Message-ID: <2ac232dd4a.2dd4a2ac23@bms.com> I thought Sendu rolled back some changes I've made. I was planning to commit changes both to the module and the tests, but I am not done yet. Stefan ----- Original Message ----- From: Chris Fields Date: Sunday, November 26, 2006 5:04 pm Subject: [Bioperl-l] EntrezGene test failures > I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ > Build test --test_files t/entrezgene.t --verbose': > > .. > ok 1367 > ok 1368 - correct number of loops for T18 > # Looks like you planned 1417 tests but only ran 1368. > # Looks like you failed 22 tests of 1368 run. > dubious > Test returned status 22 (wstat 5632, 0x1600) > DIED. FAILED tests 56, 162, 182, 184, 367, 512, 603, 631, 667, 711, > > 766, 920, 998, 1107, 1140, 1192, 1225, 1248, 1270, 1297, 1320, > 1345, > 1369-1417 > Failed 71/1417 tests, 94.99% okay > Failed Test Stat Wstat Total Fail List of Failed > -------------------------------------------------------------------- > ---- > ------- > t/entrezgene.t 22 5632 1417 120 56 162 182 184 367 512 603 > 631 > 667 711 > 766 920 998 1107 1140 1192 > 1225 1248 1270 > 1297 1320 1345 1369-1417 > Failed 1/1 test scripts. 71/1417 subtests failed. > Files=1, Tests=1417, 3 wallclock secs ( 3.06 cusr + 0.09 csys = > 3.15 CPU) > Failed 1/1 test programs. 71/1417 subtests failed. > > > > Looks like not all tests are run. Of the tests that fail, all are > from unmatched values. A few examples: > > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '14' > # expected: '16' > not ok 56 - correct number of loops for T15 > > ... > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '28' > # expected: '30' > > ... > > not ok 162 - correct number of loops for T15 > > # Failed test in t/entrezgene.t at line 456. > # got: '0' > # expected: '1' > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '6' > # expected: '5' > > > > chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at uiuc.edu Sun Nov 26 23:14:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 22:14:32 -0600 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4568BEFB.4070201@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> <4568BEFB.4070201@sendu.me.uk> Message-ID: <34BAD635-8C9F-4A22-B114-B3EFB5B544DD@uiuc.edu> On Nov 25, 2006, at 4:08 PM, Sendu Bala wrote: > Jason Stajich wrote: >> >> The circular ref is from Bio::Species when you have >> $self->{tree} = Bio::Tree::Tree->new(-root => $self); >> >> I added a weaken call in Bio::Species code explicitly -- we can't >> generally weaken the ref to the root node in Bio::Tree::Tree as that >> breaks some other things as you saw. > > Thanks. Though there's still the issue with > Bio::Tree::Node::node_cleanup not doing anything. > > >> I'm not sure I am digging what you've done with Bio::Tree::Tree. Why >> didn't you make a specialized Tree object for Taxonomy stuff so >> that you >> can add methods like lineage_node, etc? > > http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree > > get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because > it's > a Tree function. It goes hand in hand with get_lca(), which was > already > there. > > I suppose you're saying it would have been more appropriate to have a > new Tree-based object that only differed in its new() instead of > adding > an option to Tree's new()? > > My thinking was that both the -node option and get_lineage_nodes() are > useful for trees in general, not just Bio::Taxon. Jason's fixes seem to fix the problem (I tested on Mac OS X). However, does Scalar::Utils come as core with perl 5.6.1? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Sun Nov 26 23:58:14 2006 From: jason at bioperl.org (Jason Stajich) Date: Sun, 26 Nov 2006 20:58:14 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4568BEFB.4070201@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> <4568BEFB.4070201@sendu.me.uk> Message-ID: On Nov 25, 2006, at 2:08 PM, Sendu Bala wrote: > Jason Stajich wrote: >> The circular ref is from Bio::Species when you have >> $self->{tree} = Bio::Tree::Tree->new(-root => $self); >> I added a weaken call in Bio::Species code explicitly -- we can't >> generally weaken the ref to the root node in Bio::Tree::Tree as >> that breaks some other things as you saw. > > Thanks. Though there's still the issue with > Bio::Tree::Node::node_cleanup not doing anything. > right - well I am not sure that it is going to get called if you have to remove the cleanup_methods from the object (or does this mean at all?). I don't have any time to debug it any more so we'll just have to wait till later to figure it out. I'd really like to re-visit the tree bjects to see about making them faster anyways so maybe the memory cycle issue can be revisited as well. > >> I'm not sure I am digging what you've done with Bio::Tree::Tree. >> Why didn't you make a specialized Tree object for Taxonomy stuff >> so that you can add methods like lineage_node, etc? > > http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree > > get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because > it's a Tree function. It goes hand in hand with get_lca(), which > was already there. > > I suppose you're saying it would have been more appropriate to have > a new Tree-based object that only differed in its new() instead of > adding an option to Tree's new()? > > My thinking was that both the -node option and get_lineage_nodes() > are useful for trees in general, not just Bio::Taxon. > I guess I was talking about this code in new() - seems like a Tree::Taxon object could have been made to deal with the special case, but probably I am just not seeing the whole picture so no worries. # to stop us pulling in entire database of a Bio::Taxon when we later do # get_nodes() or similar, specifically set ancestor() for each node if ($node->isa('Bio::Taxon')) { push(@lineage, $node) unless $node eq $root; my $ancestor = $root; foreach my $lineage_node (@lineage) { $lineage_node->ancestor($ancestor); } continue { $ancestor = $lineage_node; } } -- Jason Stajich jason at bioperl.org http://jason.open-bio.org/ From anhthu.tieu at gsf.de Mon Nov 27 03:38:36 2006 From: anhthu.tieu at gsf.de (Anh-Thu Tieu) Date: Mon, 27 Nov 2006 09:38:36 +0100 Subject: [Bioperl-l] exention files for bioperl1.5.2 Message-ID: <456AA40C.3050207@gsf.de> Hi, I noticed there has been a new release for bioperl1.5.2 and I wondered whether there is/ will also be an extension file for this version also (as for version 1.4 or 1.5.1). Until now I have only found the core, network, db and the run files. Is it sufficient to install those four packages (+ various additional perl modules) to make bioperl1.5.2 run or do I need any exention files. Thank you. Best regards, Anh Thu From n.haigh at sheffield.ac.uk Mon Nov 27 04:52:39 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 09:52:39 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456AB567.2010601@sheffield.ac.uk> I just checked out RC5 and ran "perl Build.PL" I get: Can't locate object method "new" via package "Module::Build::Notes" (perhaps you forgot to load "Module::Build::Notes"?) at /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. Nath From bix at sendu.me.uk Mon Nov 27 09:50:08 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 14:50:08 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456AB567.2010601@sheffield.ac.uk> References: <4566B3AF.2050305@sendu.me.uk> <456AB567.2010601@sheffield.ac.uk> Message-ID: <456AFB20.4050102@sendu.me.uk> Nathan Haigh wrote: > I just checked out RC5 and ran "perl Build.PL" I get: > > Can't locate object method "new" via package "Module::Build::Notes" > (perhaps you forgot to load "Module::Build::Notes"?) at > /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. What version of Module::Build do you have installed? Does your Module/Build/Base.pm not 'use Modules::Build::Notes' somewhere near the top? Try upgrading to v0.2805 of Module::Build and let me know if that solves the problem. (If you don't have Module::Build installed at all, didn't you get some kind of prompt to install it?) Thank you, Sendu. From bix at sendu.me.uk Mon Nov 27 11:01:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 16:01:16 +0000 Subject: [Bioperl-l] exention files for bioperl1.5.2 In-Reply-To: <456AA40C.3050207@gsf.de> References: <456AA40C.3050207@gsf.de> Message-ID: <456B0BCC.2020202@sendu.me.uk> Anh-Thu Tieu wrote: > Hi, > > I noticed there has been a new release for bioperl1.5.2 and I wondered > whether there is/ will also be an extension file for this version also > (as for version 1.4 or 1.5.1). Until now I have only found the core, > network, db and the run files. Is it sufficient to install those four > packages (+ various additional perl modules) to make bioperl1.5.2 run or > do I need any exention files. What do you mean by 'extension' file? If you mean the bioperl-ext package then hopefully whatever old version you have will still work. It hasn't been tested, nor will it be updated for 1.5.2 From n.haigh at sheffield.ac.uk Mon Nov 27 11:05:40 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 16:05:40 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456AFB20.4050102@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456AB567.2010601@sheffield.ac.uk> <456AFB20.4050102@sendu.me.uk> Message-ID: <456B0CD4.1060602@sheffield.ac.uk> Sendu Bala wrote: > Nathan Haigh wrote: >> I just checked out RC5 and ran "perl Build.PL" I get: >> >> Can't locate object method "new" via package "Module::Build::Notes" >> (perhaps you forgot to load "Module::Build::Notes"?) at >> /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. > > What version of Module::Build do you have installed? Does your > Module/Build/Base.pm not 'use Modules::Build::Notes' somewhere near > the top? > > Try upgrading to v0.2805 of Module::Build and let me know if that > solves the problem. > > (If you don't have Module::Build installed at all, didn't you get some > kind of prompt to install it?) > > > Thank you, > Sendu. I have v0.2612 installed. Upgrading to Module::Build 0.2805 fixed the problem. Nath From bix at sendu.me.uk Mon Nov 27 11:18:35 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 16:18:35 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> Message-ID: <456B0FDB.9020208@sendu.me.uk> Chris Fields wrote: > On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: [snip] >> t/SearchIO...................ok >> 1/1340 >> -------------------- WARNING --------------------- >> MSG: XML::SAX::Expat not currently supported; must have local >> copies of >> NCBI DTD docs! >> --------------------------------------------------- >> >> -------------------- WARNING --------------------- >> MSG: error in parsing a report: >> >> 404 File >> `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >> NCBI_BlastOutput.dtd' >> does not exist >> file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >> NCBI_BlastOutput.dtd >> Handler couldn't resolve external entity at line 2, column 82, byte >> 104 >> error in processing external entity reference at line 2, column 82, >> byte >> 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm >> line 187 [snip] > There is an eval{} block set up to catch that error but apparently it > doesn't work. I'll have a look at it. The test script has nothing to catch in the eval because blastxml.pm catches the error and emits a warning. You'll either have to make blastxml.pm throw (instead of returning undef + warn), or figure something else out. It's a behaviour change, but would anyone care if it threw thanks to this problem? From cjfields at uiuc.edu Mon Nov 27 11:41:53 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 27 Nov 2006 10:41:53 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B0FDB.9020208@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> <456B0FDB.9020208@sendu.me.uk> Message-ID: On Nov 27, 2006, at 10:18 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: > [snip] >>> t/SearchIO...................ok >>> 1/1340 >>> -------------------- WARNING --------------------- >>> MSG: XML::SAX::Expat not currently supported; must have local >>> copies of >>> NCBI DTD docs! >>> --------------------------------------------------- >>> >>> -------------------- WARNING --------------------- >>> MSG: error in parsing a report: >>> >>> 404 File >>> `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >>> NCBI_BlastOutput.dtd' >>> does not exist >>> file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >>> NCBI_BlastOutput.dtd >>> Handler couldn't resolve external entity at line 2, column 82, >>> byte 104 >>> error in processing external entity reference at line 2, column >>> 82, byte >>> 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/ >>> Parser.pm line 187 > > [snip] > >> There is an eval{} block set up to catch that error but apparently >> it doesn't work. I'll have a look at it. > > The test script has nothing to catch in the eval because > blastxml.pm catches the error and emits a warning. You'll either > have to make blastxml.pm throw (instead of returning undef + warn), > or figure something else out. > > It's a behaviour change, but would anyone care if it threw thanks > to this problem? Ah, that's my fault. I had changed that to a throw but didn't commit it. In a nutshell, we can't/won't support XML::SAX::Expat for a number of reasons. One is the problem with the BLAST DTDs (no explicit web address, so XML validation fails). There may be a way to turn validation off. However, the other, more serious issue is that it is no longer maintained (it hasn't been updated in three years). There were plans a year ago for XML::SAX::ExpatXS to take over the XML::SAX::Expat namespace but no one has bothered to make the changeover, apparently. I have committed the change from warn to throw and made the error message more explicit. You can look it over and merge to 1.5.2 at your discretion. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cain.cshl at gmail.com Mon Nov 27 12:39:09 2006 From: cain.cshl at gmail.com (Scott Cain) Date: Mon, 27 Nov 2006 12:39:09 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <45657C65.50200@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> Message-ID: <1164649150.2575.57.camel@localhost.localdomain> Hi Sendu, I won't have time to do testing on Windows until much later in the day, but I at least want to throw out a little more information. In ActivePerl 819, DBI appears to be installed by default, but the method 'available_drivers' doesn't appear to be available (not implemented? returns something invalid when there are none? not sure at the moment). Anyway, as a result, when I run perl Build.PL and there are no drivers installed, it crashes. I'll try to tease out what is going on later tonight. Scott On Thu, 2006-11-23 at 10:48 +0000, Sendu Bala wrote: > Sendu Bala wrote: > > Scott Cain wrote: > >> Hello, > >> > >> I just wanted to mention that I made a few minor changes to Build.PL so > >> that I could get `perl Build.PL` to complete successfully. I am using > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > >> present either. The main thing I did was to have the BioDBGFF test > >> subroutine quit without asking any questions if Build.PL detected that > >> it was running on Windows. > > > > Is it completely impossible for it to pass under Windows? I find that > > quite a shame! > > > > I'm surprised it was necessary to make your changes, because it already > > had to return true from: > [snip] > > Sorry, that all made no sense because I didn't pay attention to what > changes you actually made. > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > being on mswin still causes a problem, or can the excludes_os > restriction on line 78 of Build.PL be lifted now? > > > Cheers, > Sendu. -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain.cshl at gmail.com GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From n.haigh at sheffield.ac.uk Mon Nov 27 12:48:59 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 17:48:59 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456B250B.4050607@sheffield.ac.uk> When running ./Build test for bioperl-run, the tests for DrawGram and DrawTree require me to manually close the window that is opened and press return in the console in order for the test to complete. Nath From bix at sendu.me.uk Mon Nov 27 12:54:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 17:54:58 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B250B.4050607@sheffield.ac.uk> References: <4566B3AF.2050305@sendu.me.uk> <456B250B.4050607@sheffield.ac.uk> Message-ID: <456B2672.5030405@sendu.me.uk> Nathan Haigh wrote: > When running ./Build test for bioperl-run, the tests for DrawGram and > DrawTree require me to manually close the window that is opened and > press return in the console in order for the test to complete. Hasn't that always been the case in the past? Or did you only recently install some optional pre-req? Does anyone know a way around this? From n.haigh at sheffield.ac.uk Mon Nov 27 13:31:18 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 18:31:18 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B2672.5030405@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456B250B.4050607@sheffield.ac.uk> <456B2672.5030405@sendu.me.uk> Message-ID: <456B2EF6.10808@sheffield.ac.uk> Sendu Bala wrote: > Nathan Haigh wrote: >> When running ./Build test for bioperl-run, the tests for DrawGram and >> DrawTree require me to manually close the window that is opened and >> press return in the console in order for the test to complete. > > Hasn't that always been the case in the past? Or did you only recently > install some optional pre-req? > > Does anyone know a way around this? I've always had Phylip installed, and I know I've run the tests remotely without X11 forwarding - which obviously wouldn't allow the windows to appear (tests were still successful). I'm also sure I've run the test locally previously - but I've not noticed it before - starting to think I'm going mad! :-P Nath From cjfields at uiuc.edu Mon Nov 27 16:47:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 27 Nov 2006 15:47:12 -0600 Subject: [Bioperl-l] DBSOURCE parsing Message-ID: Jason, I am working on stockholm and GenPept format parsing, both which have DBLink objects. I have a couple of questions. First, (not a huge issue really, more like a curiosity), is it possible to pass a callback to Annotation objects for the overloaded operators? I'm just thinking of situations where the data is displayed differently in other formats (like Stockholm). Also, would it be feasible to have DBLink objects also contain annotations (comments, other DBLink objects, etc) for more complex data? In particular this regards GenPept stuff, like the following examples: DBSOURCE swissprot: locus BRCA1_HUMAN, accession P38398; class: standard. created: Oct 1, 1994. sequence updated: Feb 1, 1995. annotation updated: Nov 14, 2006. xrefs: U14680.1, AAA73985.1, L78833.1, AAC37594.1, AY273801.1, AAP12647.1, A58881, 1JM7A, 1JNXX, 1N5OX, 1OQAA, 1T15A, 1T29A, 1T2UA, 1T2VA, 1T2VB, 1T2VC, 1T2VD, 1T2VE, 1Y98A xrefs (non-sequence databases): UniGene:Hs.194143, IntAct:P38398, TRANSFAC:T04074, Ensembl:ENSG00000012048, KEGG:hsa:672, HGNC:1100, MIM:113705, MIM:114480, Reactome:P38398, ArrayExpress:P38398, GO:0031436, GO:0008274, GO:0005634, GO:0000151, GO:0050681, GO:0003677, GO:0019899, GO:0003713, GO:0015631, GO:0008270, GO:0030521, GO:0007059, GO:0006978, GO:0008630, GO:0042759, GO:0046600, GO:0016481, GO:0045739, GO:0031398, GO:0045893, GO:0016567, GO:0042981, GO:0042127, GO:0006357, GO:0006359, InterPro:IPR011364, InterPro:IPR001357, InterPro:IPR002378, InterPro:IPR001841, PANTHER:PTHR13763, Pfam:PF00533, Pfam:PF00097, PIRSF:PIRSF001734, PRINTS:PR00493, SMART:SM00292, SMART:SM00184, PROSITE:PS50172, PROSITE:PS00518, PROSITE:PS50089 ... DBSOURCE pdb: molecule 1T2U, chain 65, release Apr 22, 2004; deposition: Apr 22, 2004; class: Antitumor Protein; source: Mol_id: 1; Organism_scientific: Homo Sapiens; Organism_common: Human; Gene: Brca1; Expression_system: Escherichia Coli; Expression_system_common: Bacteria; Exp. method: X-Ray Diffraction. ... DBSOURCE pir: locus I49350; summary: #length 1812 #molecular-weight 198788 #checksum 8813 ; genetic: #gene Brca1 ; superfamily: transcriptional regulator, BRCA1 type; RING finger homology ; PIR dates: 02-Jul-1996 #sequence_revision 02-Jul-1996 #text_change 09-May-2004 . ... DBSOURCE prf: locus 2202221A; state: hepatoma/colonic tumor; taxonomy: Mammalia. My thought is, the first line would be the main DBLink object data, with all subsequent lines as annotation objects (comments, DBLinks, etc) in an annotation collection contained within the main DBLink object. I don't think there would be any danger of circular references if handled correctly. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From chhalling at verizon.net Mon Nov 27 22:25:00 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:25:00 -0500 Subject: [Bioperl-l] A procedure for efficient testing of the installation of BioPerl Message-ID: <456BAC0C.10503@verizon.net> I have devised the following procedure that lets me repeatedly install BioPerl release candidates for testing the installation process. I am performing these tests under Mac OS X 10.4.8. I thought it would be useful to document this process for anyone else who is testing the installation process. I downloaded the tarball for Perl 5.8.8 and ran the following commands to set up the code for installation: cd /Volumes/CHHalling/Perl/Perl-5.8.8 tar -xzf perl-5.8.8.tgz cd perl-5.8.8 sh Configure -Dprefix=/test/perl -Dcc=gcc -des make make test For each round of testing, I run the following commands to install a fresh copy of Perl 5.8.8 and then initialize the cpan utility: cd /Volumes/CHHalling/Perl/Perl-5.8.8/perl-5.8.8 sudo rm -rf /test sudo mkdir /test sudo make install sudo rm -rf ~/.cpan export PATH=/test/perl/bin:$PATH sudo cpan Then I run my cpan commands. For installing BioPerl without having installed the dependencies, I enter the command: cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz For installing the dependencies, then installing BioPerl, I enter the commands: cpan> install Bundle::BioPerl cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz For testing modifications to Bundle::BioPerl (the subject of my next post), I execute the following commands (which exit the cpan utility after I have initialized it, create the Bundle subdirectory, copy the BioPerl.pm file that contains the Bundle::BioPerl package to the .cpan/Bundle directory, start the cpan utility, and install Bundle::BioPerl and BioPerl 1.5.2 RC5): cpan> exit $ sudo mkdir ~/.cpan/Bundle $ sudo cp /Volumes/CHHalling/Perl/BioPerl/BioPerl.pm ~/.cpan/Bundle/ $ sudo cpan cpan> install Bundle::BioPerl cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz When I have finished testing the installation, I loop back to step 2, where I remove the /test directory and reinstall Perl 5.8.8. A note: I was going to use the same procedure to test installing BioPerl 1.5.2 under Perl 5.6.1, but I discovered that Perl 5.6.1 is *so old* that there is no Makefile for Mac OS X. -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Mon Nov 27 22:02:59 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:02:59 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456BA6E3.3010908@verizon.net> I compiled and installed Perl 5.8.8 under Mac OS X 10.4.8 into a directory named /test/perl. Then I used the cpan utility to attempt to install BioPerl 1.5.2 RC5 without having installed any of its dependencies. The installation failed because of the following test failures: t/SeqFeature t/SeqHound_DB t/SeqVersion Here are the pertinent details: t/SeqFeature.................IO::String or LWP::UserAgent or HTTP::Request not installed - skipping DB tests... Can't locate URI/Escape.pm in @INC (@INC contains: t /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/arch /test/perl/lib/5.8.8/darwin-2level /test/perl/lib/5.8.8 /test/perl/lib/site_perl/5.8.8/darwin-2level /test/perl/lib/site_perl/5.8.8 /test/perl/lib/site_perl .) at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/SeqFeature/Annotated.pm line 86. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/SeqFeature/Annotated.pm line 86. Compilation failed in require at t/SeqFeature.t line 52. BEGIN failed--compilation aborted at t/SeqFeature.t line 52. t/SeqFeature.................dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/SeqHound_DB................ok 1/14Can't locate LWP/UserAgent.pm in @INC (@INC contains: /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/arch /test/perl/lib/5.8.8/darwin-2level /test/perl/lib/5.8.8 /test/perl/lib/site_perl/5.8.8/darwin-2level /test/perl/lib/site_perl/5.8.8 /test/perl/lib/site_perl .) at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/WebDBSeqI.pm line 78. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/WebDBSeqI.pm line 78. Compilation failed in require at (eval 19) line 3. ...propagated at /test/perl/lib/5.8.8/base.pm line 85. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/SeqHound.pm line 88. Compilation failed in require at t/SeqHound_DB.t line 41. BEGIN failed--compilation aborted at t/SeqHound_DB.t line 41. Use of uninitialized value in -f at t/SeqHound_DB.t line 34. t/SeqHound_DB................dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/SeqVersion.................NOK 1 # Failed test 'use Bio::DB::SeqVersion;' # in t/SeqVersion.t at line 21. # Tried to use 'Bio::DB::SeqVersion'. # Error: Base class package "LWP::UserAgent" is empty. # (Perhaps you need to 'use' the module which defines that package first.) # at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/WebAgent.pm line 90 # BEGIN failed--compilation aborted at t/SeqVersion.t line 21. # Compilation failed in require at (eval 4) line 3. # ...propagated at /test/perl/lib/5.8.8/base.pm line 85. # BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/SeqVersion.pm line 71. # Compilation failed in require at (eval 3) line 2. # BEGIN failed--compilation aborted at (eval 3) line 2. Can't locate object method "new" via package "Bio::DB::SeqVersion" at t/SeqVersion.t line 23. # Looks like you planned 10 tests but only ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test died just after 1. t/SeqVersion.................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-10 Failed 10/10 tests, 0.00% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/SeqFeature.t 2 512 211 0 0.00% ?? t/SeqHound_DB.t 2 512 14 0 0.00% ?? t/SeqVersion.t 255 65280 10 19 190.00% 1-10 9 tests and 228 subtests skipped. Failed 3/235 test scripts, 98.72% okay. 10/11535 subtests failed, 99.91% okay. make: *** [test_dynamic] Error 255 /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > [*snip*] > Thank you, > Sendu. -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Mon Nov 27 22:51:14 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:51:14 -0500 Subject: [Bioperl-l] A new Bundle::BioPerl Message-ID: <456BB232.4020808@verizon.net> After experimenting with the existing Bundle::BioPerl version 2.1.8 under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install all of the BioPerl dependencies unless run multiple times. I edited the the order that the dependencies were listed so I could get all the dependencies to install on the first try. Then I got carried away and ran some grep commands on the bioperl-live source code to identify all of the dependencies that are use'd or require'd, and I added these dependencies to the Bundle::BioPerl package. Many of these dependencies are core Perl modules, which it doesn't hurt to update. After a few rounds of testing during Thanksgiving weekend festivities, I have completed a new Bundle::BioPerl package that installs virtually all of the dependencies on the first try. There are two modules that won't install. The first is Bio::ASN1::EntrezGene, and the second is CORBA::ORBit. Bio::ASN1::EntrezGene won't install because it is dependent on Bio::Index::AbstractSeq, which is part of BioPerl. CORBA::ORBit won't install because its tarball appears to be corrupted. The cpan utility also reports that Math::Trig and Text::Balanced didn't install, but this is an error, because they are installed correctly. The cpan commands for installing the BioPerl dependencies, Bio::ASN1::EntrezGene, and BioPerl 1.5.2 RC5, will become: cpan> install Bundle::BioPerl cpan> force install Bio::ASN1::EntrezGene cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz I have filed a Bugzilla bug report (bug #2153) and attached my Bundle::BioPerl package (attachment #508) to it for consideration. -- Conrad Halling chhalling at verizon.net From DGroskreutz at twt.com Tue Nov 28 02:00:40 2006 From: DGroskreutz at twt.com (DGroskreutz at twt.com) Date: Tue, 28 Nov 2006 01:00:40 -0600 Subject: [Bioperl-l] CN=Deb Groskreutz/OU=MSN/O=TWT is out of the office. Message-ID: I will be out of the office starting 11/27/2006 and will not return until 12/04/2006. NOTICE OF CONFIDENTIALITY: The information contained in this communication, including attachments, is intended for the specific delivery to and use by the individual(s) to whom it is addressed. This email includes confidential information that may be attorney-client privileged. Any review, retransmission, dissemination, or unauthorized use of this communication is strictly prohibited and may be unlawful. If you have received this communication in error, please reply to the sender immediately and delete the original communication and any copy of it from your computer system, including all attachments. From bix at sendu.me.uk Tue Nov 28 05:53:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 10:53:10 +0000 Subject: [Bioperl-l] A new Bundle::BioPerl In-Reply-To: <456BB232.4020808@verizon.net> References: <456BB232.4020808@verizon.net> Message-ID: <456C1516.5050900@sendu.me.uk> Conrad Halling wrote: > After experimenting with the existing Bundle::BioPerl version 2.1.8 > under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install > all of the BioPerl dependencies unless run multiple times. > > I edited the the order that the dependencies were listed so I could get > all the dependencies to install on the first try. Thank you so much for all your hard work. Its extremely valuable. That said, I'm no longer recommending the usage of Bundle::BioPerl. Instead what I'll do is apply your discovered order to the new Build.PL installation system. You're welcome of course to contact Chris Dagdigian to make sure he knows about your new version of Bundle::BioPerl. He can then upload it to CPAN if he's happy with it, and people who choose to still use the Makefile.PL installation process will surely appreciate the new version of Bundle::BioPerl. Thanks again, Sendu. From st537 at york.ac.uk Tue Nov 28 06:02:07 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Tue, 28 Nov 2006 11:02:07 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... Message-ID: <456C172F.4060008@york.ac.uk> Hi, I am trying to learn bioperl and I'm attempting a few basic thing! I seem to be ok with reading in and outputting sequences and files now I am trying to do a simple BLAST search using a sequence (a sequence object in fact). The code I am attempting to run is at the bottom of the message... I am probably making a dumb mistake and don't understand the capabilities of the objects well enough, but the info for the remoteblast->submit_blast function says that it can take sequences as an argument, I've also tried sending the fasta file name containing my sequence as an argument to submit_blast, with the same result.... I have also tried sending $seqio_obj->next_seq........... i.e the following error message displayed on my terminal: Can't call method "submit_blast" on an undefined value at bioptest2.pl line 22, line 1. I haven't got around to figuring out how to process the returned data from this yet, just trying to get the function to run first! Thanks for any help that anyone can offer me with this... Samantha Thompson #******************************** use Bio::Seq; use Bio::SeqIO; use Bio::Tools::Run::RemoteBlast; use Bio::SearchIO; #seq bit $seq_obj = Bio::Seq->new(-format => 'fasta'); $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); $seq_obj = $seqio_obj->next_seq; #blast bit $remote_blast = Bio::Tools::Run::RemoteBlast->new ( -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); #end From bix at sendu.me.uk Tue Nov 28 07:39:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 12:39:29 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C172F.4060008@york.ac.uk> References: <456C172F.4060008@york.ac.uk> Message-ID: <456C2E01.5070805@sendu.me.uk> Samantha Thompson wrote: > Hi, > I am trying to learn bioperl and I'm attempting a few basic thing! I > seem to be ok with reading in and outputting sequences and files now I > am trying to do a simple BLAST search using a sequence (a sequence > object in fact). The code I am attempting to run is at the bottom of the > message... > I am probably making a dumb mistake and don't understand the > capabilities of the objects well enough, but the info for the > remoteblast->submit_blast function says that it can take sequences as an > argument, I've also tried sending the fasta file name containing my > sequence as an argument to submit_blast, with the same result.... I > have also tried sending $seqio_obj->next_seq........... i.e the > following error message displayed on my terminal: > > Can't call method "submit_blast" on an undefined value at bioptest2.pl > line 22, line 1. Always start your perl scripts with 'use strict;'. This will help you find and fix the main problem with your script, that you made a RemoteBlast object and stored it as $remote_blast, but then tried to use submit_blast() on $remoteBlast which doesn't exist. I've rewritten your code below: use strict; > use Bio::Seq; > use Bio::SeqIO; > > use Bio::Tools::Run::RemoteBlast; > use Bio::SearchIO; > > #seq bit > # $seq_obj = Bio::Seq->new(-format => 'fasta'); # above line doesn't do anything, $seq_obj gets overwritten below > my $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > my $seq_obj = $seqio_obj->next_seq; > > > > #blast bit > my $remote_blast = Bio::Tools::Run::RemoteBlast->new(-prog => 'blastp', -db => 'nr', -expect => '1e-15' ); # submit_blast takes the sequence object, not the sequence string my $blastreturn_obj = $remote_blast->submit_blast($seq_obj); From n.haigh at sheffield.ac.uk Tue Nov 28 08:10:45 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 28 Nov 2006 13:10:45 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C172F.4060008@york.ac.uk> References: <456C172F.4060008@york.ac.uk> Message-ID: <456C3555.3040807@sheffield.ac.uk> Samantha Thompson wrote: > Hi, > I am trying to learn bioperl and I'm attempting a few basic thing! I > seem to be ok with reading in and outputting sequences and files now I > am trying to do a simple BLAST search using a sequence (a sequence > object in fact). The code I am attempting to run is at the bottom of the > message... > I am probably making a dumb mistake and don't understand the > capabilities of the objects well enough, but the info for the > remoteblast->submit_blast function says that it can take sequences as an > argument, I've also tried sending the fasta file name containing my > sequence as an argument to submit_blast, with the same result.... I > have also tried sending $seqio_obj->next_seq........... i.e the > following error message displayed on my terminal: > > Can't call method "submit_blast" on an undefined value at bioptest2.pl > line 22, line 1. > > I haven't got around to figuring out how to process the returned data > from this yet, just trying to get the function to run first! > Thanks for any help that anyone can offer me with this... > > Samantha Thompson > > #******************************** > > > use Bio::Seq; > use Bio::SeqIO; > > use Bio::Tools::Run::RemoteBlast; > use Bio::SearchIO; > > #seq bit > > $seq_obj = Bio::Seq->new(-format => 'fasta'); > > $seqio_obj = Bio::SeqIO->new(-file => > "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > > $seq_obj = $seqio_obj->next_seq; > > > > #blast bit > > $remote_blast = Bio::Tools::Run::RemoteBlast->new ( > -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); > > $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); > > > > > #end > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > Hi Samantha, At first glance and without running any code, the first thing I can see that is incorrect is: $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); I believe that submit_blast() would be likely to take the actual sequence object ($seq_obj) as the argument and not the actual sequence string itself (e.g. "ACTGCTG") that you get by calling $seq_obj->seq. So swap this line for: $blastreturn_obj = $remoteBlast->submit_blast($seq_obj); And see how you get on. Nath From hlapp at gmx.net Tue Nov 28 11:20:59 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 28 Nov 2006 11:20:59 -0500 Subject: [Bioperl-l] load_seqdatabase.pl question In-Reply-To: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> Message-ID: <53C6D534-6E36-4061-B955-E74537839265@gmx.net> Hi Derek, first off, I'd recommend to always post such questions to the mailing list; sometimes I may not have a chance to check my email for a while or respond right away but someone else may know the answer too. In your case it looks like you didn't install bioperl-db. You need to install bioperl-db from CVS (using the main trunk). Instructions for how to do this are on the bioperl web site. Let me (and the list) know if you have trouble finding those. Let me know if you did install bioperl-db. (If you did, did you also set PERL5LIB if you installed it in non-standard place, such as your home directory?) -hilmar On Nov 27, 2006, at 12:07 PM, Derek Buchfink wrote: > Hi, I am new to BioSQL and I am looking to use the > load_seqdatabase.pl script to load some data into a PostgreSQL > 8.1.4 database. I am using version 1.24 of the script. However, I > am getting the following error: > > Can't locate Bio/DB/BioDB.pm in @INC (@INC contains: /usr/lib/ > perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/ > perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/ > site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/ > 5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386- > linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread- > multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/ > lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/ > perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/ > site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/ > site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi / > usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/ > perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/ > vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/ > vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/ > vendor_perl .) at load_seqdatabase.pl line 337. > BEGIN failed--compilation aborted at load_seqdatabase.pl line 337. > > Do you know how to solve this issue or do you have any helpful > suggestions? Thank you very much. > > Derek Buchfink -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cain at cshl.edu Tue Nov 28 11:42:23 2006 From: cain at cshl.edu (Scott Cain) Date: Tue, 28 Nov 2006 11:42:23 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164649150.2575.57.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> Message-ID: <1164732143.2584.33.camel@localhost.localdomain> Hi Sendu, It looks like what you've done did the trick--bioperl installed on both ActivePerl 817 and 819 using Module::Build (though I must admit I didn't look at the tests--I just wanted `perl Build.PL` to work). Nice work! Scott On Mon, 2006-11-27 at 12:39 -0500, Scott Cain wrote: > Hi Sendu, > > I won't have time to do testing on Windows until much later in the day, > but I at least want to throw out a little more information. In > ActivePerl 819, DBI appears to be installed by default, but the method > 'available_drivers' doesn't appear to be available (not implemented? > returns something invalid when there are none? not sure at the moment). > Anyway, as a result, when I run perl Build.PL and there are no drivers > installed, it crashes. I'll try to tease out what is going on later > tonight. > > Scott > > > On Thu, 2006-11-23 at 10:48 +0000, Sendu Bala wrote: > > Sendu Bala wrote: > > > Scott Cain wrote: > > >> Hello, > > >> > > >> I just wanted to mention that I made a few minor changes to Build.PL so > > >> that I could get `perl Build.PL` to complete successfully. I am using > > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > > >> present either. The main thing I did was to have the BioDBGFF test > > >> subroutine quit without asking any questions if Build.PL detected that > > >> it was running on Windows. > > > > > > Is it completely impossible for it to pass under Windows? I find that > > > quite a shame! > > > > > > I'm surprised it was necessary to make your changes, because it already > > > had to return true from: > > [snip] > > > > Sorry, that all made no sense because I didn't pay attention to what > > changes you actually made. > > > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > > being on mswin still causes a problem, or can the excludes_os > > restriction on line 78 of Build.PL be lifted now? > > > > > > Cheers, > > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From bix at sendu.me.uk Tue Nov 28 11:56:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 16:56:04 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164732143.2584.33.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> <1164732143.2584.33.camel@localhost.localdomain> Message-ID: <456C6A24.5090105@sendu.me.uk> Scott Cain wrote: > Hi Sendu, > > It looks like what you've done did the trick--bioperl installed on both > ActivePerl 817 and 819 using Module::Build (though I must admit I didn't > look at the tests--I just wanted `perl Build.PL` to work). Nice work! ... I didn't do anything yet :O Can you check on an export of bioperl-release-1-5-2-rc5 and compare to an export of branch-1-5-2 and let me know if you see the bug in the former and no bug in the latter? From gwu at molbio.mgh.harvard.edu Tue Nov 28 16:13:11 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 28 Nov 2006 16:13:11 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <53C6D534-6E36-4061-B955-E74537839265@gmx.net> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> Message-ID: <456CA667.6010609@molbio.mgh.harvard.edu> Hi everyone, I'm using load_seqdatabase.pl to upload some Genbank genome sequences to my Oracle BioSQL database. I saw some errors(See attached warning message) related to seqfeature_qualifier_value (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data type of maximum 4000 bytes. Did anybody mention this issue before? Should I just modify the column to a type being able store more data such as LONG or CLOB? Thanks. Gang Log information: ============================================ load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank /genomeseq/arabidopsis//NC_003070.gbk Loading /genomeseq/arabidopsis//NC_003070.gbk ... -------------------- WARNING --------------------- MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement execution: ORA-01461: can bind a LONG value only for insert into a LONG column (DBD ERROR: error possibly near <*> indicator at char 12 in 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, rank) VALUES (:p1, :p2, :p3, :p4)') name: INSERT ASSOC [2] Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue values: FK[Bio::SeqFeature::Generic]:14898, FK[Bio::Annotation::SimpleValue]:800, value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFVGTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADRGTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEILASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFPWEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERASVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRYIQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEAEDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDINQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDWRLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFALDIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDNQGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRYMRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYTFESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGLVQATYQASAPLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKVHLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAYTDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFVSVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSEKETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLGNFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEVTAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQLEVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTLSVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVTILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRLMLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAVPDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEYTYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVDISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLRVKLDFNFMYASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQSQVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSNTYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCLSIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWDILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSEIAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASVTRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGLHGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSSKPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDFQTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGLHIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVARLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCLLISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRNGRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVENSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPLWLSVGADASVLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVYLTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITNDSYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQESAGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTSDRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSVFSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESWQFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIVRISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMSVQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRVYPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAMSPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDILGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAKSSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLRPYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMGQRKFIPAKDACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQAINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", rank:"1" -------------------------------------------------- ============================================= From cain.cshl at gmail.com Tue Nov 28 15:18:02 2006 From: cain.cshl at gmail.com (Scott Cain) Date: Tue, 28 Nov 2006 15:18:02 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <456C6A24.5090105@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> <1164732143.2584.33.camel@localhost.localdomain> <456C6A24.5090105@sendu.me.uk> Message-ID: <536f21b00611281218v3e6fd7a1ia2c9e81ef7ad678c@mail.gmail.com> Sendu, I've tried exports of both branches and they both work. Scott On 11/28/06, Sendu Bala wrote: > > Scott Cain wrote: > > Hi Sendu, > > > > It looks like what you've done did the trick--bioperl installed on both > > ActivePerl 817 and 819 using Module::Build (though I must admit I didn't > > look at the tests--I just wanted `perl Build.PL` to work). Nice work! > > ... > > I didn't do anything yet :O > > Can you check on an export of bioperl-release-1-5-2-rc5 and compare to > an export of branch-1-5-2 and let me know if you see the bug in the > former and no bug in the latter? > > From lincoln.stein at gmail.com Tue Nov 28 21:15:38 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 28 Nov 2006 21:15:38 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph Message-ID: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> Hi, I had to back out a change I made to Bio/Graphics/Glyph recently (on both live and 1.52 branches). It caused a bizarre problem in which some features had twice the expected height. Lincoln On 11/23/06, Sendu Bala wrote: > > Sendu Bala wrote: > > Scott Cain wrote: > >> Hello, > >> > >> I just wanted to mention that I made a few minor changes to Build.PL so > >> that I could get `perl Build.PL` to complete successfully. I am using > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > >> present either. The main thing I did was to have the BioDBGFF test > >> subroutine quit without asking any questions if Build.PL detected that > >> it was running on Windows. > > > > Is it completely impossible for it to pass under Windows? I find that > > quite a shame! > > > > I'm surprised it was necessary to make your changes, because it already > > had to return true from: > [snip] > > Sorry, that all made no sense because I didn't pay attention to what > changes you actually made. > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > being on mswin still causes a problem, or can the excludes_os > restriction on line 78 of Build.PL be lifted now? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From hlapp at gmx.net Tue Nov 28 23:54:53 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 28 Nov 2006 23:54:53 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <456CA667.6010609@molbio.mgh.harvard.edu> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> Message-ID: These are the protein translations stored in the feature table as tags of features, right? You can change the type of the column (although there may be some issues when you update the column because the NVL() clause won't work if I recall that correctly), but doing so will deprive you of any 'normal' searches against that column. (You can still use functions from the DBMS_LOB package, but they will be much slower and are completely non-standard.) It is up to you whether that is too big of a price to pay for having some redundant protein translations (translating the feature's DNA sequence should give you the same) in the database. I always trimmed those feature tags off (using a custom SeqProcessor). An alternative is to convert these feature tags into actual bioentries (i.e., Bio::Seq objects; again, a custom SeqProcessor will allow you to do that). -hilmar On Nov 28, 2006, at 4:13 PM, gang wu wrote: > Hi everyone, > > I'm using load_seqdatabase.pl to upload some Genbank genome > sequences to > my Oracle BioSQL database. I saw some errors(See attached warning > message) related to seqfeature_qualifier_value > (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data > type of maximum 4000 bytes. Did anybody mention this issue before? > Should I just modify the column to a type being able store more data > such as LONG or CLOB? > > Thanks. > > Gang > > > Log information: > ============================================ > > load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser > biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank > /genomeseq/arabidopsis//NC_003070.gbk > > > Loading /genomeseq/arabidopsis//NC_003070.gbk ... > > > -------------------- WARNING --------------------- > MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement > execution: ORA-01461: can bind a LONG value only for insert into a > LONG > column (DBD ERROR: error possibly near <*> indicator at char 12 in > 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, > rank) VALUES (:p1, :p2, :p3, :p4)') > name: INSERT ASSOC [2] > Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue > values: FK[Bio::SeqFeature::Generic]:14898, > FK[Bio::Annotation::SimpleValue]:800, > value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFV > GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADR > GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEI > LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFP > WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERA > SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRY > IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEA > EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDI > NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDW > RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFAL > DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDN > QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRY > MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYT > FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGL > VQATYQASA! > > PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKV > HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAY > TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFV > SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSE > KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLG > NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEV > TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQL > EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTL > SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVT > ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRL > MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAV > PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEY > TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVD > ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLR > VKLDFNFM! > > YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQS > QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSN > TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCL > SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWD > ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSE > IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASV > TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGL > HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSS > KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDF > QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGL > HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVA > RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCL > LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRN > GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVE > NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPL > WLSVGADAS! > > VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVY > LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITND > SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQES > AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTS > DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSV > FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESW > QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIV > RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMS > VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRV > YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAM > SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDI > LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAK > SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLR > PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMG > QRKFIPAK! > > DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQ > AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", > rank:"1" > -------------------------------------------------- > > > ============================================= > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Wed Nov 29 04:32:24 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 09:32:24 +0000 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> Message-ID: <456D53A8.80800@sendu.me.uk> Lincoln Stein wrote: > Hi, > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > both live and 1.52 branches). It caused a bizarre problem in which some > features had twice the expected height. Exactly which recent commits are the necessary reversion? Just 'fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height'? I'm confused by 'removed debugging warning' since you did different things during that named commit in HEAD (you removed a warn()) vs branch-1-5-2 (you added a bunch of non-warn related stuff). From lincoln.stein at gmail.com Wed Nov 29 09:41:25 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 29 Nov 2006 09:41:25 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <456D53A8.80800@sendu.me.uk> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> Message-ID: <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> There were two branch-1-5-2 commits last night. Both are needed to back out the changes. Lincoln On 11/29/06, Sendu Bala wrote: > > Lincoln Stein wrote: > > Hi, > > > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > > both live and 1.52 branches). It caused a bizarre problem in which some > > features had twice the expected height. > > Exactly which recent commits are the necessary reversion? Just 'fixed > minor bug which caused some features drawn with the "box" glyph to have > an unexpected height'? > > I'm confused by 'removed debugging warning' since you did different > things during that named commit in HEAD (you removed a warn()) vs > branch-1-5-2 (you added a bunch of non-warn related stuff). > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From lincoln.stein at gmail.com Wed Nov 29 09:38:18 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 29 Nov 2006 09:38:18 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <456D53A8.80800@sendu.me.uk> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> Message-ID: <6dce9a0b0611290638h46dc7d95o7ce5f7977fddfc81@mail.gmail.com> Uh oh. Perhaps I made a mistake during the commits. I will check what's up. Lincoln On 11/29/06, Sendu Bala wrote: > > Lincoln Stein wrote: > > Hi, > > > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > > both live and 1.52 branches). It caused a bizarre problem in which some > > features had twice the expected height. > > Exactly which recent commits are the necessary reversion? Just 'fixed > minor bug which caused some features drawn with the "box" glyph to have > an unexpected height'? > > I'm confused by 'removed debugging warning' since you did different > things during that named commit in HEAD (you removed a warn()) vs > branch-1-5-2 (you added a bunch of non-warn related stuff). > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bix at sendu.me.uk Wed Nov 29 10:53:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 15:53:04 +0000 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> Message-ID: <456DACE0.5060401@sendu.me.uk> Lincoln Stein wrote: > There were two branch-1-5-2 commits last night. Both are needed to back > out the changes. I'm not seeing the changes as a true revert. cvs diff -r 1.113.4.6 Bio/Graphics/Glyph.pm Index: Bio/Graphics/Glyph.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph.pm,v retrieving revision 1.113.4.6 retrieving revision 1.113.4.9 diff -r1.113.4.6 -r1.113.4.9 3c3 < # $Id: Glyph.pm,v 1.113.4.6 2006/11/19 17:18:45 lstein Exp $ --- > # $Id: Glyph.pm,v 1.113.4.9 2006/11/29 02:38:33 lstein Exp $ 126a127,128 > my $feature = $self->feature; > return 1 if $feature->can('compound') && $feature->compound; 1636a1639 > cvs diff -r 1.40.2.2 Bio/Graphics/Glyph/generic.pm Index: Bio/Graphics/Glyph/generic.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/generic.pm,v retrieving revision 1.40.2.2 retrieving revision 1.40.2.4 diff -r1.40.2.2 -r1.40.2.4 113,115c113,115 < my $md = $self->SUPER::maxdepth; < return $md if defined $md; < return 0; --- > my $maxdepth = $self->option('maxdepth'); > return $maxdepth if defined $maxdepth; > return 1; cvs diff -r 1.6.8.1 Bio/Graphics/Glyph/box.pm Index: Bio/Graphics/Glyph/box.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/box.pm,v retrieving revision 1.6.8.1 retrieving revision 1.6.8.2 diff -r1.6.8.1 -r1.6.8.2 14a15,21 > sub maxdepth { > my $self = shift; > my $maxdepth = $self->option('maxdepth'); > return $maxdepth if defined $maxdepth; > return 0; > } > Is this intended? Are you sure this is safe to go into final release for 1.5.2? From cjfields at uiuc.edu Wed Nov 29 10:55:33 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 09:55:33 -0600 Subject: [Bioperl-l] URI, Graph, and Module::Build Message-ID: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> Sendu, For the Build.PL dependencies, do we want to use the absolute module requirements (URI::Escape, Graph::Directed, XML::SAX::Base) or the distributions they are in (URI, Graph, XML::SAX)? Or does it really make a difference? Also, you had mentioned that Bundle::Bioperl is no longer needed since you can have them installed via Build. Does that also hold true for Windows (since CPAN is, at best, very testy installing on Windows)? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 29 11:04:07 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 16:04:07 +0000 Subject: [Bioperl-l] URI, Graph, and Module::Build In-Reply-To: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> References: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> Message-ID: <456DAF77.6050609@sendu.me.uk> Chris Fields wrote: > Sendu, > > For the Build.PL dependencies, do we want to use the absolute module > requirements (URI::Escape, Graph::Directed, XML::SAX::Base) or the > distributions they are in (URI, Graph, XML::SAX)? Or does it really > make a difference? It makes a difference right now only where the absolute module doesn't have a version (because in Build.PL we ask for at least version 0, which fails if version in the modules is actually undef). I'll fix that in the future, so it is best to use the absolute module for clarity. > Also, you had mentioned that Bundle::Bioperl is no longer needed since > you can have them installed via Build. Does that also hold true for > Windows (since CPAN is, at best, very testy installing on Windows)? In what way is it testy? I set up a new WinXP machine today and installed ActiveState. My Build.PL script happily offered to install Module::Build for me with CPAN and it almost worked up until CPAN needed nmake. After installing nmake I upgraded CPAN with no problems and then everything worked after that (I only tried to install one optional dep with Build.PL via CPAN, and that worked fine). So yes, I'd say it holds true for Windows. Though I haven't sorted out the ppd stuff yet. From cjfields at uiuc.edu Wed Nov 29 12:06:37 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 11:06:37 -0600 Subject: [Bioperl-l] URI, Graph, and Module::Build In-Reply-To: <456DAF77.6050609@sendu.me.uk> References: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> <456DAF77.6050609@sendu.me.uk> Message-ID: On Nov 29, 2006, at 10:04 AM, Sendu Bala wrote: > Chris Fields wrote: >> Sendu, >> For the Build.PL dependencies, do we want to use the absolute >> module requirements (URI::Escape, Graph::Directed, XML::SAX::Base) >> or the distributions they are in (URI, Graph, XML::SAX)? Or does >> it really make a difference? > > It makes a difference right now only where the absolute module > doesn't have a version (because in Build.PL we ask for at least > version 0, which fails if version in the modules is actually > undef). I'll fix that in the future, so it is best to use the > absolute module for clarity. That sounds fine to me. If I remember correctly, at least one example (XML::SAX::Base) used to be a separate distribution, but it should install XML::SAX now. >> Also, you had mentioned that Bundle::Bioperl is no longer needed >> since you can have them installed via Build. Does that also hold >> true for Windows (since CPAN is, at best, very testy installing on >> Windows)? > > In what way is it testy? I set up a new WinXP machine today and > installed ActiveState. My Build.PL script happily offered to > install Module::Build for me with CPAN and it almost worked up > until CPAN needed nmake. After installing nmake I upgraded CPAN > with no problems and then everything worked after that (I only > tried to install one optional dep with Build.PL via CPAN, and that > worked fine). It all depends on the modules installed. For instance, a few that include C code or required external compiled libraries had generally been much harder to install, or they were historically; I admittedly haven't tried them recently. GD, (I think) DBD::mysql, and anything using precompiled dynamic libraries were the most problematic, but PPMs and Win-compatible dynamic libraries were always available somewhere which made installing them via nmake a non-issue. One thing I noticed (and mentioned previously) is that using 'Build' also generated HTML docs on WinXP (I didn't see this on Mac OS X); I don't know if this still occurs, so I'll give it a run today. This may be a problem since the pod2html-generated formatting differs significantly from the PPM-generated docs. I'm not even sure they install in the same location as the PPM-generated pages or whether this will cause any issues. Do you also see this on your local WinXP? > So yes, I'd say it holds true for Windows. Though I haven't sorted > out the ppd stuff yet. I think recommending PPM for BioPerl installation on Windows is still the best option for now, at least until we are sure about CPAN installation and the HTML issue above. Frankly, there will just be too much demand for it just for the HTML docs alone (they are quite nice). If the prereqs are listed correctly it should install those first, but who knows with PPM4! It will also generate HTML on the fly and install it in the doc tree as expected, which I have tested. As for a new PPD/PPM, I haven't tried generating it yet via Module::Build (I thought maybe Nathan was doing this). I may give it a go today on WinXP with a fresh ActiveState install (most of my important work is now on Mac OS X, so that shouldn't interfere). My guess is the PPD will be in old PPM3 XML format. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From chhalling at verizon.net Wed Nov 29 20:25:45 2006 From: chhalling at verizon.net (Conrad Halling) Date: Wed, 29 Nov 2006 20:25:45 -0500 Subject: [Bioperl-l] A new Bundle::BioPerl In-Reply-To: <456C1516.5050900@sendu.me.uk> References: <456BB232.4020808@verizon.net> <456C1516.5050900@sendu.me.uk> Message-ID: <456E3319.5090703@verizon.net> Sendu Bala wrote: > Conrad Halling wrote: > >> After experimenting with the existing Bundle::BioPerl version 2.1.8 >> under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install >> all of the BioPerl dependencies unless run multiple times. >> >> I edited the the order that the dependencies were listed so I could get >> all the dependencies to install on the first try. >> > > Thank you so much for all your hard work. Its extremely valuable. That > said, I'm no longer recommending the usage of Bundle::BioPerl. Instead > what I'll do is apply your discovered order to the new Build.PL > installation system. > > You're welcome of course to contact Chris Dagdigian to make sure he > knows about your new version of Bundle::BioPerl. He can then upload it > to CPAN if he's happy with it, and people who choose to still use the > Makefile.PL installation process will surely appreciate the new version > of Bundle::BioPerl. > Good. Having Build.PL do all the work is the best solution. -- Conrad -- Conrad Halling chhalling at verizon.net From hlapp at gmx.net Wed Nov 29 23:03:08 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 29 Nov 2006 23:03:08 -0500 Subject: [Bioperl-l] release timetable Message-ID: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Sendu - what is the timetable in your mind for getting the release out? The NESCent phyloinformatics hackathon is impending and if at all possible I'd really like to see the release be out of the way when it starts so that all new code can simply go the main trunk and has no chance of interfering with the release. Do you think this won't be a problem, or should we start thinking about how to expedite the release in a sensible manner? If anyone else on the list has any concerns about that code going right into the main trunk, please let me know. We (the hackathon attendees) may have to relax the must-pass-all- tests rule, so it may take until a couple days after the end of the event until some sharp edges are smoothened out. I would rather not make any guarantees as to what we will not break, and instead focus on getting the work committed. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Wed Nov 29 23:59:50 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 22:59:50 -0600 Subject: [Bioperl-l] release timetable In-Reply-To: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Message-ID: <8BA20ADA-5114-4DAA-A95F-CBD22C80CC26@uiuc.edu> On Nov 29, 2006, at 10:03 PM, Hilmar Lapp wrote: > Sendu - > > what is the timetable in your mind for getting the release out? The > NESCent phyloinformatics hackathon is impending and if at all > possible I'd really like to see the release be out of the way when it > starts so that all new code can simply go the main trunk and has no > chance of interfering with the release. > > Do you think this won't be a problem, or should we start thinking > about how to expedite the release in a sensible manner? > > If anyone else on the list has any concerns about that code going > right into the main trunk, please let me know. > > We (the hackathon attendees) may have to relax the must-pass-all- > tests rule, so it may take until a couple days after the end of the > event until some sharp edges are smoothened out. I would rather not > make any guarantees as to what we will not break, and instead focus > on getting the work committed. > > -hilmar I think most everyone would agree that the final rel. 1.5.2 should be out soon. I vote for a release before the hackathon, essentially for the same reasons you already outlined. This will get the 1.5.2 code out in the wild for testing, which will (hopefully) iron out any kinks with Module::Build and other residual bugs. If needed we could always have another developer release in the spring to clean up anything from the hackathon, fix bugs from this release, etc. Like you mentioned before, this is (and should be considered by all) a developer release, so not all tests need to pass. Saying that, I applaud Sendu and Nathan (and everyone else) for their hard work. I think this is the first time I can remember where all tests pass for all systems (though I only used since rel 1.0). Even if it's for a finite period of time. -chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 30 02:50:06 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 07:50:06 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Message-ID: <456E8D2E.60908@sendu.me.uk> Hilmar Lapp wrote: > Sendu - > > what is the timetable in your mind for getting the release out? The > NESCent phyloinformatics hackathon is impending and if at all possible > I'd really like to see the release be out of the way when it starts so > that all new code can simply go the main trunk and has no chance of > interfering with the release. I'm going to do one final merge from HEAD to branch-1-5-2 and then set the final release tags later today, so a) anything done at the hackathon won't make any difference, and b) the release should go out soon. The release will go ahead when I've sorted out the Windows PPM and the Change Log (neither of which require code changes on the branch). On this schedule I won't be able to implement Conrad's pre-req installation order in Build.PL since that would require a substantial change to ModuleBuildBioperl.pm and another RC. I'll do that after release so that 1.5.3 benefits. From n.haigh at sheffield.ac.uk Thu Nov 30 03:35:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 08:35:08 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E8D2E.60908@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> Message-ID: <456E97BC.9000800@sheffield.ac.uk> Sendu Bala wrote: > Hilmar Lapp wrote: > >> Sendu - >> >> what is the timetable in your mind for getting the release out? The >> NESCent phyloinformatics hackathon is impending and if at all possible >> I'd really like to see the release be out of the way when it starts so >> that all new code can simply go the main trunk and has no chance of >> interfering with the release. >> > > I'm going to do one final merge from HEAD to branch-1-5-2 and then set > the final release tags later today, so a) anything done at the hackathon > won't make any difference, and b) the release should go out soon. > > The release will go ahead when I've sorted out the Windows PPM and the > Change Log (neither of which require code changes on the branch). > > On this schedule I won't be able to implement Conrad's pre-req > installation order in Build.PL since that would require a substantial > change to ModuleBuildBioperl.pm and another RC. I'll do that after > release so that 1.5.3 benefits. > > _______________________________________________ > I've not had the time to test out the new CPAN installation until now. I've just tried it on a clan install of ActivePerl 5.8.8.819 and it didn't install: Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/RemoteBlast.t 9 2304 13 0 0.00% ?? t/rnamotif.t 2 512 72 144 200.00% 1-72 2 tests and 197 subtests skipped. How can I get the test output from CPAN to go to a log file so I can look at the errors more closely? Nath p.s. I think nmake will need to be installed for windows but I'll doublecheck. --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-0, 29/11/2006 Tested on: 30/11/2006 08:35:09 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From bix at sendu.me.uk Thu Nov 30 03:46:44 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 08:46:44 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E97BC.9000800@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> Message-ID: <456E9A74.9020404@sendu.me.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: >> Hilmar Lapp wrote: >> >>> Sendu - >>> >>> what is the timetable in your mind for getting the release out? The >>> NESCent phyloinformatics hackathon is impending and if at all >>> possible I'd really like to see the release be out of the way when it >>> starts so that all new code can simply go the main trunk and has no >>> chance of interfering with the release. >>> >> >> I'm going to do one final merge from HEAD to branch-1-5-2 and then set >> the final release tags later today, so a) anything done at the >> hackathon won't make any difference, and b) the release should go out >> soon. >> >> The release will go ahead when I've sorted out the Windows PPM and the >> Change Log (neither of which require code changes on the branch). >> >> On this schedule I won't be able to implement Conrad's pre-req >> installation order in Build.PL since that would require a substantial >> change to ModuleBuildBioperl.pm and another RC. I'll do that after >> release so that 1.5.3 benefits. >> >> _______________________________________________ >> > > I've not had the time to test out the new CPAN installation until now. > I've just tried it 'it' being RC5? On Windows? > on a clan install of ActivePerl 5.8.8.819 and it > didn't install: > Failed Test Stat Wstat Total Fail Failed List of Failed > ------------------------------------------------------------------------------- > > t/RemoteBlast.t 9 2304 13 0 0.00% ?? > t/rnamotif.t 2 512 72 144 200.00% 1-72 > 2 tests and 197 subtests skipped. > > How can I get the test output from CPAN to go to a log file so I can > look at the errors more closely? I don't know about log files, but you can configure the cmd window to have a large history and then just copy/paste the results. You can also go into the directory that CPAN extracted the archive to and run the tests there manually. Please send me the results of those tests. From n.haigh at sheffield.ac.uk Thu Nov 30 04:28:36 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 09:28:36 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456EA444.1010705@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sendu Bala wrote: >>> Hilmar Lapp wrote: >>> >>>> Sendu - >>>> >>>> what is the timetable in your mind for getting the release out? The >>>> NESCent phyloinformatics hackathon is impending and if at all >>>> possible I'd really like to see the release be out of the way when >>>> it starts so that all new code can simply go the main trunk and has >>>> no chance of interfering with the release. >>>> >>> >>> I'm going to do one final merge from HEAD to branch-1-5-2 and then >>> set the final release tags later today, so a) anything done at the >>> hackathon won't make any difference, and b) the release should go >>> out soon. >>> >>> The release will go ahead when I've sorted out the Windows PPM and >>> the Change Log (neither of which require code changes on the branch). >>> >>> On this schedule I won't be able to implement Conrad's pre-req >>> installation order in Build.PL since that would require a >>> substantial change to ModuleBuildBioperl.pm and another RC. I'll do >>> that after release so that 1.5.3 benefits. >>> >>> _______________________________________________ >>> >> >> I've not had the time to test out the new CPAN installation until >> now. I've just tried it > > 'it' being RC5? On Windows? > > >> on a clan install of ActivePerl 5.8.8.819 and it didn't install: >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ------------------------------------------------------------------------------- >> >> t/RemoteBlast.t 9 2304 13 0 0.00% ?? >> t/rnamotif.t 2 512 72 144 200.00% 1-72 >> 2 tests and 197 subtests skipped. >> >> How can I get the test output from CPAN to go to a log file so I can >> look at the errors more closely? > > I don't know about log files, but you can configure the cmd window to > have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the archive to > and run the tests there manually. > > Please send me the results of those tests. > > While I figure this out, I've come across the following: The version of CPAN that ships with ActivePerl 5.8.8.819 is 1.7602 and the first version of CPAN to support setting the preference of Module::Build over MakeMaker with "o conf prefer_installer MB" is 1.81 according to their change log. As a result, the default installation of Bioperl on ActivePerl 5.8.8.819 will always use Makefile.PL if it's available. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-0, 29/11/2006 Tested on: 30/11/2006 09:28:37 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From n.haigh at sheffield.ac.uk Thu Nov 30 07:50:57 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 12:50:57 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456ED3B1.9060208@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sendu Bala wrote: >>> Hilmar Lapp wrote: >>> >>>> Sendu - >>>> >>>> what is the timetable in your mind for getting the release out? The >>>> NESCent phyloinformatics hackathon is impending and if at all >>>> possible I'd really like to see the release be out of the way when >>>> it starts so that all new code can simply go the main trunk and has >>>> no chance of interfering with the release. >>>> >>> >>> I'm going to do one final merge from HEAD to branch-1-5-2 and then >>> set the final release tags later today, so a) anything done at the >>> hackathon won't make any difference, and b) the release should go >>> out soon. >>> >>> The release will go ahead when I've sorted out the Windows PPM and >>> the Change Log (neither of which require code changes on the branch). >>> >>> On this schedule I won't be able to implement Conrad's pre-req >>> installation order in Build.PL since that would require a >>> substantial change to ModuleBuildBioperl.pm and another RC. I'll do >>> that after release so that 1.5.3 benefits. >>> >>> _______________________________________________ >>> >> >> I've not had the time to test out the new CPAN installation until >> now. I've just tried it > > 'it' being RC5? On Windows? > > >> on a clan install of ActivePerl 5.8.8.819 and it didn't install: >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ------------------------------------------------------------------------------- >> >> t/RemoteBlast.t 9 2304 13 0 0.00% ?? >> t/rnamotif.t 2 512 72 144 200.00% 1-72 >> 2 tests and 197 subtests skipped. >> >> How can I get the test output from CPAN to go to a log file so I can >> look at the errors more closely? > > I don't know about log files, but you can configure the cmd window to > have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the archive to > and run the tests there manually. > > Please send me the results of those tests. > > > Hi Sendu, Installation on a clean install of ActivePerl 5.8.8.819 n WindowsXP: 1) nmake is required for CPAN installations 2) I updated CPAN to the latest version 3) Restarted CPAN and did "o conf prefer_installer MB" and "o conf commit" 4) Restarted CPAN and tried the install of bioperl 1.5.2 RC5. I still get the message saying it's using Makefile.PL and not Build.PL - not sure why! I'm going to see if updating Module::Build helps. For the time being I installed anyway..... 5) towards the end of dependency checking I get this: -- snip -- Checking if your kit is complete... Looks good Warning: prerequisite DB_File 0 not found. Writing Makefile for Bio ---- Unsatisfied dependencies detected during [S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz] ----- DB_File Shall I follow them and prepend them to the queue of modules we are processing right now? [yes] -- snip -- 6) When running the install, DB_File fails to install and that appears to be the root of the rnamotif test failing: -- snip -- t/rnamotif...................Can't locate DB_File.pm in @INC (@INC contains: t/lib C:\Perl\cpan \build\bioperl-1.5.2_005-RC\blib\lib C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\arch C:/Perl/ site/lib C:/Perl/lib .) at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SeqFeature/Coll ection.pm line 133. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SeqFe ature/Collection.pm line 133. Compilation failed in require at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Tools/RNA Motif.pm line 145. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Tools /RNAMotif.pm line 145. Compilation failed in require at t/rnamotif.t line 27. BEGIN failed--compilation aborted at t/rnamotif.t line 27. t/rnamotif...................dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-72 Failed 72/72 tests, 0.00% okay -- snip -- 7) The RemoteBlast seems to fail due to XML/SAX not being installed: --s nip t/RemoteBlast................ok 10/13Bio::SearchIO: blastxml cannot be found Exception ------------- EXCEPTION ------------- MSG: Failed to load module Bio::SearchIO::blastxml. Can't locate XML/SAX.pm in @INC (@INC conta ins: t C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib C:\Perl\cpan\build\bioperl-1.5.2_005-RC \blib\arch C:/Perl/site/lib C:/Perl/lib .) at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/ Bio\SearchIO\blastxml.pm line 112. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio\Searc hIO\blastxml.pm line 112. Compilation failed in require at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Root/Root .pm line 425. STACK Bio::Root::Root::_load_module C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Root/R oot.pm:427 STACK (eval) C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm:397 STACK Bio::SearchIO::_load_format_module C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/S earchIO.pm:396 STACK Bio::SearchIO::new C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm:176 STACK Bio::Tools::Run::RemoteBlast::retrieve_blast C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib \lib/Bio/Tools/Run/RemoteBlast.pm:603 STACK toplevel t/RemoteBlast.t:185 -------------------------------------- For more information about the SearchIO system please see the SearchIO docs. This includes ways of checking for formats at compile time, not run time Use of uninitialized value in numeric lt (<) at t/RemoteBlast.t line 187. Can't locate object method "new" via package "Bio::SearchIO::blastxml" at C:\Perl\cpan\build\bi operl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm line 177. t/RemoteBlast................dubious Test returned status 9 (wstat 2304, 0x900) after all the subtests completed successfully -- snip -- HTH, Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-1, 30/11/2006 Tested on: 30/11/2006 12:50:59 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From n.haigh at sheffield.ac.uk Thu Nov 30 07:58:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 12:58:08 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456ED560.1020001@sheffield.ac.uk> More updates: After the failed install I updating Module::Build, and re-ran the install, I get: -- snip -- Creating new 'Build' script for 'bioperl' version '1.005002005' Warning: while trying to determine prerequisites for S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi th the help of Module::Build the following error occurred: 'Failed to re-load 'ModuleBuildBiope rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: _build\lib C:\Perl\site\lib C:\ Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. ' Falling back to META.yml for prerequisites 'YAML' not installed, cannot parse 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' -- snip -- Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-1, 30/11/2006 Tested on: 30/11/2006 12:58:09 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From djupiter at tamu.edu Thu Nov 30 01:22:57 2006 From: djupiter at tamu.edu (Daniel Jupiter) Date: Thu, 30 Nov 2006 00:22:57 -0600 Subject: [Bioperl-l] Large databases Message-ID: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> Hi all. I'm new to this list, so if my question is misdirected, or inappropriate, please let me know. The question concerns databases/hashes. I would like to have a rather large hash file. Say 10,000 keys, each with a data field containing roughly 50,000 integers. For whatever reason, the dbm implementation on Mac OSX does not seem to like things of this size. Several strange things happen. First, file size seem to increase exponentially, as I increase the data field size. Additionally, in certain situations, I am returned a rather strange error concerning an uninitialized variable, which has in fact been initialized. In great confusion, I'm just curious as to whether there is a work around for dealing with such large amounts of data, or somewhere with good documentation on using hashes. Thanks. Daniel C. Jupiter, Ph.D. Postdoctoral Research Associate Department of Systems Biology and Translational Medicine College of Medicine Texas A&M University Health Science Center 702 SW H.K. Dodgen Loop Temple, TX 76504 979.997.2106 | Fax 254.742.7145 djupitern at tamu.edu | www.tamhsc.edu ? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: -1.jpeg Type: image/jpeg Size: 19402 bytes Desc: not available URL: From cjfields at uiuc.edu Thu Nov 30 11:13:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 10:13:58 -0600 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> Message-ID: <01b801c7149a$8a9777d0$15327e82@pyrimidine> > Nathan S. Haigh wrote: ... > > How can I get the test output from CPAN to go to a log file > so I can > > look at the errors more closely? > > I don't know about log files, but you can configure the cmd > window to have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the > archive to and run the tests there manually. > > Please send me the results of those tests. Like Sendu, I usually copy from the buffer in the terminal window when running from CPAN (you can set the buffer size for Windows cmd.exe). When running tests manually, I may redirect all output to a temp file, which is a bit easier to scan through since it doesn't wrap text like a cut&paste from the terminal: # Mac OS X ./Build tests &> results.txt # WinXP Build tests > results.txt 2>&1 With Windows I find it sometimes easier to just redirect STDOUT, to avoid all of the 'Subroutine x redefined' warnings. If the CPAN tests go to STDERR you could try redirectly only that stream to a temp file. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Thu Nov 30 11:29:51 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 11:29:51 -0500 Subject: [Bioperl-l] Large databases In-Reply-To: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> References: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> Message-ID: You are aware that you are getting close (or possibly beyond, depending on the exact numbers and if there is any overhead for each integer) the 2GB signed int boundary? Did you make sure that your dbm version is 64-bit enabled and supports 64 bit for filesize? -hilmar On Nov 30, 2006, at 1:22 AM, Daniel Jupiter wrote: > Hi all. > > I'm new to this list, so if my question is misdirected, or > inappropriate, please let me know. > > The question concerns databases/hashes. I would like to have a > rather large hash file. Say 10,000 keys, each with a data field > containing roughly 50,000 integers. For whatever reason, the dbm > implementation on Mac OSX does not seem to like things of this size. > > Several strange things happen. First, file size seem to increase > exponentially, as I increase the data field size. Additionally, in > certain situations, I am returned a rather strange error concerning > an uninitialized variable, which has in fact been initialized. > > In great confusion, I'm just curious as to whether there is a work > around for dealing with such large amounts of data, or somewhere > with good documentation on using hashes. > > Thanks. > > > > Daniel C. Jupiter, Ph.D. > Postdoctoral Research Associate > Department of Systems Biology and Translational Medicine > College of Medicine > Texas A&M University Health Science Center > 702 SW H.K. Dodgen Loop > Temple, TX 76504 > > 979.997.2106 | Fax 254.742.7145 > djupitern at tamu.edu | www.tamhsc.edu > > > <-1.jpeg> > > > > > > > <-1.jpeg> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From st537 at york.ac.uk Thu Nov 30 11:52:27 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Thu, 30 Nov 2006 16:52:27 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C2E01.5070805@sendu.me.uk> References: <456C172F.4060008@york.ac.uk> <456C2E01.5070805@sendu.me.uk> Message-ID: <456F0C4B.2000502@york.ac.uk> Hi, Thanks for helping me with the BLAST code, when I made the corections in ran fine, I'm assuming the returned object $blast_result is a kind of searchio object, although I'm not sure. I tried the code on the bioperl tutorial page for processing a searchio object returned from blast.... http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FASTA_reports_with_Search_and_SearchIO this seems to be the next stage after blasting in the bioperl tutorial but I'm sure how to process it correctly to get hit and alignment information regards, Samantha Thompson Sendu Bala wrote: >Samantha Thompson wrote: > > >>Hi, >>I am trying to learn bioperl and I'm attempting a few basic thing! I >>seem to be ok with reading in and outputting sequences and files now I >>am trying to do a simple BLAST search using a sequence (a sequence >>object in fact). The code I am attempting to run is at the bottom of the >>message... >>I am probably making a dumb mistake and don't understand the >>capabilities of the objects well enough, but the info for the >>remoteblast->submit_blast function says that it can take sequences as an >>argument, I've also tried sending the fasta file name containing my >>sequence as an argument to submit_blast, with the same result.... I >>have also tried sending $seqio_obj->next_seq........... i.e the >>following error message displayed on my terminal: >> >>Can't call method "submit_blast" on an undefined value at bioptest2.pl >>line 22, line 1. >> >> > >Always start your perl scripts with 'use strict;'. This will help you >find and fix the main problem with your script, that you made a >RemoteBlast object and stored it as $remote_blast, but then tried to use >submit_blast() on $remoteBlast which doesn't exist. > >I've rewritten your code below: > >use strict; > > >>use Bio::Seq; >>use Bio::SeqIO; >> >>use Bio::Tools::Run::RemoteBlast; >>use Bio::SearchIO; >> >>#seq bit >> >> >> ># $seq_obj = Bio::Seq->new(-format => 'fasta'); ># above line doesn't do anything, $seq_obj gets overwritten below > > >my $seqio_obj = Bio::SeqIO->new(-file => >"/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > > >my $seq_obj = $seqio_obj->next_seq; > > >> >>#blast bit >> >> >> >my $remote_blast = Bio::Tools::Run::RemoteBlast->new(-prog => 'blastp', >-db => 'nr', -expect => '1e-15' ); > ># submit_blast takes the sequence object, not the sequence string >my $blastreturn_obj = $remote_blast->submit_blast($seq_obj); > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at uiuc.edu Thu Nov 30 12:12:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 11:12:32 -0600 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456F0C4B.2000502@york.ac.uk> Message-ID: <01ba01c714a2$b9659c10$15327e82@pyrimidine> > Hi, > Thanks for helping me with the BLAST code, when I made the > corections in ran fine, I'm assuming the returned object > $blast_result is a kind of searchio object, although I'm not > sure. I tried the code on the bioperl tutorial page for > processing a searchio object returned from blast.... > http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FA > STA_reports_with_Search_and_SearchIO > this seems to be the next stage after blasting in the bioperl > tutorial but I'm sure how to process it correctly to get hit > and alignment information regards, > > Samantha Thompson It is a SearchIO object. FYI, you also have the option of saving the raw BLAST output to a file if needed (it should be described in the RemoteBlast POD). There is also a great HOWTO which goes into more detail about hits/HSPs and how to get alignments: http://www.bioperl.org/wiki/HOWTO:SearchIO chris From bix at sendu.me.uk Thu Nov 30 12:44:38 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 17:44:38 +0000 Subject: [Bioperl-l] Please help with the change log Message-ID: <456F1886.2090708@sendu.me.uk> I'm hoping someone out there is willing to help add summaries for each release to the Change Log: http://bioperl.org/wiki/Change_log Basically, just add a few bullet points about what was new or especially interesting in each release. Thank you, Sendu. From cjfields at uiuc.edu Thu Nov 30 12:50:03 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 11:50:03 -0600 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <438954.89098.qm@web50815.mail.yahoo.com> Message-ID: <000001c714a7$f6ee1300$15327e82@pyrimidine> Katie, Make sure you keep the posts on the mail list, just in case I can't respond but someone else can. > Hi all. > > I just ran the following test script: > > use strict; > use Bio::SearchIO; > my $in = new Bio::SearchIO(-format => 'blast', > -file => 'report.bls'); > while( my $result = $in->next_result ) { > while( my $hit = $result->next_hit ) { > while( my $hsp = $hit->next_hsp ) { > if( $hsp->length('total') > 100 ) { > if ( $hsp->percent_identity >= 75 ) { > print "Hit= ", $hit->name, > ",Length=", $hsp->length('total'), > ",Percent_id=", $hsp->percent_identity, "\n"; > } > } > } > } > } > > and saw the following output: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Could not open report.bls: No such file or directory > STACK: Error::throw > STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:350 > STACK: Bio::Root::IO::_initialize_io > C:/Perl/site/lib/Bio/Root/IO.pm:310 > STACK: Bio::Root::IO::new C:/Perl/site/lib/Bio/Root/IO.pm:223 > STACK: Bio::SearchIO::new C:/Perl/site/lib/Bio/SearchIO.pm:145 > STACK: Bio::SearchIO::new C:/Perl/site/lib/Bio/SearchIO.pm:177 > STACK: test.pl:3 > ----------------------------------------------------------- > > I'm using BioPerl 1.5.2 RC2 > Perl 5.8.8 (Build 819). > WinXP (SP2) > > Thanks, > > ~Katie Is there a BLAST report file named 'report.bls' in the same directory as your script? That's what the error indicates. Chris From n.haigh at sheffield.ac.uk Thu Nov 30 13:24:59 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 18:24:59 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456F2017.8000008@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> <456F2017.8000008@sendu.me.uk> Message-ID: <456F21FB.7090702@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> More updates: >> >> After the failed install I updating Module::Build, and re-ran the >> install, I get: >> >> -- snip -- >> Creating new 'Build' script for 'bioperl' version '1.005002005' >> Warning: while trying to determine prerequisites for >> S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi >> th the help of Module::Build the following error occurred: 'Failed to >> re-load 'ModuleBuildBiope >> rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: >> _build\lib C:\Perl\site\lib C:\ >> Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. >> ' >> >> Falling back to META.yml for prerequisites >> 'YAML' not installed, cannot parse >> 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' >> -- snip -- > > I had that problem fleetingly and it drove me crazy because later I > couldn't reproduce it. Is it reproducible on your end? > I've seen it several time and i'm sure I could reproduce it....give me a few mins and i'll see what I can report. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 18:25:01 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From bix at sendu.me.uk Thu Nov 30 13:16:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 18:16:55 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456ED560.1020001@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> Message-ID: <456F2017.8000008@sendu.me.uk> Nathan S. Haigh wrote: > More updates: > > After the failed install I updating Module::Build, and re-ran the > install, I get: > > -- snip -- > Creating new 'Build' script for 'bioperl' version '1.005002005' > Warning: while trying to determine prerequisites for > S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi > th the help of Module::Build the following error occurred: 'Failed to > re-load 'ModuleBuildBiope > rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: > _build\lib C:\Perl\site\lib C:\ > Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. > ' > > Falling back to META.yml for prerequisites > 'YAML' not installed, cannot parse > 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' > -- snip -- I had that problem fleetingly and it drove me crazy because later I couldn't reproduce it. Is it reproducible on your end? From cjfields at uiuc.edu Thu Nov 30 14:11:47 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 13:11:47 -0600 Subject: [Bioperl-l] Intermittent MySQL problems on BioPerl wiki Message-ID: <000201c714b3$6198e4e0$15327e82@pyrimidine> I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and WinXP): Database error >From BioPerl Jump to: navigation, search A database query syntax error has occurred. This may indicate a bug in the software. The last attempted database query was: (SQL query hidden) from within function "MediaWikiBagOStuff::_doquery". MySQL returned error "1205: Lock wait timeout exceeded; try restarting transaction (localhost)". This occurs intermittently when editting pages, logging in, etc. Also, pages loading to the browser seem much slower. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 30 14:19:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 13:19:34 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl5.8.8.819 In-Reply-To: <456F2017.8000008@sendu.me.uk> Message-ID: <000301c714b4$7846e790$15327e82@pyrimidine> > Nathan S. Haigh wrote: > > More updates: > > > > After the failed install I updating Module::Build, and re-ran the > > install, I get: > > > > -- snip -- > > Creating new 'Build' script for 'bioperl' version '1.005002005' > > Warning: while trying to determine prerequisites for > > S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi th the help of > > Module::Build the following error occurred: 'Failed to re-load > > 'ModuleBuildBiope > > rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: > > _build\lib C:\Perl\site\lib C:\ > > Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. > > ' > > > > Falling back to META.yml for prerequisites 'YAML' not installed, > > cannot parse 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' > > -- snip -- > > I had that problem fleetingly and it drove me crazy because > later I couldn't reproduce it. Is it reproducible on your end? During Module::Build installation I see this: ... t\metadata........ok 8/43 skipped: YAML_support feature is not enabled t\metadata2.......ok 4/18 skipped: YAML_support feature is not enabled t\moduleinfo......ok t\notes...........ok t\parents.........ok t\pod_parser......ok t\ppm.............skipped all skipped: C_support not enabled t\runthrough......ok 7/32 skipped: YAML_support feature is not enabled t\signature.......skipped all skipped: $ENV{TEST_SIGNATURE} is not set t\tilde...........ok t\versions........ok t\xs..............skipped all skipped: C_support not enabled All tests successful, 3 tests and 27 subtests skipped. Files=21, Tests=679, 262 wallclock secs ( 0.00 cusr + 0.00 csys = 0.00 CPU) C:\WINDOWS\nmake.EXE test -- OK Running make install ... Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From st537 at york.ac.uk Thu Nov 30 13:50:17 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Thu, 30 Nov 2006 18:50:17 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <01ba01c714a2$b9659c10$15327e82@pyrimidine> References: <01ba01c714a2$b9659c10$15327e82@pyrimidine> Message-ID: <456F27E9.70205@york.ac.uk> Chris Fields wrote: >>Hi, >>Thanks for helping me with the BLAST code, when I made the >>corections in ran fine, I'm assuming the returned object >>$blast_result is a kind of searchio object, although I'm not >>sure. I tried the code on the bioperl tutorial page for >>processing a searchio object returned from blast.... >>http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FA >>STA_reports_with_Search_and_SearchIO >>this seems to be the next stage after blasting in the bioperl >>tutorial but I'm sure how to process it correctly to get hit >>and alignment information regards, >> >>Samantha Thompson >> >> > >It is a SearchIO object. FYI, you also have the option of saving the raw >BLAST output to a file if needed (it should be described in the RemoteBlast >POD). > >There is also a great HOWTO which goes into more detail about hits/HSPs and >how to get alignments: > >http://www.bioperl.org/wiki/HOWTO:SearchIO > > >chris > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/bioper > > Hi, OK, I tried the code at the SearchIO HOWTO, I've pasted it below, you can see where I've added the SearchIO handling part I've changed $in to the $blast_report as this is returned from the submit_blast ... what happens when I run this however is that I get the following error: Can't call method "next_result" without a package or object reference at bioptest2.pl line 31, line 1. Line 31 being: while( my $result = $blast_report->next_result ) { Not sure why this is happening. Thanks for any help... Samantha Thompson use strict; use Bio::Perl; use Bio::Seq; use Bio::SeqIO; use Bio::Tools::Run::RemoteBlast; use Bio::SearchIO; #seq bit #$seq_obj = Bio::Seq->new(-format => 'fasta'); my $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); my $seq_obj = $seqio_obj->next_seq; #blast bit my $remote_blast = Bio::Tools::Run::RemoteBlast->new ( -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); my $blast_report = $remote_blast->submit_blast($seq_obj); #new part for SearchIO... while( my $result = $blast_report->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { if( $hsp->length('total') > 100 ) { if ( $hsp->percent_identity >= 75 ) { print "Hit= ", $hit->name, ",Length=", $hsp->length('total'), ",Percent_id=", $hsp->percent_identity, "\n"; } } } } } From dag at sonsorol.org Thu Nov 30 14:25:16 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 30 Nov 2006 14:25:16 -0500 Subject: [Bioperl-l] [Root-l] Intermittent MySQL problems on BioPerl wiki In-Reply-To: <000201c714b3$6198e4e0$15327e82@pyrimidine> References: <000201c714b3$6198e4e0$15327e82@pyrimidine> Message-ID: Reports like this need to go to support at helpdesk.open-bio.org so that they enter our RT helpdesk queue -- the main reason is that sometimes emails to the root-l at open-bio.org administrators mailing list can get lost in the shuffle. I am going to bounce this message into RT and will restart mysql on the portal box. This is probably something we should be doing anyway to free up memory -- the wikis in particular seem to be pretty hard on mysql and free memory. -Chris On Nov 30, 2006, at 2:11 PM, Chris Fields wrote: > I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and > WinXP): > > Database error >> From BioPerl > Jump to: navigation, search > A database query syntax error has occurred. This may indicate a bug > in the > software. The last attempted database query was: > > (SQL query hidden) > > from within function "MediaWikiBagOStuff::_doquery". MySQL returned > error > "1205: Lock wait timeout exceeded; try restarting transaction > (localhost)". > > > This occurs intermittently when editting pages, logging in, etc. > Also, > pages loading to the browser seem much slower. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > _______________________________________________ > Root-l mailing list > Root-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/root-l From n.haigh at sheffield.ac.uk Thu Nov 30 15:07:24 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 20:07:24 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456F21FB.7090702@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> <456F2017.8000008@sendu.me.uk> <456F21FB.7090702@sheffield.ac.uk> Message-ID: <456F39FC.9070805@sheffield.ac.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: > >> Nathan S. Haigh wrote: >> >>> More updates: >>> >>> After the failed install I updating Module::Build, and re-ran the >>> install, I get: >>> >>> -- snip -- >>> Creating new 'Build' script for 'bioperl' version '1.005002005' >>> Warning: while trying to determine prerequisites for >>> S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi >>> th the help of Module::Build the following error occurred: 'Failed to >>> re-load 'ModuleBuildBiope >>> rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: >>> _build\lib C:\Perl\site\lib C:\ >>> Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. >>> ' >>> >>> Falling back to META.yml for prerequisites >>> 'YAML' not installed, cannot parse >>> 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' >>> -- snip -- >>> >> I had that problem fleetingly and it drove me crazy because later I >> couldn't reproduce it. Is it reproducible on your end? >> >> > > I've seen it several time and i'm sure I could reproduce it....give me a > few mins and i'll see what I can report. > > Nath > > > --- > avast! Antivirus: Outbound message clean. > Virus Database (VPS): 0652-2, 30/11/2006 > Tested on: 30/11/2006 18:25:01 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > --- > avast! Antivirus: Inbound message clean. > Virus Database (VPS): 0652-2, 30/11/2006 > Tested on: 30/11/2006 18:50:39 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > > Reproduce: 1) clean install of ActivePerl 5.8.8.819 on WinXP 2) Install nmake in path 3) run "cpan CPAN" to install the latest version of CPAN module 4) ran cpan, accepted default for new CPAN configuration, ran "o conf prefer_installer MB" and "o conf commit" then "q" 5) run "cpan Module::Build" to install the latest version of Module::Build 6) run "cpan" and then "install S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" 7) Choose not to install optional modules 8) Error shows here Installing all optional modules doesn't produce the error. However, It produces the problem i've told you about missing "scripts" dir (actually, it's not just the scripts dir - it's all but the base dir it was unpacked into). Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 20:07:25 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From cjfields at uiuc.edu Thu Nov 30 15:48:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 14:48:26 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXPActivePerl 5.8.8.819 In-Reply-To: <456F39FC.9070805@sheffield.ac.uk> Message-ID: <000801c714c0$e26eff70$15327e82@pyrimidine> > Nathan S. Haigh wrote: > Reproduce: > 1) clean install of ActivePerl 5.8.8.819 on WinXP > 2) Install nmake in path > 3) run "cpan CPAN" to install the latest version of CPAN module > 4) ran cpan, accepted default for new CPAN configuration, ran > "o conf prefer_installer MB" and "o conf commit" then "q" > 5) run "cpan Module::Build" to install the latest version of > Module::Build > 6) run "cpan" and then "install > S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" > 7) Choose not to install optional modules > 8) Error shows here > > Installing all optional modules doesn't produce the error. > However, It produces the problem i've told you about missing > "scripts" dir (actually, it's not just the scripts dir - it's > all but the base dir it was unpacked into). > > Nath Confirmed, using same setup as Nathan. chris From cjfields at uiuc.edu Thu Nov 30 16:27:17 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 15:27:17 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <000801c714c0$e26eff70$15327e82@pyrimidine> Message-ID: <002401c714c6$53f65080$15327e82@pyrimidine> > > Nathan S. Haigh wrote: > > Reproduce: > > 1) clean install of ActivePerl 5.8.8.819 on WinXP > > 2) Install nmake in path > > 3) run "cpan CPAN" to install the latest version of CPAN module > > 4) ran cpan, accepted default for new CPAN configuration, > ran "o conf > > prefer_installer MB" and "o conf commit" then "q" > > 5) run "cpan Module::Build" to install the latest version of > > Module::Build > > 6) run "cpan" and then "install > > S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" > > 7) Choose not to install optional modules > > 8) Error shows here > > > > Installing all optional modules doesn't produce the error. > > However, It produces the problem i've told you about > missing "scripts" > > dir (actually, it's not just the scripts dir - it's all but > the base > > dir it was unpacked into). > > > > Nath > > Confirmed, using same setup as Nathan. > > chris Okay, revise that. I get the message you mentioned, but installation only fails after tests are run. The single failed test (rnamotif.t) is due to DB_File not being installed, which Sendu has corrected in CVS and (I think) the 1.5.2 branch. However, I can't get DB_File to install via CPAN (I have VC++ Express Edition installed). I think XML::SAX and a few others fail as well. Chris From n.haigh at sheffield.ac.uk Thu Nov 30 16:41:30 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 21:41:30 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <002401c714c6$53f65080$15327e82@pyrimidine> References: <002401c714c6$53f65080$15327e82@pyrimidine> Message-ID: <456F500A.7010707@sheffield.ac.uk> Chris Fields wrote: >>> Nathan S. Haigh wrote: >>> Reproduce: >>> 1) clean install of ActivePerl 5.8.8.819 on WinXP >>> 2) Install nmake in path >>> 3) run "cpan CPAN" to install the latest version of CPAN module >>> 4) ran cpan, accepted default for new CPAN configuration, >>> >> ran "o conf >> >>> prefer_installer MB" and "o conf commit" then "q" >>> 5) run "cpan Module::Build" to install the latest version of >>> Module::Build >>> 6) run "cpan" and then "install >>> S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" >>> 7) Choose not to install optional modules >>> 8) Error shows here >>> >>> Installing all optional modules doesn't produce the error. >>> However, It produces the problem i've told you about >>> >> missing "scripts" >> >>> dir (actually, it's not just the scripts dir - it's all but >>> >> the base >> >>> dir it was unpacked into). >>> >>> Nath >>> >> Confirmed, using same setup as Nathan. >> >> chris >> > > Okay, revise that. I get the message you mentioned, but installation only > fails after tests are run. The single failed test (rnamotif.t) is due to > DB_File not being installed, which Sendu has corrected in CVS and (I think) > the 1.5.2 branch. However, I can't get DB_File to install via CPAN (I have > VC++ Express Edition installed). I think XML::SAX and a few others fail as > well. > > Chris > > > Yes that's correct, I get the message but things then seem to proceed normally (not that I know what normal is!). I had to install DB_File via PPM and install XML::SAX explicitly in CPAN. That then seems to have cleared things up and the tests pass and bioperl core is installed. However, there are other optional dependencies that didn't install successfully - I suppose I should investigate those tomorrow. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 21:41:31 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From gwu at molbio.mgh.harvard.edu Thu Nov 30 17:08:08 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Thu, 30 Nov 2006 17:08:08 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> Message-ID: <456F5648.6070207@molbio.mgh.harvard.edu> Thanks Hilmar. Do you mean the NVL() clause will make load_seqdatabase.pl not work when update? I have problem with updating. Seems load_seqdatabase.pl only tries to insert instead of update. I used one of the test genbank file coming whith bioperl-db. Please take a look at the attached output. Thanks. Gang ========================================= >perl load_seqdatabase.pl -lookup -host elegans -driver Oracle -dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank -namespace test /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/AP000868.gb Loading /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/AP000868.gb ... -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("This sequence was reannotated via the Ensembl system. Please visit the Ensembl web site, http://www.ensembl.org/ for more information. ","1") FKs (389109) ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) violated (DBD ERROR: OCIStmtExecute) --------------------------------------------------- -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("The /gene indicates a unique id for a gene, /cds a unique id for a translation and a /exon a unique id for an exon. These ids are maintained wherever possible between versions. For more information on how to interpret the feature table, please visit http://www.ensembl.org/Docs/embl.html. ","2") FKs (389109) ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) violated (DBD ERROR: OCIStmtExecute) --------------------------------------------------- ... ... ========================================================== Hilmar Lapp wrote: > These are the protein translations stored in the feature table as > tags of features, right? > > You can change the type of the column (although there may be some > issues when you update the column because the NVL() clause won't work > if I recall that correctly), but doing so will deprive you of any > 'normal' searches against that column. (You can still use functions > from the DBMS_LOB package, but they will be much slower and are > completely non-standard.) > > It is up to you whether that is too big of a price to pay for having > some redundant protein translations (translating the feature's DNA > sequence should give you the same) in the database. I always trimmed > those feature tags off (using a custom SeqProcessor). An alternative > is to convert these feature tags into actual bioentries (i.e., > Bio::Seq objects; again, a custom SeqProcessor will allow you to do > that). > > -hilmar > > On Nov 28, 2006, at 4:13 PM, gang wu wrote: > > >> Hi everyone, >> >> I'm using load_seqdatabase.pl to upload some Genbank genome >> sequences to >> my Oracle BioSQL database. I saw some errors(See attached warning >> message) related to seqfeature_qualifier_value >> (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data >> type of maximum 4000 bytes. Did anybody mention this issue before? >> Should I just modify the column to a type being able store more data >> such as LONG or CLOB? >> >> Thanks. >> >> Gang >> >> >> Log information: >> ============================================ >> >> load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser >> biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank >> /genomeseq/arabidopsis//NC_003070.gbk >> >> >> Loading /genomeseq/arabidopsis//NC_003070.gbk ... >> >> >> -------------------- WARNING --------------------- >> MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement >> execution: ORA-01461: can bind a LONG value only for insert into a >> LONG >> column (DBD ERROR: error possibly near <*> indicator at char 12 in >> 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, >> rank) VALUES (:p1, :p2, :p3, :p4)') >> name: INSERT ASSOC [2] >> Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue >> values: FK[Bio::SeqFeature::Generic]:14898, >> FK[Bio::Annotation::SimpleValue]:800, >> value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFV >> GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADR >> GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEI >> LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFP >> WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERA >> SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRY >> IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEA >> EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDI >> NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDW >> RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFAL >> DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDN >> QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRY >> MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYT >> FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGL >> VQATYQASA! >> >> PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKV >> HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAY >> TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFV >> SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSE >> KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLG >> NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEV >> TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQL >> EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTL >> SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVT >> ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRL >> MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAV >> PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEY >> TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVD >> ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLR >> VKLDFNFM! >> >> YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQS >> QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSN >> TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCL >> SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWD >> ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSE >> IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASV >> TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGL >> HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSS >> KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDF >> QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGL >> HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVA >> RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCL >> LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRN >> GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVE >> NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPL >> WLSVGADAS! >> >> VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVY >> LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITND >> SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQES >> AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTS >> DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSV >> FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESW >> QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIV >> RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMS >> VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRV >> YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAM >> SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDI >> LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAK >> SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLR >> PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMG >> QRKFIPAK! >> >> DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQ >> AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", >> rank:"1" >> -------------------------------------------------- >> >> >> ============================================= >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > From cjfields at uiuc.edu Thu Nov 30 17:16:02 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 16:16:02 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <456F500A.7010707@sheffield.ac.uk> References: <002401c714c6$53f65080$15327e82@pyrimidine> <456F500A.7010707@sheffield.ac.uk> Message-ID: <202B1F50-E905-46DE-9EB5-5F206AC04523@uiuc.edu> On Nov 30, 2006, at 3:41 PM, Nathan S. Haigh wrote: > ... >> >> Okay, revise that. I get the message you mentioned, but >> installation only >> fails after tests are run. The single failed test (rnamotif.t) is >> due to >> DB_File not being installed, which Sendu has corrected in CVS and >> (I think) >> the 1.5.2 branch. However, I can't get DB_File to install via >> CPAN (I have >> VC++ Express Edition installed). I think XML::SAX and a few >> others fail as >> well. >> >> Chris >> >> >> > > Yes that's correct, I get the message but things then seem to > proceed normally (not that I know what normal is!). > I had to install DB_File via PPM and install XML::SAX explicitly in > CPAN. That then seems to have cleared things up and the tests pass > and bioperl core is installed. However, there are other optional > dependencies that didn't install successfully - I suppose I should > investigate those tomorrow. > > Nath The DB_File failure is due to compilation problems. BTW, I can get XML::SAX to install, so that shouldn't be an issue. I know that setting up the PPM is a pain, but I have to say it is much faster, and all required PPMs are available. Which makes me curious: why bother with trying out a CPAN installation process at this point, especially when you have to use PPM to install some of the prereqs properly anyway? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From pelikan at cs.pitt.edu Thu Nov 30 17:19:29 2006 From: pelikan at cs.pitt.edu (pelikan at cs.pitt.edu) Date: Thu, 30 Nov 2006 17:19:29 -0500 (EST) Subject: [Bioperl-l] Error with supplied lineages importing uniprot data Message-ID: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> Hello all, I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows, without Cygwin. The "make test"s have all completed without error. This is my first time dealing with bioperl, so bear with me. I've successfully loaded the most recent taxonomy information using the biosql-schema scripts. After this, I attempted to load the most recent release of the uniprot flat file dataset with the following command: load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat I am subsequently greeted by many of the following errors: Could not store Q7N3Q6: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: The supplied lineage does not start near 'Photorhabdus luminescens subsp. laumondii' STACK: Error::throw STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio\Root\Root.pm:359 STACK: Bio::Species::classification C:/Perl/site/lib/Bio\Species.pm:166 STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:55 STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row C:/Perl/site/lib/Bio\DB\BioSQL\SpeciesAdaptor.pm:281 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key C:/Perl/site/lib/Bio/DB/BioSQL/BasePersisten STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenc STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: STACK: Bio::DB::Persistent::PersistentObject::create C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:244 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:2 STACK: Bio::DB::Persistent::PersistentObject::store C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:271 STACK: C:\DATA\MYSQL\cvs\src\bioperl\bioperl-db-1.5.2_005-RC\scripts\biosql\load_seqdatabase.pl:620 ----------------------------------------------------------- Can someone shed some light on why this may be taking place? -Richard From hlapp at gmx.net Thu Nov 30 18:28:40 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 18:28:40 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <456F5648.6070207@molbio.mgh.harvard.edu> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> <456F5648.6070207@molbio.mgh.harvard.edu> Message-ID: <70B28FBB-0250-4EB8-8775-CD0537369A3D@gmx.net> Right. You need to tell it to lookup sequences first if you know that you are loading sequences which may be in the database already (see the POD of load_seqdatabase.pl, switch --lookup; there are several other command line options that control what will happen if a sequence entry is already present in the database.). The messages in you report are warnings, not errors. It looks like some of the comments are duplicated for a sequence, it doesn't look like reason for concern. Is not so good if you get errors thrown. -hilmar On Nov 30, 2006, at 5:08 PM, gang wu wrote: > Thanks Hilmar. Do you mean the NVL() clause will make > load_seqdatabase.pl not work when update? > > I have problem with updating. Seems load_seqdatabase.pl only tries > to insert instead of update. I used one of the test genbank file > coming whith bioperl-db. Please take a look at the attached output. > > Thanks. > > Gang > > ========================================= > >perl load_seqdatabase.pl -lookup -host elegans -driver Oracle - > dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank - > namespace test /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/ > biosql/data/AP000868.gb > Loading /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/ > AP000868.gb ... > > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, > values were ("This sequence was reannotated via the Ensembl system. > Please visit the Ensembl web site, http://www.ensembl.org/ for more > information. ","1") FKs (389109) > ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) > violated (DBD ERROR: OCIStmtExecute) > --------------------------------------------------- > > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, > values were ("The /gene indicates a unique id for a gene, /cds a > unique id for a translation and a /exon a unique id for an exon. > These ids are maintained wherever possible between versions. For > more information on how to interpret the feature table, please > visit http://www.ensembl.org/Docs/embl.html. ","2") FKs (389109) > ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) > violated (DBD ERROR: OCIStmtExecute) > --------------------------------------------------- > ... > ... > ========================================================== > Hilmar Lapp wrote: >> These are the protein translations stored in the feature table as >> tags of features, right? You can change the type of the column >> (although there may be some issues when you update the column >> because the NVL() clause won't work if I recall that correctly), >> but doing so will deprive you of any 'normal' searches against >> that column. (You can still use functions >from the DBMS_LOB >> package, but they will be much slower and are completely non- >> standard.) It is up to you whether that is too big of a price to >> pay for having some redundant protein translations (translating >> the feature's DNA sequence should give you the same) in the >> database. I always trimmed those feature tags off (using a custom >> SeqProcessor). An alternative is to convert these feature tags >> into actual bioentries (i.e., Bio::Seq objects; again, a custom >> SeqProcessor will allow you to do that). -hilmar On Nov 28, 2006, >> at 4:13 PM, gang wu wrote: >>> Hi everyone, I'm using load_seqdatabase.pl to upload some Genbank >>> genome sequences to my Oracle BioSQL database. I saw some errors >>> (See attached warning message) related to >>> seqfeature_qualifier_value (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE >>> column), which has Varchar2 data type of maximum 4000 bytes. Did >>> anybody mention this issue before? Should I just modify the >>> column to a type being able store more data such as LONG or CLOB? >>> Thanks. Gang Log information: >>> ============================================ load_seqdatabase.pl - >>> host elegans -driver Oracle -dbname sparc -dbuser biosqldb- >>> sgowner -dbpass PASS -format genbank -namespace genbank / >>> genomeseq/arabidopsis//NC_003070.gbk Loading /genomeseq/ >>> arabidopsis//NC_003070.gbk ... -------------------- WARNING >>> --------------------- MSG: SimpleValueAdaptor::add_assoc: >>> unexpected failure of statement execution: ORA-01461: can bind a >>> LONG value only for insert into a LONG column (DBD ERROR: error >>> possibly near <*> indicator at char 12 in 'INSERT INTO >>> <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, rank) >>> VALUES (:p1, :p2, :p3, :p4)') name: INSERT ASSOC [2] >>> Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue values: FK >>> [Bio::SeqFeature::Generic]:14898, FK >>> [Bio::Annotation::SimpleValue]:800, >>> value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSG >>> FV >>> GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASA >>> DR >>> GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSS >>> EI >>> LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNS >>> FP >>> WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFE >>> RA >>> SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYT >>> RY >>> IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRT >>> EA >>> EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIV >>> DI >>> NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENI >>> DW >>> RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRF >>> AL >>> DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGS >>> DN >>> QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPT >>> RY >>> MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYL >>> YT >>> FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLR >>> GL VQATYQASA! >>> PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGG >>> KV >>> HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDED >>> AY >>> TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSD >>> FV >>> SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSD >>> SE >>> KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGT >>> LG >>> NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQ >>> EV >>> TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLG >>> QL >>> EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVP >>> TL >>> SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRT >>> VT >>> ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEM >>> RL >>> MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRIL >>> AV >>> PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGID >>> EY >>> TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDG >>> VD >>> ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKL >>> LR VKLDFNFM! >>> YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNL >>> QS >>> QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAV >>> SN >>> TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVY >>> CL >>> SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSG >>> WD >>> ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADD >>> SE >>> IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEA >>> SV >>> TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLD >>> GL >>> HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQ >>> SS >>> KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDED >>> DF >>> QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAK >>> GL >>> HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKG >>> VA >>> RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNG >>> CL >>> LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSM >>> RN >>> GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPK >>> VE >>> NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSK >>> PL WLSVGADAS! >>> VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRP >>> VY >>> LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWIT >>> ND >>> SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQ >>> ES >>> AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNM >>> TS >>> DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPF >>> SV >>> FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSE >>> SW >>> QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKN >>> IV >>> RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILY >>> MS >>> VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDL >>> RV >>> YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSM >>> AM >>> SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGV >>> DI >>> LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEG >>> AK >>> SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSL >>> LR >>> PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNI >>> MG QRKFIPAK! >>> DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAI >>> DQ AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", >>> rank:"1" -------------------------------------------------- >>> ============================================= >>> _______________________________________________ Bioperl-l mailing >>> list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/ >>> mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Nov 30 18:31:41 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 18:31:41 -0500 Subject: [Bioperl-l] Error with supplied lineages importing uniprot data In-Reply-To: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> References: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> Message-ID: <24C694D6-1124-48A9-8C7C-FA58AB598F01@gmx.net> Maybe Sendu can shed light on what might be happening here? On Nov 30, 2006, at 5:19 PM, pelikan at cs.pitt.edu wrote: > Hello all, > > I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows, > without Cygwin. The "make test"s have all completed without error. > This > is my first time dealing with bioperl, so bear with me. > > I've successfully loaded the most recent taxonomy information > using the > biosql-schema scripts. After this, I attempted to load the most recent > release of the uniprot flat file dataset with the following command: > > load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass > ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat > > I am subsequently greeted by many of the following errors: > > Could not store Q7N3Q6: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: The supplied lineage does not start near 'Photorhabdus > luminescens > subsp. laumondii' > STACK: Error::throw > STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio\Root\Root.pm:359 > STACK: Bio::Species::classification C:/Perl/site/lib/Bio\Species.pm: > 166 > STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:55 > STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row > C:/Perl/site/lib/Bio\DB\BioSQL\SpeciesAdaptor.pm:281 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersisten > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenc > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: > STACK: Bio::DB::Persistent::PersistentObject::create > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:244 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:2 > STACK: Bio::DB::Persistent::PersistentObject::store > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:271 > STACK: > C:\DATA\MYSQL\cvs\src\bioperl\bioperl-db-1.5.2_005-RC\scripts\biosql > \load_seqdatabase.pl:620 > ----------------------------------------------------------- > > Can someone shed some light on why this may be taking place? > > -Richard > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From The_Polymorph at rocketmail.com Thu Nov 30 18:58:22 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 30 Nov 2006 15:58:22 -0800 (PST) Subject: [Bioperl-l] Upgrading my BioPerl RC via ppm? In-Reply-To: <000001c714a7$f6ee1300$15327e82@pyrimidine> Message-ID: <519167.29410.qm@web50804.mail.yahoo.com> Hi all. I'm currently using BioPerl 1.5.2 RC2 but I've seen multiple references to 1.5.2 RC5. Can anyone tell me how to upgrade to the latest version? The ppm GUI (ActivePerl Build 819) doesn't include any BioPerl packages among those deemed upgradable. Thanks, ~Katie "Be who you are and say what you feel because those who mind don't matter and those who matter don't mind." - Dr. Seuss, "Oh the Places You'll Go" ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com From arareko at campus.iztacala.unam.mx Thu Nov 30 19:56:02 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Thu, 30 Nov 2006 18:56:02 -0600 Subject: [Bioperl-l] [Root-l] Intermittent MySQL problems on BioPerl wiki In-Reply-To: References: <000201c714b3$6198e4e0$15327e82@pyrimidine> Message-ID: <456F7DA2.7000408@campus.iztacala.unam.mx> Chris & Chris, I've run the maintenance scripts for MediaWiki (just in case they weren't run in the upgrade to 1.8.2), restarted Apache (with no significant changes on website response), then rebooted the machine (seems like MySQL restart didn't do the trick) and apparently its behaving much better. Please check if the reported error still happens. Regards, Mauricio. Chris Dagdigian wrote: > Reports like this need to go to support at helpdesk.open-bio.org so that > they enter our RT helpdesk queue -- the main reason is that > sometimes emails to the root-l at open-bio.org administrators mailing > list can get lost in the shuffle. > > I am going to bounce this message into RT and will restart mysql on > the portal box. This is probably something we should be doing anyway > to free up memory -- the wikis in particular seem to be pretty hard > on mysql and free memory. > > -Chris > > On Nov 30, 2006, at 2:11 PM, Chris Fields wrote: > >> I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and >> WinXP): >> >> Database error >>> From BioPerl >> Jump to: navigation, search >> A database query syntax error has occurred. This may indicate a bug >> in the >> software. The last attempted database query was: >> >> (SQL query hidden) >> >> from within function "MediaWikiBagOStuff::_doquery". MySQL returned >> error >> "1205: Lock wait timeout exceeded; try restarting transaction >> (localhost)". >> >> >> This occurs intermittently when editting pages, logging in, etc. >> Also, >> pages loading to the browser seem much slower. >> >> Christopher Fields >> Postdoctoral Researcher - Switzer Lab >> Dept. of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> _______________________________________________ >> Root-l mailing list >> Root-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/root-l > > _______________________________________________ > Root-l mailing list > Root-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/root-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From bosborne11 at verizon.net Wed Nov 1 02:31:49 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 31 Oct 2006 22:31:49 -0400 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: Message-ID: Nancy, It looks like a good place to start would be the get_header() and _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that the author, at some point, wanted get_header to return meaningful information but stepping through the test shows it returning a lot of UNDEF. Now I don't know if this is due to the method or the source SCF file, but you might be able to get these methods to work yourself. But to answer your questions, yes, it certainly sounds reasonable that these values would be extracted by Bio::SeqIO::scf. Brian O. On 10/31/06 3:51 PM, "Nancy Hansen" wrote: > > Hello, > > As sequencing centers begin to deposit trace data from "Medical > Sequencing" projects into the public archives, there is now the need to > "anonymize" sequence trace files by removing embedded information which > might be used to identify the individual who was the original source of > the DNA being sequenced. > > I was hoping I might be able to use Bio::SeqIO to manipulate the > comments contained in an SCF-formatted trace file, but I'm finding that > Bio::SeqIO/Bio::Seq::SequenceTrace doesn't seem to store this information. > Since SCF is a widely-accepted standard for trace files, would it be > reasonable to include fields like "scf_comments" and "scf_header" in a > Bio::Seq::SequenceTrace object and have Bio::SeqIO::scf populate them? > Likewise, it would be great if write_seq could pull these values right > from a SequenceTrace object rather than requiring them as arguments. > > I'd be happy to help in this effort if necessary. > > Thanks, > --Nancy > > ************************************* > Nancy F. Hansen, PhD nhansen at nhgri.nih.gov > Bioinformatics Group > NIH Intramural Sequencing Center (NISC) > 5625 Fishers Lane > Rockville, MD 20852 > Phone: (301) 435-1560 Fax: (301) 435-6170 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From huangyi1 at hkusua.hku.hk Wed Nov 1 08:25:10 2006 From: huangyi1 at hkusua.hku.hk (Huang Yi) Date: Wed, 1 Nov 2006 16:25:10 +0800 Subject: [Bioperl-l] bioperl1.5 and GD2.35 - solved In-Reply-To: <1A4207F8295607498283FE9E93B775B4023B5F3C@EX02.asurite.ad.asu.edu> Message-ID: <200611010825.kA18PGWu022850@hkusua.hku.hk> The problem was solved. I re-emerged gd-2.0.33 with png USE flag. Thanks again! Huang Yi -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Kevin Brown Sent: Tuesday, October 31, 2006 11:35 PM To: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] bioperl1.5 and GD2.35 Not really a Bioperl issue per se, but sounds like when you had Gentoo emerge GD it didn't include libpng and so didn't build the needed parts to create PNG type graphics. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Huang Yi > Sent: Monday, October 30, 2006 10:46 PM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] bioperl1.5 and GD2.35 > > Hi, > > > > I just installed bioperl 1.4 from CPAN to my Gentoo linux > computer. But the > installation was failed. I had to install by force. > > > > However, the GD module couldn't be installed for some unknown reasons. > > > > I therefore use "emerge" tool of Gentoo to get bioperl and GD > again. They > are fine. The version of bioperl became upgrade to1.5 and GD was 2.35. > > > > However, when I tested it by using the program in HOWTO wiki page > (http://www.bioperl.org/wiki/HOWTO:Graphics), it always told me: > > > > Can't locate object method "png" via package "GD::Image" at > /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Panel.pm line > 799, <> line 9. > > > > In my other computer, bioperl1.4 and GD2.34 work fine. I > therefore want to > remove the CPAN bioperl from the system and re-install it, > but it seems to > be impossible. > > > > Would you please give me some advices on how to let my GD and > bioperl work. > > > > Thanks! > > > > Huang Yi > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/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 nhansen at nhgri.nih.gov Wed Nov 1 13:43:32 2006 From: nhansen at nhgri.nih.gov (Nancy Hansen) Date: Wed, 1 Nov 2006 08:43:32 -0500 (EST) Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: References: Message-ID: On Tue, 31 Oct 2006, Brian Osborne wrote: > It looks like a good place to start would be the get_header() and > _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that > the author, at some point, wanted get_header to return meaningful > information but stepping through the test shows it returning a lot of UNDEF. > Now I don't know if this is due to the method or the source SCF file, but > you might be able to get these methods to work yourself. > > But to answer your questions, yes, it certainly sounds reasonable that these > values would be extracted by Bio::SeqIO::scf. Sounds great! So, if I make these changes, is there someone I should run them by before checking them into CVS? Is Chad Matsalla still involved in bioperl? I've never contributed to the project, so I'm not sure how things work... Thanks! --Nancy ************************************* Nancy F. Hansen, PhD nhansen at nhgri.nih.gov Bioinformatics Group NIH Intramural Sequencing Center (NISC) 5625 Fishers Lane Rockville, MD 20852 Phone: (301) 435-1560 Fax: (301) 435-6170 From arareko at campus.iztacala.unam.mx Wed Nov 1 14:30:34 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed, 01 Nov 2006 08:30:34 -0600 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: References: Message-ID: <4548AF8A.6090205@campus.iztacala.unam.mx> The usual way is to send your modifications as an 'enhancement' through the Bugzilla system (please add your patches as attachments after creating the report, not into the description field): http://bugzilla.open-bio.org/ Thanks for contributing! Regards, Mauricio. Nancy Hansen wrote: > On Tue, 31 Oct 2006, Brian Osborne wrote: > >> It looks like a good place to start would be the get_header() and >> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can see that >> the author, at some point, wanted get_header to return meaningful >> information but stepping through the test shows it returning a lot of UNDEF. >> Now I don't know if this is due to the method or the source SCF file, but >> you might be able to get these methods to work yourself. >> >> But to answer your questions, yes, it certainly sounds reasonable that these >> values would be extracted by Bio::SeqIO::scf. > > Sounds great! So, if I make these changes, is there someone I should run > them by before checking them into CVS? Is Chad Matsalla still involved in > bioperl? I've never contributed to the project, so I'm not sure how > things work... > > Thanks! > --Nancy > > ************************************* > Nancy F. Hansen, PhD nhansen at nhgri.nih.gov > Bioinformatics Group > NIH Intramural Sequencing Center (NISC) > 5625 Fishers Lane > Rockville, MD 20852 > Phone: (301) 435-1560 Fax: (301) 435-6170 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From cjfields at uiuc.edu Wed Nov 1 14:39:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 1 Nov 2006 08:39:38 -0600 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: Message-ID: <000c01c6fdc3$8ed54770$15327e82@pyrimidine> > On Tue, 31 Oct 2006, Brian Osborne wrote: > >> It looks like a good place to start would be the get_header() and >> _get_header methods in Bio::SeqIO::scf. If you read t/scf.t you can >> see that the author, at some point, wanted get_header to return >> meaningful information but stepping through the test shows it >> returning a lot of UNDEF. Now I don't know if this is due to the >> method or the source SCF file, but you might be able to get these >> methods to work yourself. >> >> But to answer your questions, yes, it certainly sounds reasonable >> that these values would be extracted by Bio::SeqIO::scf. > > Sounds great! So, if I make these changes, is there someone > I should run them by before checking them into CVS? Is Chad > Matsalla still involved in bioperl? I've never contributed > to the project, so I'm not sure how things work... > > Thanks! > --Nancy You can check them into Bugzilla as a patch to a bug: http://bugzilla.open-bio.org/ There is a HOWTO for patch submission here: http://www.bioperl.org/wiki/HOWTO:SubmitPatch You could also send them to Brian or me. Bugzilla is probably your best bet as anyone with a developer account can check in the fix. You should also write up some tests for your code changes. You can use the test file mentioned above (t/scf.t) as a start. -chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Wed Nov 1 13:00:53 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 01 Nov 2006 09:00:53 -0400 Subject: [Bioperl-l] Bio::SeqIO::scf header/comments handling In-Reply-To: Message-ID: Nancy, I suggest doing this through Bugzilla, http://bugzilla.open-bio.org. First add your proposal as a bug or as an enhancement, sounds like it could be either but I'd say it doesn't matter. Then contribute patches to the "bug" as you work, some one will apply them. Also add tests to t/scf.t, if you're working on scf.pm. Thank you in advance for your contributions. As for Chad, I have no idea but strictly speaking no one "owns" a module in Bioperl. Brian O. On 11/1/06 9:43 AM, "Nancy Hansen" wrote: > Sounds great! So, if I make these changes, is there someone I should run > them by before checking them into CVS? Is Chad Matsalla still involved in > bioperl? I've never contributed to the project, so I'm not sure how > things work... From keithplayer at hotmail.com Thu Nov 2 00:22:07 2006 From: keithplayer at hotmail.com (Keith Player) Date: Thu, 2 Nov 2006 00:22:07 +0000 (UTC) Subject: [Bioperl-l] Article Message-ID: Sorry I didn't attach the article link originally. You can view the full-text for free: http://www.genome.org/cgi/content/abstract/12/10/1599 When I was talking about the R-tree I was talking about the current implementation. I should point out that I didn't actually try the perl module directly but implemented the binning schema straight in mysql. I found that by using the SQL I mentioned previously the database performed better compared to using the binning schema, I assume because of less disk seeks. I tested on a dataset of around 30k records and another the same size as the paper. The binning outperformed the queries as described in the paper, but the SQL I mentioned in the first post outperformed the binning schema by around a factor of 3. The new binning schema might make all this moot, especially if it removes layers so that groups/features next to each other are saved on the same/adjacent pages. The only question then would be whether database optimization is effected by the binning. Also does needing to know the largest length of a group/feature make the SQL statement I created impractical? From limericksean at gmail.com Wed Nov 1 16:28:58 2006 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 1 Nov 2006 17:28:58 +0100 Subject: [Bioperl-l] Can't locate object method "new_instance" via package "Bio::DB::SeqFeature::Store::dbi::mysql" at /project/gbrowse/httpd_perllib_new/Bio/DB/SeqFeature/Store.pm line 336. Message-ID: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> Hi, I am currently in the process of trying testing Gbrowse with the (relatively new) Bio::DB::SeqFeature::Store adaptor method. A couple of teething problems, just wondering if anyone else had encountered the message above. Any insight appreciated. Also the package called (Bio::DB::SeqFeature::Store::dbi::mysql) had to be copied into the lowercase 'dbi' from its original DBI form - don't know if this was a previously reported bug. Thanks, Sean. From ybolo001 at student.ucr.edu Thu Nov 2 00:15:57 2006 From: ybolo001 at student.ucr.edu (Eugene Bolotin) Date: Wed, 1 Nov 2006 16:15:57 -0800 Subject: [Bioperl-l] Check sequence format, question Message-ID: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> Dear bioperl mailing list, I trying to get sequence from a file using Bio::SeqIO, before I do anything, I want to make sure that the file is in a correct Fasta sequence format. I want it to spit out an error message if it is in any other format. What is the easiest way to do it? Thanks, Eugene Bolotin Sladek Lab. From cjfields at uiuc.edu Thu Nov 2 04:28:11 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 1 Nov 2006 22:28:11 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> References: <941fcc750611011615j6f55764hb9e1cd880fb4396c@mail.gmail.com> Message-ID: <24DED46C-4630-4E95-94D0-87810183F191@uiuc.edu> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: > Dear bioperl mailing list, > I trying to get sequence from a file using Bio::SeqIO, before I do > anything, > I want to make sure that the file is in a correct Fasta sequence > format. I > want it to spit out an error message if it is in any other format. > What is the easiest way to do it? > Thanks, > Eugene Bolotin > Sladek Lab. There is no formal FASTA definition that is universally accepted beyond having the first line start with '>' and an optional description, with the sequence in subsequent lines. http://www.bioperl.org/wiki/FASTA_sequence_format Bio::SeqIO isn't currently set up to validate sequence formats directly, but you could try preparsing the data using Bio::Tools::GuessSeqFormat. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Thu Nov 2 02:21:35 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 1 Nov 2006 21:21:35 -0500 Subject: [Bioperl-l] Can't locate object method "new_instance" via package "Bio::DB::SeqFeature::Store::dbi::mysql" at /project/gbrowse/httpd_perllib_new/Bio/DB/SeqFeature/Store.pm line 336. In-Reply-To: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> References: <462784640611010828g7d472550p53912db2401b5fd3@mail.gmail.com> Message-ID: <6dce9a0b0611011821l45cd7f8enb2e77f286f7cf6f5@mail.gmail.com> Hi, DBI should be uppercased in the gbrowse config file: [GENERAL] description = C. elegans GFF3 Database db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn ws164_gff3 You shouldn't have to change anything to lowercase. Lincoln On 11/1/06, Sean O'Keeffe wrote: > > Hi, > I am currently in the process of trying testing Gbrowse with the > (relatively new) Bio::DB::SeqFeature::Store adaptor method. A couple > of teething problems, just wondering if anyone else had encountered > the message above. Any insight appreciated. > Also the package called (Bio::DB::SeqFeature::Store::dbi::mysql) had > to be copied into the lowercase 'dbi' from its original DBI form - > don't know if this was a previously reported bug. > > Thanks, > Sean. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From Bernhard.Schmalhofer at biomax.com Thu Nov 2 08:53:14 2006 From: Bernhard.Schmalhofer at biomax.com (Bernhard Schmalhofer) Date: Thu, 02 Nov 2006 09:53:14 +0100 Subject: [Bioperl-l] Is it possible to parse BLAST output using IO:String? In-Reply-To: <716af09c0610301244q1c6d4cd6y23e72371dda4fa4d@mail.gmail.com> References: <00e301c6fc5f$a36de9e0$e6028a0a@GOLHARMOBILE1> <716af09c0610301244q1c6d4cd6y23e72371dda4fa4d@mail.gmail.com> Message-ID: <4549B1FA.1020506@biomax.com> Bernd Web wrote: > Hi Ryan, > > I parse blastn output using IO::String w/o problems: > > my $stringfh = new IO::String($input); > my $in = new Bio::SearchIO(-format => 'blast', -fh => $stringfh); I do the same with implicitly using IO::String. Works like a charm at leaset with Perl 5.8.0. # get $blast_report from MySQL open my $blast_report_fh, '<', \$blast_report; my $in = Bio::SearchIO->new( -format => 'blast', -fh => $blast_report_fh ); Regards, Bernhard -- ************************************************** Dipl.-Physiker Bernhard Schmalhofer Senior Developer Biomax Informatics AG Lochhamer Str. 11 82152 Martinsried, Germany Tel: +49 89 895574-839 Fax: +49 89 895574-825 eMail: Bernhard.Schmalhofer at biomax.com Website: www.biomax.com ************************************************** From cjfields at uiuc.edu Thu Nov 2 15:11:01 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 09:11:01 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <85304914-322B-46BA-BED2-09722FE08D57@uiuc.edu> Brian, I think the validation issue is worthwhile but I can see logistical nightmares having every SeqIO parser validate sequence while parsing; GenBank and EMBL do this to some extent already but it isn't foolproof. Much of SeqIO (e.g. GenBank/EMBL/Swiss parsing) is already in dire need of an overhaul as is w/o adding validation. I wonder if it would be better if SeqIO has-a validator object instead of acting as a validator itself, i.e. SeqIO would focus on parsing and writing, the validator would focus on validation. It might be easier from the maintenance aspect. It's probably worthwhile exploring using Bio::Tools::GuessSeqFormat within SeqIO, or setting up a new system altogether. Validation using the sequence validator could then be enabled by having a validation option when instantiating SeqIO. We could even enable XML format validation using the DTD/Schema, which should be fairly straightforward. Of course, this all depends on someone writing it up... Chris On Nov 2, 2006, at 6:49 AM, Brian Osborne wrote: > Chris et al., > > As you know the question of whether SeqIO should or should not > validate or > check the given format is still an open one. In fact, some SeqIO > modules do > validate to some extent. See: > > http://bugzilla.open-bio.org/show_bug.cgi?id=1508 > > I can see that you've commented on this enhancement, I'm replying > just to > bring this to the attention of others. > > Brian O. > > > On 11/2/06 12:28 AM, "Chris Fields" wrote: > >> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: >> >>> Dear bioperl mailing list, >>> I trying to get sequence from a file using Bio::SeqIO, before I do >>> anything, >>> I want to make sure that the file is in a correct Fasta sequence >>> format. I >>> want it to spit out an error message if it is in any other format. >>> What is the easiest way to do it? >>> Thanks, >>> Eugene Bolotin >>> Sladek Lab. >> >> There is no formal FASTA definition that is universally accepted >> beyond having the first line start with '>' and an optional >> description, with the sequence in subsequent lines. >> >> http://www.bioperl.org/wiki/FASTA_sequence_format >> >> Bio::SeqIO isn't currently set up to validate sequence formats >> directly, but you could try preparsing the data using >> Bio::Tools::GuessSeqFormat. >> >> Chris >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Thu Nov 2 14:38:36 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 10:38:36 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <85304914-322B-46BA-BED2-09722FE08D57@uiuc.edu> Message-ID: Chris, Yes, and validation should always be optional. SeqIO is not always as fast as some want it to be and sometimes you're certain that your files don't need to be validated. Brian O. On 11/2/06 11:11 AM, "Chris Fields" wrote: > Brian, > > I think the validation issue is worthwhile but I can see logistical > nightmares having every SeqIO parser validate sequence while parsing; > GenBank and EMBL do this to some extent already but it isn't > foolproof. Much of SeqIO (e.g. GenBank/EMBL/Swiss parsing) is > already in dire need of an overhaul as is w/o adding validation. > > I wonder if it would be better if SeqIO has-a validator object > instead of acting as a validator itself, i.e. SeqIO would focus on > parsing and writing, the validator would focus on validation. It > might be easier from the maintenance aspect. It's probably > worthwhile exploring using Bio::Tools::GuessSeqFormat within SeqIO, > or setting up a new system altogether. Validation using the sequence > validator could then be enabled by having a validation option when > instantiating SeqIO. We could even enable XML format validation > using the DTD/Schema, which should be fairly straightforward. > > Of course, this all depends on someone writing it up... > > Chris > > On Nov 2, 2006, at 6:49 AM, Brian Osborne wrote: > >> Chris et al., >> >> As you know the question of whether SeqIO should or should not >> validate or >> check the given format is still an open one. In fact, some SeqIO >> modules do >> validate to some extent. See: >> >> http://bugzilla.open-bio.org/show_bug.cgi?id=1508 >> >> I can see that you've commented on this enhancement, I'm replying >> just to >> bring this to the attention of others. >> >> Brian O. >> >> >> On 11/2/06 12:28 AM, "Chris Fields" wrote: >> >>> On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: >>> >>>> Dear bioperl mailing list, >>>> I trying to get sequence from a file using Bio::SeqIO, before I do >>>> anything, >>>> I want to make sure that the file is in a correct Fasta sequence >>>> format. I >>>> want it to spit out an error message if it is in any other format. >>>> What is the easiest way to do it? >>>> Thanks, >>>> Eugene Bolotin >>>> Sladek Lab. >>> >>> There is no formal FASTA definition that is universally accepted >>> beyond having the first line start with '>' and an optional >>> description, with the sequence in subsequent lines. >>> >>> http://www.bioperl.org/wiki/FASTA_sequence_format >>> >>> Bio::SeqIO isn't currently set up to validate sequence formats >>> directly, but you could try preparsing the data using >>> Bio::Tools::GuessSeqFormat. >>> >>> Chris >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > From bosborne11 at verizon.net Thu Nov 2 12:49:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 08:49:01 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <24DED46C-4630-4E95-94D0-87810183F191@uiuc.edu> Message-ID: Chris et al., As you know the question of whether SeqIO should or should not validate or check the given format is still an open one. In fact, some SeqIO modules do validate to some extent. See: http://bugzilla.open-bio.org/show_bug.cgi?id=1508 I can see that you've commented on this enhancement, I'm replying just to bring this to the attention of others. Brian O. On 11/2/06 12:28 AM, "Chris Fields" wrote: > On Nov 1, 2006, at 6:15 PM, Eugene Bolotin wrote: > >> Dear bioperl mailing list, >> I trying to get sequence from a file using Bio::SeqIO, before I do >> anything, >> I want to make sure that the file is in a correct Fasta sequence >> format. I >> want it to spit out an error message if it is in any other format. >> What is the easiest way to do it? >> Thanks, >> Eugene Bolotin >> Sladek Lab. > > There is no formal FASTA definition that is universally accepted > beyond having the first line start with '>' and an optional > description, with the sequence in subsequent lines. > > http://www.bioperl.org/wiki/FASTA_sequence_format > > Bio::SeqIO isn't currently set up to validate sequence formats > directly, but you could try preparsing the data using > Bio::Tools::GuessSeqFormat. > > Chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Thu Nov 2 18:07:45 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 12:07:45 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <93F383D1-6DDF-4238-954A-96CE1218C641@uiuc.edu> On Nov 2, 2006, at 8:38 AM, Brian Osborne wrote: > Chris, > > Yes, and validation should always be optional. SeqIO is not always > as fast > as some want it to be and sometimes you're certain that your files > don't > need to be validated. > > Brian O. Agreed. We could use the original Bugzilla bug (1508?) to track this and maybe gather ideas, but the wiki is probably a better place... Chris > On 11/2/06 11:11 AM, "Chris Fields" wrote: > >> ... Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bosborne11 at verizon.net Thu Nov 2 18:08:45 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 02 Nov 2006 14:08:45 -0400 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: <93F383D1-6DDF-4238-954A-96CE1218C641@uiuc.edu> Message-ID: Chris, Yes, in the Project priority list page. Speaking of this page, why is all of the text on the bottom half of this page crossed out? Many of these items have _not_ been done. Brian O. On 11/2/06 2:07 PM, "Chris Fields" wrote: > Agreed. We could use the original Bugzilla bug (1508?) to track this > and maybe gather ideas, but the wiki is probably a better place... From cjfields at uiuc.edu Thu Nov 2 19:22:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 2 Nov 2006 13:22:48 -0600 Subject: [Bioperl-l] Check sequence format, question In-Reply-To: References: Message-ID: <0DA38665-F4CB-4000-974F-47915F0524A2@uiuc.edu> On Nov 2, 2006, at 12:08 PM, Brian Osborne wrote: > Chris, > > Yes, in the Project priority list page. > > Speaking of this page, why is all of the text on the bottom half of > this > page crossed out? Many of these items have _not_ been done. > > Brian O. You're right; they shouldn't be crossed out unless they are completed. If someone takes on a project then they attach their signature to it, not cross it off the list. I'll change that and add a disclaimer to the top of the page. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stewarta at nmrc.navy.mil Thu Nov 2 20:26:08 2006 From: stewarta at nmrc.navy.mil (Andrew Stewart) Date: Thu, 2 Nov 2006 15:26:08 -0500 Subject: [Bioperl-l] Bio::DB::GFF and feature order Message-ID: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> In attempting to determine some statistics on the distances between CDS features in my Bio::DB::GFF database, I ran a query on all CDS features as follows... my @CDS = $segment->features('CDS'); ...only to find that the features returned are not in order. Is there a way of returning the features in order or sorting them through some internal Bio::DB::GFF related method, aside from the more obvious path of sorting through the array itself (somehow)? -A -- Andrew Stewart Research Assistant, Genomics Team Navy Medical Research Center (NMRC) Biological Defense Research Directorate (BDRD) BDRD Annex 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 email: stewarta at nmrc.navy.mil phone: 301-231-6700 Ext 270 From lincoln.stein at gmail.com Thu Nov 2 20:41:06 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 2 Nov 2006 15:41:06 -0500 Subject: [Bioperl-l] [Gmod-gbrowse] Bio::DB::GFF and feature order In-Reply-To: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> References: <3505E983-B3D1-46A9-A648-1147B81DB2FA@nmrc.navy.mil> Message-ID: <6dce9a0b0611021241i35f602f2q6ca59f23738d1013@mail.gmail.com> How do you want them sorted? To sort them by their start positions: my @CDS = sort {$a->start<=>$b->start} $segment->features('CDS'); Other people may want to sort features by end position, length, name, or who knows what. Lincoln On 11/2/06, Andrew Stewart wrote: > > In attempting to determine some statistics on the distances between CDS > features in my Bio::DB::GFF database, I ran a query on all CDS features as > follows... > my @CDS = $segment->features('CDS'); > > ...only to find that the features returned are not in order. Is there a > way of returning the features in order or sorting them through some internal > Bio::DB::GFF related method, aside from the more obvious path of sorting > through the array itself (somehow)? > > > -A > > -- > Andrew Stewart > Research Assistant, Genomics Team > Navy Medical Research Center (NMRC) > Biological Defense Research Directorate (BDRD) > BDRD Annex > 12300 Washington Avenue, 2nd Floor > Rockville, MD 20852 > > email: stewarta at nmrc.navy.mil > phone: 301-231-6700 Ext 270 > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From n.haigh at sheffield.ac.uk Thu Nov 2 22:12:28 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 02 Nov 2006 22:12:28 +0000 Subject: [Bioperl-l] $Bio::Root::Version:VERSION Message-ID: <454A6D4C.3020605@sheffield.ac.uk> When does $Bio::Root::Version::VERSION get incremented? immediately prior to a tag or straight after a tag so that CVS code is seen as more recent than an official release? For example, $VERSION is currently set to 1.52_01 but the code in CVS HEAD is passed 1.5.2 RC2 now so should is read 1.52_02 or be 1.52_03 for the upcoming 1.52 RC3? Cheers Nath From bix at sendu.me.uk Thu Nov 2 23:14:57 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 02 Nov 2006 23:14:57 +0000 Subject: [Bioperl-l] $Bio::Root::Version:VERSION In-Reply-To: <454A6D4C.3020605@sheffield.ac.uk> References: <454A6D4C.3020605@sheffield.ac.uk> Message-ID: <454A7BF1.1060705@sendu.me.uk> Nathan S. Haigh wrote: > When does $Bio::Root::Version::VERSION get incremented? immediately > prior to a tag or straight after a tag so that CVS code is seen as more > recent than an official release? Normally nothing happens. > For example, $VERSION is currently set to 1.52_01 but the code in CVS > HEAD is passed 1.5.2 RC2 now so should is read 1.52_02 or be 1.52_03 for > the upcoming 1.52 RC3? Once I've decided what to do based on the discussion we had, I'll update it. I'll currently leaning toward the 'clean break', pugs-style suggestion from Chris. If you've strong views in another direction, post in that thread. From bernd.web at gmail.com Fri Nov 3 12:57:03 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 3 Nov 2006 13:57:03 +0100 Subject: [Bioperl-l] Bio::DB::Query::GenBank Message-ID: <716af09c0611030457p678f4d30v935215ba3c4dd5dc@mail.gmail.com> Hi, In contrast to the doc of Bio::DB::Query::GenBank at http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Query/GenBank.html this following seems not the case: "If you provide an array reference of IDs in -ids, the query will be ignored and the list of IDs will be used when the query is passed to a Bio::DB::GenBank object's get_Stream_by_query() method" I used # $Id: GenBank.pm,v 1.19 2006/09/26 22:03:07 sendu Exp $ It looks like query always overrules the array(ref) given in -ids. bernd From staffa at niehs.nih.gov Fri Nov 3 16:29:19 2006 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Fri, 03 Nov 2006 12:29:19 -0400 Subject: [Bioperl-l] Bio::Tools::RestrictionEnzyme Message-ID: The module Bio::Tools::RestrictionEnzyme Uses the perl split function to generate the fragments of a digestion, Using the recognition pattern as the delimiter. It then glues onto the resulting strings that part of the pattern representing the sequence before and after the cut. This is fine for non-ambiguous patterns, but starts looking funny for patterns having ambiguities. Worse that in doing a double digest, one enzyme after another, the ambiguity code character can mask a true cut site. I was using BsaHI [GRCGYC] followed by HpaII [CCGG] Below is the example of the CCGG pattern being masked by a Y And the different results of the digestion. CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAA As opposed to the real thing: CGCCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAA Which when cut by HpaII [CCGG] really yields first A_B_frag : CGC Instead of : first A_B_frag = CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTAGAAAG ACTTGCTAGTGCTGTTGGGTCTCC TTGACTCTGAGACAATGATAACAATGTTGAAGGTGGTCTAGGCATTTGGGTGCTGTGGAGTTATAAAGAGGAAAAG AAAAGATAAAACAAAAAAAAATAG GAAACAAATGATTAAGCCACTACTAAGGGGTCTAGTCTAATGCCAACTGGGTAAATTCATGGGAACAATGTGTGCC AGTCTTTAGAAACACTGTTTCATA TTGCATATATTATGGCATGGTATTACATTGATTAATTTTACTTTAGAGATGAAGAAGCTGAGATTTGGGGTGAATA GCAATTATCCCAAAGTCTCTCAGA TAGCTGGAGGCAGCAGGGTCTGGGGTATTCACAGTCCCTACTCCATATTGTGTGGTCAGAACCAAATGAGACAGAT AAAGGGCAGACAAAAGAGAAAGTG GGGAGTATGATTTGAAAATGATGGTGTGACCCAGATTTCTGATGGAAATATCTAATGGCTGCAGACTGGATAGCTG TGACCATTTTAGTTACTGAATTCA GGAGATCTTATCTCAATGGAGGCATGTTGTCAACCAAAAGCCAGGATAAGCAAGGGTCAGTGTCTAGACATTGGAG TAAGGTTTGCCTGGATATTTCCAC AGGGAACCAAGTGTCATGGAGTCTTATTCATTGGGAGGTTATCTTTGTTACACACATGGACATATCATCAAGCCAG CAATTCAGCAAAACTGTCAACACA CAAATAGAGATGTATTGACAACGGGGAACCACAAGTCATGCTTATTCCAAGCTAAAGCCCTCATGTGGAACTTGTT TTGTATGGCATTTGTCTCATCTAC ACATTGATGGGAAGGGTAAAAGGAAGTCTTTGGTGGGATTACAGAAGTCAGTAAAAAAGCAAAAGGAAAGATTTAG AAAACAAAGAAAAAGAAAAGGGAG GAAAGGAAAAGAAAAAAGATTTCAGAGATCTCAACATCAATTCAGACCAAGGGTGCCTCTTATACTATGTCCAAGC CAGTAAGTGGGGTTGTTCTTGTTA ACTACAGCCATGTATAGAGGTGAACTTCAGGCTCCTGACTGATCCTCTGAGGTAGAAAGTAAACAGTACTCTTATG ACACACGCAGTTGTTCAGTGCTGA CATGAAAATGTCATTGCTTACAGCGCTAGGAGAC This subroutine yields, I believe, the true sequence, Although I don't know how efficient it is. I'm thinking it must be more efficient than having to turn each fragment from the first digestion into a BioPerl Sequence Object before applying the cut_seq method. sub cut_seq { my $number= 0; my @frags = (); my $bigline = shift @_; my $recognition_site = shift @_; my $cutsite = shift @_; my $pat = &expanded_string($recognition_site); while ($bigline){ #my $offset = index $bigline, $pat; if ($bigline =~/($pat)/){ my $first = substr $&,0,$cutsite; my $last = substr $&,$cutsite; my $frag = $`.$first; push @frags, $frag; $number++; #print "fragment # $number:\n$frag\n"; my $rest_of_bigline = $last.$'; $bigline = $rest_of_bigline;} else {push @frags, $bigline; #Last one $number++; #print "fragment # $number:\n$bigline\n"; $bigline = "";} } return @frags; } Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Information Technology Support Services Contract (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov ) National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From cjfields at uiuc.edu Fri Nov 3 18:28:53 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 3 Nov 2006 12:28:53 -0600 Subject: [Bioperl-l] Bio::Tools::RestrictionEnzyme In-Reply-To: References: Message-ID: <915FE028-7F12-4BCE-AD9D-7D8D7D74AD6F@uiuc.edu> Nick, Could you file this as a bug? Chris On Nov 3, 2006, at 10:29 AM, Staffa, Nick (NIH/NIEHS) wrote: > The module Bio::Tools::RestrictionEnzyme > Uses the perl split function to generate the fragments of a digestion, > Using the recognition pattern as the delimiter. It then glues onto > the > resulting strings that part of the pattern representing the > sequence before > and after the cut. This is fine for non-ambiguous patterns, but > starts > looking funny for patterns having ambiguities. > Worse that in doing a double digest, one enzyme after another, the > ambiguity > code character can mask a true cut site. > I was using BsaHI [GRCGYC] followed by HpaII [CCGG] > Below is the example of the CCGG pattern being masked by a Y > And the different results of the digestion. > > > CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAA > As opposed to the real thing: > CGCCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAA > > Which when cut by HpaII [CCGG] really yields > first A_B_frag : > CGC > > Instead of : > first A_B_frag = > > CGYCGGCATGTCGATGGTGACCATGTGACAGCACGAGTCACTGCTGCTTTCAAGTTCCGAACAGGAATTA > GAAAG > ACTTGCTAGTGCTGTTGGGTCTCC > TTGACTCTGAGACAATGATAACAATGTTGAAGGTGGTCTAGGCATTTGGGTGCTGTGGAGTTATAAAGAG > GAAAAG > AAAAGATAAAACAAAAAAAAATAG > GAAACAAATGATTAAGCCACTACTAAGGGGTCTAGTCTAATGCCAACTGGGTAAATTCATGGGAACAATG > TGTGCC > AGTCTTTAGAAACACTGTTTCATA > TTGCATATATTATGGCATGGTATTACATTGATTAATTTTACTTTAGAGATGAAGAAGCTGAGATTTGGGG > TGAATA > GCAATTATCCCAAAGTCTCTCAGA > TAGCTGGAGGCAGCAGGGTCTGGGGTATTCACAGTCCCTACTCCATATTGTGTGGTCAGAACCAAATGAG > ACAGAT > AAAGGGCAGACAAAAGAGAAAGTG > GGGAGTATGATTTGAAAATGATGGTGTGACCCAGATTTCTGATGGAAATATCTAATGGCTGCAGACTGGA > TAGCTG > TGACCATTTTAGTTACTGAATTCA > GGAGATCTTATCTCAATGGAGGCATGTTGTCAACCAAAAGCCAGGATAAGCAAGGGTCAGTGTCTAGACA > TTGGAG > TAAGGTTTGCCTGGATATTTCCAC > AGGGAACCAAGTGTCATGGAGTCTTATTCATTGGGAGGTTATCTTTGTTACACACATGGACATATCATCA > AGCCAG > CAATTCAGCAAAACTGTCAACACA > CAAATAGAGATGTATTGACAACGGGGAACCACAAGTCATGCTTATTCCAAGCTAAAGCCCTCATGTGGAA > CTTGTT > TTGTATGGCATTTGTCTCATCTAC > ACATTGATGGGAAGGGTAAAAGGAAGTCTTTGGTGGGATTACAGAAGTCAGTAAAAAAGCAAAAGGAAAG > ATTTAG > AAAACAAAGAAAAAGAAAAGGGAG > GAAAGGAAAAGAAAAAAGATTTCAGAGATCTCAACATCAATTCAGACCAAGGGTGCCTCTTATACTATGT > CCAAGC > CAGTAAGTGGGGTTGTTCTTGTTA > ACTACAGCCATGTATAGAGGTGAACTTCAGGCTCCTGACTGATCCTCTGAGGTAGAAAGTAAACAGTACT > CTTATG > ACACACGCAGTTGTTCAGTGCTGA > CATGAAAATGTCATTGCTTACAGCGCTAGGAGAC > > > This subroutine yields, I believe, the true sequence, > Although I don't know how efficient it is. > I'm thinking it must be more efficient than having to turn each > fragment > from the first digestion into a BioPerl Sequence Object before > applying the > cut_seq method. > > sub cut_seq { > my $number= 0; > my @frags = (); > my $bigline = shift @_; > my $recognition_site = shift @_; > my $cutsite = shift @_; > my $pat = &expanded_string($recognition_site); > while ($bigline){ > #my $offset = index $bigline, $pat; > if ($bigline =~/($pat)/){ > my $first = substr $&,0,$cutsite; > my $last = substr $&,$cutsite; > my $frag = $`.$first; > push @frags, $frag; > $number++; > #print "fragment # $number:\n$frag\n"; > my $rest_of_bigline = $last.$'; > $bigline = $rest_of_bigline;} > else {push @frags, $bigline; #Last one > $number++; > #print "fragment # $number:\n$bigline\n"; > $bigline = "";} > } > return @frags; > } > > > > > Nick Staffa > Telephone: 919-316-4569 (NIEHS: 6-4569) > Scientific Computing Support Group > NIEHS Information Technology Support Services Contract > (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov ) > National Institute of Environmental Health Sciences > National Institutes of Health > Research Triangle Park, North Carolina > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From johnson.biotech at gmail.com Fri Nov 3 16:47:56 2006 From: johnson.biotech at gmail.com (Seth Johnson) Date: Fri, 3 Nov 2006 11:47:56 -0500 Subject: [Bioperl-l] BioSQL load_seqdatabase.pl -pipeline option Message-ID: Hello guys, I'm populating biosql database using "load_seqdatabase.pl" from genbank release files for primates. However, I only need sequences that belong to humans (taxon id: 9606). I assume that best way to filter the necessary sequences is to use '-pipeline' option of the script. The documentation seems a little vague to me on how to create my own processor to accomplish the task. Can anyone clarify the steps??? -- Best Regards, Seth Johnson Senior Bioinformatics Associate From er at xs4all.nl Fri Nov 3 19:59:47 2006 From: er at xs4all.nl (Erik) Date: Fri, 3 Nov 2006 20:59:47 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error Message-ID: <10596.156.83.1.241.1162583987.squirrel@webmail.xs4all.nl> Hi all, I noticed the parsing is borked with newest swisprot files: UniProt Knowledgebase Release 9 consists of: UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines in swissprot/trembl according to the new specification (see http://expasy.org/sprot/relnotes/sp_news.html). Basically, the change is as follows: ID EntryName DataClass; MoleculeType; SequenceLength. is changed to: ID EntryName DataClass; SequenceLength. The change I made was only in the regex capturing the entry name: method next_seq (Bio/SeqIO/swiss.pm) : =============== unless( m/ ^ ID \s+ # (\S+) \s+ # $1 entryname ([^\s;]+); \s+ # $2 DataClass [0-9]+[ ]AA \. # Sequencelength (capture?) $ /ox ) { $self->throw("swissprot stream with no ID. Not swissprot in my book"); } =============== I tested this (=entry parsable and SeqIO created) against several hundred Swissprot and Trembl entries. Of course, files with the older format are now broken - it may be better to leave old and new format, and try both (newest first). hth, Erik From er at xs4all.nl Fri Nov 3 20:56:47 2006 From: er at xs4all.nl (Erik) Date: Fri, 3 Nov 2006 21:56:47 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error - Message-ID: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> I should have mentioned two more changes needed in Bio/SeqIO/swiss.pm for the new Swissprot format: In Bio/SeqIO/swiss.pm, next_seq(): =============== $params{'-namespace'} = ($2 eq 'Reviewed' ) ? 'Swiss-Prot' : ($2 eq 'Unreviewed' ) ? 'TrEMBL' : # ($2 eq 'STANDARD' ) ? 'Swiss-Prot' : # ($2 eq 'PRELIMINARY') ? 'TrEMBL' : $2; =============== and in Bio/SeqIO/swiss.pm, write_seq(): =============== $div = ($ns eq 'Swiss-Prot') ? 'Reviewed' : ($ns eq 'TrEMBL') ? 'Unreviewed' : # ($ns eq 'Swiss-Prot') ? 'STANDARD' : # ($ns eq 'TrEMBL') ? 'PRELIMINARY' : $ns; =============== above, the old lines are shown as outcommented. again, hth, Erik From pllv_shrm at yahoo.com Fri Nov 3 21:14:14 2006 From: pllv_shrm at yahoo.com (pallavi sharma) Date: Fri, 3 Nov 2006 13:14:14 -0800 (PST) Subject: [Bioperl-l] need help Message-ID: <20061103211414.56111.qmail@web31712.mail.mud.yahoo.com> hii could ny one plz tell me how to convert bioperl module like Bio::SearchIO n Bio::alignIO module into perl lang --------------------------------- Check out the New Yahoo! Mail - Fire up a more powerful email and get things done faster. From hlapp at gmx.net Fri Nov 3 22:54:08 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 3 Nov 2006 17:54:08 -0500 Subject: [Bioperl-l] BioSQL load_seqdatabase.pl -pipeline option In-Reply-To: References: Message-ID: Close. It's not the --pipeline option you want to use for this purpose but the --seqfilter option. For example, to retain only sequence with taxon id 9606 you would say --seqfilter 'sub {my $s=shift->{"-species"}; return 1 unless $s; return 1 unless $s->ncbi_taxid; return 1 if $s->ncbi_taxid == 9606; return 0;}' Note that when formulating the conditions upon which to accept or reject the object you need to take into account that the closure may be called multiple times for one object, at various stages of completion of the properties hash. So, the above sequence of logic says, accept the object if there is no species attached (yet), or if the species doesn't have a taxon ID (yet; in Genbank format, the taxon ID is actually in the feature table, and hence will only be populated later, after parsing the organism lines), or if the taxon ID is 9606. Otherwise (i.e., there is a species object, it has a taxon ID defined, and the taxon ID is not 9606) reject the object. (Note that --seqfilter will read and parse a file if the argument refers to an existing and readable file. So if you are going to use this construct often, you may want to put into a file.) -hilmar On Nov 3, 2006, at 11:47 AM, Seth Johnson wrote: > Hello guys, > > I'm populating biosql database using "load_seqdatabase.pl" from > genbank release files for primates. However, I only need sequences > that belong to humans (taxon id: 9606). I assume that best way to > filter the necessary sequences is to use '-pipeline' option of the > script. The documentation seems a little vague to me on how to create > my own processor to accomplish the task. Can anyone clarify the > steps??? > > -- > Best Regards, > > > Seth Johnson > Senior Bioinformatics Associate > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From akozik at atgc.org Fri Nov 3 22:29:49 2006 From: akozik at atgc.org (Alexander Kozik) Date: Fri, 03 Nov 2006 14:29:49 -0800 Subject: [Bioperl-l] SCF files Message-ID: <454BC2DD.5050405@atgc.org> Hi all, There is a contradiction in opinions (I have used google search) what type of data SCF files (sequencing chromatograms) carry. Could you help to clarify following topics: are these statements true or false: 1. SCF files can be generated by Phred program only. 2. new version of Phred can read SCF files produced by older version of Phred and re-do basecalling with new quality scores [new quality scores could be different because of the improvements/changes in a basecalling algorithm] 3. SCF files contain no less information as original AB1 files [in other words, no information lost during conversion of AB1 to SCF] Thanks, -Alex ======================================== Alexander Kozik Bioinformatics Specialist Genome and Biomedical Sciences Facility 451 East Health Sciences Drive University of California Davis, CA 95616-8816 Phone: (530) 754-9127 email: akozik at atgc.org web: http://www.atgc.org/ ======================================== From cjfields at uiuc.edu Sun Nov 5 21:56:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 5 Nov 2006 15:56:08 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error - In-Reply-To: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> References: <15518.156.83.1.241.1162587407.squirrel@webmail.xs4all.nl> Message-ID: <73A15B2C-A8FE-4F1B-B17E-B43A46B82140@uiuc.edu> We'll try to get these in. THe problem is we need to try and make this backwards compatible. I'll post this as a bug for now as a reminder. Chris On Nov 3, 2006, at 2:56 PM, Erik wrote: > > I should have mentioned two more changes needed > in Bio/SeqIO/swiss.pm for the new Swissprot > format: > > In Bio/SeqIO/swiss.pm, next_seq(): > =============== > $params{'-namespace'} = ($2 eq 'Reviewed' ) ? 'Swiss-Prot' : > ($2 eq 'Unreviewed' ) ? 'TrEMBL' : > # ($2 eq 'STANDARD' ) ? 'Swiss-Prot' : > # ($2 eq 'PRELIMINARY') ? 'TrEMBL' : > $2; > =============== > > > and in Bio/SeqIO/swiss.pm, write_seq(): > =============== > $div = ($ns eq 'Swiss-Prot') ? 'Reviewed' : > ($ns eq 'TrEMBL') ? 'Unreviewed' : > # ($ns eq 'Swiss-Prot') ? 'STANDARD' : > # ($ns eq 'TrEMBL') ? 'PRELIMINARY' : > $ns; > =============== > > above, the old lines are shown as outcommented. > > > again, hth, > > Erik > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From adsj at novozymes.com Mon Nov 6 13:03:21 2006 From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=) Date: Mon, 06 Nov 2006 14:03:21 +0100 Subject: [Bioperl-l] Subclassing Bio::Seq ? Extending Bio::Perl References: <934F95E71B6C9347A873C42AE3C196191299DFBF@NZT0004E.dknz.nzcorp.n et> <934F95E71B6C9347A873C42AE3C196190B84C5FC@NZT0004E.dknz.nzcorp.net> Message-ID: <87zmb4ohgm.fsf@topper.koldfront.dk> On Tue, 24 Oct 2006 14:57:02 -0400, Hilmar wrote: > On Oct 24, 2006, at 1:59 PM, JK ((Jesper Agerbo Krogh)) wrote: >>> The reason that this is a Bio::PrimarySeq and not a Bio::Seq or your >>> extension of the latter is that the Perl garbage collector can't deal >>> with circular references. >> Doesn't Scalar::Util::weaken solve that? > You're welcome to test and try. It should be a simple change in > Bio::Seq::add_SeqFeature(). You will see that it is this method and > not the feature object that makes sure the wrapped primarySeq gets > passed as sequence reference. Just change that to creating a new > reference to the sequence object and make it a weak reference before > passing it to the feature object. > (The feature object has no requirement (or knowledge) that the > referenced sequence object is a PrimarySeq.) I've tried implementing this approach - the only test that failed was FootPrinter.t, which I "solved" by not weakening if the object is a Bio::PrimarySeq. I am not sure how fragile this approach is; any comments (patch attached)? [...] > I'm not following you why this would make any difference (it would be > $seq->message_digest() compared to $seqCompute->message_digest > ($seq)), unless what you are saying is that you would like to cache > the result of the computation. You would have to create, or pass around, a $seqCompute object everywhere your $seq-object's digest was needed, which would be a bit of a pain? Best regards, Adam -- Adam Sj?gren adsj at novozymes.com -------------- next part -------------- A non-text attachment was scrubbed... Name: feature_seq_weaken.patch Type: text/x-patch Size: 3675 bytes Desc: not available URL: From n.haigh at sheffield.ac.uk Mon Nov 6 15:12:37 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 15:12:37 +0000 Subject: [Bioperl-l] return undef Message-ID: <454F50E5.3030702@sheffield.ac.uk> Is there any reason why a "return undef" can't simply be swapped over to just "return"? Cheers Nath From n.haigh at sheffield.ac.uk Mon Nov 6 16:19:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 16:19:08 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F5BED.6040406@sendu.me.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> Message-ID: <454F607C.5020808@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Is there any reason why a "return undef" can't simply be swapped over to >> just "return"? > > No, in fact if you see any 'return undef's, please change them to > 'return' since the former can lead to subtle bugs. We did do an audit > earlier to fix most of those; presumably there was some kind of issue > with the remainder (or they just weren't caught), so check that no > problems arise when you make the change. > Just been checking the bioperl-run modules and changed the ones I found. Running "make test" doesn't seem to show up any errors so I'll commit them shortly. On a similar note, is it safe to simply substitute "use vars" for "our" and correctly commenting the list of variables if qw() was previously used? e.g.: use vars qw($variable1 @array1 %hash1); # to: our ($variable1, @array1, %hash1); If so, there are 340+ "use vars" in the bioperl-run......any wise ideas on a generic script that can do an intelligent search and replace. Bearing in mind that these lists can span multiple lines? I set up the following page a couple of days ago to house some scripts that can be used to do audit checks of code: http://www.bioperl.org/wiki/Auditing If anyone has any scripts, Perl, shell or otherwise fell free to add them! :-) Cheers Nath -- > A: Yes. >> Q: Are you sure? >> >>> A: Because it reverses the logical flow of conversation. >>> >>>> Q: Why is top posting frowned upon? >>>> Get Thunderbird From bix at sendu.me.uk Mon Nov 6 15:59:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 15:59:41 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F50E5.3030702@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> Message-ID: <454F5BED.6040406@sendu.me.uk> Nathan S. Haigh wrote: > Is there any reason why a "return undef" can't simply be swapped over to > just "return"? No, in fact if you see any 'return undef's, please change them to 'return' since the former can lead to subtle bugs. We did do an audit earlier to fix most of those; presumably there was some kind of issue with the remainder (or they just weren't caught), so check that no problems arise when you make the change. From cjfields at uiuc.edu Mon Nov 6 16:35:52 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 10:35:52 -0600 Subject: [Bioperl-l] AlignIO::stockholm write_aln() Message-ID: I have added some experimental write_aln() support for Stockholm format to CVS along with some basic tests to AlignIO.t. I plan on cleaning it up a bit and adding more tests, along with possibly adding a builder option (similar to SeqIO::genbank) to have annotation parsing optional. Right now it is always on by default. It doesn't print meta data yet but does parse and store it; I'll probably add that in the next day or two. Be forewarned if testing this: I haven't tried clustal/msf/etc- >stockholm conversions yet so don't know if that works, but it should (it just won't print annotations). I'll add tests for that when I get time. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 6 16:55:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 16:55:55 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <454F607C.5020808@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> Message-ID: <454F691B.3090900@sendu.me.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: >> Nathan S. Haigh wrote: >>> Is there any reason why a "return undef" can't simply be swapped over to >>> just "return"? >> >> No, in fact if you see any 'return undef's, please change them to >> 'return' since the former can lead to subtle bugs. We did do an audit >> earlier to fix most of those; presumably there was some kind of issue >> with the remainder (or they just weren't caught), so check that no >> problems arise when you make the change. > > Just been checking the bioperl-run modules and changed the ones I found. > Running "make test" doesn't seem to show up any errors so I'll commit > them shortly. Thanks. > On a similar note, is it safe to simply substitute "use vars" for "our" > and correctly commenting the list of variables if qw() was previously used? Should be. But note that we didn't officially agree on having the Run package require Perl 5.6... Is there a particular person who maintains the Run package, or does that fall to the pumpkin of Core? > If so, there are 340+ "use vars" in the bioperl-run......any wise ideas > on a generic script that can do an intelligent search and replace. > Bearing in mind that these lists can span multiple lines? It'll need a little futzing, just be very careful it is working perfectly before applying it to everything. All of Core and the other packages need the same work done on them... > I set up the following page a couple of days ago to house some scripts > that can be used to do audit checks of code: > http://www.bioperl.org/wiki/Auditing > > If anyone has any scripts, Perl, shell or otherwise fell free to add > them! :-) I created a one-off for the conversion to 'use base', but its a bit of delirium-induced hack. I'll add it when I get the chance; its essentially a more complex version of what you want to do. It also ought to be applied to all the other Bioperl packages... (You should make mention of the existing audit scripts in CVS for bioperl-live in maintenance/) From cjfields at uiuc.edu Mon Nov 6 17:58:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 11:58:27 -0600 Subject: [Bioperl-l] return undef In-Reply-To: <454F691B.3090900@sendu.me.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> <454F691B.3090900@sendu.me.uk> Message-ID: <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> >> On a similar note, is it safe to simply substitute "use vars" for >> "our" >> and correctly commenting the list of variables if qw() was >> previously used? > > Should be. But note that we didn't officially agree on having the Run > package require Perl 5.6... Is there a particular person who maintains > the Run package, or does that fall to the pumpkin of Core? I believe Albert Vilella was taking care of bioperl-run, but I'm not absolutely sure. I think we can assume that, if core rel. 1.5.2 requires perl 5.6.1, anything that requires bioperl rel. 1.5.2 should likewise require perl 5.6.1 as well. Probably should make that explicitly stated somewhere. >> If so, there are 340+ "use vars" in the bioperl-run......any wise >> ideas >> on a generic script that can do an intelligent search and replace. >> Bearing in mind that these lists can span multiple lines? > > It'll need a little futzing, just be very careful it is working > perfectly before applying it to everything. All of Core and the other > packages need the same work done on them... I have gone through a few and manually switched 'use vars' over to 'our'. You can always try making the necessary changes globally but I think you'll see a lot of failed tests. >> I set up the following page a couple of days ago to house some >> scripts >> that can be used to do audit checks of code: >> http://www.bioperl.org/wiki/Auditing >> >> If anyone has any scripts, Perl, shell or otherwise fell free to add >> them! :-) > > I created a one-off for the conversion to 'use base', but its a bit of > delirium-induced hack. I'll add it when I get the chance; its > essentially a more complex version of what you want to do. It also > ought > to be applied to all the other Bioperl packages... > > (You should make mention of the existing audit scripts in CVS for > bioperl-live in maintenance/) Not sure how much more global code auditing should be done before the 1.5.2 final release, but if it passes tests then I don't have a problem. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 6 18:08:38 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 06 Nov 2006 18:08:38 +0000 Subject: [Bioperl-l] return undef In-Reply-To: <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> <454F691B.3090900@sendu.me.uk> <588CFC9D-F078-43E7-9A30-116AFD256A88@uiuc.edu> Message-ID: <454F7A26.9090800@sendu.me.uk> Chris Fields wrote: >>> I set up the following page a couple of days ago to house some scripts >>> that can be used to do audit checks of code: >>> http://www.bioperl.org/wiki/Auditing >>> >>> If anyone has any scripts, Perl, shell or otherwise fell free to add >>> them! :-) >> >> I created a one-off for the conversion to 'use base', but its a bit of >> delirium-induced hack. I'll add it when I get the chance; its >> essentially a more complex version of what you want to do. It also ought >> to be applied to all the other Bioperl packages... >> >> (You should make mention of the existing audit scripts in CVS for >> bioperl-live in maintenance/) > > Not sure how much more global code auditing should be done before the > 1.5.2 final release None; I won't add any to the branch (bug fixes and documentation only, for the most part). It is still valuable to do for the next release though! From n.haigh at sheffield.ac.uk Mon Nov 6 20:29:23 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 06 Nov 2006 20:29:23 +0000 Subject: [Bioperl-l] StandAloneFasta::version Message-ID: <454F9B23.8010302@sheffield.ac.uk> Hi Sendu, I've written a version method for StandAloneFasta.pm. However, because of the way in which FASTA is versioned, it makes for difficult version comparisons i.e. they contain non-numeric characters e.g. 3.4t26. I have employed a private function that does a conversion of the non-numeric characters into their ascii value representation to build a float. e.g. the above version would result in: 3.411626 which can then be compared easily. At the moment, this is accessed via $factory->version like other modules as this will give access to a version number that is easily comparable. However, should there be a different function to return the unconverted version string e.g. 3.4t26? Or should there be a function that does a compare internally so it can be accessed something like: print "we have met the min version requirement\n" if $factory->at_least_version('3.4t26'); Ideas welcome! Nath From cjfields at uiuc.edu Mon Nov 6 21:21:10 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 6 Nov 2006 15:21:10 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <454F9B23.8010302@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> Message-ID: <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> Nathan, Weren't the problems with the reported StandAloneFasta.pm test fails due to differences in the returned order of the Hits/HSPs in the FASTA reports from the different versions? The test results you posted on the wiki (where I commented on this) seem to indicate that: not ok 11 # Test 11 got: "0" (t/StandAloneFasta.t at line 75) # Expected: "994" # t/StandAloneFasta.t line 75 is: ok $hsp->num_identical, 994; not ok 12 # Test 12 got: "1977" (t/StandAloneFasta.t at line 76) # Expected: "994" # t/StandAloneFasta.t line 76 is: ok $hsp->length, 994; ok 13 not ok 14 # Test 14 got: "0" (t/StandAloneFasta.t at line 88) # Expected: "994" # t/StandAloneFasta.t line 88 is: ok $hsp->num_identical, 994; not ok 15 # Test 15 got: "1977" (t/StandAloneFasta.t at line 89) # Expected: "994" # t/StandAloneFasta.t line 89 is: ok $hsp->length, 994; It looks like a value is returned for the tests, so parsing isn't broken. They just aren't returned in the order specified, so the tests are faulty, not the parsing. The tests could be fixed by using id/score key/value pairs in a hash or something similar. We probably shouldn't limit to a specific version unless parsing is actually broken. Chris On Nov 6, 2006, at 2:29 PM, Nathan S. Haigh wrote: > Hi Sendu, > > I've written a version method for StandAloneFasta.pm. However, because > of the way in which FASTA is versioned, it makes for difficult version > comparisons i.e. they contain non-numeric characters e.g. 3.4t26. > > I have employed a private function that does a conversion of the > non-numeric characters into their ascii value representation to > build a > float. e.g. the above version would result in: 3.411626 which can then > be compared easily. At the moment, this is accessed via > $factory->version like other modules as this will give access to a > version number that is easily comparable. However, should there be a > different function to return the unconverted version string e.g. > 3.4t26? > Or should there be a function that does a compare internally so it can > be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26'); > > Ideas welcome! > Nath > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From torsten.seemann at infotech.monash.edu.au Mon Nov 6 20:41:24 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Tue, 07 Nov 2006 07:41:24 +1100 Subject: [Bioperl-l] return undef In-Reply-To: <454F607C.5020808@sheffield.ac.uk> References: <454F50E5.3030702@sheffield.ac.uk> <454F5BED.6040406@sendu.me.uk> <454F607C.5020808@sheffield.ac.uk> Message-ID: <454F9DF4.80702@infotech.monash.edu.au> > I set up the following page a couple of days ago to house some scripts > that can be used to do audit checks of code: > http://www.bioperl.org/wiki/Auditing Your 'grep' patterns should probably have "\s+" rather than " " between keywords as often coders have used multiple spaces or tabs. Your 'die/confess/...' patterns require a "(" after them. I'd say those functions are used without parentheses about half the time, eg. die "ech!"; Explicit "return undef" aren't too hard to find. It's the hidden ones where it's "my $value; ...lots of code...; return $value;" which are hard to identify. -- Torsten Seemann Victorian Bioinformatics Consortium, Monash University, Australia From n.appleby at uq.edu.au Tue Nov 7 02:11:06 2006 From: n.appleby at uq.edu.au (Nikki Appleby) Date: Tue, 7 Nov 2006 12:11:06 +1000 Subject: [Bioperl-l] go-perl error: ')' missing Message-ID: <005d01c70211$fbaf55a0$1b776682@IMBPC.AD> Thanks for being there when things go wrong. I have installed required modules as listed in Chris' instructions, then get stuck on this. C:\Perl\go-perl\go-perl-0.05>perl Makefile.PL The system cannot find the path specified. NOTICE: ** You do not have xsltproc ** This tool is not required for go-perl, but it is useful for for certain kinds of format conversion (eg converting to OWL format). You will also need this tool if you are installing go-db-perl You can safely ignore this notification message; Even if you do intend to use go-db-perl later, you can install xsltproc at a later date xsltproc is available as part of libxslt. See http://xmlsoft.org/XSLT/ for details Writing Makefile for GO C:\Perl\go-perl\go-perl-0.05>nmake Microsoft (R) Program Maintenance Utility Version 1.50 Copyright (c) Microsoft Corp 1988-94. All rights reserved. makefile(1706) : fatal error U1000: syntax error : ')' missing in macro invocati on Stop. Nikki Appleby. 07 334 62634 From n.haigh at sheffield.ac.uk Tue Nov 7 07:05:40 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 07 Nov 2006 07:05:40 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> Message-ID: <45503044.30000@sheffield.ac.uk> Chris Fields wrote: > Nathan, > > Weren't the problems with the reported StandAloneFasta.pm test fails > due to differences in the returned order of the Hits/HSPs in the FASTA > reports from the different versions? The test results you posted on > the wiki (where I commented on this) seem to indicate that: > > not ok 11 > # Test 11 got: "0" (t/StandAloneFasta.t at line 75) > # Expected: "994" > # t/StandAloneFasta.t line 75 is: ok $hsp->num_identical, 994; > not ok 12 > # Test 12 got: "1977" (t/StandAloneFasta.t at line 76) > # Expected: "994" > # t/StandAloneFasta.t line 76 is: ok $hsp->length, 994; > ok 13 > not ok 14 > # Test 14 got: "0" (t/StandAloneFasta.t at line 88) > # Expected: "994" > # t/StandAloneFasta.t line 88 is: ok $hsp->num_identical, 994; > not ok 15 > # Test 15 got: "1977" (t/StandAloneFasta.t at line 89) > # Expected: "994" > # t/StandAloneFasta.t line 89 is: ok $hsp->length, 994; > > It looks like a value is returned for the tests, so parsing isn't > broken. They just aren't returned in the order specified, so the > tests are faulty, not the parsing. The tests could be fixed by using > id/score key/value pairs in a hash or something similar. We probably > shouldn't limit to a specific version unless parsing is actually broken. > > Chris > Chris, I agree, I was going to update the tests later this morning :-P Any thoughts about version() or should I just leave it be for now? Cheers Nath From bix at sendu.me.uk Tue Nov 7 09:15:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 09:15:41 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45503044.30000@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> Message-ID: <45504EBD.2000708@sendu.me.uk> Nathan S. Haigh wrote: > I agree, I was going to update the tests later this morning :-P Any > thoughts about version() or should I just leave it be for now? If its no trouble, go ahead with a version() method. Its nice to have in any case. I'd suggest your latter option of 'there be a function that does a compare internally so it can be accessed something like: print "we have met the min version requirement\n" if $factory->at_least_version('3.4t26');' In fact, it ought to work with '34t26b3' as well (I guess the method would try what it was given, and on failure, try again with the last 2 characters removed, then try both cases again with a decimal added if there wasn't one). From n.haigh at sheffield.ac.uk Tue Nov 7 09:50:52 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 07 Nov 2006 09:50:52 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45504EBD.2000708@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> Message-ID: <455056FC.90608@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> I agree, I was going to update the tests later this morning :-P Any >> thoughts about version() or should I just leave it be for now? > > If its no trouble, go ahead with a version() method. Its nice to have > in any case. I'd suggest your latter option of 'there be a function > that does a compare internally so it can be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26');' > In fact, it ought to work with '34t26b3' as well (I guess the method > would try what it was given, and on failure, try again with the last 2 > characters removed, then try both cases again with a decimal added if > there wasn't one). I've contacted Bill Pearson to clarify his versioning scheme. Ideally, we could do as you say, compare variants of '34t26b3'. However, the software doesn't report the b3 part of the version string only 3.4t26 followed by a date. Therefore, I'm not sure it's possible to distinguish between 3.4t26b1 and 3.4t26b3 - unless we consider the date also returned by the software :-( . Bill said he is currently busy with a course at Cold Spring Harbor but will respond in full later. Therefore, until he's informed me of how he versions his releases, I'll hold off with the version() method for the time being. Nath From cjfields at uiuc.edu Tue Nov 7 15:58:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 09:58:48 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <45504EBD.2000708@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> Message-ID: <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> On Nov 7, 2006, at 3:15 AM, Sendu Bala wrote: > Nathan S. Haigh wrote: >> I agree, I was going to update the tests later this morning :-P Any >> thoughts about version() or should I just leave it be for now? > > If its no trouble, go ahead with a version() method. Its nice to > have in > any case. I'd suggest your latter option of 'there be a function that > does a compare internally so it can be accessed something like: > print "we have met the min version requirement\n" if > $factory->at_least_version('3.4t26');' > In fact, it ought to work with '34t26b3' as well (I guess the method > would try what it was given, and on failure, try again with the last 2 > characters removed, then try both cases again with a decimal added if > there wasn't one). Is it possible to have the interface base class contain an abstract program_version() (or similar) method? One that could be implemented to just grab the current version of the program? I was thinking about something like this for the RNA-based wrappers I want to add but it seems to be something that most Run modules would benefit from. Just haven't had time to look into it with much detail. Almost wonder if it would be easier to have all bioperl-run modules have a Run-specific Root object for common methods, regardless of the other interfaces used. Maybe something inheriting Bio::Root::Root... chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Nov 7 16:54:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 10:54:48 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550AF3B.8000807@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> Message-ID: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: ... >> Is it possible to have the interface base class contain an >> abstract program_version() (or similar) method? One that could be >> implemented to just grab the current version of the program? I >> was thinking about something like this for the RNA-based wrappers >> I want to add but it seems to be something that most Run modules >> would benefit from. Just haven't had time to look into it with >> much detail. > > What's wrong with version() ? Didn't realize there was a version() already. >> Almost wonder if it would be easier to have all bioperl-run >> modules have a Run-specific Root object for common methods, >> regardless of the other interfaces used. Maybe something >> inheriting Bio::Root::Root... > > What's wrong with Bio::Tools::Run::WrapperBase ? I agree that WrapperBase fulfills most of this functionality. However, don't a few bioperl-run wrappers 'roll their own', i.e. not implement WrapperBase? Requiring all bioperl-run module inherit the same Run-specific base object would integrate them a bit more and distinguish them from the core modules (which would inherit Bio::Root::Root). Anyway, it's just a suggestion. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Tue Nov 7 15:54:06 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 07 Nov 2006 10:54:06 -0500 Subject: [Bioperl-l] Bio::SeqIO::gcg bug Message-ID: <4550AC1E.2070500@bms.com> Bio::SeqIO::gcg is checking the checksum against the GCG generated one. There is a problem with the way this is done: 1. Bio::SeqIO::gcg removes all characters, except [A-Za-z] (which by the way is always wrong). 2. GCG calculates the checksum on uppercase I assume Hilmar removed the $_ = uc($_); line for a very good reason, but the call to validate should be: _validate_checksum(uc($sequence),$chksum)) Also I believe the regexp for checking the alphabet should remove explicitly numbers and whitespaces. Removing everything else is not a good idea because gaps, end of translation are removed also and possible parsing errors might be suppressed incorrectly. Let me know if I am missing some other considerations here. If not I will commit these changes. Stefan From bix at sendu.me.uk Tue Nov 7 17:25:22 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 17:25:22 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> Message-ID: <4550C182.3000308@sendu.me.uk> Chris Fields wrote: > > On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: > >>> Almost wonder if it would be easier to have all bioperl-run modules >>> have a Run-specific Root object for common methods, regardless of the >>> other interfaces used. Maybe something inheriting Bio::Root::Root... >> >> What's wrong with Bio::Tools::Run::WrapperBase ? > > I agree that WrapperBase fulfills most of this functionality. However, > don't a few bioperl-run wrappers 'roll their own', i.e. not implement > WrapperBase? Requiring all bioperl-run module inherit the same > Run-specific base object would integrate them a bit more and distinguish > them from the core modules (which would inherit Bio::Root::Root). > Anyway, it's just a suggestion. Well, how would you 'require' them to use anything at all? There's not even anything 'requiring' that a core module inherit from Bio::Root::Root(I). We just (very strongly) advise that you inherit from there. So we can also advise that bioperl-run wrappers do not roll their own but use Bio::Tools::Run::WrapperBase. From cjfields at uiuc.edu Tue Nov 7 17:40:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 11:40:32 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C182.3000308@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> Message-ID: <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> > Well, how would you 'require' them to use anything at all? There's not > even anything 'requiring' that a core module inherit from > Bio::Root::Root(I). We just (very strongly) advise that you inherit > from > there. So we can also advise that bioperl-run wrappers do not roll > their > own but use Bio::Tools::Run::WrapperBase. Like I said, it's a suggestion. No need to get snippy. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Tue Nov 7 16:07:23 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 16:07:23 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> Message-ID: <4550AF3B.8000807@sendu.me.uk> Chris Fields wrote: > > On Nov 7, 2006, at 3:15 AM, Sendu Bala wrote: > >> Nathan S. Haigh wrote: >>> I agree, I was going to update the tests later this morning :-P Any >>> thoughts about version() or should I just leave it be for now? >> >> If its no trouble, go ahead with a version() method. Its nice to have in >> any case. I'd suggest your latter option of 'there be a function that >> does a compare internally so it can be accessed something like: >> print "we have met the min version requirement\n" if >> $factory->at_least_version('3.4t26');' >> In fact, it ought to work with '34t26b3' as well (I guess the method >> would try what it was given, and on failure, try again with the last 2 >> characters removed, then try both cases again with a decimal added if >> there wasn't one). > > Is it possible to have the interface base class contain an abstract > program_version() (or similar) method? One that could be implemented to > just grab the current version of the program? I was thinking about > something like this for the RNA-based wrappers I want to add but it > seems to be something that most Run modules would benefit from. Just > haven't had time to look into it with much detail. What's wrong with version() ? > Almost wonder if it would be easier to have all bioperl-run modules have > a Run-specific Root object for common methods, regardless of the other > interfaces used. Maybe something inheriting Bio::Root::Root... What's wrong with Bio::Tools::Run::WrapperBase ? From n.haigh at sheffield.ac.uk Tue Nov 7 17:48:56 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 07 Nov 2006 17:48:56 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> Message-ID: <4550C708.5060209@sheffield.ac.uk> Chris Fields wrote: > On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: > ... > > >>> Is it possible to have the interface base class contain an >>> abstract program_version() (or similar) method? One that could be >>> implemented to just grab the current version of the program? I >>> was thinking about something like this for the RNA-based wrappers >>> I want to add but it seems to be something that most Run modules >>> would benefit from. Just haven't had time to look into it with >>> much detail. >>> >> What's wrong with version() ? >> > > Didn't realize there was a version() already. > > >>> Almost wonder if it would be easier to have all bioperl-run >>> modules have a Run-specific Root object for common methods, >>> regardless of the other interfaces used. Maybe something >>> inheriting Bio::Root::Root... >>> >> What's wrong with Bio::Tools::Run::WrapperBase ? >> > > I agree that WrapperBase fulfills most of this functionality. > However, don't a few bioperl-run wrappers 'roll their own', i.e. not > implement WrapperBase? Requiring all bioperl-run module inherit the > same Run-specific base object would integrate them a bit more and > distinguish them from the core modules (which would inherit > Bio::Root::Root). Anyway, it's just a suggestion. > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > >From what i've seen of Bioperl-run there is not a whole lot of consistency between modules. I think it would be a good idea to have all run modules inherit WrapperBase - would this be a big change?? Nath From bix at sendu.me.uk Tue Nov 7 17:49:09 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 07 Nov 2006 17:49:09 +0000 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> Message-ID: <4550C715.5090608@sendu.me.uk> Chris Fields wrote: >> Well, how would you 'require' them to use anything at all? There's not >> even anything 'requiring' that a core module inherit from >> Bio::Root::Root(I). We just (very strongly) advise that you inherit from >> there. So we can also advise that bioperl-run wrappers do not roll their >> own but use Bio::Tools::Run::WrapperBase. > > Like I said, it's a suggestion. No need to get snippy. You took that completely the wrong way. I am applying absolutely no value judgment on your suggestion. It may be an excellent one. I was simply explaining we have no programmatic way of requiring that modules use other modules - we rely on people following the advice/ status quo. Given that, are you still suggesting that it would be better to advise people to use Bio::Root::SomeNewRunThing, or is Bio::Tools::Run::WrapperBase satisfactory? From hlapp at gmx.net Tue Nov 7 17:55:12 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 7 Nov 2006 12:55:12 -0500 Subject: [Bioperl-l] Bio::SeqIO::gcg bug In-Reply-To: <4550AC1E.2070500@bms.com> References: <4550AC1E.2070500@bms.com> Message-ID: On Nov 7, 2006, at 10:54 AM, Stefan Kirov wrote: > I assume Hilmar removed the $_ = uc($_); line for a very good reason, > but the call to validate should be: > _validate_checksum(uc($sequence),$chksum)) I agree. The case of the sequence letters should remain untouched though for other purposes. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Tue Nov 7 17:55:22 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 11:55:22 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C708.5060209@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C708.5060209@sheffield.ac.uk> Message-ID: <8132EB4F-2FE0-4A46-A96D-E406CCB0F047@uiuc.edu> On Nov 7, 2006, at 11:48 AM, Nathan Haigh wrote: ... > From what i've seen of Bioperl-run there is not a whole lot of > consistency between modules. I think it would be a good idea to > have all > run modules inherit WrapperBase - would this be a big change?? > > Nath We really have no idea how many wrappers don't implement WrapperBase at the moment; until then we don't know how much work it would take. This might be a job for a maintenance script... Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From natalia.grabar at club-internet.fr Tue Nov 7 17:48:53 2006 From: natalia.grabar at club-internet.fr (natalia.grabar at club-internet.fr) Date: Tue, 7 Nov 2006 18:48:53 +0100 Subject: [Bioperl-l] perl conference in Paris Message-ID: hi all, are you fine? next 25 & 26 November there will be a Perl conference in Paris http://conferences.mongueurs.net/fpw2006/ I wonder if it would be possible to have a presentation (tutorial?) of the bioperl package during this conference. thanks have a nice day natalia From cjfields at uiuc.edu Tue Nov 7 19:49:47 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 7 Nov 2006 13:49:47 -0600 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C715.5090608@sendu.me.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C182.3000308@sendu.me.uk> <983EA6F9-E30A-48D3-B9DA-AE2C0D2B866D@uiuc.edu> <4550C715.5090608@sendu.me.uk> Message-ID: <4AC53CE6-20EC-4841-A28C-E083823F8487@uiuc.edu> On Nov 7, 2006, at 11:49 AM, Sendu Bala wrote: >> Like I said, it's a suggestion. No need to get snippy. > > You took that completely the wrong way. I am applying absolutely no > value judgment on your suggestion. It may be an excellent one. I > was simply explaining we have no programmatic way of requiring that > modules use other modules - we rely on people following the advice/ > status quo. There may not be a programmatic way of enforcing one to use WrapperBase or other base classes beyond using maintenance scripts. However, if we as a community agree on following a basic set of bioperl coding standards (Best Practices, using Bio::Root::Root/ RootI, POD, etc), then anyone should reasonably expect that their code may be changed to conform more with those standards, at least within reason. We recently enforced this with Bio::Root::Root/RootI, 'return undef', 'use base', and others, so I don't see the problem with doing so here. There will always be some controversial or grey areas (use of AUTOLOAD comes to mind), but in my opinion it is very reasonable to require that new modules use a particular base class or implement a specific interface if the new code is expected to interact properly with other BioPerl classes/objects. One could always use the mail list to express their opinions if they disagree or want some clarification or guidance. Sorry, Election Day in the States. Lots of snippiness around on this end (overdosed of negative ads)! > Given that, are you still suggesting that it would be better to > advise people to use Bio::Root::SomeNewRunThing, or is > Bio::Tools::Run::WrapperBase satisfactory? Either way will work, but.... I was thinking of something like this: Run-based |---WrapperBase Root class---| |---Non-WrapperBase (web apps and others) Bio::Root::Root works in this capacity already, but I was thinking of a base class unique to bioperl-run classes which could integrate similar methods from WrapperBase and non-WrapperBase'd modules. I suppose we could also have it as a simple interface; modules which implement it could be distinguished from core if needed. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Tue Nov 7 19:58:10 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 7 Nov 2006 11:58:10 -0800 Subject: [Bioperl-l] (no subject) Message-ID: Lincoln - I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql which call $sth->finish in the offset_boundary call and the fetch_sequence method as my code which does GFF3 -> CDS dumping was getting lots of " statement handle DBI::st=HASH(0x189bf8c) still Active at" Changes are here: http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/Bio/DB/ SeqFeature/Store/DBI/mysql.pm.diff?r1=1.25&r2=1.26 These changes should be migrated to the branch before the release if all is okay. Please let me know. -jason From jason at bioperl.org Tue Nov 7 18:27:27 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 7 Nov 2006 10:27:27 -0800 Subject: [Bioperl-l] StandAloneFasta::version In-Reply-To: <4550C708.5060209@sheffield.ac.uk> References: <454F9B23.8010302@sheffield.ac.uk> <5D443D1B-B653-47FF-862B-9AA2A3BA0A03@uiuc.edu> <45503044.30000@sheffield.ac.uk> <45504EBD.2000708@sendu.me.uk> <9DDCFF91-376B-4112-9C9C-02D7B8E32626@uiuc.edu> <4550AF3B.8000807@sendu.me.uk> <11C075A5-6133-4005-A6EA-6040382624AE@uiuc.edu> <4550C708.5060209@sheffield.ac.uk> Message-ID: <4A984083-23FA-42F6-8C73-901FD87DB5F6@bioperl.org> i think it is important - we just have not had a dedicated developer who enforced these requirements by auditing the code. I had tried to establish a standard through WrapperBase but some contributions ignored this and some modules had grown up before the wrapperbase was in place. I also think the ontology of applications is a bit screwed up so people were putting modules in directories willy-nilly. I think bioperl-run is even more cat-herding than the other aspects of the project because applications change and there are very many combinations of parameters and version of applications. There was a flurry of contributions and no good way to marshall them initially. So what to do - I guess make do with how it is but not rename anything at this point but try and standardize things - it will depend on your desire to really take this on. The PISE modules may need to be re-evaluated to insure they are still working - there was hope that some of them could be simplified through some automated class generation from the XML they are based on, but that was never developed. We will try and a have an open-bio linux server available as a platform where we can have a consistent testing environment but I am not sure if we want this to represent every possible version of apps or just the most recent. -jason On Nov 7, 2006, at 9:48 AM, Nathan Haigh wrote: > Chris Fields wrote: >> On Nov 7, 2006, at 10:07 AM, Sendu Bala wrote: >> ... >> >> >>>> Is it possible to have the interface base class contain an >>>> abstract program_version() (or similar) method? One that could be >>>> implemented to just grab the current version of the program? I >>>> was thinking about something like this for the RNA-based wrappers >>>> I want to add but it seems to be something that most Run modules >>>> would benefit from. Just haven't had time to look into it with >>>> much detail. >>>> >>> What's wrong with version() ? >>> >> >> Didn't realize there was a version() already. >> >> >>>> Almost wonder if it would be easier to have all bioperl-run >>>> modules have a Run-specific Root object for common methods, >>>> regardless of the other interfaces used. Maybe something >>>> inheriting Bio::Root::Root... >>>> >>> What's wrong with Bio::Tools::Run::WrapperBase ? >>> >> >> I agree that WrapperBase fulfills most of this functionality. >> However, don't a few bioperl-run wrappers 'roll their own', i.e. not >> implement WrapperBase? Requiring all bioperl-run module inherit the >> same Run-specific base object would integrate them a bit more and >> distinguish them from the core modules (which would inherit >> Bio::Root::Root). Anyway, it's just a suggestion. >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> From what i've seen of Bioperl-run there is not a whole lot of > consistency between modules. I think it would be a good idea to > have all > run modules inherit WrapperBase - would this be a big change?? > > Nath > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Wed Nov 8 10:24:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 08 Nov 2006 10:24:41 +0000 Subject: [Bioperl-l] (no subject) Message-ID: <4551B069.6060305@sendu.me.uk> [forwarded on behalf of Dave Howorth] Jason Stajich wrote: > Lincoln - > I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql > which call $sth->finish in the offset_boundary call and the > fetch_sequence method as my code which does GFF3 -> CDS dumping was > getting lots of " statement handle DBI::st=HASH(0x189bf8c) still > Active at" What version of DBD::mysql are you using? It sounds like this: http://rt.cpan.org/Public/Bug/Display.html?id=20464 Cheers, Dave From bix at sendu.me.uk Wed Nov 8 11:12:12 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 08 Nov 2006 11:12:12 +0000 Subject: [Bioperl-l] Bioperl versioning In-Reply-To: <6dce9a0b0610311224x79256b29sf102eb5c35865caf@mail.gmail.com> References: <453E309B.9090007@sendu.me.uk> <000001c6f78b$d1c65a30$15327e82@pyrimidine> <6dce9a0b0610311224x79256b29sf102eb5c35865caf@mail.gmail.com> Message-ID: <4551BB8C.5040606@sendu.me.uk> Lincoln Stein wrote: > Are you going to go ahead with 1.52_XX ? If so, I will code GBrowse to > look for 1.52 or higher. You should do the equivalent of use Bio::Root::Version 1.5.2; Eg. unless (eval{"require $Bio::Root::Version;" || ${Bio::Root::Version::VERSION'} < 1.005002) { #complain } Since most core modules get their version from Bio::Root::Version, you could also check the core module you're actually using in GBrowse, instead of asking Bio::Root::Version itself. So, if you do actually need to use Bio::Whatever in your module, the best thing to do is say: use Bio::Whatever 1.5.2; From jason at bioperl.org Wed Nov 8 15:56:55 2006 From: jason at bioperl.org (Jason Stajich) Date: Wed, 8 Nov 2006 07:56:55 -0800 Subject: [Bioperl-l] (no subject) In-Reply-To: <4551B069.6060305@sendu.me.uk> References: <4551B069.6060305@sendu.me.uk> Message-ID: <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> sounds like it. I am running 3.0006 The added sth->finish did take care of it for now since I assume a fair number of people are stuck with these vers? On Nov 8, 2006, at 2:24 AM, Sendu Bala wrote: > [forwarded on behalf of Dave Howorth] > > > Jason Stajich wrote: >> Lincoln - >> I'm checking two lines to Bio::DB::SeqFeature::Store::DBI::mysql >> which call $sth->finish in the offset_boundary call and the >> fetch_sequence method as my code which does GFF3 -> CDS dumping was >> getting lots of " statement handle DBI::st=HASH(0x189bf8c) still >> Active at" > > What version of DBD::mysql are you using? It sounds like this: > > http://rt.cpan.org/Public/Bug/Display.html?id=20464 > > Cheers, Dave > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California Dept of Plant and Microbial Biology 321 Koshland Hall #3102 Berkeley, CA 94720-3102 lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From dhoworth at mrc-lmb.cam.ac.uk Wed Nov 8 16:16:05 2006 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Wed, 08 Nov 2006 16:16:05 +0000 Subject: [Bioperl-l] (no subject) In-Reply-To: <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> References: <4551B069.6060305@sendu.me.uk> <5457B464-4982-4045-8A27-BB6B06813E2F@bioperl.org> Message-ID: <455202C5.9060609@mrc-lmb.cam.ac.uk> Jason Stajich wrote: > sounds like it. > > I am running 3.0006 > > The added sth->finish did take care of it for now since I assume a fair > number of people are stuck with these vers? Well, the current version on CPAN is fixed and the bug breaks lots of applications so upgrading DBD::mysql is a better cure. Or even downgrading to the one before it broke :) Cheers, Dave From bix at sendu.me.uk Thu Nov 9 10:28:34 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 10:28:34 +0000 Subject: [Bioperl-l] bptutorial.pl 0 In-Reply-To: <000601c6fc4a$c3e43450$15327e82@pyrimidine> References: <000601c6fc4a$c3e43450$15327e82@pyrimidine> Message-ID: <455302D2.1000901@sendu.me.uk> Chris Fields wrote: > What version of Bioperl are you running? > > As a warning, the bptutorial.pl script has been removed from CVS and will > not be included in future versions of Bioperl. It can be found on the > bioperl wiki instead: > > http://www.bioperl.org/wiki/Bptutorial It hasn't been removed, but should it be? AFAIK there was still a request from at least one person to keep it. But is it still out of date wrt the wiki version? From bix at sendu.me.uk Thu Nov 9 10:31:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 10:31:16 +0000 Subject: [Bioperl-l] bptutorial.pl 0 In-Reply-To: <455302D2.1000901@sendu.me.uk> References: <000601c6fc4a$c3e43450$15327e82@pyrimidine> <455302D2.1000901@sendu.me.uk> Message-ID: <45530374.1010001@sendu.me.uk> Sendu Bala wrote: > Chris Fields wrote: >> What version of Bioperl are you running? >> As a warning, the bptutorial.pl script has been removed from CVS and will >> not be included in future versions of Bioperl. It can be found on the >> bioperl wiki instead: >> >> http://www.bioperl.org/wiki/Bptutorial > > It hasn't been removed, but should it be? AFAIK there was still a > request from at least one person to keep it. But is it still out of date > wrt the wiki version? Scratch that, it was still in the 1.5.2 branch but I've removed it. From bix at sendu.me.uk Thu Nov 9 12:04:56 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 09 Nov 2006 12:04:56 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 Message-ID: <45531968.6080607@sendu.me.uk> Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. See http://www.bioperl.org/wiki/Release_1.5.2 for instructions on getting and testing this RC. Developers: Once again I'm hopeful that this is the last RC. If all goes well expect final release in about a weeks time. Please check and update documentation. Users: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into. Thank you, Sendu. From avilella at gmail.com Thu Nov 9 12:15:20 2006 From: avilella at gmail.com (Albert Vilella) Date: Thu, 9 Nov 2006 12:15:20 +0000 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln Message-ID: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> Hi, I am musing on how to add trees to the AlignIO::Nexus objects. In PAML we have this "add_tree" method, and "get_rst_trees", which we could also apply to this case. I also would like to hear some feedback on how to write_aln nexus files that contain one or more trees in the object instance. Do we want this by default? Only if a "with_trees" parameter is set? Cheers, Albert. From n.haigh at sheffield.ac.uk Thu Nov 9 13:55:59 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Thu, 09 Nov 2006 13:55:59 +0000 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> Message-ID: <4553336F.2000000@sheffield.ac.uk> Albert Vilella wrote: > Hi, > > I am musing on how to add trees to the AlignIO::Nexus objects. > > In PAML we have this "add_tree" method, and "get_rst_trees", which we > could also apply to this case. > > I also would like to hear some feedback on how to write_aln nexus > files that contain one or more trees in the object instance. Do we > want this by default? Only if a "with_trees" parameter is set? > > Cheers, > > Albert. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > Hi Albert, I don't know if you are aware of this resource, so here it is: http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all I would suggest that if there are trees in the object instance, then write_aln should print them by default and then have a "no_trees" option. Nath From cjfields at uiuc.edu Thu Nov 9 14:13:09 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 08:13:09 -0600 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <4553336F.2000000@sheffield.ac.uk> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> <4553336F.2000000@sheffield.ac.uk> Message-ID: <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> On Nov 9, 2006, at 7:55 AM, Nathan Haigh wrote: > Albert Vilella wrote: >> Hi, >> >> I am musing on how to add trees to the AlignIO::Nexus objects. >> >> In PAML we have this "add_tree" method, and "get_rst_trees", which we >> could also apply to this case. >> >> I also would like to hear some feedback on how to write_aln nexus >> files that contain one or more trees in the object instance. Do we >> want this by default? Only if a "with_trees" parameter is set? >> >> Cheers, >> >> Albert. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > Hi Albert, > > I don't know if you are aware of this resource, so here it is: > http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all > > I would suggest that if there are trees in the object instance, then > write_aln should print them by default and then have a "no_trees" > option. > > Nath Another option is to store them in the SimpleAlign object as a queue of Tree objects. Stockholm format allows trees in the annotation section, so it makes sense that if some alignments contain this data then we should have a way of parsing and storing it, as long as we read/write support the particular tree format. Something like: my $aln = $alnin->next_aln(); # iterate... while (my $tree = $aln->next_tree()) { ... } # or SimpleAlign-like for my $tree ($aln->each_tree()) { ... } # all trees @trees = $aln->each_tree(); etc. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 9 15:28:45 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 09:28:45 -0600 Subject: [Bioperl-l] nexus add_tree, get_trees, write tree in write_aln In-Reply-To: <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> References: <358f4d650611090415v2a8ee2b3p32f5060b24926917@mail.gmail.com> <4553336F.2000000@sheffield.ac.uk> <19EA4559-54CF-4CDE-8C59-6CCCFCE3239A@uiuc.edu> Message-ID: <112C051C-0868-4933-A1CE-87E773B7FD05@uiuc.edu> On Nov 9, 2006, at 8:13 AM, Chris Fields wrote: > On Nov 9, 2006, at 7:55 AM, Nathan Haigh wrote: > >> Albert Vilella wrote: >>> Hi, >>> >>> I am musing on how to add trees to the AlignIO::Nexus objects. >>> >>> In PAML we have this "add_tree" method, and "get_rst_trees", >>> which we >>> could also apply to this case. >>> >>> I also would like to hear some feedback on how to write_aln nexus >>> files that contain one or more trees in the object instance. Do we >>> want this by default? Only if a "with_trees" parameter is set? >>> >>> Cheers, >>> >>> Albert. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> Hi Albert, >> >> I don't know if you are aware of this resource, so here it is: >> http://search.cpan.org/search?query=bio%3A%3Anexus&mode=all >> >> I would suggest that if there are trees in the object instance, then >> write_aln should print them by default and then have a "no_trees" >> option. >> >> Nath > > Another option is to store them in the SimpleAlign object as a queue > of Tree objects. Stockholm format allows trees in the annotation > section, so it makes sense that if some alignments contain this data > then we should have a way of parsing and storing it, as long as we > read/write support the particular tree format. .... Forgot to mention the option of using a builder object, analogous to the one used for Bio::SeqIO::genbank (Bio::Seq::SeqBuilder); this would be similar to Nathan's suggestion but would tell the parser what data you want parsed (alignment annotation, tree data, sequences, accession/id, etc) based on 'slots' and particular conditions, and therefore determines what data is stored in SimpleAlign objects. I planned on setting one up for Bio::AlignIO::stockholm in the near future for optional annotation parsing, but tree parsing could be included as well. Were you thinking of something along those lines? Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bernd.web at gmail.com Thu Nov 9 23:07:48 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 10 Nov 2006 00:07:48 +0100 Subject: [Bioperl-l] Blast Writer Message-ID: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> Hi, I am using Bio::SearchIO and Bio::SearchIO::Writer::HTMLResultWriter and its filter, as my $writer = new Bio::SearchIO::Writer::HTMLResultWriter(); $writer->filter('hsp', \&hsp_filter); Can I change the contents of the HSP objects (apart from true/false filtering)? I would like to change some HSP values. Would it be possible to do so with HTMLResultWriter's filters? And if so, how to access the Hit/HSP objects in the filter? I'd be grateful for any suggestions. Best regards, Bernd From jason at bioperl.org Thu Nov 9 23:21:34 2006 From: jason at bioperl.org (Jason Stajich) Date: Thu, 9 Nov 2006 15:21:34 -0800 Subject: [Bioperl-l] Blast Writer In-Reply-To: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> References: <716af09c0611091507i46e18626ibc4d6e9c6ec594c5@mail.gmail.com> Message-ID: <15C2FE1E-F0C8-43DD-96E7-FADA3421AA82@bioperl.org> You can always do this before you pass the Result object to the writer. The for loop will pass back the actual hit or hsp objects and so any updates should be stored. for my $hit ( $result->hits ) { for my $hsp ( $hit->hsps ) { # change the HSP } } -jason On Nov 9, 2006, at 3:07 PM, Bernd Web wrote: > Hi, > > I am using Bio::SearchIO and Bio::SearchIO::Writer::HTMLResultWriter > and its filter, as > my $writer = new Bio::SearchIO::Writer::HTMLResultWriter(); > $writer->filter('hsp', \&hsp_filter); > > Can I change the contents of the HSP objects (apart from true/ > false filtering)? > I would like to change some HSP values. Would it be possible to do so > with HTMLResultWriter's filters? And if so, how to access the Hit/HSP > objects in the filter? > > I'd be grateful for any suggestions. > > Best regards, > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California Dept of Plant and Microbial Biology 321 Koshland Hall #3102 Berkeley, CA 94720-3102 lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From James.Rose at UCHSC.edu Thu Nov 9 22:56:00 2006 From: James.Rose at UCHSC.edu (James.Rose at UCHSC.edu) Date: Thu, 9 Nov 2006 15:56:00 -0700 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI Message-ID: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Hi- apologies if this subject has been addressed before, but I can't seem to find a way to search prior threads short of downloading the entire archives. I'm trying to use Bioperl to do something I thought would be fairly simple: Ingredients: one file containing a list of GI numbers for various proteins 1) Read GI number from file. 2) run a remote tblastn search against the sequenced Spermophilus tridecemlineatus genome with the GI number as query. 3) save resultant BLAST file to disk for later parsing. As it stands, several hours of browsing and scripting has failed to turn up anything that might be useful in this regard. Any advice is very much appreciated. Thanks, James From ak at ebi.ac.uk Fri Nov 10 00:01:55 2006 From: ak at ebi.ac.uk (Andreas Kahari) Date: Fri, 10 Nov 2006 00:01:55 +0000 Subject: [Bioperl-l] Archive searching (was Re: Remote tblastn against a sequenced genome at NCBI) In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: <20061110000155.GA27524@ebi.ac.uk> On Thu, Nov 09, 2006 at 03:56:00PM -0700, James.Rose at UCHSC.edu wrote: > > > Hi- apologies if this subject has been addressed before, but I can't > seem to find a way to search prior threads short of downloading the > entire archives. [cut] See here: http://www.bioperl.org/wiki/Mailing_lists -- Andreas K?h?ri :: Ensembl Software Developer European Bioinformatics Institute (EMBL-EBI) -------------------------------------------- contentsofsignaturemightsettleduringtransfer From cjfields at uiuc.edu Fri Nov 10 00:46:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 18:46:35 -0600 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: <43D47332-B9A9-4D01-87FD-433D86B68853@uiuc.edu> > Hi- apologies if this subject has been addressed before, but I > can't seem to find a way to search prior threads short of > downloading the entire archives. I'm trying to use Bioperl to do > something I thought would be fairly simple: > > Ingredients: one file containing a list of GI numbers for various > proteins > > 1) Read GI number from file. > 2) run a remote tblastn search against the sequenced Spermophilus > tridecemlineatus genome with the GI number as query. > 3) save resultant BLAST file to disk for later parsing. > > As it stands, several hours of browsing and scripting has failed to > turn up anything that might be useful in this regard. > > Any advice is very much appreciated. > > Thanks, > > James NCBI has a little-known (but very useful) list of databases available for remote BLAST searches: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastdblist.html If you replace the database parameter with the exact string listed under the table, then it should work. 'Trace/ Spermophilus_tridecemlineatus_WGS' for the WGS sequences is probably what you want. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Nov 10 00:49:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 9 Nov 2006 18:49:24 -0600 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> References: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: On Nov 9, 2006, at 4:56 PM, wrote: > > > Hi- apologies if this subject has been addressed before, but I > can't seem to find a way to search prior threads short of > downloading the entire archives. I'm trying to use Bioperl to do > something I thought would be fairly simple: > > Ingredients: one file containing a list of GI numbers for various > proteins > > 1) Read GI number from file. > 2) run a remote tblastn search against the sequenced Spermophilus > tridecemlineatus genome with the GI number as query. > 3) save resultant BLAST file to disk for later parsing. > > As it stands, several hours of browsing and scripting has failed to > turn up anything that might be useful in this regard. > > Any advice is very much appreciated. > > Thanks, > > James Oops, sent you an old page. Here's the more up-to-date one: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/ remote_accessible_blastdblist.html Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sayali_salodkar at persistent.co.in Fri Nov 10 05:10:35 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Fri, 10 Nov 2006 10:40:35 +0530 Subject: [Bioperl-l] Bioperl parser for PolyPhred? Message-ID: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> Hi, I want to parse the output of polyphred http://droog.gs.washington.edu/PolyPhred.html. Is there a parser already available in Bioperl which would help me in doing the same. Thanks, Sayali DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From bix at sendu.me.uk Fri Nov 10 10:15:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 10:15:41 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) Message-ID: <4554514D.2020001@sendu.me.uk> Hi all, Since I'm seeing inadequacies with the current Makefile.PL scripts we have, I'm thinking of converting from ExtUtils::MakeMaker and the Makefile.PL scripts to Module::Build Build.PL scripts. The advantages this will bring would be creation and installation of documentation, sane handling of required and optional dependencies, and hopefully good META.yml output, for CPAN compatibility wrt version numbers. I'll be able to use Module::Build::Compat to automatically generate Makefile.PL scripts in 'passthrough' style (if an end-user tries to use Makefile.PL without having Module::Build installed, it will offer to install Module::Build for them) when it comes time to make distributions, but Makefile.PL would no longer be in CVS. One thing I'm not clear on with the current situation is what is supposed to happen when the user chooses to install scripts. Where are they supposed to get installed to, and where do end-users normally run them from and how? How does this compare to expectations from other perl module distributions that have installable scripts? Please comment and discuss, but I'd like to get this done for the 1.5.2 release so that the CPAN distribution will be happy. From Derek.Fairley at bll.n-i.nhs.uk Fri Nov 10 10:15:52 2006 From: Derek.Fairley at bll.n-i.nhs.uk (Fairley, Derek) Date: Fri, 10 Nov 2006 10:15:52 -0000 Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI In-Reply-To: <28A674A3948E8D4981E47C16052840440CBC12@latte.uchsc.edu> Message-ID: James, Try the nabble.com mirror of this forum for easy searching of prior threads: http://www.nabble.com/BioPerl-f13596.html Derek. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of James.Rose at UCHSC.edu Sent: 09 November 2006 22:56 To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI Hi- apologies if this subject has been addressed before, but I can't seem to find a way to search prior threads short of downloading the entire archives. I'm trying to use Bioperl to do something I thought would be fairly simple: Ingredients: one file containing a list of GI numbers for various proteins 1) Read GI number from file. 2) run a remote tblastn search against the sequenced Spermophilus tridecemlineatus genome with the GI number as query. 3) save resultant BLAST file to disk for later parsing. As it stands, several hours of browsing and scripting has failed to turn up anything that might be useful in this regard. Any advice is very much appreciated. Thanks, James _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Fri Nov 10 12:31:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 12:31:29 +0000 Subject: [Bioperl-l] Distribution files, versions Message-ID: <45547121.6040904@sendu.me.uk> Does anyone know what the following files are supposed to do and if they still used/needed? bioperl.lisp maintenance/symlink_scripts.pl maintenance/symlink_scripts.PLS doc/makedoc.PL scripts/install_bioperl_scripts.pl Most modules in the distribution take their version from Bio::Root::Version, but some do not. Is there some reason they must keep the version they currently have, or can they be made like the others? These are the modules that seem to define their own version (based on a quick grep): Bio/DB/NCBIHelper.pm Bio/DB/Expression/geo.pm Bio/DB/EUtilities/elink.pm Bio/SeqIO/tinyseq.pm Bio/Graphics/Glyph/cds.pm Bio/Graphics/Glyph/translation.pm Bio/Graphics/Glyph/so_transcript.pm Bio/Index/Blast.pm Bio/Index/Hmmer.pm Bio/Tools/WebBlat.pm Bio/Tools/HMM.pm Bio/Tools/dpAlign.pm From JK at novozymes.com Fri Nov 10 12:41:19 2006 From: JK at novozymes.com (JK (Jesper Agerbo Krogh)) Date: Fri, 10 Nov 2006 13:41:19 +0100 Subject: [Bioperl-l] Bio::SeqIO::fasta patch. Message-ID: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> Hi. Just a small patch for outputting stuff on the descriptionline i fasta format. Stuff like: DE test DE test2 DE test3 converted to fasta becomes: > testtest2test3 and not > test test2 test3 Index: fasta.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/fasta.pm,v retrieving revision 1.60 diff -r1.60 fasta.pm 203c203 < $desc =~ s/\n//g; --- > $desc =~ s/\n/ /g; Should probably be applied to the stable-branch . Jesper From arareko at campus.iztacala.unam.mx Fri Nov 10 15:14:18 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Fri, 10 Nov 2006 09:14:18 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: <4554974A.4010206@campus.iztacala.unam.mx> Sendu Bala wrote: > Does anyone know what the following files are supposed to do and if they > still used/needed? > > bioperl.lisp This a module template for Emacs users. > maintenance/symlink_scripts.pl > maintenance/symlink_scripts.PLS The 1st is created by Makefile.PL (basically its a rename of the 2nd) and is run during 'make install'. From the POD: "This script will create a symlink in the 'installscript' directory (as defined during install) to a script in that same directory. It was written to create a symlink with the name 'bp_pg_bulk_load_gff.pl' that targeted 'bp_bulk_load_gff.pl' but can be extended by adding files to the %symlink_scripts hash. Perl function 'symlink' is used to keep the script from crashing on systems that don't allow symbolic linking." > doc/makedoc.PL I have no idea :) > scripts/install_bioperl_scripts.pl This is also run automatically on 'make install'. Cheers, Mauricio. -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From aaron.j.mackey at gsk.com Fri Nov 10 13:59:55 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Fri, 10 Nov 2006 08:59:55 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> Message-ID: > bioperl.lisp This is a set of convenience macros for developers who use Emacs, but it's pretty out of date. Some may still use it, though. It's of no use being in the package distribution, however. > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must keep > the version they currently have, or can they be made like the others? if their current version is greater than the bioperl version, then they must keep it for backwards compatibility (as otherwise a "require" statement for a certain version of Bio::SeqIO::tinyseq won't work properly). -Aaron From dmessina at wustl.edu Fri Nov 10 14:55:44 2006 From: dmessina at wustl.edu (David Messina) Date: Fri, 10 Nov 2006 08:55:44 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: <256AAE6A-2ACC-4CFE-B66E-F94C536FA8C5@wustl.edu> > bioperl.lisp This is the emacs template for bioperl module writing. Should be kept I think. http://www.bioperl.org/wiki/Emacs_template > maintenance/symlink_scripts.pl > maintenance/symlink_scripts.PLS Don't know if they're still needed, but Makefile.PL still refers to them. > doc/makedoc.PL I think this does similar to what you propose below, namely redefining modules' version strings to be the same as Bio::Root::Version's. I don't see any reason to remove it, but I like your suggestion to have all the modules get their version from Bio::Root::Version. > scripts/install_bioperl_scripts.pl Does what it says. Don't know if it's still needed; I think Makefile.PL handles script installation. Re your other post about switching over to Build.PL, I think scripts go into /usr/local/bin by default, or wherever specified if PREFIX or the like is set when the user runs 'perl Makefile.PL'. That seems to fit with other CPAN distros' model, and is what I (as an end-user) would expect. Dave > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must > keep > the version they currently have, or can they be made like the others? > > These are the modules that seem to define their own version (based > on a > quick grep): > Bio/DB/NCBIHelper.pm > Bio/DB/Expression/geo.pm > Bio/DB/EUtilities/elink.pm > Bio/SeqIO/tinyseq.pm > Bio/Graphics/Glyph/cds.pm > Bio/Graphics/Glyph/translation.pm > Bio/Graphics/Glyph/so_transcript.pm > Bio/Index/Blast.pm > Bio/Index/Hmmer.pm > Bio/Tools/WebBlat.pm > Bio/Tools/HMM.pm > Bio/Tools/dpAlign.pm From cjfields at uiuc.edu Fri Nov 10 15:50:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 09:50:58 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > Hi all, > > Since I'm seeing inadequacies with the current Makefile.PL scripts we > have, I'm thinking of converting from ExtUtils::MakeMaker and the > Makefile.PL scripts to Module::Build Build.PL scripts. > > The advantages this will bring would be creation and installation of > documentation, sane handling of required and optional dependencies, > and > hopefully good META.yml output, for CPAN compatibility wrt version > numbers. > > I'll be able to use Module::Build::Compat to automatically generate > Makefile.PL scripts in 'passthrough' style (if an end-user tries to > use > Makefile.PL without having Module::Build installed, it will offer to > install Module::Build for them) when it comes time to make > distributions, but Makefile.PL would no longer be in CVS. > > > One thing I'm not clear on with the current situation is what is > supposed to happen when the user chooses to install scripts. Where are > they supposed to get installed to, and where do end-users normally run > them from and how? How does this compare to expectations from other > perl > module distributions that have installable scripts? > > > Please comment and discuss, but I'd like to get this done for the > 1.5.2 > release so that the CPAN distribution will be happy. I don't have a problem with this as long as it works for all systems. It sounds like a good long-term solution, esp. for CPAN developer releases. However, we've already had three RC's using the regular old Makefile.PL setup, which seems to work fine for now. It also sounds like we will need to update all relevant installation documentation (since we can't run 'perl Makefile.PL' w/o Makefile.PL, unless I'm missing something). Hence I'm a bit worried about adding something new like this after three RCs and just before a final release. I think it's something we should do, but I'm not sure we should have it for this release. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From dmessina at wustl.edu Fri Nov 10 15:40:21 2006 From: dmessina at wustl.edu (David Messina) Date: Fri, 10 Nov 2006 09:40:21 -0600 Subject: [Bioperl-l] Bioperl parser for PolyPhred? In-Reply-To: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> References: <000c01c70486$8e748c40$4bc7580a@persistent.co.in> Message-ID: Sayali, I don't believe there is a BioPerl polyphred parser yet. This question came up on the list previously, however, and there was mention of a Perl script that appears to parse polyphred output: http://portal.open-bio.org/pipermail/bioperl-l/2003-December/014206.html Dave From bix at sendu.me.uk Fri Nov 10 15:59:54 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 15:59:54 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> Message-ID: <4554A1FA.6080003@sendu.me.uk> Chris Fields wrote: > On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > >> Hi all, >> >> Since I'm seeing inadequacies with the current Makefile.PL scripts we >> have, I'm thinking of converting from ExtUtils::MakeMaker and the >> Makefile.PL scripts to Module::Build Build.PL scripts. [snip] > I don't have a problem with this as long as it works for all systems. > It sounds like a good long-term solution, esp. for CPAN developer releases. > > However, we've already had three RC's using the regular old Makefile.PL > setup, which seems to work fine for now. It also sounds like we will > need to update all relevant installation documentation (since we can't > run 'perl Makefile.PL' w/o Makefile.PL, unless I'm missing something). > Hence I'm a bit worried about adding something new like this after three > RCs and just before a final release. > > I think it's something we should do, but I'm not sure we should have it > for this release. Now that I'm looking into it, it seems like quite a job, and yes, especially with all the documentation updates that need to be carefully looked at. Though to answer your question, Makefile.PL would be auto-generated by Build.PL immediately prior to a release and included in the distribution file for end users to use, but it wouldn't be in CVS. Such a Makefile.PL is essentially a front-end to the Build.PL for backwards-compatibility. For 1.5.2 I may just manually create a META.yml (the one generated via Makefile.PL isn't good enough) which only affects CPAN behaviour and nothing else we've been testing in the RCs. From bix at sendu.me.uk Fri Nov 10 16:03:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 10 Nov 2006 16:03:04 +0000 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554974A.4010206@campus.iztacala.unam.mx> References: <45547121.6040904@sendu.me.uk> <4554974A.4010206@campus.iztacala.unam.mx> Message-ID: <4554A2B8.4010207@sendu.me.uk> Mauricio Herrera Cuadra wrote: > Sendu Bala wrote: >> Does anyone know what the following files are supposed to do and if >> they still used/needed? >> >> bioperl.lisp > > This a module template for Emacs users. I propose moving it to the wiki and removing it from CVS. >> maintenance/symlink_scripts.pl >> maintenance/symlink_scripts.PLS > The 1st is created by Makefile.PL (basically its a rename of the 2nd) > and is run during 'make install'. From the POD: > > "This script will create a symlink in the 'installscript' directory (as > defined during install) to a script in that same directory. It was > written to create a symlink with the name 'bp_pg_bulk_load_gff.pl' that > targeted 'bp_bulk_load_gff.pl' but can be extended by adding files to > the %symlink_scripts hash. > > Perl function 'symlink' is used to keep the script from crashing on > systems that don't allow symbolic linking." The question is, do we need this symlink? Is the bulk_load_gff stuff still relevant? Why was it needed in the first place? For me, it doesn't seem to do anything useful; it just creates a broken symlink in PREFIX/bin. >> scripts/install_bioperl_scripts.pl > This is also run automatically on 'make install'. Not any more it isn't. Makefile.PL has (some of, at least) this script's methods. Does anyone use it manually? I propose removing it from CVS. AFAICT, Makefile.PL only ever installs to scripts_temp? How would people normally expect to define the script installation directory? Maybe it used to install scripts to user-defined or typical places (eg. /usr/local/bin as David Messina suggests) but that got broken in a recent commit? Can anyone confirm if script installation works properly for them, and how they got it to work? From cjfields at uiuc.edu Fri Nov 10 16:11:17 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:11:17 -0600 Subject: [Bioperl-l] Bio::SeqIO::fasta patch. In-Reply-To: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> References: <934F95E71B6C9347A873C42AE3C196190B84C622@NZT0004E.dknz.nzcorp.net> Message-ID: <7BBF2CEB-B012-4145-9818-6B69D10C7E8F@uiuc.edu> On Nov 10, 2006, at 6:41 AM, JK ((Jesper Agerbo Krogh)) wrote: > Hi. > > Just a small patch for outputting stuff on the descriptionline i > fasta format. > > Stuff like: > > DE test > DE test2 > DE test3 > > converted to fasta becomes: > >> testtest2test3 > > and not > >> test test2 test3 ... Actually, this should be fixed in the original input parser, not in fasta.pm. Was this from EMBL format? Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Fri Nov 10 16:16:24 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Fri, 10 Nov 2006 11:16:24 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> Message-ID: <4554A5D8.8000700@bms.com> I personally like the idea. Why not have both for this release to ensure smooth transition? Sendu, would having Makefile.PL (I mean the old one) along with the build script be a problem? I am not very familiar with both modules, but from the pdoc it seems it should not be too hard: Note that if you want to provide both a Makefile.PL and a Build.PL for your distribution, you probably want to add the following to "WriteMakefile" in your Makefile.PL so that MakeMaker doesn?t try to run your Build.PL as a nor? mal .PL file: PL_FILES => {}, Stefan Chris Fields wrote: > On Nov 10, 2006, at 4:15 AM, Sendu Bala wrote: > > >> Hi all, >> >> Since I'm seeing inadequacies with the current Makefile.PL scripts we >> have, I'm thinking of converting from ExtUtils::MakeMaker and the >> Makefile.PL scripts to Module::Build Build.PL scripts. >> >> The advantages this will bring would be creation and installation of >> documentation, sane handling of required and optional dependencies, >> and >> hopefully good META.yml output, for CPAN compatibility wrt version >> numbers. >> >> I'll be able to use Module::Build::Compat to automatically generate >> Makefile.PL scripts in 'passthrough' style (if an end-user tries to >> use >> Makefile.PL without having Module::Build installed, it will offer to >> install Module::Build for them) when it comes time to make >> distributions, but Makefile.PL would no longer be in CVS. >> >> >> One thing I'm not clear on with the current situation is what is >> supposed to happen when the user chooses to install scripts. Where are >> they supposed to get installed to, and where do end-users normally run >> them from and how? How does this compare to expectations from other >> perl >> module distributions that have installable scripts? >> >> >> Please comment and discuss, but I'd like to get this done for the >> 1.5.2 >> release so that the CPAN distribution will be happy. >> > > I don't have a problem with this as long as it works for all > systems. It sounds like a good long-term solution, esp. for CPAN > developer releases. > > However, we've already had three RC's using the regular old > Makefile.PL setup, which seems to work fine for now. It also sounds > like we will need to update all relevant installation documentation > (since we can't run 'perl Makefile.PL' w/o Makefile.PL, unless I'm > missing something). Hence I'm a bit worried about adding something > new like this after three RCs and just before a final release. > > I think it's something we should do, but I'm not sure we should have > it for this release. > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at uiuc.edu Fri Nov 10 16:21:07 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:21:07 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: ... > Most modules in the distribution take their version from > Bio::Root::Version, but some do not. Is there some reason they must > keep > the version they currently have, or can they be made like the others? > > These are the modules that seem to define their own version (based > on a > quick grep): > Bio/DB/NCBIHelper.pm > Bio/DB/Expression/geo.pm > Bio/DB/EUtilities/elink.pm > Bio/SeqIO/tinyseq.pm > Bio/Graphics/Glyph/cds.pm > Bio/Graphics/Glyph/translation.pm > Bio/Graphics/Glyph/so_transcript.pm > Bio/Index/Blast.pm > Bio/Index/Hmmer.pm > Bio/Tools/WebBlat.pm > Bio/Tools/HMM.pm > Bio/Tools/dpAlign.pm They probably shouldn't have their own unless there is a good reason (and I can't really think of one). The elink $VERSION is for the NCBI elink DTD, not the bioperl version, but that should be changed in elinks to something else beside $VERSION (my bad). The same reasoning may be relevant for the other modules; we'll just have to check them one-by-one. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Nov 10 16:29:42 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 10 Nov 2006 10:29:42 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554A5D8.8000700@bms.com> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> Message-ID: On Nov 10, 2006, at 10:16 AM, Stefan Kirov wrote: > I personally like the idea. Why not have both for this release to > ensure smooth transition? Sendu, would having Makefile.PL (I mean > the old one) along with the build script be a problem? I am not > very familiar with both modules, but from the pdoc it seems it > should not be too hard: > > Note that if you want to provide both a Makefile.PL and a > Build.PL for your distribution, you probably want to add > the following to "WriteMakefile" in your Makefile.PL so > that MakeMaker doesn?t try to run your Build.PL as a nor > mal .PL file: > > PL_FILES => {}, > > > Stefan ... Sounds like a good compromise to me. Like I said, the only problem I had is introducing something drastically new after three RCs (and just prior to a final release; I think Sendu wanted to release the final 1.5.2 next week, just before Thanksgiving here.). There is no problem though if we have the old Makefile.PL to fall back to for this release. In fact, you could remove it from HEAD when needed; the file still exists on the 1.5.2 branch, right? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bernd.web at gmail.com Fri Nov 10 17:39:30 2006 From: bernd.web at gmail.com (Bernd Web) Date: Fri, 10 Nov 2006 18:39:30 +0100 Subject: [Bioperl-l] Bio::Graphics Message-ID: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> Hi, Lincoln made an excellent help on Graphics. Thanks for that!(http://www.bioperl.org/wiki/HOWTO:Graphics) I am just looking at the imagemap creation with my $map=$panel->create_web_map('mapname',\&linkrule,'bbb'); and would like to connect the PNG from a blast report to the blast results. I just realize that this likely has been done many times. Does someone have a pointer to code for creating an imagemap from a BLAST report and also write the blast results with links? Bernd From bosborne11 at verizon.net Fri Nov 10 18:10:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Fri, 10 Nov 2006 13:10:01 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554A2B8.4010207@sendu.me.uk> Message-ID: Sendu, No, no scripts installed either by bioperl-live or by 1.5.2-RC3 (Mac OS X, Perl 5.8.6). But yes, bioperl-live has certainly been capable of installing scripts in the past. Brian O. On 11/10/06 11:03 AM, "Sendu Bala" wrote: > Can anyone confirm if script installation works properly for them, and > how they got it to work? From hlapp at gmx.net Fri Nov 10 23:33:48 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:33:48 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <45547121.6040904@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> Message-ID: On Nov 10, 2006, at 7:31 AM, Sendu Bala wrote: > bioperl.lisp This is the macros file for emacs. Do not delete it from the repository ... -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Nov 10 23:37:32 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:37:32 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: References: Message-ID: <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: >> bioperl.lisp > > This is a set of convenience macros for developers who use Emacs, > but it's > pretty out of date. What is out of date in there? > Some may still use it, though. E.g., dinosaurs like me. > It's of no use being in the package distribution, however. I agree. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Nov 10 23:40:40 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 18:40:40 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <4554A2B8.4010207@sendu.me.uk> References: <45547121.6040904@sendu.me.uk> <4554974A.4010206@campus.iztacala.unam.mx> <4554A2B8.4010207@sendu.me.uk> Message-ID: <2E617B21-BBFA-4865-AC50-6D6694B6CE2F@gmx.net> On Nov 10, 2006, at 11:03 AM, Sendu Bala wrote: >>> bioperl.lisp >> >> This a module template for Emacs users. > > I propose moving it to the wiki and removing it from CVS. This is not a good idea because the wiki is a bad platform for version controlling source code files, and this is a source code file. I don't have a problem with putting it up on the wiki, too. Better yet, link to the version in CVS. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Sat Nov 11 00:35:06 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 10 Nov 2006 19:35:06 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: Sounds like a good thing to do to me - I'd just be hesitant to do this for the 1.5.2 release. But I'm not the release master. -hilmar On Nov 10, 2006, at 5:15 AM, Sendu Bala wrote: > Hi all, > > Since I'm seeing inadequacies with the current Makefile.PL scripts we > have, I'm thinking of converting from ExtUtils::MakeMaker and the > Makefile.PL scripts to Module::Build Build.PL scripts. > > The advantages this will bring would be creation and installation of > documentation, sane handling of required and optional dependencies, > and > hopefully good META.yml output, for CPAN compatibility wrt version > numbers. > > I'll be able to use Module::Build::Compat to automatically generate > Makefile.PL scripts in 'passthrough' style (if an end-user tries to > use > Makefile.PL without having Module::Build installed, it will offer to > install Module::Build for them) when it comes time to make > distributions, but Makefile.PL would no longer be in CVS. > > > One thing I'm not clear on with the current situation is what is > supposed to happen when the user chooses to install scripts. Where are > they supposed to get installed to, and where do end-users normally run > them from and how? How does this compare to expectations from other > perl > module distributions that have installable scripts? > > > Please comment and discuss, but I'd like to get this done for the > 1.5.2 > release so that the CPAN distribution will be happy. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From kaboroev at sfu.ca Fri Nov 10 22:51:21 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Fri, 10 Nov 2006 14:51:21 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical Message-ID: <45550269.9050407@sfu.ca> Hi, I am attempting to add a few methods (ie. matching_bands_list) to the fpc map class but I am having a hard time inheriting the class properly. My first attempt was to inherit the "Bio::Map::Physical" class but the "next_map" package is not found. So I tried inheriting "Bio::MapIO" instead, and get a cannot find "matching_bands_list" via package "Bio::Map::Physical" The only way I can get it to work is with no inheritance and passing the map class variable to the function, but this isn't very elegant. Is there a correct way to inherit these classes that will allow me to execute this properly? keith From bernd.web at gmail.com Fri Nov 10 23:10:09 2006 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 11 Nov 2006 00:10:09 +0100 Subject: [Bioperl-l] POD HTML ResultWriter Message-ID: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> Hi, I just found the POD for HTMLResultWriter is truncated in Internet Explorer. http://doc.bioperl.org/bioperl-live/Bio/SearchIO/Writer/HTMLResultWriter.html. It stops with start_report. I think this is due to the tag (and , <BODY> tags in the text of start_report. In Firefox the page is rendered OK. Bernd From bix at sendu.me.uk Sat Nov 11 08:38:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 11 Nov 2006 08:38:27 +0000 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45550269.9050407@sfu.ca> References: <45550269.9050407@sfu.ca> Message-ID: <45558C03.8020903@sendu.me.uk> Keith Anthony Boroevich wrote: > Hi, > > I am attempting to add a few methods (ie. matching_bands_list) to the > fpc map class but I am having a hard time inheriting the class properly. > > My first attempt was to inherit the "Bio::Map::Physical" class but the > "next_map" package is not found. > So I tried inheriting "Bio::MapIO" instead, and get a cannot find > "matching_bands_list" via package "Bio::Map::Physical" > The only way I can get it to work is with no inheritance and passing the > map class variable to the function, but this isn't very elegant. Is > there a correct way to inherit these classes that will allow me to > execute this properly? It's hard to diagnose the problem without knowing exactly what you've tried. Please post some relevant code. Also, what version of Bioperl are you using? From bernd.web at gmail.com Sat Nov 11 13:53:55 2006 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 11 Nov 2006 14:53:55 +0100 Subject: [Bioperl-l] Bio::DB::Fasta index Message-ID: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Hi, A maybe strange question: is it possible to force Bio::DB::Fasta NOT to index the fasta file at any time (if there is already an index)? In the doc (http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Fasta.html), I read: " If one of the source fasta files is updated, the module reindexes just that one file. (You can also force reindexing manually)." Can I also switch off reindexing? (I realize that with Bio::Index::Fasta indexing can be separated). bernd From mkiwala at watson.wustl.edu Sat Nov 11 15:54:55 2006 From: mkiwala at watson.wustl.edu (mkiwala at watson.wustl.edu) Date: Sat, 11 Nov 2006 09:54:55 -0600 (CST) Subject: [Bioperl-l] Bio::DB::Fasta index In-Reply-To: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> References: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Message-ID: <58605.24.107.18.143.1163260495.squirrel@gscmail.wustl.edu> > A maybe strange question: is it possible to force Bio::DB::Fasta NOT > to index the fasta file at any time (if there is already an index)? I don't think so, but you could set the time stamp on the index file just before you run your script that uses the index. On a unix-like machine you would use the touch command. From cjfields at uiuc.edu Sat Nov 11 16:26:31 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 11 Nov 2006 10:26:31 -0600 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> References: <OF981FA506.80BA9953-ON85257222.004C99FF-85257222.004CE6C4@gsk.com> <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> Message-ID: <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> On Nov 10, 2006, at 5:37 PM, Hilmar Lapp wrote: > > On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: > >>> bioperl.lisp >> >> This is a set of convenience macros for developers who use Emacs, >> but it's >> pretty out of date. > > What is out of date in there? > >> Some may still use it, though. > > E.g., dinosaurs like me. > >> It's of no use being in the package distribution, however. > > I agree. > > -hilmar Maybe move it to it's own folder? It would be convenient if anyone else has helper macros (Komodo, vim, etc) or other developer stuff donated that we don't want included in the package distribution. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Sat Nov 11 16:31:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 11 Nov 2006 10:31:26 -0600 Subject: [Bioperl-l] POD HTML ResultWriter In-Reply-To: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> References: <716af09c0611101510o1970de01x10bff5375f6cc31@mail.gmail.com> Message-ID: <27593A76-29AE-4295-A229-36A92F9F92F6@uiuc.edu> Bernd, Could you submit this as a bug? It likely has to do with PDOC. Include the IE version etc. Chris On Nov 10, 2006, at 5:10 PM, Bernd Web wrote: > Hi, > > I just found the POD for HTMLResultWriter is truncated in Internet > Explorer. > http://doc.bioperl.org/bioperl-live/Bio/SearchIO/Writer/ > HTMLResultWriter.html. > It stops with start_report. > I think this is due to the <HTML> tag (and <TITLE>, <BODY> tags in the > text of start_report. In Firefox the page is rendered OK. > > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Sat Nov 11 18:02:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 11 Nov 2006 13:02:18 -0500 Subject: [Bioperl-l] Distribution files, versions In-Reply-To: <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> References: <OF981FA506.80BA9953-ON85257222.004C99FF-85257222.004CE6C4@gsk.com> <5191D763-E7FB-4F99-8FEF-2489F971A884@gmx.net> <779F60A8-CA61-4CAD-B91F-B94A274EFD34@uiuc.edu> Message-ID: <6E07DFB4-4D2A-4D66-9FAA-FEC20F6DE1B2@gmx.net> On Nov 11, 2006, at 11:26 AM, Chris Fields wrote: > > On Nov 10, 2006, at 5:37 PM, Hilmar Lapp wrote: > >> >> On Nov 10, 2006, at 8:59 AM, aaron.j.mackey at gsk.com wrote: >> >>>> bioperl.lisp >> >>> It's of no use being in the package distribution, however. >> >> I agree. >> >> -hilmar > > Maybe move it to it's own folder? It would be convenient if anyone > else has helper macros (Komodo, vim, etc) or other developer stuff > donated that we don't want included in the package distribution. Good idea, I agree. -hilmar > > chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From chhalling at verizon.net Sun Nov 12 18:11:54 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 12 Nov 2006 13:11:54 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC Message-ID: <455763EA.8080300@verizon.net> Quick summary: 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but not by Bio::Restriction::Enzyme. Should 'X' be removed from Bio::Tools::IUPAC or should it be added to Bio::Restriction::Enzyme? Detailed explanation: I tried to use the Bio::Restriction modules to perform a simple restriction analysis of some sequences I'm using at work, and I found the documentation and code confusing. So I'm volunteering to overhaul and redocument these modules. As part of this effort, I am also volunteering to fix the Bio::Restriction::IO::bairoch module. I have begun writing a test suite, RestrictionEnzyme.t, for the Bio::Restriction::Enzyme module. For one of the tests, I created a Bio::Restriction::Enzyme object with a recognition sequence that includes all of the IUPAC base symbols along with the caret ('^') symbol. A code excerpt is: use Bio::Tools::IUPAC; my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); ok $enzyme = Bio::Restriction::Enzyme->new( -name => 'IUPAC-IUB', -site => $site ); This test fails because Bio::Tools::IUPAC module includes 'X' as a valid base symbol, whereas Bio::Restriction::Enzyme does not. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 STACK: t/RestrictionEnzyme.t:184 ----------------------------------------------------------- The symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC need to be synchronized. Since 'X' is not recommended by "Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences" (see http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it stands for xanthine), I am in favor of removing it as a valid symbol. But I have a feeling that if 'X' is removed as a valid symbol from Bio::Tools::IUPAC, this will break a lot of existing code. So the simplest solution seems to be to add 'X' to the symbols recognized by Bio::Restriction::Enzyme. Does anyone have a recommendation? -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Sun Nov 12 22:21:06 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 12 Nov 2006 17:21:06 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> References: <455763EA.8080300@verizon.net> Message-ID: <45579E52.3010606@verizon.net> A followup: Bio::Tools::IUPAC::iupac_iub() also returns 'U' as a valid base. My idea of getting an authoritative set of base symbols from Bio::Tools::IUPAC does not work well. I will leave the valid bases in Bio::Restriction::Enzyme set to what is already used in the module ('ABCDGHKMNRSTVWY'). -- Conrad Conrad Halling wrote: > Quick summary: > > 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but not by > Bio::Restriction::Enzyme. Should 'X' be removed from Bio::Tools::IUPAC > or should it be added to Bio::Restriction::Enzyme? > > Detailed explanation: > > I tried to use the Bio::Restriction modules to perform a simple > restriction analysis of some sequences I'm using at work, and I found > the documentation and code confusing. So I'm volunteering to overhaul > and redocument these modules. As part of this effort, I am also > volunteering to fix the Bio::Restriction::IO::bairoch module. > > I have begun writing a test suite, RestrictionEnzyme.t, for the > Bio::Restriction::Enzyme module. For one of the tests, I created a > Bio::Restriction::Enzyme object with a recognition sequence that > includes all of the IUPAC base symbols along with the caret ('^') > symbol. A code excerpt is: > > use Bio::Tools::IUPAC; > my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); > my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); > ok $enzyme = > Bio::Restriction::Enzyme->new( > -name => 'IUPAC-IUB', > -site => $site ); > > This test fails because Bio::Tools::IUPAC module includes 'X' as a valid > base symbol, whereas Bio::Restriction::Enzyme does not. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 > STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 > STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 > STACK: t/RestrictionEnzyme.t:184 > ----------------------------------------------------------- > > The symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC > need to be synchronized. Since 'X' is not recommended by "Nomenclature > for Incompletely Specified Bases in Nucleic Acid Sequences" (see > http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it > stands for xanthine), I am in favor of removing it as a valid symbol. > > But I have a feeling that if 'X' is removed as a valid symbol from > Bio::Tools::IUPAC, this will break a lot of existing code. So the > simplest solution seems to be to add 'X' to the symbols recognized by > Bio::Restriction::Enzyme. > > Does anyone have a recommendation? > > -- Conrad Halling chhalling at verizon.net From dmessina at wustl.edu Sun Nov 12 22:30:59 2006 From: dmessina at wustl.edu (David Messina) Date: Sun, 12 Nov 2006 16:30:59 -0600 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> References: <455763EA.8080300@verizon.net> Message-ID: <C5C56BF0-8135-4CBE-BF30-B931E79B39C7@wustl.edu> > The symbols recognized by Bio::Restriction::Enzyme and > Bio::Tools::IUPAC > need to be synchronized. Since 'X' is not recommended by "Nomenclature > for Incompletely Specified Bases in Nucleic Acid Sequences" (see > http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it > stands for xanthine), I am in favor of removing it as a valid symbol. > > But I have a feeling that if 'X' is removed as a valid symbol from > Bio::Tools::IUPAC, this will break a lot of existing code. So the > simplest solution seems to be to add 'X' to the symbols recognized by > Bio::Restriction::Enzyme. How about adding a -strict option which would require valid IUPAC symbols (i.e. not 'X')? And the permissive, 'X'-okay behavior would be the default. Dave From cjfields at uiuc.edu Mon Nov 13 00:15:37 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 12 Nov 2006 18:15:37 -0600 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <45579E52.3010606@verizon.net> References: <455763EA.8080300@verizon.net> <45579E52.3010606@verizon.net> Message-ID: <59337785-5E63-4FD3-A490-FA9AC4715BBE@uiuc.edu> On Nov 12, 2006, at 4:21 PM, Conrad Halling wrote: > A followup: > > Bio::Tools::IUPAC::iupac_iub() also returns 'U' as a valid base. My > idea > of getting an authoritative set of base symbols from Bio::Tools::IUPAC > does not work well. > > I will leave the valid bases in Bio::Restriction::Enzyme set to > what is > already used in the module ('ABCDGHKMNRSTVWY'). > > -- Conrad Conrad, You could grab a hash of DNA/RNA codes from Bio::Tools::IUPAC using iupac_iub(), then modify that for internal use in Bio::Restriction modules by adding/deleting what you want. Or add a method to Bio::Tools::IUPAC that adds/deletes key-value pairs in the object to your specifications. If there are non-IUPAC symbols present in the module we should consider the reasons why they are there. Were they added as a quick fix, or for other reasons? Strictly speaking, I would say a module named Bio::Tools::IUPAC should not contain non-IUPAC symbols, and modifications should be made on a case-by-case basis (in objects), vs. universally (in classes). You could always remove any non- standard symbols and see what breaks. By the way, I think I can speak for many here by saying that we are happy you will take up the Bio::Restriction classes. They definitely need some work! Chris > Conrad Halling wrote: >> Quick summary: >> >> 'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but >> not by >> Bio::Restriction::Enzyme. Should 'X' be removed from >> Bio::Tools::IUPAC >> or should it be added to Bio::Restriction::Enzyme? >> >> Detailed explanation: >> >> I tried to use the Bio::Restriction modules to perform a simple >> restriction analysis of some sequences I'm using at work, and I found >> the documentation and code confusing. So I'm volunteering to overhaul >> and redocument these modules. As part of this effort, I am also >> volunteering to fix the Bio::Restriction::IO::bairoch module. >> >> I have begun writing a test suite, RestrictionEnzyme.t, for the >> Bio::Restriction::Enzyme module. For one of the tests, I created a >> Bio::Restriction::Enzyme object with a recognition sequence that >> includes all of the IUPAC base symbols along with the caret ('^') >> symbol. A code excerpt is: >> >> use Bio::Tools::IUPAC; >> my %iupac_iub = Bio::Tools::IUPAC::iupac_iub(); >> my $site = join( '', '^', sort( keys( %iupac_iub ) ) ); >> ok $enzyme = >> Bio::Restriction::Enzyme->new( >> -name => 'IUPAC-IUB', >> -site => $site ); >> >> This test fails because Bio::Tools::IUPAC module includes 'X' as a >> valid >> base symbol, whereas Bio::Restriction::Enzyme does not. >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY] >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359 >> STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441 >> STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337 >> STACK: t/RestrictionEnzyme.t:184 >> ----------------------------------------------------------- >> >> The symbols recognized by Bio::Restriction::Enzyme and >> Bio::Tools::IUPAC >> need to be synchronized. Since 'X' is not recommended by >> "Nomenclature >> for Incompletely Specified Bases in Nucleic Acid Sequences" (see >> http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it >> stands for xanthine), I am in favor of removing it as a valid symbol. >> >> But I have a feeling that if 'X' is removed as a valid symbol from >> Bio::Tools::IUPAC, this will break a lot of existing code. So the >> simplest solution seems to be to add 'X' to the symbols recognized by >> Bio::Restriction::Enzyme. >> >> Does anyone have a recommendation? >> >> > > -- > Conrad Halling > chhalling at verizon.net > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Mon Nov 13 09:59:34 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 13 Nov 2006 09:59:34 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 Message-ID: <45584206.2040506@sheffield.ac.uk> I've done a test of the bioperl-run 1.5.2 RC3. I've posted results etc to the wiki. I have quite a lot of changes to commit regarding changing "return undef" to "return" and other issues about "bioperl best practices" - they are mainly only obvious changes. I also, moved some tests over to Test::More and added a few further tests for those modules. The test suite passes OK for me (other than the same issues for 1.5.2 RC3). Should It be OK to commit the to HEAD? or shall I wait till after the 1.5.2 release? Cheers Nath From avilella at gmail.com Mon Nov 13 13:25:44 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 13 Nov 2006 13:25:44 +0000 Subject: [Bioperl-l] new methods -- wiki or bugzilla? Message-ID: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Hi, Should the new methods/features be declared as ENH bugs in bugzilla or using the wiki? Cheers, Albert. From cjfields at uiuc.edu Mon Nov 13 15:10:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 09:10:27 -0600 Subject: [Bioperl-l] new methods -- wiki or bugzilla? In-Reply-To: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Message-ID: <013f01c70735$dbc09140$15327e82@pyrimidine> > Hi, > > Should the new methods/features be declared as ENH bugs in > bugzilla or using the wiki? > > Cheers, > > Albert. Historically we have used Bugzilla so we can keep track of them (the enhancement tag is also available there for that reason). You could use the wiki, but I personally think the wiki better serves as primarily a documentation site, both for current code and for the direction we plan on taking Bioperl. We could add a code requests page, though. We already have a Projects Priority page that details what we think are the top issues with Bioperl that need to be addressed; there have been a number of things added to that page that should be separated out into a code request page. However, I don't know how much will be implemented unless someone interested takes it up. Frankly, there are quite a number of requests in bugzilla that haven't been added b/c of lack of interest/time by the other developers. Either that, or we have a lack of knowledge about a certain format or program, as I had with the XMFA and ARP AlignIO parsers (see the POD for my comments; the parsing is pretty minimal). Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Mon Nov 13 15:17:03 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 09:17:03 -0600 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <45584206.2040506@sheffield.ac.uk> Message-ID: <014001c70736$c6e20c80$15327e82@pyrimidine> > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Nathan S. Haigh > Sent: Monday, November 13, 2006 4:00 AM > To: bioperl-l; sendu Bala > Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 > > I've done a test of the bioperl-run 1.5.2 RC3. I've posted > results etc to the wiki. > > I have quite a lot of changes to commit regarding changing > "return undef" to "return" and other issues about "bioperl > best practices" - they are mainly only obvious changes. I > also, moved some tests over to Test::More and added a few > further tests for those modules. The test suite passes OK for > me (other than the same issues for 1.5.2 RC3). > Should It be OK to commit the to HEAD? or shall I wait till after the > 1.5.2 release? > > Cheers > Nath I would say, if the tests pass, commit away. As an aside, I'm not sure how versioning works in the other bioperl distributions. We generally package them up at the same time but I don't remember them getting a specific version number upon release. For instance, bioperl-db was considered at version 0.1 for a long time, but I can't remember if it was officially assigned that. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 13 15:18:43 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 15:18:43 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <014001c70736$c6e20c80$15327e82@pyrimidine> References: <014001c70736$c6e20c80$15327e82@pyrimidine> Message-ID: <45588CD3.5020407@sendu.me.uk> Chris Fields wrote: > > As an aside, I'm not sure how versioning works in the other bioperl > distributions. We generally package them up at the same time but I don't > remember them getting a specific version number upon release. For instance, > bioperl-db was considered at version 0.1 for a long time, but I can't > remember if it was officially assigned that. I'm making their versions match that of core, which seems appropriate. From avilella at gmail.com Mon Nov 13 13:36:44 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 13 Nov 2006 13:36:44 +0000 Subject: [Bioperl-l] new methods -- wiki or bugzilla? In-Reply-To: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> References: <358f4d650611130525y7e8facf2tf3437023fb55d043@mail.gmail.com> Message-ID: <358f4d650611130536sd99bc51u9df42f8bd71cb3a8@mail.gmail.com> and related to the previous question: can an email (presumably with a certain template format) be sent somewhere so that either one or the other system create a new feature ticket somewhere? I've been told that it can be done with wikis, but never seen it done. On 11/13/06, Albert Vilella <avilella at gmail.com> wrote: > Hi, > > Should the new methods/features be declared as ENH bugs in bugzilla or > using the wiki? > > Cheers, > > Albert. > From cjfields at uiuc.edu Mon Nov 13 16:51:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 10:51:24 -0600 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <45588CD3.5020407@sendu.me.uk> Message-ID: <000001c70743$f45b5ce0$15327e82@pyrimidine> > Chris Fields wrote: > > > > As an aside, I'm not sure how versioning works in the other bioperl > > distributions. We generally package them up at the same time but I > > don't remember them getting a specific version number upon > release. > > For instance, bioperl-db was considered at version 0.1 for a long > > time, but I can't remember if it was officially assigned that. > > I'm making their versions match that of core, which seems appropriate. Sounds good to me. We could at least state that run, db, and network 1.5.2 releases require bioperl rel. 1.5.2 (i.e. they are not guaranteed to work with older bioperl core versions), since that's what they were tested against. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 13 16:52:15 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 16:52:15 +0000 Subject: [Bioperl-l] bioperl-run 1.5.2 RC3 In-Reply-To: <000001c70743$f45b5ce0$15327e82@pyrimidine> References: <000001c70743$f45b5ce0$15327e82@pyrimidine> Message-ID: <4558A2BF.7000405@sendu.me.uk> Chris Fields wrote: >> Chris Fields wrote: >>> As an aside, I'm not sure how versioning works in the other bioperl >>> distributions. We generally package them up at the same time but I >>> don't remember them getting a specific version number upon >> release. >>> For instance, bioperl-db was considered at version 0.1 for a long >>> time, but I can't remember if it was officially assigned that. >> I'm making their versions match that of core, which seems appropriate. > > Sounds good to me. We could at least state that run, db, and network 1.5.2 > releases require bioperl rel. 1.5.2 (i.e. they are not guaranteed to work > with older bioperl core versions), since that's what they were tested > against. Yes, they will (do already) require core 1.5.2 for Makefile.PL (Build.PL) to succeed. From alessandro.botton at unipd.it Mon Nov 13 18:10:36 2006 From: alessandro.botton at unipd.it (Alessandro Botton) Date: Mon, 13 Nov 2006 19:10:36 +0100 Subject: [Bioperl-l] Installation problems... Message-ID: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Sorry to disturb you... I tried to install BioPerl by means of cpan. I have previously installed Bundle::BioPerl and everything was ok, and then tried to force the Bioperl installation. Anyway, I attach the "make test" part taken from my shell during Bioperl installation and the result of the second test (tut1.pl, also in attachment) suggested to detect a good installation of Biopelr (the first one was ok). if you need further information please ask me. Thank you in advance for your precious help. Best wishes, A.Botton ??? ======================================= ALESSANDRO BOTTON, PhD student Department of Environmental Agronomy and Crop Science University of Padova AGRIPOLIS - V.le dell'Universit?, 16 35020 Legnaro (PD)-ITALY Fax ++39 049 8272850 Phone ++39 049 8272889 E-mail: alessandro.botton at unipd.it _______________________________________ Doctorate School of Crop Science www.daapv.unipd.it/spv _______________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0016.html> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: make_test_part.txt URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0008.txt> -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0017.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: tut1.pl Type: text/x-perl-script Size: 137 bytes Desc: not available URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0004.bin> -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0018.html> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: test_tut1.pl.txt URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0009.txt> -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061113/5ee0a8ae/attachment-0019.html> From bix at sendu.me.uk Mon Nov 13 19:16:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 13 Nov 2006 19:16:58 +0000 Subject: [Bioperl-l] Installation problems... In-Reply-To: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> References: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Message-ID: <4558C4AA.6020004@sendu.me.uk> Alessandro Botton wrote: > Sorry to disturb you... > I tried to install BioPerl by means of cpan. I have previously installed > Bundle::BioPerl and everything was ok, and then tried to force the > Bioperl installation. Anyway, I attach the "make test" part taken from > my shell during Bioperl installation and the result of the second test > (tut1.pl, also in attachment) suggested to detect a good installation of > Biopelr (the first one was ok). if you need further information please > ask me. Unfortunately Bioperl 1.4 (the latest 'stable' edition in CPAN) is very old and yes, you're likely to get all sorts of failures. tut1.pl tries to do something that indeed no longer works in 1.4. We have a 'developer' release called 1.5.2 soon to be released which should in fact be suitable for use by everyone and everything should work. You can download a pre-release version and install it manually: http://bioperl.org/wiki/Release_1.5.2 Or wait a week or two and you'll be able to find the final release on CPAN. Hope that helps, Sendu. From n.haigh at sheffield.ac.uk Mon Nov 13 19:50:53 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 13 Nov 2006 19:50:53 +0000 Subject: [Bioperl-l] Installation problems... In-Reply-To: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> References: <10E34D30-8163-4C2D-A0B5-2B9ADC2277B5@unipd.it> Message-ID: <4558CC9D.2050507@sheffield.ac.uk> Alessandro Botton wrote: > Sorry to disturb you... > I tried to install BioPerl by means of cpan. I have previously > installed Bundle::BioPerl and everything was ok, and then tried to > force the Bioperl installation. Anyway, I attach the "make test" part > taken from my shell during Bioperl installation and the result of the > second test (tut1.pl, also in attachment) suggested to detect a good > installation of Biopelr (the first one was ok). if you need further > information please ask me. > Thank you in advance for your precious help. > Best wishes, > A.Botton > Hi Alessandro, The Bioperl 1.4 release is now somewhat out-of-date and you might be better to install the latest 1.5.x developer release. We are currently working towards a 1.5.2 release, which should be out within the next week or so. The latest version is 1.5.2 release candidate 3 - it should be installable via CPAN. I will refer you to what has been said about the 1.5.2 RC3 release: "Users: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into." At the moment CPAN doesn't see 1.5.x as a developer release (which should be fixed shortly). Therefore you should still be able to install it with: prompt> perl -MCPAN -e shell CPAN> install Bioperl Once the 1.5.2 RC3 distribution file is fixed, the above will not work. Let me know how you get on and if you get 1.5.2 RC3 installed. Cheers Nathan From jdw at ou.edu Mon Nov 13 23:50:15 2006 From: jdw at ou.edu (James D. White) Date: Mon, 13 Nov 2006 17:50:15 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> Message-ID: <455904B7.50504@ou.edu> "Erik" <er at xs4all.nl> wrote: >Hi all, > >I noticed the parsing is borked with newest swisprot files: > UniProt Knowledgebase Release 9 consists of: > UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 > UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 > > >I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines >in swissprot/trembl according to the new specification (see >http://expasy.org/sprot/relnotes/sp_news.html). > >Basically, the change is as follows: > ID EntryName DataClass; MoleculeType; SequenceLength. >is changed to: > ID EntryName DataClass; SequenceLength. > > > >The change I made was only in the regex capturing the entry name: >method next_seq (Bio/SeqIO/swiss.pm) : > >=============== > > unless( m/ > ^ > ID \s+ # > (\S+) \s+ # $1 entryname > ([^\s;]+); \s+ # $2 DataClass > [0-9]+[ ]AA \. # Sequencelength (capture?) > $ > /ox ) > { > $self->throw("swissprot stream with no ID. Not swissprot in my book"); > } > >=============== > > How about something like the following to recognize both old and new formats =============== unless( m/ ^ ID \s+ # (\S+) \s+ # $1 entryname ( (: [^\s;]+; \s+ )? ) # $2 DataClass (including ";\s+") [0-9]+[ ]AA \. # Sequencelength (capture?) $ /ox ) { $self->throw("swissprot stream with no ID. Not swissprot in my book"); } # Because $2 now contains a trailing ";\s+" in the new format, it needs to be fixed $DataClass = $2 || 'default DataClass'; # provide default for old file format $DataClass =~ s/;\s+$//; # remove trailing ";\s+" =============== The code trailing the unless block should be modified to use the appropriate variable names. This is provided only to show what post-match modification is needed. > >I tested this (=entry parsable and SeqIO created) against several >hundred Swissprot and Trembl entries. > >Of course, files with the older format are now broken - it may be better >to leave old and new format, and try both (newest first). > >hth, > >Erik > > > > > > From lincoln.stein at gmail.com Mon Nov 13 17:43:50 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 13 Nov 2006 12:43:50 -0500 Subject: [Bioperl-l] Bio::DB::Fasta index In-Reply-To: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> References: <716af09c0611110553h438e0465vb8f56773734d291f@mail.gmail.com> Message-ID: <6dce9a0b0611130943n28600d66xb3fa37f7bb4a68b6@mail.gmail.com> You can always remove write permissions from the index file, in which case the attempted reindexing will fail quickly. Lincoln On 11/11/06, Bernd Web <bernd.web at gmail.com> wrote: > > Hi, > > A maybe strange question: is it possible to force Bio::DB::Fasta NOT > to index the fasta file at any time (if there is already an index)? In > the doc ( > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/DB/Fasta.html > ), > I read: " If one of the source fasta files is updated, the module > reindexes just that one file. (You can also force reindexing > manually)." > > Can I also switch off reindexing? (I realize that with > Bio::Index::Fasta indexing can be separated). > > bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Tue Nov 14 04:44:09 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 13 Nov 2006 22:44:09 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <455904B7.50504@ou.edu> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> Message-ID: <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> On Nov 13, 2006, at 5:50 PM, James D. White wrote: > "Erik" <er at xs4all.nl> wrote: > >> Hi all, >> >> I noticed the parsing is borked with newest swisprot files: >> UniProt Knowledgebase Release 9 consists of: >> UniProtKB/Swiss-Prot Release 51.0 of 31-Oct-2006 >> UniProtKB/TrEMBL Release 34.0 of 31-Oct-2006 >> >> >> I edited my local copy of Bio/SeqIO/swiss.pm to parse the ID lines >> in swissprot/trembl according to the new specification (see >> http://expasy.org/sprot/relnotes/sp_news.html). >> >> Basically, the change is as follows: >> ID EntryName DataClass; MoleculeType; SequenceLength. >> is changed to: >> ID EntryName DataClass; SequenceLength. >> >> >> >> The change I made was only in the regex capturing the entry name: >> method next_seq (Bio/SeqIO/swiss.pm) : >> >> =============== >> >> unless( m/ >> ^ >> ID \s+ # >> (\S+) \s+ # $1 entryname >> ([^\s;]+); \s+ # $2 DataClass >> [0-9]+[ ]AA \. # Sequencelength >> (capture?) >> $ >> /ox ) >> { >> $self->throw("swissprot stream with no ID. Not swissprot in my >> book"); >> } >> >> =============== >> >> > > How about something like the following to recognize both old and > new formats > > =============== > > unless( m/ > ^ > ID \s+ # > (\S+) \s+ # $1 entryname > ( (: [^\s;]+; \s+ )? ) # $2 DataClass > (including ";\s+") > [0-9]+[ ]AA \. # > Sequencelength (capture?) > $ > /ox ) > { > $self->throw("swissprot stream with no ID. Not swissprot in my > book"); > } > # Because $2 now contains a trailing ";\s+" in the new format, it > needs to be fixed > $DataClass = $2 || 'default DataClass'; # provide default > for old file format > $DataClass =~ s/;\s+$//; # remove trailing "; > \s+" > > =============== > > The code trailing the unless block should be modified to use the > appropriate > variable names. This is provided only to show what post-match > modification is > needed. > >> >> I tested this (=entry parsable and SeqIO created) against several >> hundred Swissprot and Trembl entries. >> >> Of course, files with the older format are now broken - it may be >> better >> to leave old and new format, and try both (newest first). >> >> hth, >> >> Erik This has been fixed to match old and new formats in CVS and passes all tests so far. You can try it out if you want. The regex is made to match up to (but not include) the ';', so there is no need to remove the extra space. ... unless( m{^ ID \s+ # (\S+) \s+ # $1 entryname ([^\s;]+); \s+ # $2 DataClass (?:PRT;)? \s+ # Molecule Type (optional) [0-9]+[ ]AA \. # Sequencelength (capture?) $ }ox ) { ... The molecule type was always PRT and was a carryover from EMBL format divisions. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From kaboroev at sfu.ca Tue Nov 14 05:55:46 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Mon, 13 Nov 2006 21:55:46 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45558C03.8020903@sendu.me.uk> References: <45550269.9050407@sfu.ca> <45558C03.8020903@sendu.me.uk> Message-ID: <45595A62.7090704@sfu.ca> Hi, I am using an up-to-date bioperl-live. The precise code is insignificant so I wrote some additional (shorter) code to attempt to explain my problem. What I want to do is the following. I want to add some functionality to the Bio::Map::Physical module so i created a module that inherits Physical module, Extended::FPC.pm. #----Test.pl-BEGIN---# use strict; use diagnostics; use Extended::FPC; my $mapio = new Extended::FPC(-format => "fpc",-file => $ARGV[0],-readcor => 1); my $map = $mapio->next_map(); $map->fpc_test(); exit 0; #---Test.pl-END------# #----Extended::FPC.pm-BEGIN---# package Extended::FPC; use strict; use base qw(Bio::Map::Physical Bio::MapIO); sub fpc_test { print STDERR "testing\n"; return 0; } 1; #----Extended::FPC.pm-END-----# The execution of test.pl results in a "Can't locate object method "next_map" via package "Extended::FPC"" error; Then I added the "Bio::MapIO" module to the "use base qw(Bio::Map::Physical Bio::MapIO);", because that is the module in which next_map is declared. When I again execute test.pl I now get the exception: Uncaught exception from user code: #-------- EXCEPTION ------- # ------------- EXCEPTION: Bio::Root::NotImplemented ------------- MSG: Abstract method "Bio::Factory::MapFactoryI::next_map" is not implemented by package Extended::FPC. This is not your fault - author of Extended::FPC should be blamed! STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.7/Bio/Root/Root.pm:359 STACK: Bio::Root::RootI::throw_not_implemented /usr/lib/perl5/site_perl/5.8.7/Bio/Root/RootI.pm:522 STACK: Bio::Factory::MapFactoryI::next_map /usr/lib/perl5/site_perl/5.8.7/Bio/Factory/MapFactoryI.pm:84 STACK: ./fpc.pl:12 ---------------------------------------------------------------- at /usr/lib/perl5/site_perl/5.8.7/Error.pm line 187 Error::throw('Bio::Root::NotImplemented', '-class', 'Bio::Root::NotImplemented', '-object', 'Extended::FPC=HASH(0x109ce10)', '-text', 'Abstract method "Bio::Factory::MapFactoryI::next_map" is not ...') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Root/Root.pm line 359 Bio::Root::Root::throw('Extended::FPC=HASH(0x109ce10)', '-text', 'Abstract method "Bio::Factory::MapFactoryI::next_map" is not ...', '-class', 'Bio::Root::NotImplemented') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Root/RootI.pm line 522 Bio::Root::RootI::throw_not_implemented('Extended::FPC=HASH(0x109ce10)') called at /usr/lib/perl5/site_perl/5.8.7/Bio/Factory/MapFactoryI.pm line 84 Bio::Factory::MapFactoryI::next_map('Extended::FPC=HASH(0x109ce10)') called at ./fpc.pl line 12 #---- EXCEPTION END ----# This is where I am now and have no real idea of where to begin. I suppose the easiest way is to pass the $map variable to the function of interest and not to bother with inheriting any modules. Sendu Bala wrote: > Keith Anthony Boroevich wrote: > >> Hi, >> >> I am attempting to add a few methods (ie. matching_bands_list) to the >> fpc map class but I am having a hard time inheriting the class properly. >> >> My first attempt was to inherit the "Bio::Map::Physical" class but the >> "next_map" package is not found. >> So I tried inheriting "Bio::MapIO" instead, and get a cannot find >> "matching_bands_list" via package "Bio::Map::Physical" >> The only way I can get it to work is with no inheritance and passing the >> map class variable to the function, but this isn't very elegant. Is >> there a correct way to inherit these classes that will allow me to >> execute this properly? >> > > It's hard to diagnose the problem without knowing exactly what you've > tried. Please post some relevant code. Also, what version of Bioperl are > you using? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- ><)))?> -cGRASP- <?(((>< Keith Anthony Boroevich Simon Fraser University Tel: 604-268-7276 From bix at sendu.me.uk Tue Nov 14 08:49:52 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 14 Nov 2006 08:49:52 +0000 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <45595A62.7090704@sfu.ca> References: <45550269.9050407@sfu.ca> <45558C03.8020903@sendu.me.uk> <45595A62.7090704@sfu.ca> Message-ID: <45598330.20400@sendu.me.uk> Keith Anthony Boroevich wrote: > Hi, > > I am using an up-to-date bioperl-live. The precise code is > insignificant so I wrote some additional (shorter) code to attempt to > explain my problem. What I want to do is the following. I want to add > some functionality to the Bio::Map::Physical module so i created a > module that inherits Physical module, Extended::FPC.pm. > > #----Test.pl-BEGIN---# > use strict; > use diagnostics; > use Extended::FPC; > my $mapio = new Extended::FPC(-format => "fpc",-file => > $ARGV[0],-readcor => 1); > my $map = $mapio->next_map(); > $map->fpc_test(); > exit 0; > #---Test.pl-END------# > > #----Extended::FPC.pm-BEGIN---# > package Extended::FPC; > use strict; > use base qw(Bio::Map::Physical Bio::MapIO); > > sub fpc_test { > print STDERR "testing\n"; > return 0; > } > > 1; > #----Extended::FPC.pm-END-----# > > The execution of test.pl results in a "Can't locate object method > "next_map" via package "Extended::FPC"" error; > Then I added the "Bio::MapIO" module to the "use base > qw(Bio::Map::Physical Bio::MapIO);", because that is the module in which > next_map is declared. Well I think alarm bells should have been ringing at that point. I think you're trying to inherit from the wrong module to do whatever it is you want to do. Bio::Map::Physical has no next_map() because it isn't a Map::IO module. It represents a /single/ map (only), and is the sort of object you might /receive/ as the result of calling next_map() on an actual Map::IO module. So perhaps you should take another look at the various Map modules and figure out the correct thing to inherit from, or you just need to correct your usage (only call next_map() on a Map::IO). From er at xs4all.nl Tue Nov 14 09:40:20 2006 From: er at xs4all.nl (Erik) Date: Tue, 14 Nov 2006 10:40:20 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> Message-ID: <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> Btw and FYI: I have run this regex through SwissProt and Trembl and a previous version of those two files (to be version-precise: swissprot 51 and 50; trembl 33 and 34). It matched all ID lines. Thanks :) Erik > ... > unless( m{^ > ID \s+ # > (\S+) \s+ # $1 entryname > ([^\s;]+); \s+ # $2 DataClass > (?:PRT;)? \s+ # Molecule Type (optional) > [0-9]+[ ]AA \. # Sequencelength (capture?) > $ > }ox ) { > ... > > The molecule type was always PRT and was a carryover from EMBL format > divisions. From cjfields at uiuc.edu Tue Nov 14 12:35:24 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 14 Nov 2006 06:35:24 -0600 Subject: [Bioperl-l] Bio/SeqIO/swiss.pm parsing error In-Reply-To: <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> References: <mailman.2570.1162825957.2429.bioperl-l@lists.open-bio.org> <455904B7.50504@ou.edu> <E4158F8E-8794-4247-A2F8-DBBF7AA8F8F4@uiuc.edu> <7997.156.83.1.251.1163497220.squirrel@webmail.xs4all.nl> Message-ID: <B5AD2308-6CC0-4250-ABFA-1E728196693F@uiuc.edu> On Nov 14, 2006, at 3:40 AM, Erik wrote: > Btw and FYI: > > I have run this regex through SwissProt and Trembl and a previous > version > of those two files (to be version-precise: swissprot 51 and 50; > trembl 33 > and 34). > > It matched all ID lines. > > Thanks :) > > Erik ... Thanks for letting us know. We like success stories! Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From gcarbajosa at cnio.es Tue Nov 14 10:39:41 2006 From: gcarbajosa at cnio.es (guillermo) Date: Tue, 14 Nov 2006 11:39:41 +0100 Subject: [Bioperl-l] Error while indexing whole genbank Message-ID: <80337800c106ece5f0c78ed0b098b8f8@cnio.es> Hello, I am trying to index the whole of genbank nucleotide (release number 156, October 15 2006), with the script (which uses Bio::Index::GenBank) that is attached at the end of this message the process crashes with this error message: sdbm store returned -1, errno 9, key "BF460808" at /usr/local/lib/perl5/site_perl/5.8.8/Bio/Index/Abstract.pm line 714, <GenBank> line 164732819. why could this be? Thanks, Guillermo #!/usr/local/bin/perl -w # Perl pragma to restrict unsafe constructs use strict; # Issue warnings about suspicious programming. use warnings; # Use the code module that contains BioPerl Services. use Bio::Index::GenBank; # Use to index GenBank file use Bio::SeqIO; # be prepare for command-line options/arguments use Getopt::Std; sub help { return<<"END_HELP"; Description: Make index from GenBank database Usage: createGenBankIndex.pl -d {index file} -g {GenBank database} -d path and file name of index database -g GenBank database path END_HELP } BEGIN { # Determines the options with values from program use vars qw/$opt_d $opt_g/; # these are switches taking an argument (a value) my $switches = 'dg'; # Get the switches getopt($switches); # If the user does not write nothing, skip to help unless (defined($opt_d) || defined($opt_g)){ print help; exit 0; } } ######################################################################## ####### # # DESCRIPTION: The next program creates an BioPerl index aside GenBank database. # # INPUT (BY CONSOLE): - (-d) Path where the Uniprot index is going to store. # - (-g) Path where GenBank database is located # # OUTPUT: - O => The program has finished sucessfully # - 1 => Some of database files has not founded # - 2 => There was an error while the process was running # # AUTHOR: Jos?? Manuel Rodr??guez Carrasco -jmrc at cnb.uam.es- (INB-CNB) ######################################################################## ####### # Check if the path of GenBank database is able to read unless (-f $opt_g && -r $opt_g) { # The GenBank database has not been found print "Error of createGenBankIndex program: The GenBank database has not been found\n"; # Return an error exit 1; } # Store the database paths my @DBList = ($opt_g); # Create new instance to index file. It is used the option my $indexSW = Bio::Index::GenBank->new ('-filename' => $opt_d, '-write_flag' => 1); # Make the index my $numFiles = $indexSW->make_index(@DBList); # Check how many databases have been indexed if ($numFiles == 1) { # There has been not exist error. print "\nThe creation of GenBank index has been executed successfully\n"; exit 0; } else { # There has been exist an process error print "\nThere was a problem while the creation of GenBank index was running\n"; exit 2; } **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From gcarbajosa at cnio.es Tue Nov 14 10:57:01 2006 From: gcarbajosa at cnio.es (guillermo) Date: Tue, 14 Nov 2006 11:57:01 +0100 Subject: [Bioperl-l] indexing with several processors Message-ID: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> Hello, While using the Bio::Index::GenBank module for indexing Genbank, is there any option to run the process with more than one processor. Thanks **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From lincoln.stein at gmail.com Tue Nov 14 16:08:55 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 14 Nov 2006 11:08:55 -0500 Subject: [Bioperl-l] Bio::Graphics In-Reply-To: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> References: <716af09c0611100939l4e3083c1re0fed16aa0384799@mail.gmail.com> Message-ID: <6dce9a0b0611140808md4edbe7ye2632714621da52d@mail.gmail.com> I don't think the dots have been connected on this. It should be straightforward following the example in the BioGraphics HOWTO. Lincoln On 11/10/06, Bernd Web <bernd.web at gmail.com> wrote: > > Hi, > > Lincoln made an excellent help on Graphics. Thanks for > that!(http://www.bioperl.org/wiki/HOWTO:Graphics) > I am just looking at the imagemap creation with > my $map=$panel->create_web_map('mapname',\&linkrule,'bbb'); > and would like to connect the PNG from a blast report to the blast > results. > > I just realize that this likely has been done many times. Does someone > have a pointer to code for creating an imagemap from a BLAST report > and also write the blast results with links? > > Bernd > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bosborne11 at verizon.net Tue Nov 14 21:54:25 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 14 Nov 2006 16:54:25 -0500 Subject: [Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC In-Reply-To: <455763EA.8080300@verizon.net> Message-ID: <C17FA541.B55D%bosborne11@verizon.net> Conrad, The typical solution is to declare an alphabet, as in: my $seq = Bio::Seq->new(-seq => "xxxx", -alphabet => "dna") Then Bioperl will not check your sequence. This works since you'll know that the alphabet, in this case, has to be "dna". Brian O. On 11/12/06 1:11 PM, "Conrad Halling" <chhalling at verizon.net> wrote: > This test fails because Bio::Tools::IUPAC module includes 'X' as a valid > base symbol, whereas Bio::Restriction::Enzyme does not. From stewarta at nmrc.navy.mil Tue Nov 14 22:47:26 2006 From: stewarta at nmrc.navy.mil (Andrew Stewart) Date: Tue, 14 Nov 2006 17:47:26 -0500 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast Message-ID: <8AF15F1F-0C81-4506-97C4-D25A12804731@nmrc.navy.mil> Anyone have any opinions as to how easy/difficult it would be to incorporate mpiblast into Bio::Tools::Run::StandAloneBlast? It runs essentially the same way as blastall, and its output is nearly identical. -A -- Andrew Stewart Research Assistant, Genomics Team Navy Medical Research Center (NMRC) Biological Defense Research Directorate (BDRD) BDRD Annex 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 email: stewarta at nmrc.navy.mil phone: 301-231-6700 Ext 270 From bosborne11 at verizon.net Wed Nov 15 03:10:00 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 14 Nov 2006 22:10:00 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <45531968.6080607@sendu.me.uk> Message-ID: <C17FEF38.B565%bosborne11@verizon.net> Sendu, RC3 can't be released as it doesn't install its scripts and some of these scripts are critical (e.g. the bp_*load_gff.pl and bp_process*.pl scripts, used by GMOD and chado users). I believe I've fixed this though, the problem was in Makefile.PL, no surprise. BIO On 11/9/06 7:04 AM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Developers: > Once again I'm hopeful that this is the last RC. If all goes well > expect final release in about a weeks time. Please check and update > documentation. > > Users: > Even though 1.5.2 is a 'developer' release, we consider it the most > stable and capable version of Bioperl, and recommend that you use > it in all but the most critical production environments. Please > try it out and let us know of any problems or difficulties you run > into. > > > Thank you, > Sendu. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sayali_salodkar at persistent.co.in Wed Nov 15 14:15:52 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Wed, 15 Nov 2006 19:45:52 +0530 Subject: [Bioperl-l] Help needed urgently Message-ID: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> I wish to fetch consensus sequence and the names of the trace (chromat) files used in the assembly from the .ace file For this purpose, I am using Bio::Assembly::IO. But I am unable to find the appropriate methods which would enable me to fetch this information. Note: The BS line (base segment) in the .ace file indicates which read phrap has chosen to be the consensus at a particular position. For example: BS 1 515 K26-572c gives BS <padded start consensus position> <padded end consensus position> <read name> respectively. How do I retrieve this information contig wise? Kindly help. Regards, Sayali D Salodkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From cjfields at uiuc.edu Wed Nov 15 14:22:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 08:22:38 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <C17FEF38.B565%bosborne11@verizon.net> Message-ID: <000a01c708c1$80d37300$15327e82@pyrimidine> > Sendu, > > RC3 can't be released as it doesn't install its scripts and > some of these scripts are critical (e.g. the bp_*load_gff.pl > and bp_process*.pl scripts, used by GMOD and chado users). I > believe I've fixed this though, the problem was in > Makefile.PL, no surprise. > > BIO ... This is definitely something to think about with Sendu's proposed changeover to Module::Build, which would obviate having a Makefile.PL. The issue with broken script installation was raised previously, but there were few responses (probably b/c itr came up somewhat indirectly in relation to other files in CVS). Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 14:24:25 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 08:24:25 -0600 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast In-Reply-To: <8AF15F1F-0C81-4506-97C4-D25A12804731@nmrc.navy.mil> Message-ID: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> > Anyone have any opinions as to how easy/difficult it would be > to incorporate mpiblast into > Bio::Tools::Run::StandAloneBlast? It runs essentially the > same way as blastall, and its output is nearly identical. > > > -A > > -- > Andrew Stewart > Research Assistant, Genomics Team > Navy Medical Research Center (NMRC) > Biological Defense Research Directorate (BDRD) BDRD Annex > 12300 Washington Avenue, 2nd Floor Rockville, MD 20852 > > email: stewarta at nmrc.navy.mil > phone: 301-231-6700 Ext 270 I think plans were to rewrite StandAloneBlast and RemoteBlast to make them more 'generic' (i.e. capable of running other BLAST-related programs), though I'm not sure at what stage everything is. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From sayali_salodkar at persistent.co.in Wed Nov 15 14:15:52 2006 From: sayali_salodkar at persistent.co.in (Sayali) Date: Wed, 15 Nov 2006 19:45:52 +0530 Subject: [Bioperl-l] Help needed urgently Message-ID: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> I wish to fetch consensus sequence and the names of the trace (chromat) files used in the assembly from the .ace file For this purpose, I am using Bio::Assembly::IO. But I am unable to find the appropriate methods which would enable me to fetch this information. Note: The BS line (base segment) in the .ace file indicates which read phrap has chosen to be the consensus at a particular position. For example: BS 1 515 K26-572c gives BS <padded start consensus position> <padded end consensus position> <read name> respectively. How do I retrieve this information contig wise? Kindly help. Regards, Sayali D Salodkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Pvt. Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Pvt. Ltd. does not accept any liability for virus infected mails. From bix at sendu.me.uk Wed Nov 15 15:35:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 15:35:29 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <4554514D.2020001@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> Message-ID: <455B33C1.1010800@sendu.me.uk> Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I propose removing it from CVS. Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL when a user does a normal install of Bioperl? Or can it safely be ignored, only run manually by people who want to install Deobfuscator? From nhansen at nhgri.nih.gov Wed Nov 15 15:52:05 2006 From: nhansen at nhgri.nih.gov (Nancy Hansen) Date: Wed, 15 Nov 2006 10:52:05 -0500 (EST) Subject: [Bioperl-l] Inheritance Bio::Map::Physical Message-ID: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Keith Anthony Boroevich wrote: > > I am using an up-to-date bioperl-live. The precise code is > insignificant so I wrote some additional (shorter) code to attempt to > explain my problem. What I want to do is the following. I want to add > some functionality to the Bio::Map::Physical module so i created a > module that inherits Physical module, Extended::FPC.pm. > > #----Test.pl-BEGIN---# > use strict; > use diagnostics; > use Extended::FPC; > my $mapio = new Extended::FPC(-format => "fpc",-file => > $ARGV[0],-readcor => 1); > my $map = $mapio->next_map(); > $map->fpc_test(); > exit 0; > #---Test.pl-END------# You're right that your Extended::FPC should inherit from Bio::Map::Physical, but you really don't want to use it to parse the fpc file (Bio::MapIO does that just fine, and gets all the data you need into the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical object using Bio::MapIO, then forcing it to be an Extended::FPC, which will allow it to use your method(s): my $mapio = Bio::MapIO->new(-format => 'fpc', -file => $ARGV[0], -readcor => 1); my $fpc_map = $mapio->next_map(); bless $fpc_map, Extended::FPC; my $ra_bands = $fpc_map->my_new_extended_method(); I've actually written my own method to return the band sizes as well, so it would probably make a good enhancement to Bio::Map::Physical, which already has a "matching_bands" method that returns the (scalar) number of bands that match at a given tolerance. If that method were "enhanced" to return an array of matching band sizes rather than the scalar number of bands, it would still return the number in scalar context, but give you the matching band info in list context. I'd be happy to submit a patch for this if others think it's backwardly-compatible enough. --Nancy ************************************* Nancy F. Hansen, PhD nhansen at nhgri.nih.gov Bioinformatics Group NIH Intramural Sequencing Center (NISC) 5625 Fishers Lane Rockville, MD 20852 Phone: (301) 435-1560 Fax: (301) 435-6170 From cjfields at uiuc.edu Wed Nov 15 16:24:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 10:24:57 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> Message-ID: <000001c708d2$97c9d610$15327e82@pyrimidine> > Does anyone know what purpose Bio/DB/Makefile.PL serves? If > none, I propose removing it from CVS. > > Dave: Do you need anything to happen with > doc/Deobfuscator/Makefile.PL when a user does a normal > install of Bioperl? Or can it safely be ignored, only run > manually by people who want to install Deobfuscator? The Bio/DB/Makefile.PL and MANIFEST could be GMOD- or Chado-related (they are both related to Bio::DB::GFF). I'm not sure though; I'm cc'ing this to Lincoln to see if they are still needed. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From arareko at campus.iztacala.unam.mx Wed Nov 15 16:23:45 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed, 15 Nov 2006 10:23:45 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> Message-ID: <455B3F11.6070102@campus.iztacala.unam.mx> I think Deobfuscator code should be manually installed only. Mauricio. Sendu Bala wrote: > Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I > propose removing it from CVS. > > Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL > when a user does a normal install of Bioperl? Or can it safely be > ignored, only run manually by people who want to install Deobfuscator? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From kaboroev at sfu.ca Wed Nov 15 17:14:14 2006 From: kaboroev at sfu.ca (Keith Anthony Boroevich) Date: Wed, 15 Nov 2006 09:14:14 -0800 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> References: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Message-ID: <455B4AE6.509@sfu.ca> Thanks, this is exactly what I was looking for. I didn't know how to get Bio::MapIO to return "my" class and I was unaware that bless could be used in such a manner. Not to nit-pick, but just in case anyone else has such a problem, quotes are required around the class. bless $fpc_map "Extended::FPC"; Nancy Hansen wrote: > > > You're right that your Extended::FPC should inherit from > Bio::Map::Physical, but you really don't want to use it to parse the fpc > file (Bio::MapIO does that just fine, and gets all the data you need into > the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical > object using Bio::MapIO, then forcing it to be an Extended::FPC, which > will allow it to use your method(s): > > my $mapio = Bio::MapIO->new(-format => 'fpc', > -file => $ARGV[0], > -readcor => 1); > > my $fpc_map = $mapio->next_map(); > > bless $fpc_map, Extended::FPC; > my $ra_bands = $fpc_map->my_new_extended_method(); > -- ><)))?> -cGRASP- <?(((>< Keith Anthony Boroevich Simon Fraser University Tel: 604-268-7276 From pmiguel at purdue.edu Wed Nov 15 17:00:50 2006 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 15 Nov 2006 12:00:50 -0500 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <455B47C2.8020400@purdue.edu> Sayali wrote: > I wish to fetch consensus sequence and the names of the trace (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar > Hi Sayali, I don't think there is a pre-rolled bioperl method to do what you ask. (But it seems like one is under construction?) You can extract the contig sequences from a phrap .ace file with the following plain perl code: my $print_it = 0; while (<>){ $print_it = /^CO / ? 1 : /^$/ ? 0 : $print_it ; s/^CO />/; s/\*//g; #removes "pads"--optional print if $print_it; } To find the reads that went into each contig, you do *not* want the BS tagged records. My understanding is that BS is just what consed uses to populate its consensus line from the ace file. The simplest way is: egrep '^CO|AF' acefilename if you are on a unix system. Or with perl while (<>) { print if (/^CO|AF/); } -- Phillip Purdue Genomics Core Facility From cjfields at uiuc.edu Wed Nov 15 17:00:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:00:05 -0600 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> > I wish to fetch consensus sequence and the names of the trace > (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to > find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read > phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus > position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar It looks like the relevant part of the Bio::Assembly::IO::ace parser responsible for parsing this is commented out: # Loading base segments definitions (Base Segment field) # /^BS (\d+) (\d+) (\S+)/ && do { # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} {'segments'})) { # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . " " . $2; # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = $1 . " " . $2 } # }; I'm not sure why to be honest as I'm not very familiar with the Bio::Assembly. Have you tried removing the comments to see what happens? You could file a bug report noting this using Bugzilla: http://bugzilla.open-bio.org/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 17:00:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:00:05 -0600 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> Message-ID: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> > I wish to fetch consensus sequence and the names of the trace > (chromat) > files used in the assembly from the .ace file > > For this purpose, I am using Bio::Assembly::IO. But I am unable to > find the > appropriate methods which would enable me to fetch this information. > > > > Note: > > The BS line (base segment) in the .ace file indicates which read > phrap has > chosen to be the consensus at a particular position. > > For example: > > BS 1 515 K26-572c gives > > BS <padded start consensus position> <padded end consensus > position> <read > name> respectively. > > > > How do I retrieve this information contig wise? > > Kindly help. > > Regards, > > Sayali D Salodkar It looks like the relevant part of the Bio::Assembly::IO::ace parser responsible for parsing this is commented out: # Loading base segments definitions (Base Segment field) # /^BS (\d+) (\d+) (\S+)/ && do { # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} {'segments'})) { # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . " " . $2; # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = $1 . " " . $2 } # }; I'm not sure why to be honest as I'm not very familiar with the Bio::Assembly. Have you tried removing the comments to see what happens? You could file a bug report noting this using Bugzilla: http://bugzilla.open-bio.org/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 17:37:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 11:37:35 -0600 Subject: [Bioperl-l] Inheritance Bio::Map::Physical In-Reply-To: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> References: <Pine.GSO.4.58.0611151042090.2737@stout.nhgri.nih.gov> Message-ID: <D7DFA98D-2107-4C4C-9BBA-8B029DD9CC41@uiuc.edu> On Nov 15, 2006, at 9:52 AM, Nancy Hansen wrote: > Keith Anthony Boroevich wrote: >> >> I am using an up-to-date bioperl-live. The precise code is >> insignificant so I wrote some additional (shorter) code to attempt to >> explain my problem. What I want to do is the following. I want >> to add >> some functionality to the Bio::Map::Physical module so i created a >> module that inherits Physical module, Extended::FPC.pm. >> >> #----Test.pl-BEGIN---# >> use strict; >> use diagnostics; >> use Extended::FPC; >> my $mapio = new Extended::FPC(-format => "fpc",-file => >> $ARGV[0],-readcor => 1); >> my $map = $mapio->next_map(); >> $map->fpc_test(); >> exit 0; >> #---Test.pl-END------# > > You're right that your Extended::FPC should inherit from > Bio::Map::Physical, but you really don't want to use it to parse > the fpc > file (Bio::MapIO does that just fine, and gets all the data you > need into > the Bio::Map::Physical object). Try retrieving a Bio::Map::Physical > object using Bio::MapIO, then forcing it to be an Extended::FPC, which > will allow it to use your method(s): > > my $mapio = Bio::MapIO->new(-format => 'fpc', > -file => $ARGV[0], > -readcor => 1); > > my $fpc_map = $mapio->next_map(); > > bless $fpc_map, Extended::FPC; > my $ra_bands = $fpc_map->my_new_extended_method(); > > I've actually written my own method to return the band sizes as > well, so > it would probably make a good enhancement to Bio::Map::Physical, which > already has a "matching_bands" method that returns the (scalar) > number of > bands that match at a given tolerance. If that method were > "enhanced" to > return an array of matching band sizes rather than the scalar > number of > bands, it would still return the number in scalar context, but give > you > the matching band info in list context. I'd be happy to submit a > patch > for this if others think it's backwardly-compatible enough. > > --Nancy Keith, Nancy, Sendu Bala has taken over maintenance of the Bio::Map modules. I have cc'd him this in case he has missed it (he's in the middle of getting a bioperl developer release put together). In general we are more than happy to take new modules and patches for current ones. There is a HOWTO on submitting patches and new code: http://www.bioperl.org/wiki/HOWTO:SubmitPatch If you plan on submitting a patch, you should also consider adding some tests as well. I think the relevant tests for Bio::Map modules are in t/Map.t and t/MapIO.t. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 18:15:48 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 18:15:48 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> Message-ID: <455B5954.1080209@sendu.me.uk> Chris Fields wrote: > On Nov 10, 2006, at 10:16 AM, Stefan Kirov wrote: > >> I personally like the idea. Why not have both for this release to >> ensure smooth transition? Sendu, would having Makefile.PL (I mean >> the old one) along with the build script be a problem? [snip] > Sounds like a good compromise to me. Like I said, the only problem I > had is introducing something drastically new after three RCs (and > just prior to a final release; I think Sendu wanted to release the > final 1.5.2 next week, just before Thanksgiving here.). There is no > problem though if we have the old Makefile.PL to fall back to for > this release. In fact, you could remove it from HEAD when needed; > the file still exists on the 1.5.2 branch, right? I think the compromise isn't worth it. The old Makefile.PL is just too inadequate and I don't want to support it. Build.pl is simply far too superior and I really want all users to be using it. I've now made the changeover in HEAD for core only (so far). Can people please try it out, especially wrt to installation in default and user-specified locations? First, clean out your system of the old Makefile.PL stuff: perl Makefile.PL make clean rm Makefile.PL Makefile.old cvs update -d -P Now try out the new Build.PL: perl Build.PL ./Build test ./Build install Try out other things: http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm You'll notice you don't have a Makefile.PL anymore. Distributions will include one, and as a cvs user you can generate one by: ./Build manifest ./Build distmeta Now you can try out the things you used to be able to do: make test make install Please let me know how you get on, Sendu. From bosborne11 at verizon.net Wed Nov 15 18:33:06 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 13:33:06 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> Message-ID: <C180C792.B596%bosborne11@verizon.net> Sendu, I see: 175 ~/bioperl-live>perl Build.PL Checking prerequisites... ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Which is incorrect since there no "modules indicated above". Brian O. On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Please let me know how you get on, From gcarbajosa at cnio.es Wed Nov 15 17:43:10 2006 From: gcarbajosa at cnio.es (guillermo) Date: Wed, 15 Nov 2006 18:43:10 +0100 Subject: [Bioperl-l] Fwd: Error while indexing whole genbank Message-ID: <68874599fabff74a65fcc62568022288@cnio.es> Hello, I just indexed BCT without problems and now I am going to do it in parts, different indexes for each one, for PLN, PRI, ROD, etc. Anyways, I??l try to do it for the whole genbank and if it works I?ll let you know. Thanks for the support, Guille Inicio mensaje reenviado: > De: guillermo <gcarbajosa at cnio.es> > Fecha: 14 de noviembre de 2006 11:39:41 GMT+01:00 > Para: bioperl-l at bioperl.org > Asunto: Error while indexing whole genbank > > Hello, > > I am trying to index the whole of genbank nucleotide (release number > 156, October 15 2006), with the script (which uses > Bio::Index::GenBank) that is attached at the end of this message the > process crashes with this error message: > > sdbm store returned -1, errno 9, key "BF460808" at > /usr/local/lib/perl5/site_perl/5.8.8/Bio/Index/Abstract.pm line 714, > <GenBank> line 164732819. > > why could this be? > > Thanks, > Guillermo > > > #!/usr/local/bin/perl -w > > # Perl pragma to restrict unsafe constructs > use strict; > > # Issue warnings about suspicious programming. > use warnings; > > # Use the code module that contains BioPerl Services. > use Bio::Index::GenBank; # Use to index GenBank file > use Bio::SeqIO; > > # be prepare for command-line options/arguments > use Getopt::Std; > > sub help { > return<<"END_HELP"; > Description: Make index from GenBank database > Usage: > > createGenBankIndex.pl -d {index file} -g {GenBank database} > -d path and file name of index database > -g GenBank database path > > END_HELP > > } > > > BEGIN { > > # Determines the options with values from program > use vars qw/$opt_d $opt_g/; > > # these are switches taking an argument (a value) > my $switches = 'dg'; > > # Get the switches > getopt($switches); > > # If the user does not write nothing, skip to help > unless (defined($opt_d) || defined($opt_g)){ > print help; > exit 0; > } > > } > > ####################################################################### > ######## > # > # DESCRIPTION: The next program creates an BioPerl index aside GenBank > database. > # > # INPUT (BY CONSOLE): - (-d) Path where the Uniprot index is going to > store. > # - (-g) Path where GenBank database is located > # > # OUTPUT: - O => The program has finished sucessfully > # - 1 => Some of database files has not founded > # - 2 => There was an error while the process was running > # > # AUTHOR: Jos?? Manuel Rodr??guez Carrasco -jmrc at cnb.uam.es- (INB-CNB) > ####################################################################### > ######## > > > # Check if the path of GenBank database is able to read > unless (-f $opt_g && -r $opt_g) { > > # The GenBank database has not been found > print "Error of createGenBankIndex program: The GenBank database has > not been found\n"; > > # Return an error > exit 1; > } > > > # Store the database paths > my @DBList = ($opt_g); > > # Create new instance to index file. It is used the option > my $indexSW = Bio::Index::GenBank->new ('-filename' => $opt_d, > '-write_flag' => 1); > > # Make the index > my $numFiles = $indexSW->make_index(@DBList); > > # Check how many databases have been indexed > if ($numFiles == 1) { > > # There has been not exist error. > print "\nThe creation of GenBank index has been executed > successfully\n"; > exit 0; > > > } else { > > # There has been exist an process error > print "\nThere was a problem while the creation of GenBank index was > running\n"; > exit 2; > } > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3585 bytes Desc: not available URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061115/64a3cab3/attachment-0004.bin> From cain at cshl.edu Wed Nov 15 17:45:52 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 15 Nov 2006 12:45:52 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <000001c708d2$97c9d610$15327e82@pyrimidine> References: <000001c708d2$97c9d610$15327e82@pyrimidine> Message-ID: <1163612752.2599.2.camel@localhost.localdomain> I didn't even know those files were in the repository. I suspect they are leftovers from original Bio::DB::GFF development. Given that the last time they were touched was over five years ago, and neither GBrowse nor any other GMOD project use them (that I know of), I think they can be safely removed. Scott On Wed, 2006-11-15 at 10:24 -0600, Chris Fields wrote: > > Does anyone know what purpose Bio/DB/Makefile.PL serves? If > > none, I propose removing it from CVS. > > > > Dave: Do you need anything to happen with > > doc/Deobfuscator/Makefile.PL when a user does a normal > > install of Bioperl? Or can it safely be ignored, only run > > manually by people who want to install Deobfuscator? > > The Bio/DB/Makefile.PL and MANIFEST could be GMOD- or Chado-related (they > are both related to Bio::DB::GFF). I'm not sure though; I'm cc'ing this to > Lincoln to see if they are still needed. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20061115/e5f0620c/attachment.sig> From pabignone at gmail.com Wed Nov 15 14:51:43 2006 From: pabignone at gmail.com (Paola Bignone) Date: Wed, 15 Nov 2006 14:51:43 +0000 Subject: [Bioperl-l] reverse complement - and features Message-ID: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Hi all, do you know of an easy way to reverse complement the sequence of an embl entry and the features associated with that sequence. I'm looking at genomic syntenic regions, and in some organisms the gene is in the plus strand while in others is in the minus. Thanks in advance, PAB From cjfields at uiuc.edu Wed Nov 15 19:16:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:16:34 -0600 Subject: [Bioperl-l] Fwd: Error while indexing whole genbank In-Reply-To: <68874599fabff74a65fcc62568022288@cnio.es> References: <68874599fabff74a65fcc62568022288@cnio.es> Message-ID: <E99B3889-1800-4A69-9F40-FEED774FD653@uiuc.edu> On Nov 15, 2006, at 11:43 AM, guillermo wrote: > Hello, > > I just indexed BCT without problems and now I am going to do it in > parts, different indexes for each one, for PLN, PRI, ROD, etc. > Anyways, I??l try to do it for the whole genbank and if it works I > ?ll let you know. > > Thanks for the support, > Guille My guess is that the full genbank file was way too large, so breaking them up by division is probably the way to go. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Nov 15 19:18:18 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:18:18 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> <455B5954.1080209@sendu.me.uk> Message-ID: <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> On Nov 15, 2006, at 12:15 PM, Sendu Bala wrote: > ... > I think the compromise isn't worth it. The old Makefile.PL is just too > inadequate and I don't want to support it. Build.pl is simply far too > superior and I really want all users to be using it. > > I've now made the changeover in HEAD for core only (so far). > > Can people please try it out, especially wrt to installation in > default > and user-specified locations? > > First, clean out your system of the old Makefile.PL stuff: > perl Makefile.PL > make clean > rm Makefile.PL Makefile.old > cvs update -d -P > > Now try out the new Build.PL: > perl Build.PL > ./Build test > ./Build install > > Try out other things: > http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm > > You'll notice you don't have a Makefile.PL anymore. Distributions will > include one, and as a cvs user you can generate one by: > ./Build manifest > ./Build distmeta > > Now you can try out the things you used to be able to do: > make test > make install > > > Please let me know how you get on, > Sendu. Will do. We'll need to change all docs in CVS/wiki to conform with the new install routine. You'll probably want to post another interim RC before a final release just to make sure any residual bugs are worked out, unless you are just doing this in CVS HEAD. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 19:22:08 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:22:08 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> References: <4554514D.2020001@sendu.me.uk> <72ADB20A-22C4-4452-829F-614D1060AC1C@uiuc.edu> <4554A5D8.8000700@bms.com> <BC70790C-0A9C-4408-8F24-68D43E600F1C@uiuc.edu> <455B5954.1080209@sendu.me.uk> <C506A6FD-AD93-47D8-B1C4-413E81D497E2@uiuc.edu> Message-ID: <455B68E0.9090308@sendu.me.uk> Chris Fields wrote: > Will do. We'll need to change all docs in CVS/wiki to conform with the > new install routine. You'll probably want to post another interim RC > before a final release just to make sure any residual bugs are worked > out, unless you are just doing this in CVS HEAD. There needs to be another RC for 1.5.2 for the remaining run package problems, so what I'll do is wait a little while longer for Build.PL feedback and when all seems well it'll go into 1.5.2 branch and become part of RC4. From bix at sendu.me.uk Wed Nov 15 19:33:33 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:33:33 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <OFAAF39FAB.9EB9DA23-ON85257227.00675002-85257227.00676C9E@gsk.com> References: <OFAAF39FAB.9EB9DA23-ON85257227.00675002-85257227.00676C9E@gsk.com> Message-ID: <455B6B8D.30508@sendu.me.uk> Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: > What actual needs prompted the change from ExtUtils::MakeMaker to > Module::Build? For the old Makefile.PL: At the time I started, script installation was broken. Documentation installation hasn't worked in a very long time. Handling of true requirements and optional pre-requisites is completely inadequate. It can't generate a suitable META.yml, and leaves the package non-ideal for distribution on CPAN. It was also a nightmare keeping the Makefile.PL scripts in each cvs module (live, run, db, network) in sync with each other. Now they can have simple module-specific Build.PL scripts, with all the advanced functionality in a rarely-updated and unchanged-between-modules ModuleBuildBioperl.pm. > It seems that the switch was made without a complete understanding of > all the bits and bobs in the existing Makefile.PL I hope that's not the case; I tried to understand everything. Please let me know if I've missed something. (To tidy up a question I asked about the symlink script, I've resolved that and the symlink should also work given the proviso outlined in the POD for maintenance/symlink_script.pl) > For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered > by the main Makefile.PL) such that users can choose whether to test > the install vs. a live database or not. The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such functionality. Letting the user choose to do live database tests was a function of the main Makefile.PL, which I have carried over to the new Build.PL. (And made it better in the process.) > This is an example of encapsulation: the specializied testing/install > process for a module is kept with the module, and not in the > monolithic main script. From a maintenance point of view, it seems to me to be much easier if all install-related things are in one place rather than scattered where you might miss things. > For two, it seems that the ability to install bp_*.pl scripts was > "lost" in the transition. What makes you say that? It certainly shouldn't be. What should happen is you get asked what scripts you'd like to install (the same question as before), but again its done in a much nicer way. (The major difference, I suppose, is that scripts_temp is no longer generated; prior to "./Build install" you'll find the scripts in blib/script/) > For three, there's certainly a lot more that I can't remember right > now. Please try and remember. I spent a lot of time trying to make sure that Build.PL does everything Makefile.PL did, but much much better. Thank you, Sendu. From bix at sendu.me.uk Wed Nov 15 19:09:01 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:09:01 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180CA3A.B599%bosborne11@verizon.net> References: <C180CA3A.B599%bosborne11@verizon.net> Message-ID: <455B65CD.3020400@sendu.me.uk> Brian Osborne wrote: > Sendu, > > 177 ~/bioperl-live>./Build test > scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Can't copy('scripts/utilities/bp_sreformat.PLS', > 'blib/script/bp_sreformat.PLS'): Permission denied at > /Library/Perl/5.8.6/Module/Build/Base.pm line 3977. That's an odd one. Did you first start out with a clean bioperl-live (ie. one without a blib directory made by something else)? Is it consistent? If you run ./Build test again, does it keep happening? Does blib/script/bp_sreformat.PLS exist and what are its permissions? Did it manage to put anything at all in blib? Is ~/bioperl-live writable? From bix at sendu.me.uk Wed Nov 15 19:09:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 19:09:41 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <455B65F5.1030207@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > > Which is incorrect since there no "modules indicated above". Thanks, I'll look into it. Just to confirm, do you suppose that you have all pre-reqs installed? From cjfields at uiuc.edu Wed Nov 15 19:36:11 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 13:36:11 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <0FCFCA18-8FDC-4463-BF3B-1586145743CE@uiuc.edu> On Nov 15, 2006, at 12:33 PM, Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this > installation > > > Which is incorrect since there no "modules indicated above". > > > Brian O. > > > On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > >> Please let me know how you get on, Same here (Mac OS X). All tests pass, though (setting BIOPERLDEBUG=1): All tests successful, 6 subtests skipped. Files=236, Tests=12817, 398 wallclock secs (86.03 cusr + 14.12 csys = 100.15 CPU) I'll give WinXP a test to see how it fares. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Wed Nov 15 16:44:19 2006 From: jason at bioperl.org (Jason Stajich) Date: Wed, 15 Nov 2006 08:44:19 -0800 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B33C1.1010800@sendu.me.uk> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> Message-ID: <1965DDC8-DC2E-4895-A6C9-BD7A15FACDF1@bioperl.org> On Nov 15, 2006, at 7:35 AM, Sendu Bala wrote: > Does anyone know what purpose Bio/DB/Makefile.PL serves? If none, I > propose removing it from CVS. this was from when Lincoln imported Bio::DB::GFF into Bioperl from a separate code base. I don't know that it serves any purpose but I would get an okay from Lincoln first. > > Dave: Do you need anything to happen with doc/Deobfuscator/Makefile.PL > when a user does a normal install of Bioperl? Or can it safely be > ignored, only run manually by people who want to install Deobfuscator? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From bosborne11 at verizon.net Wed Nov 15 18:44:26 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 13:44:26 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B5954.1080209@sendu.me.uk> Message-ID: <C180CA3A.B599%bosborne11@verizon.net> Sendu, 177 ~/bioperl-live>./Build test scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Can't copy('scripts/utilities/bp_sreformat.PLS', 'blib/script/bp_sreformat.PLS'): Permission denied at /Library/Perl/5.8.6/Module/Build/Base.pm line 3977. Brian O. On 11/15/06 1:15 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Please let me know how you get on, From bix at sendu.me.uk Wed Nov 15 20:20:26 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 20:20:26 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <C180C792.B596%bosborne11@verizon.net> References: <C180C792.B596%bosborne11@verizon.net> Message-ID: <455B768A.8060009@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I see: > > 175 ~/bioperl-live>perl Build.PL > Checking prerequisites... > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > > Which is incorrect since there no "modules indicated above". Should be fixed now. From bix at sendu.me.uk Wed Nov 15 20:23:22 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 20:23:22 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C180E071.B5B0%bosborne11@verizon.net> References: <C180E071.B5B0%bosborne11@verizon.net> Message-ID: <455B773A.5080608@sendu.me.uk> Brian Osborne wrote: > Sendu, > > I just looked at the most recent bioperl-db and bioperl-run, I don't see any > Build.pl there. Are you suggesting that the Bioperl core build should be > mediated by Build.pl yet all other packages are built by some Makefile.PL? No, once it seems like Build.PL is ok in core, I'll convert db, run and network over to it as well. From bosborne11 at verizon.net Wed Nov 15 19:24:12 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 14:24:12 -0500 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B65F5.1030207@sendu.me.uk> Message-ID: <C180D38C.B5A4%bosborne11@verizon.net> Sendu, According to my install of 1.5.2 RC3 I have all of the dependencies installed: *** Optional dependencies section *** All dependencies are installed So that line "ERRORS/WARNINGS FOUND IN PREREQUISITES.." shouldn't appear. Brian O. On 11/15/06 2:09 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Brian Osborne wrote: >> Sendu, >> >> I see: >> >> 175 ~/bioperl-live>perl Build.PL >> Checking prerequisites... >> >> ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the >> versions >> of the modules indicated above before proceeding with this installation >> >> >> Which is incorrect since there no "modules indicated above". > > Thanks, I'll look into it. Just to confirm, do you suppose that you have > all pre-reqs installed? From cjfields at uiuc.edu Wed Nov 15 20:52:23 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 14:52:23 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B68E0.9090308@sendu.me.uk> Message-ID: <001601c708f7$f441dd50$15327e82@pyrimidine> > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Sendu Bala > Sent: Wednesday, November 15, 2006 1:22 PM > To: bioperl-l > Subject: Re: [Bioperl-l] No more Makefile.PL (MakeMaker -> > Module::Build) > > Chris Fields wrote: > > Will do. We'll need to change all docs in CVS/wiki to conform with > > the new install routine. You'll probably want to post > another interim > > RC before a final release just to make sure any residual bugs are > > worked out, unless you are just doing this in CVS HEAD. > > There needs to be another RC for 1.5.2 for the remaining run > package problems, so what I'll do is wait a little while > longer for Build.PL feedback and when all seems well it'll go > into 1.5.2 branch and become part of RC4. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l All tests pass for WinXP. If anyone wants to install from CVS using WinXP we'll need to get them to install Module::Build, as it doesn't come standard with ActivePerl (although a PPM is available). I'm guessing make/nmake is still required, though not explicitly. One oddity I noticed is if you use: perl Build.PL Build On Mac it manifies the POD; on WinXP it manify's and HTMLifies the POD. No idea why there is a difference between the two. I would suggest that we make this optional, though; not everybody wants the HTML/man pages. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 21:10:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 21:10:27 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <001601c708f7$f441dd50$15327e82@pyrimidine> References: <001601c708f7$f441dd50$15327e82@pyrimidine> Message-ID: <455B8243.4080809@sendu.me.uk> Chris Fields wrote: > All tests pass for WinXP. If anyone wants to install from CVS using > WinXP we'll need to get them to install Module::Build, as it doesn't > come standard with ActivePerl (although a PPM is available). I'm > guessing make/nmake is still required, though not explicitly. I think one of the benefits of Module::Build is that it is more cross-platform, and doesn't rely on a make-like thing. If you tried to install without Module::Build on WinXP, did you get some kind of meaningful error message? > One oddity I noticed is if you use: > > perl Build.PL Build > > On Mac it manifies the POD; on WinXP it manify's and HTMLifies the > POD. Nothing to do with me. I guess WinXP people like HTML docs :) > I would suggest that we make this optional, though; not everybody > wants the HTML/man pages. I disagree with making it optional, default off. I've never been aware of having the option to not install man pages for things that had man pages to install. It just happens and I'm glad of it. Its telling that there doesn't seem to be command line arg to turn doc installation off in Module::Build. Its a new functionality I'd have to add, I think. Is there actually any significant value in not installing docs? From bosborne11 at verizon.net Wed Nov 15 20:19:13 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 15:19:13 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <C180E071.B5B0%bosborne11@verizon.net> Sendu, I just looked at the most recent bioperl-db and bioperl-run, I don't see any Build.pl there. Are you suggesting that the Bioperl core build should be mediated by Build.pl yet all other packages are built by some Makefile.PL? Brian O. On 11/15/06 2:33 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: >> What actual needs prompted the change from ExtUtils::MakeMaker to >> Module::Build? > > For the old Makefile.PL: > At the time I started, script installation was broken. Documentation > installation hasn't worked in a very long time. Handling of true > requirements and optional pre-requisites is completely inadequate. It > can't generate a suitable META.yml, and leaves the package non-ideal for > distribution on CPAN. > > It was also a nightmare keeping the Makefile.PL scripts in each cvs > module (live, run, db, network) in sync with each other. Now they can > have simple module-specific Build.PL scripts, with all the advanced > functionality in a rarely-updated and unchanged-between-modules > ModuleBuildBioperl.pm. > > >> It seems that the switch was made without a complete understanding of >> all the bits and bobs in the existing Makefile.PL > > I hope that's not the case; I tried to understand everything. Please let > me know if I've missed something. (To tidy up a question I asked about > the symlink script, I've resolved that and the symlink should also work > given the proviso outlined in the POD for maintenance/symlink_script.pl) > > >> For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered >> by the main Makefile.PL) such that users can choose whether to test >> the install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such > functionality. Letting the user choose to do live database tests was a > function of the main Makefile.PL, which I have carried over to the new > Build.PL. (And made it better in the process.) > > >> This is an example of encapsulation: the specializied testing/install >> process for a module is kept with the module, and not in the >> monolithic main script. > > From a maintenance point of view, it seems to me to be much easier if > all install-related things are in one place rather than scattered where > you might miss things. > > >> For two, it seems that the ability to install bp_*.pl scripts was >> "lost" in the transition. > > What makes you say that? It certainly shouldn't be. What should happen > is you get asked what scripts you'd like to install (the same question > as before), but again its done in a much nicer way. > > (The major difference, I suppose, is that scripts_temp is no longer > generated; prior to "./Build install" you'll find the scripts in > blib/script/) > > >> For three, there's certainly a lot more that I can't remember right >> now. > > Please try and remember. I spent a lot of time trying to make sure that > Build.PL does everything Makefile.PL did, but much much better. > > > Thank you, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From aaron.j.mackey at gsk.com Wed Nov 15 18:29:30 2006 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Wed, 15 Nov 2006 13:29:30 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" Message-ID: <OFE989A597.3219BF40-ON85257227.0064E293-85257227.00659451@gsk.com> What actual needs prompted the change from ExtUtils::MakeMaker to Module::Build? It seems that the switch was made without a complete understanding of all the bits and bobs in the existing Makefile.PL For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered by the main Makefile.PL) such that users can choose whether to test the install vs. a live database or not. This is an example of encapsulation: the specializied testing/install process for a module is kept with the module, and not in the monolithic main script. For two, it seems that the ability to install bp_*.pl scripts was "lost" in the transition. For three, there's certainly a lot more that I can't remember right now. I know Module::Build is shiny and new and preferred for startup development projects, but that cruddy old Makefile.PL still works, and does a number of clever things that do have reasons for existence, even if the collective wit of the mailing list can't remember all of them right away. -Aaron -- Aaron J. Mackey, Ph.D. Principal Scientist Bioinformatics Discovery & Analysis, Upper Providence GlaxoSmithKline 1250 South Collegeville Road, UP1345 P.O. Box 5089 Collegeville, PA 19426-0989 phone: 610-917-5761/8-282-5761 fax: 610-917-7901 email: Aaron.J.Mackey at gsk.com From bix at sendu.me.uk Wed Nov 15 21:28:30 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 21:28:30 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C180E8B3.B5B6%bosborne11@verizon.net> References: <C180E8B3.B5B6%bosborne11@verizon.net> Message-ID: <455B867E.8010001@sendu.me.uk> Brian Osborne wrote: > Sendu, > > One problem here, as I see it, is the fact that this change has been > introduced just days before the intended release. My intent is to go to RC4 instead, which pushes release a week or two away. God knows I wanted to release over a month ago, but I'm a perfectionist. > http://www.bioperl.org/wiki/Release_1.5.2 > > You won't find any mention of changing the build there, nor of Build.pl, or > Module::Build. This page is a nice example of "best practice", where > everything about the release is lined up and laid out, and making a big > change at the last minute is not best practice. Now, has Bioperl always made > a big deal out of best practice? No, but that's what's been nice about this > particular release so far, an emphasis on doing things correctly. This is assuredly all valid. But I feel this is a case of a necessary last minute addition. Necessary because I don't feel the old Makefile.PL is up to the job. Its merely unfortunate that I only discovered this so late into the RC cycle. Evidently I and all the other testers don't test the installation side of things, only the test scripts in t/. > Also, I understand that you think that your approach is better but such a > central change can't be adopted without discussion and some semblance of > consensus. So far I'm not getting any sense that anyone is agreeing with the > change but I am sensing discomfort with the idea, or resignation. I asked for comments and discussions 5 days ago. The only responses were positive or neutral (with reservations regarding putting it into 1.5.2, but not for the idea itself). If you don't press on and make things happen after positive feedback, nothing will ever get done at all. So to clarify, is anyone actually uncomfortable or 'resigned' to the idea? Does anyone feel strongly in favour of keeping Makefile.PL? > I have no strong opinion one way or another, Makefile or Build, but I do not > want to see significant changes at the last minute and I do not want > significant changes coming unilaterally. I agree. But again, I'm even less happy with the idea of releasing something that I know is inadequate simply because I discovered that too late. From cjfields at uiuc.edu Wed Nov 15 22:33:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 16:33:26 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <001901c70906$1441aa50$15327e82@pyrimidine> > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: .... > > For one, the Bio::DB::GFF Makefile.PL is independent (yet > triggered by > > the main Makefile.PL) such that users can choose whether to > test the > > install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves > no such functionality. Letting the user choose to do live > database tests was a function of the main Makefile.PL, which > I have carried over to the new Build.PL. (And made it better > in the process.) Scott Cain also indicated the Bio/DB Makefile.PL and MANIFEST files were not used anymore. ... > > For three, there's certainly a lot more that I can't remember right > > now. > > Please try and remember. I spent a lot of time trying to make > sure that Build.PL does everything Makefile.PL did, but much > much better. > > > Thank you, > Sendu. We can always reinstate the Makefile.PL if things blow up; I don't think they will, but that's what CVS is good for. I haven't had any problems on WinXP or Mac OS X yet beyond the pre-req error message Brian pointed out (and scripts seem to install fine on both OS's). Personally, I would have liked to wait until after the 1.5.2 final release to avoid any confusion and documentation changes, but that's not my call. We do need to let Scott and Lincoln in on these changes (they only know about the removal of the Bio/DB Makefile.PL). I think various install scripts look for a Makefile.PL, so if it isn't there things will tank on their end. We also need to post this everywhere possible in very big neon-colored letters (with fireworks and so on), since most users are used to 'perl Makefile.PL; make; make install'. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From pabignone at gmail.com Wed Nov 15 14:51:43 2006 From: pabignone at gmail.com (Paola Bignone) Date: Wed, 15 Nov 2006 14:51:43 +0000 Subject: [Bioperl-l] reverse complement - and features Message-ID: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Hi all, do you know of an easy way to reverse complement the sequence of an embl entry and the features associated with that sequence. I'm looking at genomic syntenic regions, and in some organisms the gene is in the plus strand while in others is in the minus. Thanks in advance, PAB From bix at sendu.me.uk Wed Nov 15 23:08:00 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:08:00 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c70906$1441aa50$15327e82@pyrimidine> References: <001901c70906$1441aa50$15327e82@pyrimidine> Message-ID: <455B9DD0.5000409@sendu.me.uk> Chris Fields wrote: > > We do need to let Scott and Lincoln in on these changes (they only know > about the removal of the Bio/DB Makefile.PL). I think various install > scripts look for a Makefile.PL, so if it isn't there things will tank on > their end. We also need to post this everywhere possible in very big > neon-colored letters (with fireworks and so on), since most users are used > to 'perl Makefile.PL; make; make install'. It doesn't need to be neon because most users will still be able to do exactly that; Makefile.PL will be part of the distributions (having been generated by Build.PL). For most people, there's not going to be any significant difference with this change. It'll be more like a behind-the-scenes thing. From lincoln.stein at gmail.com Wed Nov 15 22:43:21 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 15 Nov 2006 17:43:21 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B867E.8010001@sendu.me.uk> References: <C180E8B3.B5B6%bosborne11@verizon.net> <455B867E.8010001@sendu.me.uk> Message-ID: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> > > This is assuredly all valid. But I feel this is a case of a necessary > last minute addition. Necessary because I don't feel the old Makefile.PL > is up to the job. Its merely unfortunate that I only discovered this so > late into the RC cycle. Evidently I and all the other testers don't test > the installation side of things, only the test scripts in t/ > I tested script installation last week and it was all fine as far as I could tell. Are there any details about how installation was failing? Lincoln > Also, I understand that you think that your approach is better but such a > > central change can't be adopted without discussion and some semblance of > > consensus. So far I'm not getting any sense that anyone is agreeing with > the > > change but I am sensing discomfort with the idea, or resignation. > > I asked for comments and discussions 5 days ago. The only responses were > positive or neutral (with reservations regarding putting it into 1.5.2, > but not for the idea itself). If you don't press on and make things > happen after positive feedback, nothing will ever get done at all. Sorry, but I didn't see the discussion. So to clarify, is anyone actually uncomfortable or 'resigned' to the > idea? Does anyone feel strongly in favour of keeping Makefile.PL? I'm sorry we have to push the release back. I was unaware that Makefile.PLwas broken -- my preference would have been to fix it rather than to rewrite things from scratch. Lincoln > I have no strong opinion one way or another, Makefile or Build, but I do > not > > want to see significant changes at the last minute and I do not want > > significant changes coming unilaterally. > > I agree. But again, I'm even less happy with the idea of releasing > something that I know is inadequate simply because I discovered that too > late. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Wed Nov 15 22:31:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 16:31:56 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B8243.4080809@sendu.me.uk> Message-ID: <001801c70905$dbdd7a40$15327e82@pyrimidine> > Chris Fields wrote: > > All tests pass for WinXP. If anyone wants to install from > CVS using > > WinXP we'll need to get them to install Module::Build, as > it doesn't > > come standard with ActivePerl (although a PPM is available). I'm > > guessing make/nmake is still required, though not explicitly. > > I think one of the benefits of Module::Build is that it is > more cross-platform, and doesn't rely on a make-like thing. > > If you tried to install without Module::Build on WinXP, did > you get some kind of meaningful error message? Yes: C:\Perl\src\bioperl\core>perl Build.PL Base class package "Module::Build" is empty. (Perhaps you need to 'use' the module which defines that package first.) at ModuleBuildBioperl.pm line 12 BEGIN failed--compilation aborted at ModuleBuildBioperl.pm line 12. Compilation failed in require at Build.PL line 16. BEGIN failed--compilation aborted at Build.PL line 16. Which clued me in immediately. > > One oddity I noticed is if you use: > > > > perl Build.PL Build > > > > On Mac it manifies the POD; on WinXP it manify's and HTMLifies the > > POD. > > Nothing to do with me. I guess WinXP people like HTML docs :) > > > > I would suggest that we make this optional, though; not everybody > > wants the HTML/man pages. > > I disagree with making it optional, default off. I've never > been aware of having the option to not install man pages for > things that had man pages to install. It just happens and I'm > glad of it. > > Its telling that there doesn't seem to be command line arg to > turn doc installation off in Module::Build. Its a new > functionality I'd have to add, I think. Is there actually any > significant value in not installing docs? HTML docs are made by PPM upon module installation, so there is no need for making HTML at least on WinXP (and the conversion almost triples the time for the Build step). However, oddly, using 'Build test' only manifies the docs on WinXP (using 'Build' does both man and HTML). I have a feeling we will run into this very rarely (the average WinXP user will install using PPM), so it's not an immediate problem. I would like to hear what Mauricio finds on FreeBSD and see how other OS's fare. I see that there is a PPMMaker module with Module::Build, so we'll have to look into that for WinXP PPMs.. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 15 23:19:47 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:19:47 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> References: <C180E8B3.B5B6%bosborne11@verizon.net> <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> Message-ID: <455BA093.8040603@sendu.me.uk> Lincoln Stein wrote: > Sendu Bala wrote: > This is assuredly all valid. But I feel this is a case of a necessary > last minute addition. Necessary because I don't feel the old Makefile.PL > is up to the job. Its merely unfortunate that I only discovered this so > late into the RC cycle. Evidently I and all the other testers don't test > the installation side of things, only the test scripts in t/ > > I tested script installation last week and it was all fine as far as I > could tell. Are there any details about how installation was failing? Maybe this aspect got broken since after you tested (I don't think so though, judging by the fix), but scripts only got put in scripts_temp and nowhere else. The major prompt for the change was needing a complete META.yml for CPAN... > So to clarify, is anyone actually uncomfortable or 'resigned' to the > idea? Does anyone feel strongly in favour of keeping Makefile.PL? > > I'm sorry we have to push the release back. I was unaware that > Makefile.PL was broken -- my preference would have been to fix it rather > than to rewrite things from scratch. ... I'd have had to do far more rewriting things from scratch to get a complete META.yml out of Makefile.PL. I didn't want to reinvent the wheel, and Module::Build has lots of other benefits as well. I'd already done major adjustments to Makefile.PL previously; the move to Build.PL can be seen as just one more major behind-the-scenes adjustment, since Makefile.PL will still exist in distributions (having been generated by Build.PL) and people can still install the same way they have done in the past. The only real change for most users is that they now need Module::Build installed. From bix at sendu.me.uk Wed Nov 15 23:57:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:57:14 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810D8A.B5D0%bosborne11@verizon.net> References: <C1810D8A.B5D0%bosborne11@verizon.net> Message-ID: <455BA95A.5040404@sendu.me.uk> Brian Osborne wrote: > Sendu, > > This is not right. I just removed all the build stuff, Makefile* and Build*, > and did an update. There's no Makefile.PL, it's not part of the > distribution, there is Build.PL. As I mentioned in the other thread, Makefile.PL isn't in CVS, but it will be generated and included in distributions (ie. in .tar.gz file that you download from the website or via CPAN). As a CVS user you can generate one for yourself by: perl Build.PL ./Build manifest ./Build distmeta You should now have Makefile.PL on which you can do the usual stuff: perl Makefile.PL make make test make install From bosborne11 at verizon.net Wed Nov 15 20:54:27 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 15:54:27 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B6B8D.30508@sendu.me.uk> Message-ID: <C180E8B3.B5B6%bosborne11@verizon.net> Sendu, One problem here, as I see it, is the fact that this change has been introduced just days before the intended release. Take a look at the page that's supposed to describe 1.5.2 and associated work: http://www.bioperl.org/wiki/Release_1.5.2 You won't find any mention of changing the build there, nor of Build.pl, or Module::Build. This page is a nice example of "best practice", where everything about the release is lined up and laid out, and making a big change at the last minute is not best practice. Now, has Bioperl always made a big deal out of best practice? No, but that's what's been nice about this particular release so far, an emphasis on doing things correctly. That, and having enough people to do the work! Also, I understand that you think that your approach is better but such a central change can't be adopted without discussion and some semblance of consensus. So far I'm not getting any sense that anyone is agreeing with the change but I am sensing discomfort with the idea, or resignation. I have no strong opinion one way or another, Makefile or Build, but I do not want to see significant changes at the last minute and I do not want significant changes coming unilaterally. Brian O. On 11/15/06 2:33 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Aaron J Mackey/PharmRD/GSK wrote on 11/15/2006 01:29:30 PM: >> What actual needs prompted the change from ExtUtils::MakeMaker to >> Module::Build? > > For the old Makefile.PL: > At the time I started, script installation was broken. Documentation > installation hasn't worked in a very long time. Handling of true > requirements and optional pre-requisites is completely inadequate. It > can't generate a suitable META.yml, and leaves the package non-ideal for > distribution on CPAN. > > It was also a nightmare keeping the Makefile.PL scripts in each cvs > module (live, run, db, network) in sync with each other. Now they can > have simple module-specific Build.PL scripts, with all the advanced > functionality in a rarely-updated and unchanged-between-modules > ModuleBuildBioperl.pm. > > >> It seems that the switch was made without a complete understanding of >> all the bits and bobs in the existing Makefile.PL > > I hope that's not the case; I tried to understand everything. Please let > me know if I've missed something. (To tidy up a question I asked about > the symlink script, I've resolved that and the symlink should also work > given the proviso outlined in the POD for maintenance/symlink_script.pl) > > >> For one, the Bio::DB::GFF Makefile.PL is independent (yet triggered >> by the main Makefile.PL) such that users can choose whether to test >> the install vs. a live database or not. > > The Makefile.PL in Bio/DB? As far as I can tell, it achieves no such > functionality. Letting the user choose to do live database tests was a > function of the main Makefile.PL, which I have carried over to the new > Build.PL. (And made it better in the process.) > > >> This is an example of encapsulation: the specializied testing/install >> process for a module is kept with the module, and not in the >> monolithic main script. > > From a maintenance point of view, it seems to me to be much easier if > all install-related things are in one place rather than scattered where > you might miss things. > > >> For two, it seems that the ability to install bp_*.pl scripts was >> "lost" in the transition. > > What makes you say that? It certainly shouldn't be. What should happen > is you get asked what scripts you'd like to install (the same question > as before), but again its done in a much nicer way. > > (The major difference, I suppose, is that scripts_temp is no longer > generated; prior to "./Build install" you'll find the scripts in > blib/script/) > > >> For three, there's certainly a lot more that I can't remember right >> now. > > Please try and remember. I spent a lot of time trying to make sure that > Build.PL does everything Makefile.PL did, but much much better. > > > Thank you, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Wed Nov 15 23:59:19 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 15 Nov 2006 23:59:19 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810E20.B5D2%bosborne11@verizon.net> References: <C1810E20.B5D2%bosborne11@verizon.net> Message-ID: <455BA9D7.6020906@sendu.me.uk> Brian Osborne wrote: > Lincoln, > > All I know was the scripts weren't being installed, I fixed this by adding > "use IO::File" to Makefile.PL. Sendu mentioned a problem with documentation, > I don't know what he meant by this. 'man' docs weren't being generated/installed apparently due to some kind of issue with command line length. That's been a long-standing issue. From cjfields at uiuc.edu Thu Nov 16 00:01:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 18:01:57 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1810D8A.B5D0%bosborne11@verizon.net> Message-ID: <001d01c70912$723c8a60$15327e82@pyrimidine> Brian, I think he means the actual releases or the 1.5.2 branch, not CVS. Sendu, I am seeing a general consensus towards not using Module::Build just now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar and I also had stated previously that this should probably wait until after 1.5.2 (which you seemed to agree with). I think we are all for the idea of moving forward, but it's a lot to impose just prior to a release (not to mention Thanksgiving here!). I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we should stick with that for now (i.e. not change over to Module::Build on the 1.5.2 branch). The install script fix that Brian committed to Makefile.PL in CVS HEAD prior to removal could be merged to branch-1.5.2. We could leave the Module::Build stuff in CVS for the next release to work out the bugs. I'm not sure whether we can have both Build.PL and Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl Build.PL' just overwrite the old Makefile.PL anyway? chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign > -----Original Message----- > From: Brian Osborne [mailto:bosborne11 at verizon.net] > Sent: Wednesday, November 15, 2006 5:32 PM > To: Sendu Bala; Chris Fields > Cc: aaron.j.mackey at gsk.com; bioperl-l > Subject: Re: [Bioperl-l] "progress": useful changes vs. > "shiny new thingie" > > Sendu, > > This is not right. I just removed all the build stuff, > Makefile* and Build*, and did an update. There's no > Makefile.PL, it's not part of the distribution, there is Build.PL. > > Brian O. > > > On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > > > exactly that; Makefile.PL will be part of the distributions (having > > been generated by Build.PL). > > From bix at sendu.me.uk Thu Nov 16 00:27:31 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 00:27:31 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001d01c70912$723c8a60$15327e82@pyrimidine> References: <001d01c70912$723c8a60$15327e82@pyrimidine> Message-ID: <455BB073.9040205@sendu.me.uk> Chris Fields wrote: > Brian, > > I think he means the actual releases or the 1.5.2 branch, not CVS. > > Sendu, I am seeing a general consensus towards not using Module::Build just > now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar and I also > had stated previously that this should probably wait until after 1.5.2 > (which you seemed to agree with). I think we are all for the idea of moving > forward, but it's a lot to impose just prior to a release (not to mention > Thanksgiving here!). > > I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we > should stick with that for now (i.e. not change over to Module::Build on the > 1.5.2 branch). The install script fix that Brian committed to Makefile.PL > in CVS HEAD prior to removal could be merged to branch-1.5.2. Its certainly possible to stay with Makefile.PL on the 1.5.2 branch. I /think/ that if I took a META.yml generated from HEAD's Build.PL and added it to the branch that should solve the CPAN issue at least. I would just want clarification that the consensus really is to stay with Makefile.PL for 1.5.2. The primary argument seems to be to not have anything too new and untested in the branch, but Makefile.PL itself has lots of new additions. My Makefile.PL improvements and the change to Build.PL have all been in the name of making 1.5.2 install well. The move to Build.PL was just the most appropriate way to fix some bugs and make needed changes. > We could leave the Module::Build stuff in CVS for the next release to work > out the bugs. I'm not sure whether we can have both Build.PL and > Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl Build.PL' > just overwrite the old Makefile.PL anyway? It would, but why would we want both in CVS? I'd strongly advise the cessation of development on the old Makefile.PL, and if it isn't going to be added to anymore, nor used by anyone, why keep it in CVS? It's just going to cause confusion and problems with people coming across issues in the old Makefile.PL. Wasted development time if someone tries to fix something in Makefile.PL that was already solved in Build.PL. Bizarre behaviour if you were doing something with old Makefile.PL but then managed to overwrite it with Build.PL's Makefile.PL and suddenly you're working with a whole different script. In short, not the most optimal of situations. From bosborne11 at verizon.net Wed Nov 15 23:31:38 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 18:31:38 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455B9DD0.5000409@sendu.me.uk> Message-ID: <C1810D8A.B5D0%bosborne11@verizon.net> Sendu, This is not right. I just removed all the build stuff, Makefile* and Build*, and did an update. There's no Makefile.PL, it's not part of the distribution, there is Build.PL. Brian O. On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > exactly that; Makefile.PL will be part of the distributions (having been > generated by Build.PL). From bosborne11 at verizon.net Wed Nov 15 23:34:08 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 18:34:08 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> Message-ID: <C1810E20.B5D2%bosborne11@verizon.net> Lincoln, All I know was the scripts weren't being installed, I fixed this by adding "use IO::File" to Makefile.PL. Sendu mentioned a problem with documentation, I don't know what he meant by this. Brian O. On 11/15/06 5:43 PM, "Lincoln Stein" <lincoln.stein at gmail.com> wrote: > I tested script installation last week and it was all fine as far as I could > tell. Are there any details about how installation was failing? From bosborne11 at verizon.net Thu Nov 16 01:43:32 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 20:43:32 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BA95A.5040404@sendu.me.uk> Message-ID: <C1812C74.B5E3%bosborne11@verizon.net> Sendu, If I'm understanding you correctly you're saying that someone checking out bioperl-live, HEAD, would not see a Makefile.PL if we chose to use Build.PL, yes? And there would be a Makefile.PL in the distributions, yes? Brian O. On 11/15/06 6:57 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > Brian Osborne wrote: >> Sendu, >> >> This is not right. I just removed all the build stuff, Makefile* and Build*, >> and did an update. There's no Makefile.PL, it's not part of the >> distribution, there is Build.PL. > > As I mentioned in the other thread, Makefile.PL isn't in CVS, but it > will be generated and included in distributions (ie. in .tar.gz file > that you download from the website or via CPAN). > > As a CVS user you can generate one for yourself by: > perl Build.PL > ./Build manifest > ./Build distmeta > > You should now have Makefile.PL on which you can do the usual stuff: > perl Makefile.PL > make > make test > make install From stefan.kirov at bms.com Thu Nov 16 00:34:02 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Wed, 15 Nov 2006 19:34:02 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" Message-ID: <db32bddda3.ddda3db32b@bms.com> Maybe I will just reiterate myself. I think the idea is good, but timing is bad. Sendu, from purely socialogical point of view Makefile.PL should be there. I bet that significant percent of the users would do cvs checkout, type perl Makefile.PL and start cursing. Perhaps you would not do this, but many of us do not read most of the docs, unless nothing else works. As a result you would have confusion and frustration. Many people would google 'bioperl install' and come up with old docs and wonder why it does not work. In a perfect world it would work. Just my thoughts. Stefan ----- Original Message ----- From: Chris Fields <cjfields at uiuc.edu> Date: Wednesday, November 15, 2006 7:01 pm Subject: Re: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" > Brian, > > I think he means the actual releases or the 1.5.2 branch, not CVS. > > Sendu, I am seeing a general consensus towards not using > Module::Build just > now. Lincoln, Aaron, and Brian all seem to want to wait; Hilmar > and I also > had stated previously that this should probably wait until after 1.5.2 > (which you seemed to agree with). I think we are all for the idea > of moving > forward, but it's a lot to impose just prior to a release (not to > mentionThanksgiving here!). > > I think the old Makefile.PL is still in the 1.5.2 branch. So maybe we > should stick with that for now (i.e. not change over to > Module::Build on the > 1.5.2 branch). The install script fix that Brian committed to > Makefile.PLin CVS HEAD prior to removal could be merged to branch- > 1.5.2. > > We could leave the Module::Build stuff in CVS for the next release > to work > out the bugs. I'm not sure whether we can have both Build.PL and > Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl > Build.PL'just overwrite the old Makefile.PL anyway? > > chris > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > -----Original Message----- > > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > Sent: Wednesday, November 15, 2006 5:32 PM > > To: Sendu Bala; Chris Fields > > Cc: aaron.j.mackey at gsk.com; bioperl-l > > Subject: Re: [Bioperl-l] "progress": useful changes vs. > > "shiny new thingie" > > > > Sendu, > > > > This is not right. I just removed all the build stuff, > > Makefile* and Build*, and did an update. There's no > > Makefile.PL, it's not part of the distribution, there is Build.PL. > > > > Brian O. > > > > > > On 11/15/06 6:08 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > > > > > exactly that; Makefile.PL will be part of the distributions > (having > > > been generated by Build.PL). > > > > > > _______________________________________________ > 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 Thu Nov 16 01:48:43 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 15 Nov 2006 20:48:43 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> Message-ID: <C1812DAB.B5E5%bosborne11@verizon.net> Sendu, That's right. Brian O. On 11/15/06 7:27 PM, "Sendu Bala" <bix at sendu.me.uk> wrote: > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. From joannec at bii.a-star.edu.sg Thu Nov 16 02:11:31 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 02:11:31 +0000 (UTC) Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations Message-ID: <loom.20061116T030106-109@post.gmane.org> Hi, I am a new user to BioPerl and am encountering some problems while parsing location statements. I have read the link http://www.bioperl.org/wiki/FAQ#How_do_I_parse_the_CDS_join_or_complement_statements_in_GenBank_or_EMBL_files_to_get_the_sub-locations.3F and tried to implement this. However I am encountering some problems. Given a testcase: CDS join(752472..752685,752752..753298,753335..754039) CDS complement(637431..639525) CDS 741745..741781 This means that my file has join, complement and simple location statements. Using Bio::Location::SplitLocationI object to get the coordinates, my output is: CDS 752472..752685,752752..753298,753335..754039 CDS CDS The complement and simple location statements were not parsed properly. Am I using the right BioPerl module to parse? Kindly assist on the appropriate steps to retrieve all 3 different location types. Thanks! Joanne From cjfields at uiuc.edu Thu Nov 16 02:33:25 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 20:33:25 -0600 Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations In-Reply-To: <loom.20061116T030106-109@post.gmane.org> References: <loom.20061116T030106-109@post.gmane.org> Message-ID: <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> On Nov 15, 2006, at 8:11 PM, Joanne Chen wrote: > Hi, > I am a new user to BioPerl and am encountering some problems while > parsing > location statements. > > I have read the link > http://www.bioperl.org/wiki/ > FAQ#How_do_I_parse_the_CDS_join_or_complement_statements_in_GenBank_or > _EMBL_files_to_get_the_sub-locations.3F > and tried to implement this. > > However I am encountering some problems. > > Given a testcase: > > CDS join(752472..752685,752752..753298,753335..754039) > > > CDS complement(637431..639525) > > > CDS 741745..741781 > > > This means that my file has join, complement and simple location > statements. > > Using Bio::Location::SplitLocationI object to get the coordinates, > my output is: > > CDS 752472..752685,752752..753298,753335..754039 > > CDS > > CDS > > > The complement and simple location statements were not parsed > properly. Am I > using the right BioPerl module to parse? Kindly assist on the > appropriate steps > to retrieve all 3 different location types. Thanks! > > > Joanne > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l If you are using the loop as shown in the FAQ: foreach my $feature ($seqobj->top_SeqFeatures){ if ( $feature->location->isa('Bio::Location::SplitLocationI') and $feature->primary_tag eq 'CDS' ) { foreach my $location ( $feature->location->sub_Location ) { print $location->start , ".." , $location->end, "\n"; } } } it will skip over simple locations, so the last two are passed over. You probably should use: foreach my $feature ($seqobj->top_SeqFeatures){ if ( $feature->primary_tag eq 'CDS' ) { foreach my $location ( $feature->location->each_Location ) { print $location->start , ".." , $location->end, "\n"; } } } Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 02:44:05 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 15 Nov 2006 20:44:05 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> Message-ID: <DEAB987E-4700-4677-979B-E5708F6905D3@uiuc.edu> On Nov 15, 2006, at 6:27 PM, Sendu Bala wrote: >> I think the old Makefile.PL is still in the 1.5.2 branch. So >> maybe we >> should stick with that for now (i.e. not change over to >> Module::Build on the >> 1.5.2 branch). The install script fix that Brian committed to >> Makefile.PL >> in CVS HEAD prior to removal could be merged to branch-1.5.2. > > Its certainly possible to stay with Makefile.PL on the 1.5.2 branch. I > /think/ that if I took a META.yml generated from HEAD's Build.PL and > added it to the branch that should solve the CPAN issue at least. > > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. The primary argument seems to be to not > have > anything too new and untested in the branch, but Makefile.PL itself > has > lots of new additions. My Makefile.PL improvements and the change to > Build.PL have all been in the name of making 1.5.2 install well. The > move to Build.PL was just the most appropriate way to fix some bugs > and > make needed changes. Right, but those changes were made w/o much discussion; what discussion there was seemed to end with the agreement this would wait until after rel. 1.5.2. I think that's the main point. That and the timing seems to be a little off for implementing this (after three RC's and just prior to a final release). Everyone seems to think that switching to Module::Build would be a good idea, but the move was made rather arbitrarily and (borrowing Brian's well-chosen word) unilaterally. And, although the Makefile.PL was a bit clunky, it works for now. >> We could leave the Module::Build stuff in CVS for the next release >> to work >> out the bugs. I'm not sure whether we can have both Build.PL and >> Makefile.PL in CVS HEAD, but I don't see why not. Wouldn't 'perl >> Build.PL' >> just overwrite the old Makefile.PL anyway? > > It would, but why would we want both in CVS? I'd strongly advise the > cessation of development on the old Makefile.PL, and if it isn't going > to be added to anymore, nor used by anyone, why keep it in CVS? It's > just going to cause confusion and problems with people coming across > issues in the old Makefile.PL. Wasted development time if someone > tries > to fix something in Makefile.PL that was already solved in Build.PL. > Bizarre behaviour if you were doing something with old Makefile.PL but > then managed to overwrite it with Build.PL's Makefile.PL and suddenly > you're working with a whole different script. > > In short, not the most optimal of situations. Stefan has hit upon the problem very succinctly; there is no Makefile.PL in CVS, so anyone checking out bioperl-live will immediately run into problems. Hence, there has to be a Makefile.PL in CVS HEAD, be it the old one or a new one, at least for the time being. And it seems many still want the old Makefile.PL for now (which is why I suggested it). If you left the old Makefile.PL in you could always add a deprecation message indicating the switch. It will at least give everybody some time to get used to using Module::Build and the new system (and hopefully dissuade them from working on it). Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From joannec at bii.a-star.edu.sg Thu Nov 16 03:17:27 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 03:17:27 +0000 (UTC) Subject: [Bioperl-l] =?utf-8?q?Parsing_the_CDS_join_or_complement_statemen?= =?utf-8?q?ts_to=09get_the_sub-locations?= References: <loom.20061116T030106-109@post.gmane.org> <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> Message-ID: <loom.20061116T041551-540@post.gmane.org> Thanks a lot for your help. It works. =) However I have a small problem. Now I would also like to determine its strand-ie. negative strand for complement and positive for all others. Is there a function to determine and print its strand OR a function to determine if it is a complement, join or simple? Joanne. From pmiguel at purdue.edu Thu Nov 16 03:53:02 2006 From: pmiguel at purdue.edu (Phillip SanMiguel) Date: Wed, 15 Nov 2006 22:53:02 -0500 Subject: [Bioperl-l] Help needed urgently In-Reply-To: <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> References: <000301c708c0$8f89bc20$4bc7580a@persistent.co.in> <B12C831C-6241-4B07-9379-CAE9DFAB8EF0@uiuc.edu> Message-ID: <455BE09E.4020408@purdue.edu> Chris Fields wrote: >> I wish to fetch consensus sequence and the names of the trace >> (chromat) >> files used in the assembly from the .ace file >> >> For this purpose, I am using Bio::Assembly::IO. But I am unable to >> find the >> appropriate methods which would enable me to fetch this information. >> >> >> >> [..base segment documentation elided...] >> >> >> How do I retrieve this information contig wise? >> >> Kindly help. >> >> Regards, >> >> Sayali D Salodkar >> > > It looks like the relevant part of the Bio::Assembly::IO::ace parser > responsible for parsing this is commented out: > > # Loading base segments definitions (Base Segment field) > # /^BS (\d+) (\d+) (\S+)/ && do { > # if (exists($self->{'contigs'}[$contig]{'reads'}{$3} > {'segments'})) { > # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . > " " . $2; > # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = > $1 . " " . $2 } > # }; > > I'm not sure why to be honest as I'm not very familiar with the > Bio::Assembly. Have you tried removing the comments to see what > happens? > > Chris, I'm pretty sure that the Base Segment tag (BS) is not the one Sayali wants. At least that is my reading of Sayali's wanting to get the consensus sequence and the traces names used in the assembly. I write this because of an email sent me by David Gordon in 2001 included here without his permission: > Phrap writes BS lines which > indicate, for each consensus position, which read phrap uses at that > position to become the consensus. These BS ("base segments") are > manipulated by Consed when there are changes to the assembly, such as > joins, tears, removing reads, or changing the consensus. Which is basically what Sayali quoted from the documentation from phrap. But it is not consistent with "trace names used in the assembly". -- Phillip From hlapp at gmx.net Thu Nov 16 05:52:23 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Nov 2006 00:52:23 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BB073.9040205@sendu.me.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> Message-ID: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > I would just want clarification that the consensus really is to stay > with Makefile.PL for 1.5.2. The primary argument seems to be to not > have > anything too new and untested in the branch, but Makefile.PL itself > has > lots of new additions. My Makefile.PL improvements and the change to > Build.PL have all been in the name of making 1.5.2 install well. The > move to Build.PL was just the most appropriate way to fix some bugs > and > make needed changes. My take on this, aside from having said before that the move to Module::Build is certainly a good one except with not-so-great timing, is that the distribution if at all possible should have a working Makefile.PL. If Build.PL can coexist that'd be great. That would give you the opportunity to have Makefile.PL print out a message right at the beginning that if the installation process messes up one should try Build.PL. This would spare you from fixing any problems in Makefile.PL that are fixed in the Build.PL approach. As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub that just prints out a message telling you to use Build.PL and does nothing else. If you check out bioperl-live from CVS you need to be prepared to having checked out the live edge of the code. Edges can be rough. The key thing is that the build process works. Finally let's not forget that this is still a developer release. That means that a) perfection isn't needed, rather shorter release cycles, and b) development implies change. So the main reason why I find the timing less than optimal is because it prolongs the time until the next release. Implementing changes like this do require a lot of energy. I very much appreciate that Sendu invested the time and energy to make it work, even though unfortunately at the last hour. Who knows who would have had the energy after the release. If Sendu hadn't put in the work now, the next release master may have been stuck with an even messier Makefile.PL system. Instead of Monday morning quarterbacking after no-one stopped him when he asked about it, we should all help him make the release - and the build change - successful now that he has done most if not all of the migration work already. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Thu Nov 16 07:47:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 07:47:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C1812C74.B5E3%bosborne11@verizon.net> References: <C1812C74.B5E3%bosborne11@verizon.net> Message-ID: <455C1790.3080408@sendu.me.uk> Brian Osborne wrote: > Sendu, > > If I'm understanding you correctly you're saying that someone checking out > bioperl-live, HEAD, would not see a Makefile.PL if we chose to use Build.PL, > yes? And there would be a Makefile.PL in the distributions, yes? Yes, that is what I had meant. Though now following Hilmar's suggestion, I might create a stub in CVS for Makefile.PL that tells you to use Build.PL. I don't think it appropriate to have a working Makefile.PL in CVS though; not the old one for reasons outlined previously, and not one generated by Build.PL, because generated files don't need version control and only confuse matters when they become controlled. Ok, so the current plan is: # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml # CVS core gets a Makefile.PL stub telling you to use Build.PL # CVS db, run, network stay with Makefile.PL until after final release of 1.5.2, then move to Build.PL with Makefile.PL stub (because they don't have a 1.5.2 branch) Is everyone happy with that, or are there further suggestions for something better? From joannec at bii.a-star.edu.sg Thu Nov 16 07:55:22 2006 From: joannec at bii.a-star.edu.sg (Joanne Chen) Date: Thu, 16 Nov 2006 07:55:22 +0000 (UTC) Subject: [Bioperl-l] =?utf-8?q?Parsing_the_CDS_join_or_complement_statemen?= =?utf-8?q?ts_to=09get_the_sub-locations?= References: <loom.20061116T030106-109@post.gmane.org> <F1FDF9E0-58EF-4E1E-AAE1-D8B1FC463514@uiuc.edu> <loom.20061116T041551-540@post.gmane.org> Message-ID: <loom.20061116T085446-347@post.gmane.org> Got the strand problem fixed. Thanks. =) From bix at sendu.me.uk Thu Nov 16 07:55:41 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 07:55:41 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C1790.3080408@sendu.me.uk> References: <C1812C74.B5E3%bosborne11@verizon.net> <455C1790.3080408@sendu.me.uk> Message-ID: <455C197D.6000107@sendu.me.uk> Sendu Bala wrote: > Brian Osborne wrote: >> Sendu, >> >> If I'm understanding you correctly you're saying that someone checking >> out >> bioperl-live, HEAD, would not see a Makefile.PL if we chose to use >> Build.PL, >> yes? And there would be a Makefile.PL in the distributions, yes? > > Yes, that is what I had meant. Though now following Hilmar's suggestion, > I might create a stub in CVS for Makefile.PL that tells you to use > Build.PL. I don't think it appropriate to have a working Makefile.PL in > CVS though; not the old one for reasons outlined previously, and not one > generated by Build.PL, because generated files don't need version > control and only confuse matters when they become controlled. > > Ok, so the current plan is: > # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml Also, # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who read the docs on the website/elsewhere (which will be updated to explain the new Build.PL system) don't get confused when that doesn't work, for wide testing, and to get people used to it for the next release. The old Makefile.PL will have 2 changes: Brians bug-fix and a little message pointing out that Build.PL is now the preferred installation system, but Makefile.PL still works. > # CVS core gets a Makefile.PL stub telling you to use Build.PL > # CVS db, run, network stay with Makefile.PL until after final release > of 1.5.2, then move to Build.PL with Makefile.PL stub (because they > don't have a 1.5.2 branch) > > Is everyone happy with that, or are there further suggestions for > something better? From rvosa at sfu.ca Thu Nov 16 07:19:43 2006 From: rvosa at sfu.ca (Rutger Vos) Date: Wed, 15 Nov 2006 23:19:43 -0800 Subject: [Bioperl-l] indexing with several processors In-Reply-To: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> References: <827cd8bf8688497da1fb2718b35cd7d0@cnio.es> Message-ID: <455C110F.4000600@sfu.ca> I notice nobody has responded yet. Without looking at the code I'm guessing here, but I would be very surprised if any part of bioperl is smart enough to be able to switch to some kind of mpi architecture, or any other clever way of parallelizing tasks on multi-processor architectures. If you can split the job up by hand and start scripts on the chunks, that might work. Good luck, Rutger guillermo wrote: > Hello, > > While using the Bio::Index::GenBank module for indexing Genbank, is > there any option to run the process with more than one processor. > > Thanks > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los > ficheros adjuntos, pueden contener informaci?n protegida para el uso > exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n > o cualquier otro tipo de transmisi?n por parte de otra persona que no > sea el destinatario. Si usted recibe por error este correo, se ruega > comunicarlo al remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any > attachments may contain confidential and privileged information for > the sole use of the designated recipient named above. Distribution, > reproduction or any other use of this transmission by any party other > than the intended recipient is prohibited. If you are not the intended > recipient please contact the sender and delete all copies. > > ------------------------------------------------------------------------ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > ------------------------------------------------------------------------ > > No virus found in this incoming message. > Checked by AVG Free Edition. > Version: 7.1.409 / Virus Database: 268.14.5/534 - Release Date: 11/14/2006 > -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Rutger A. Vos Postdoctoral research fellow University of British Columbia Personal site: http://www.sfu.ca/~rvosa CIPRES: http://www.phylo.org Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From n.haigh at sheffield.ac.uk Thu Nov 16 09:14:52 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 09:14:52 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> Message-ID: <455C2C0C.1080403@sheffield.ac.uk> Hilmar Lapp wrote: > On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > > >> I would just want clarification that the consensus really is to stay >> with Makefile.PL for 1.5.2. The primary argument seems to be to not >> have >> anything too new and untested in the branch, but Makefile.PL itself >> has >> lots of new additions. My Makefile.PL improvements and the change to >> Build.PL have all been in the name of making 1.5.2 install well. The >> move to Build.PL was just the most appropriate way to fix some bugs >> and >> make needed changes. >> > > My take on this, aside from having said before that the move to > Module::Build is certainly a good one except with not-so-great > timing, is that the distribution if at all possible should have a > working Makefile.PL. > I was in the process of writing a rather long e-mail to try to stem the tide of Sendu-bashing :-P But, this response serves as a better platform for my comments. I don't see the change to Build.PL as an issue - especially if we have another RC. I think it would be worse to introduce Build.PL in the "stable" 1.6 release than in the 1.5.x developer series. I think one good reason for using Build.PL when Sendu brought the issue up, is that it is more important as far as building a package for CPAN rather than an end user - and since Sendu is the release pumpkin he is the one with the strongest opinion for changing it now, rather than later - it would make his job much easier! I believe Sendu mentioned that a Makefile.PL would be included in the CPAN package but is not in CVS as it would be generated from Build.PL for backward compatibility - is that right Sendu? How does installing via CPAN affect this? Does it give higher priority to Build.PL over Makefile.PL and thus use Build.PL for the install? > If Build.PL can coexist that'd be great. That would give you the > opportunity to have Makefile.PL print out a message right at the > beginning that if the installation process messes up one should try > Build.PL. This would spare you from fixing any problems in > Makefile.PL that are fixed in the Build.PL approach. > Good idea, for anyone downloading the .tar.gz from CPAN if they issue "perl Makefile.PL" without knowing Build.PL was there it should hopefully work, but if not, issue a comment at the end to say try "perl Build.PL" if anything seemed to go wrong. > As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub > that just prints out a message telling you to use Build.PL and does > nothing else. If you check out bioperl-live from CVS you need to be > prepared to having checked out the live edge of the code. Edges can > be rough. The key thing is that the build process works. > I was going to suggest something like this with regard to a Makefile.PL in CVS. This would then be overwritten by the Makefile.PL produced from Build.PL by the release pumpkin when making the CPAN package. > Finally let's not forget that this is still a developer release. That > means that a) perfection isn't needed, rather shorter release cycles, > and b) development implies change. So the main reason why I find the > timing less than optimal is because it prolongs the time until the > next release. > If we go for short release cycles, and regular bug fix release, we will no longer have to say to users: "This is a known bug/issue in release x.y.z, it has been fixed in CVS HEAD so get it from there" we can roll out fixes in regular releases. This way CVS is then used solely by developers and those really wanting to live on the bleeding edge code. Therefore, it is important to get Build.PL in place to let the release cycle and CPAN packages built quickly, easily and without hassle - which I believe is the problem with Makefile.PL as it currently is. > Implementing changes like this do require a lot of energy. I very > much appreciate that Sendu invested the time and energy to make it > work, even though unfortunately at the last hour. Who knows who would > have had the energy after the release. If Sendu hadn't put in the > work now, the next release master may have been stuck with an even > messier Makefile.PL system. Instead of Monday morning quarterbacking > after no-one stopped him when he asked about it, we should all help > him make the release - and the build change - successful now that he > has done most if not all of the migration work already. > > -hilmar > Hear, hear - well done Sendu on all your hard work! Personally, I think the move to Build.PL is a good one - it may be a little late in this particular release, but I think that the problem is not that it is a late change, but that it wasn't picked up sooner. It fits well with the goal of making releases and big fix releases more regular, and if these are made available via CPAN, then the use of CVS is for developers and those wanting to live on the edge. Build.PL helps all this by making is easier and quicker to make CPAN packages. It also means we have a while before the "stable" 1.6 release to ensure it is working effectively - better than dropping it in on the 1.6 release isn't it? I think it's work the delay and an extra RC! Anyway, my 2 pence worth! Nath From n.haigh at sheffield.ac.uk Thu Nov 16 09:04:00 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 09:04:00 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> Message-ID: <455C2980.4000609@sheffield.ac.uk> Hilmar Lapp wrote: > On Nov 15, 2006, at 7:27 PM, Sendu Bala wrote: > > >> I would just want clarification that the consensus really is to stay >> with Makefile.PL for 1.5.2. The primary argument seems to be to not >> have >> anything too new and untested in the branch, but Makefile.PL itself >> has >> lots of new additions. My Makefile.PL improvements and the change to >> Build.PL have all been in the name of making 1.5.2 install well. The >> move to Build.PL was just the most appropriate way to fix some bugs >> and >> make needed changes. >> > > My take on this, aside from having said before that the move to > Module::Build is certainly a good one except with not-so-great > timing, is that the distribution if at all possible should have a > working Makefile.PL. > I was in the process of writing a rather long e-mail to try to stem the tide of Sendu-bashing :-P But, this response serves as a better platform for my comments. I don't see the change to Build.PL as an issue - especially if we have another RC. I think it would be worse to introduce Build.PL in the "stable" 1.6 release than in the 1.5.x developer series. I think one good reason for using Build.PL when Sendu brought the issue up, is that it is more important as far as building a package for CPAN rather than an end user - and since Sendu is the release pumpkin he is the one with the strongest opinion for changing it now, rather than later - it would make his job much easier! I believe Sendu mentioned that a Makefile.PL would be included in the CPAN package but is not in CVS as it would be generated from Build.PL for backward compatibility - is that right Sendu? How does installing via CPAN affect this? Does it give higher priority to Build.PL over Makefile.PL and thus use Build.PL for the install? > If Build.PL can coexist that'd be great. That would give you the > opportunity to have Makefile.PL print out a message right at the > beginning that if the installation process messes up one should try > Build.PL. This would spare you from fixing any problems in > Makefile.PL that are fixed in the Build.PL approach. > Good idea, for anyone downloading the .tar.gz from CPAN if they issue "perl Makefile.PL" without knowing Build.PL was there it should hopefully work, but if not, issue a comment at the end to say try "perl Build.PL" if anything seemed to go wrong. > As for CVS, I think Makefile.PL in CVS needs to be reduced to a stub > that just prints out a message telling you to use Build.PL and does > nothing else. If you check out bioperl-live from CVS you need to be > prepared to having checked out the live edge of the code. Edges can > be rough. The key thing is that the build process works. > I was going to suggest something like this with regard to a Makefile.PL in CVS. This would then be overwritten by the Makefile.PL produced from Build.PL by the release pumpkin when making the CPAN package. > Finally let's not forget that this is still a developer release. That > means that a) perfection isn't needed, rather shorter release cycles, > and b) development implies change. So the main reason why I find the > timing less than optimal is because it prolongs the time until the > next release. > If we go for short release cycles, and regular bug fix release, we will no longer have to say to users: "This is a known bug/issue in release x.y.z, it has been fixed in CVS HEAD so get it from there" we can roll out fixes in regular releases. This way CVS is then used solely by developers and those really wanting to live on the bleeding edge code. Therefore, it is important to get Build.PL in place to let the release cycle and CPAN packages built quickly, easily and without hassle - which I believe is the problem with Makefile.PL as it currently is. > Implementing changes like this do require a lot of energy. I very > much appreciate that Sendu invested the time and energy to make it > work, even though unfortunately at the last hour. Who knows who would > have had the energy after the release. If Sendu hadn't put in the > work now, the next release master may have been stuck with an even > messier Makefile.PL system. Instead of Monday morning quarterbacking > after no-one stopped him when he asked about it, we should all help > him make the release - and the build change - successful now that he > has done most if not all of the migration work already. > > -hilmar > Here, here - well done Sendu on all your hard work! Personally, I think the move to Build.PL is a good one - it may be a little late in this particular release, but I think that the problem is not that it is a late change, but that it wasn't picked up sooner. It fits well with the goal of making releases and big fix releases more regular, and if these are made available via CPAN, then the use of CVS is for developers and those wanting to live on the edge. Build.PL helps all this by making is easier and quicker to make CPAN packages. It also means we have a while before the "stable" 1.6 release to ensure it is working effectively - better than dropping it in on the 1.6 release isn't it? I think it's work the delay and an extra RC! Anyway, my 2 pence worth! Nath -- > A: Yes. >> Q: Are you sure? >> >>> A: Because it reverses the logical flow of conversation. >>> >>>> Q: Why is top posting frowned upon? >>>> Get Thunderbird <http://www.mozilla.org/products/thunderbird/> From bix at sendu.me.uk Thu Nov 16 09:26:45 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 09:26:45 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2C0C.1080403@sheffield.ac.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> <455C2C0C.1080403@sheffield.ac.uk> Message-ID: <455C2ED5.4060602@sendu.me.uk> Nathan S. Haigh wrote: > I believe Sendu mentioned that a Makefile.PL would be included in the > CPAN package but is not in CVS as it would be generated from > Build.PL for backward compatibility - is that right Sendu? Yes. > How does installing via CPAN affect this? Does it give higher > priority to Build.PL over Makefile.PL and thus use Build.PL for the > install? I don't know about priorities (but assume it would prefer Build.PL), but in any case, the generated Makefile.PL basically just calls Build.PL, so it makes no difference. > Build.PL helps all this by making is easier and quicker to make CPAN > packages. It also means we have a while before the "stable" 1.6 > release to ensure it is working effectively - better than dropping it > in on the 1.6 release isn't it? I think it's work the delay and an > extra RC! Yes, it surely needs to happen before 1.6. As suggested here and originally in the other thread, 1.5.2 can be the transition release with old Makefile.PL and Build.PL as well (set up to not overwrite Makefile.PL). From bix at sendu.me.uk Thu Nov 16 11:35:25 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 11:35:25 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <001801c70905$dbdd7a40$15327e82@pyrimidine> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> Message-ID: <455C4CFD.5080005@sendu.me.uk> Chris Fields wrote: > I see that there is a PPMMaker module with Module::Build, so we'll have to > look into that for WinXP PPMs.. Nathan, does: perl Build.PL ./Build ppmdist create anything useful? For me it generates a tar.gz containing blib, and a ppd file (the contents of which can be adjusted by supplying "an optional argument codebase which is used in the generated ppd file to specify the (usually relative) URL of the distribution. By default, this value is the distribution name without any path information", eg. ./Build ppmdist --codebase "MSWin32-x86-multi-thread/Bioperl....tar.gz"). Is this PPM4 format? What else needs to be done to it to make it suitable? I can easily extend the ppmdist action to do whatever you want, so let me know. From bix at sendu.me.uk Thu Nov 16 11:45:03 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 11:45:03 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC3 In-Reply-To: <45531968.6080607@sendu.me.uk> References: <45531968.6080607@sendu.me.uk> Message-ID: <455C4F3F.1090901@sendu.me.uk> Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 3 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Developers: > Once again I'm hopeful that this is the last RC. If all goes well > expect final release in about a weeks time. Please check and update > documentation. Sadly all didn't go well. Some remaining bugs are present in the Run package which are now being worked on (there was also a WinXP core bug already fixed by Chris). Expect RC4 sometime this week, which will also include a transitional Build.PL as an alternative to installing with Makefile.PL. From bikash_lohia2000 at yahoo.com Thu Nov 16 12:30:04 2006 From: bikash_lohia2000 at yahoo.com (bikash lohia) Date: Thu, 16 Nov 2006 04:30:04 -0800 (PST) Subject: [Bioperl-l] i am new to group, require a help Message-ID: <20061116123004.87840.qmail@web54213.mail.yahoo.com> hello group, I am new to this group and want a help.i have list of accesion id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to manually search gene database of NCBI for converting this accession no. of cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i want to do it through perl programming where the program directly takes the list of id ( such as AK105331,Ak070197) from notepad file and searches in gene database of ncbi. to give results in accession id starting with OS****** .i want only the accession id of corresponding Ak***** id. for example - AK070197 of nucleotide databse = Os02g0669100 of gene database. i want to convert all this AK***** ids to OS***** ids through programming in perl/bioperl as manually not possible for long list. please help. i have no idea how can the code be. with thanks in advance from Bikash --------------------------------- Sponsored Link Degrees for working adults in as fast as 1 year. Bachelors, Masters, Associates. Top schools From n.haigh at sheffield.ac.uk Thu Nov 16 12:45:14 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 12:45:14 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C4CFD.5080005@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> Message-ID: <455C5D5A.5020205@sheffield.ac.uk> Sendu Bala wrote: > Chris Fields wrote: >> I see that there is a PPMMaker module with Module::Build, so we'll >> have to >> look into that for WinXP PPMs.. > > Nathan, does: > > perl Build.PL > ./Build ppmdist > > create anything useful? For me it generates a tar.gz containing blib, > and a ppd file (the contents of which can be adjusted by supplying "an > optional argument codebase which is used in the generated ppd file to > specify the (usually relative) URL of the distribution. By default, > this value is the distribution name without any path information", eg. > ./Build ppmdist --codebase "MSWin32-x86-multi-thread/Bioperl....tar.gz"). > > Is this PPM4 format? What else needs to be done to it to make it > suitable? I can easily extend the ppmdist action to do whatever you > want, so let me know. Sorry, but i've been busy this last week etc so haven't be able to test RC3 on WinXP yet - hopefully Chris' tests have been sufficient. Essentially a PPM dist comprises of the .tar.gz file you described (of the blib dir) and then the XML file (.ppd) which describes the package and it's dependencies. The syntax of the XML has changed for PPM4 (which required me to do these changes by hand on the ppd that was previously output by "make ppd". For PPM4 the XML in the ppd file can be copied over to packages.xml file in our PPM repository. the codebase URL can be relative/absolute and it's exact value depends on the relative position of the XML (whether in the .ppd or package.xml file) and the .tar.gz file. Thus, by default, they would have to reside in the same dir on our server. Without looking at the XML I couldn't say if it was PPM3 or PPM4 compatible. Could you e-mail me the ppd file and I'll take a look. Cheers Nath From cjfields at uiuc.edu Thu Nov 16 12:45:13 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 06:45:13 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C197D.6000107@sendu.me.uk> References: <C1812C74.B5E3%bosborne11@verizon.net> <455C1790.3080408@sendu.me.uk> <455C197D.6000107@sendu.me.uk> Message-ID: <F9D837E4-4614-4905-A171-9738ED1D01D8@uiuc.edu> On Nov 16, 2006, at 1:55 AM, Sendu Bala wrote: ... > Also, > # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who > read the docs on the website/elsewhere (which will be updated to > explain > the new Build.PL system) don't get confused when that doesn't work, > for wide testing, and to get people used to it for the next > release. The > old Makefile.PL will have 2 changes: Brians bug-fix and a little > message > pointing out that Build.PL is now the preferred installation > system, but > Makefile.PL still works. Sounds fine to me. The old Makefile.PL is in the branch along with the new system, we leave a stub in place for Makefile.PL in CVS HEAD, and everybody's happy (hopefully). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 13:08:57 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 07:08:57 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2980.4000609@sheffield.ac.uk> References: <001d01c70912$723c8a60$15327e82@pyrimidine> <455BB073.9040205@sendu.me.uk> <C2937A9A-877B-4D08-B899-79FED3268E56@gmx.net> <455C2980.4000609@sheffield.ac.uk> Message-ID: <4723715A-551A-4402-A98C-14B64EEDD80E@uiuc.edu> On Nov 16, 2006, at 3:04 AM, Nathan S. Haigh wrote: > ... >> If Build.PL can coexist that'd be great. That would give you the >> opportunity to have Makefile.PL print out a message right at the >> beginning that if the installation process messes up one should try >> Build.PL. This would spare you from fixing any problems in >> Makefile.PL that are fixed in the Build.PL approach. > > Good idea, for anyone downloading the .tar.gz from CPAN if they issue > "perl Makefile.PL" without knowing Build.PL was there it should > hopefully work, but if not, issue a comment at the end to say try > "perl > Build.PL" if anything seemed to go wrong. That's amazingly similar to the suggestion I made ;> Seriously, when we make any changes in Bioperl they should be made with the community in mind. If I were to download RC3 directly from the website, it uses the old Makefile.PL. Therefore I would expect the new RC and the final release to have a similar installation procedure. Same with CVS. And I'll note that the CVS docs and wiki still state that Makefile.PL is the one to use. If we can redirect them to the current way, all the better. But sudden dramatic changes, even in a developer release, are probably not the way to go. > If we go for short release cycles, and regular bug fix release, we > will > no longer have to say to users: > "This is a known bug/issue in release x.y.z, it has been fixed in CVS > HEAD so get it from there" > we can roll out fixes in regular releases. This way CVS is then used > solely by developers and those really wanting to live on the bleeding > edge code. Therefore, it is important to get Build.PL in place to let > the release cycle and CPAN packages built quickly, easily and without > hassle - which I believe is the problem with Makefile.PL as it > currently is. Shorter developer cycles are definitely better. Like Hilmar suggests, they don't have to be perfect (though relatively bug- free). If you look back through the old releases I don't think you'll find many with all tests passing on all OS's. I would like to get a 1.5.3 out by spring, then start towards cleaning up for a summer-fall rel. 1.6. Maybe that's wishful thinking. >> Implementing changes like this do require a lot of energy. I very >> much appreciate that Sendu invested the time and energy to make it >> work, even though unfortunately at the last hour. Who knows who would >> have had the energy after the release. If Sendu hadn't put in the >> work now, the next release master may have been stuck with an even >> messier Makefile.PL system. Instead of Monday morning quarterbacking >> after no-one stopped him when he asked about it, we should all help >> him make the release - and the build change - successful now that he >> has done most if not all of the migration work already. >> >> -hilmar >> > > Here, here - well done Sendu on all your hard work! > Personally, I think the move to Build.PL is a good one - it may be a > little late in this particular release, but I think that the > problem is > not that it is a late change, but that it wasn't picked up sooner. It > fits well with the goal of making releases and big fix releases more > regular, and if these are made available via CPAN, then the use of CVS > is for developers and those wanting to live on the edge. Build.PL > helps > all this by making is easier and quicker to make CPAN packages. It > also > means we have a while before the "stable" 1.6 release to ensure it is > working effectively - better than dropping it in on the 1.6 release > isn't it? I think it's work the delay and an extra RC! > > Anyway, my 2 pence worth! > Nath I don't think anyone is knocking Sendu for his effort here. I will remind everybody that this was discussed in a previous thread and a decision was made (and agreed to by Sendu) to wait until after this release to implement Build, hence the backlash. Brian summed it up quite well. We all support this; the timimg was just bad. That's all. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 13:21:27 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 13:21:27 +0000 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? Message-ID: <455C65D7.5060704@sendu.me.uk> Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if the intent was that it not be included in any distribution. I've had a very quick look at it and the docs seem a little out of date. More importantly, I couldn't get it to return any results. I can't find any tests for it in the t/ directory either. Is there any interest in developing this module to get it into a working and tested state, or should I exclude it from the up-coming release of Bioperl? If no one wants to maintain it, should it be deprecated? Thank you, Sendu. From roy at colibase.bham.ac.uk Thu Nov 16 13:18:55 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Thu, 16 Nov 2006 13:18:55 +0000 Subject: [Bioperl-l] reverse complement - and features In-Reply-To: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> References: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> Message-ID: <455C653F.7010907@colibase.bham.ac.uk> > do you know of an easy way to reverse complement the sequence of an > embl entry and the features associated with that sequence. > I'm looking at genomic syntenic regions, and in some organisms the > gene is in the plus strand while in others is in the minus. Try the revcom_with_features method from Bio::SeqUtils: $revcom=Bio::SeqUtils->revcom_with_features($seq); (Apparently the documentation isn't correct for this. I have submitted a patch to Bugzilla.) Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From n.haigh at sheffield.ac.uk Thu Nov 16 13:37:33 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 13:37:33 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C6028.3060402@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455C6028.3060402@sendu.me.uk> Message-ID: <455C699D.1040407@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sorry, but i've been busy this last week etc so haven't be able to test >> RC3 on WinXP yet - hopefully Chris' tests have been sufficient. > > No problem, thanks for all your testing effort! > > >> Essentially a PPM dist comprises of the .tar.gz file you described (of >> the blib dir) and then the XML file (.ppd) which describes the package >> and it's dependencies. > > Is the .ppd ever included in the .tar.gz, or is it always separate? > > Nope - always separate. >> The syntax of the XML has changed for PPM4 (which >> required me to do these changes by hand on the ppd that was previously >> output by "make ppd". > > Is there a reference for the format anywhere? > Erm not really - that I know of. There is this thread which I use for reference: http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 > >> For PPM4 the XML in the ppd file can be copied >> over to packages.xml file in our PPM repository. the codebase URL can be >> relative/absolute and it's exact value depends on the relative position >> of the XML (whether in the .ppd or package.xml file) and the .tar.gz >> file. Thus, by default, they would have to reside in the same dir on our >> server. >> >> Without looking at the XML I couldn't say if it was PPM3 or PPM4 >> compatible. Could you e-mail me the ppd file and I'll take a look. > > It's pretty basic: > > <SOFTPKG NAME="bioperl" VERSION="1,005002003,0,0"> > <TITLE>bioperl > Bioinformatics Toolkit > Bioperl Team <bioperl-l at bioperl.org> > > > > > > If I made it output the sort of information in the current > http://bioperl.org/DIST/RC/package.xml, would that be fine? Did you > have any kind of automation for creating that package.xml, or do you > see a good potential way of automating it? This PPD doesn't contain any info about what modules it provides (ideally, it should have a provide tags for all modules in bioperl) or the dependencies via the require tag. I didn't have an automated way of making it. Previously, the output of "make ppd" used PREREQ_PM from makefile.pl to create PPM3 dependency tags for all modules in PREREQ_PM. I just modified the tags to REQUIRE and added '::' to the end of modules that didn't natively have one. This should all be detailed in the above in - here again for convenience: http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 There must be an automated way to generate the PPM4 compatible PPDs - I think there is a way to generate one from the CPAN distribution. I think this might be the way ActiveState does it? Nath From bix at sendu.me.uk Thu Nov 16 13:47:05 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 13:47:05 +0000 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> References: <455C65D7.5060704@sendu.me.uk> <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> Message-ID: <455C6BD9.6090100@sendu.me.uk> Allen Day wrote: > Hi Sendu, > > Several years ago I was asked by Jim Kent to stop maintaining it. He > was concerned it would overload the UCSC servers. It's not in the > distribution for the same reason. Thanks, I'll deprecate it then. From gcarbajosa at cnio.es Thu Nov 16 13:12:58 2006 From: gcarbajosa at cnio.es (guillermo) Date: Thu, 16 Nov 2006 14:12:58 +0100 Subject: [Bioperl-l] indexing whole genbank Message-ID: Hello, I wrote to this list before because I wasn?t able to index the whole of genebank. I?ve tried to do it spliting the work by creating small indexes and it has worked perfectly so that seems the way to do it. Thanks for your comments, Guillermo **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From cjfields at uiuc.edu Thu Nov 16 15:08:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:08:08 -0600 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <455C65D7.5060704@sendu.me.uk> Message-ID: <001501c70991$06b14fe0$15327e82@pyrimidine> > Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if > the intent was that it not be included in any distribution. > I've had a very quick look at it and the docs seem a little > out of date. More importantly, I couldn't get it to return > any results. > > I can't find any tests for it in the t/ directory either. Is > there any interest in developing this module to get it into a > working and tested state, or should I exclude it from the > up-coming release of Bioperl? > > If no one wants to maintain it, should it be deprecated? > > > Thank you, > Sendu. I would definitely exclude it if it doesn't work or have tests. Have you contacted the author (Allen Day)? I wonder if he has updated the code but hasn't committed it. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Thu Nov 16 15:17:23 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 16 Nov 2006 10:17:23 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C197D.6000107@sendu.me.uk> References: <455C1790.3080408@sendu.me.uk> <455C197D.6000107@sendu.me.uk> Message-ID: <75FDB3A6-BFB6-4120-92B1-04D54D708E4C@gmx.net> Sounds great to me. -hilmar On Nov 16, 2006, at 2:55 AM, Sendu Bala wrote: >> Ok, so the current plan is: >> # 1.5.2 keeps old Makefile.PL and gains HEAD's META.yml > Also, > # 1.5.2 gains Build.PL (and ModuleBuildBioperl.pm) so that people who > read the docs on the website/elsewhere (which will be updated to > explain > the new Build.PL system) don't get confused when that doesn't work, > for wide testing, and to get people used to it for the next > release. The > old Makefile.PL will have 2 changes: Brians bug-fix and a little > message > pointing out that Build.PL is now the preferred installation > system, but > Makefile.PL still works. > > >> # CVS core gets a Makefile.PL stub telling you to use Build.PL >> # CVS db, run, network stay with Makefile.PL until after final >> release >> of 1.5.2, then move to Build.PL with Makefile.PL stub (because they >> don't have a 1.5.2 branch) >> >> Is everyone happy with that, or are there further suggestions for >> something better? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Thu Nov 16 15:29:31 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:29:31 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C699D.1040407@sheffield.ac.uk> Message-ID: <001601c70994$02da28d0$15327e82@pyrimidine> ... > > > > Is there a reference for the format anywhere? > > > > Erm not really - that I know of. There is this thread which I use for > reference: > http://aspn.activestate.com/ASPN/Mail/Message/ppm/3243428 Looks like kobes is using PPM::Make (he should; it's his distribution). We'll need to make sure that Module::Build uses that as well, since it seems there are some significant changes. ... > There must be an automated way to generate the PPM4 > compatible PPDs - I think there is a way to generate one from > the CPAN distribution. I think this might be the way > ActiveState does it? > > Nath I think ActiveState has it's own automated build process. For PPM3 they used the PPD section from the regular makefile (from Makefile.PL and ExtUtils::MakeMaker). Notably they still indicate using 'nmake ppd' when generating Makefile.PL, so maybe they use an updated or modified ExtUtils::MakeMaker? Or they add tags for the Makefile.PL: use ExtUtils::MakeMaker; # See lib/ExtUtils/MakeMaker.pm for details of how to influence # the contents of the Makefile that is written. WriteMakefile( 'NAME' => 'Term::Control', 'VERSION_FROM' => 'Control.pm', # finds $VERSION ($] ge '5.005') ? ( 'AUTHOR' => 'Johnny Doel (johnny at doel.org)', 'ABSTRACT' => 'Control the IO for terminals', # extra tags here? ) : (), ); The reason you may not see a certain distribution built into a PPM is b/c a particular dependency is not available for one reason or another, tests fail during the make process, etc. They will try to build specific ones upon request. Many of the ones in Kobes are generated by users who want up-to-date distros or ones not built automatically by ActiveState, though Randy Kobes himself sets up most of them. Significantly, he has already switched over to PPM4; maybe we should contact him about this? Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 16 15:31:08 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 09:31:08 -0600 Subject: [Bioperl-l] indexing whole genbank In-Reply-To: Message-ID: <001701c70994$3d332400$15327e82@pyrimidine> > Hello, > > I wrote to this list before because I wasn?t able to index > the whole of genebank. I?ve tried to do it spliting the work > by creating small indexes and it has worked perfectly so that > seems the way to do it. > > Thanks for your comments, > Guillermo Thanks for the update. I think that the problem was a full GenBank file is way too large for flatfile indexing (I think it's around 800 GB unpacked now). Nice to know doing it by divisions works. chris Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 16:29:33 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 16:29:33 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <17756.36534.549232.263868@satchel.alerce.com> References: <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> <455BA093.8040603@sendu.me.uk> <17756.36534.549232.263868@satchel.alerce.com> Message-ID: <455C91ED.2030008@sendu.me.uk> George Hartzell wrote: > Sendu Bala writes: > > [...] > > The only real change for most users is that they now need Module::Build > > installed. > > Module::Build can be a real pain-in-the_%$* if you're used to > installing perl modules in a specialized place using something like > this: > > perl Makefile.PL PREFIX=~/perl-stuff > > Granted, MakeMaker's handling of that has been inconsistent across > platforms over the years, but on a single system at least it's > manageable. > > If/when bioperl swaps over to a Module::Build based system, PLEASE > make a big&loud reference to the "Installing in the same location as > ExtUtils::MakeMaker" section of the Module::Build::Cookbook so that > folks have a fighting chance of avoiding unpleasant surprises. Thanks, I've added a clarification to the INSTALL file. From hartzell at alerce.com Thu Nov 16 16:15:50 2006 From: hartzell at alerce.com (George Hartzell) Date: Thu, 16 Nov 2006 08:15:50 -0800 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455BA093.8040603@sendu.me.uk> References: <455B867E.8010001@sendu.me.uk> <6dce9a0b0611151443l412400a7g1decdd208cc91b0c@mail.gmail.com> <455BA093.8040603@sendu.me.uk> Message-ID: <17756.36534.549232.263868@satchel.alerce.com> Sendu Bala writes: > [...] > The only real change for most users is that they now need Module::Build > installed. Module::Build can be a real pain-in-the_%$* if you're used to installing perl modules in a specialized place using something like this: perl Makefile.PL PREFIX=~/perl-stuff Granted, MakeMaker's handling of that has been inconsistent across platforms over the years, but on a single system at least it's manageable. If/when bioperl swaps over to a Module::Build based system, PLEASE make a big&loud reference to the "Installing in the same location as ExtUtils::MakeMaker" section of the Module::Build::Cookbook so that folks have a fighting chance of avoiding unpleasant surprises. That section says, in part: With the introduction of "--prefix" in Module::Build 0.28 and "INSTALL_BASE" in ExtUtils::MakeMaker 6.31 its [sic] easy to get them both to install in the same locations. First, ensure you have at least version 0.28 of Module::Build installed and 6.31 of ExtUtils::MakeMaker. Prior versions have differeing installation behaviours. People may need to upgrade their installations [at least the ExtUtils::MakeMaker and Module::Build bits], but at least they'll see the train barreling down at them. g. From roy at colibase.bham.ac.uk Thu Nov 16 16:49:49 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Thu, 16 Nov 2006 16:49:49 +0000 Subject: [Bioperl-l] reverse complement - and features In-Reply-To: <40d6e6580611160828m5f7047e0gadec36f958a69990@mail.gmail.com> References: <40d6e6580611150651j32e23df0l79765c9f8e78b153@mail.gmail.com> <455C653F.7010907@colibase.bham.ac.uk> <40d6e6580611160828m5f7047e0gadec36f958a69990@mail.gmail.com> Message-ID: <455C96AD.8030804@colibase.bham.ac.uk> > that method sounds promising, although the documentation seems to be > copy-and-paste from the trunc_with_features() method. Yes, I was a bit lazy with that. It has been fixed in CVS (thanks Chris) and will be included in the new 1.5.2 release. > I included in my script, although it doesn't complaint but no being > there, it doesn't do anything with the file. > I looked at the version of bioperl in the server where I'm running, > and it is 1.5.0 and the SeqUtils.pm does not include the > revcom_with_features(). > Do you know if I can install the SeqUtils.pm module in my directory, > and call it with use lib "/home/xxxx/xxxx/lib/perl"; ? Yes, that should work. You can download the most recent version from: http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioperl-live/Bio/SeqUtils.pm?rev=HEAD&content-type=text/plain You can put that file in the directory /home/xxxx/xxxx/lib/perl/Bio/ and it should then be recognised as the preferred Bio::SeqUtils module if you use lib as you say. Good luck with it. Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From cjfields at uiuc.edu Thu Nov 16 16:55:39 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 10:55:39 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455C2ED5.4060602@sendu.me.uk> Message-ID: <001901c709a0$0b6a6d50$15327e82@pyrimidine> > Nathan S. Haigh wrote: > > I believe Sendu mentioned that a Makefile.PL would be > included in the > > CPAN package but is not in CVS as it would be generated > from Build.PL > > for backward compatibility - is that right Sendu? > > Yes. > > > > How does installing via CPAN affect this? Does it give > higher priority > > to Build.PL over Makefile.PL and thus use Build.PL for the install? > > I don't know about priorities (but assume it would prefer > Build.PL), but in any case, the generated Makefile.PL > basically just calls Build.PL, so it makes no difference. > > > > Build.PL helps all this by making is easier and quicker to > make CPAN > > packages. It also means we have a while before the "stable" 1.6 > > release to ensure it is working effectively - better than > dropping it > > in on the 1.6 release isn't it? I think it's work the delay and an > > extra RC! > > Yes, it surely needs to happen before 1.6. As suggested here > and originally in the other thread, 1.5.2 can be the > transition release with old Makefile.PL and Build.PL as well > (set up to not overwrite Makefile.PL). So far, we have these modes of installation: 1) Direct installation using CPAN -> INSTALL 2) Regular distribution (either from the Bioperl website or CPAN) using 'make/nmake' ->INSTALL, INSTALL.WIN 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN 4) PPM (Windows-only) -> INSTALL.WIN Anything using make/nmake will need to be changed in docs. Do you want to switch everything over to using 'perl Build.PL'? Also, since the 'manifying' problem is now fixed we can remove the blurb about it from INSTALL and the wiki. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 16 16:59:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 16:59:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> References: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: <455C98F0.9050909@sendu.me.uk> Chris Fields wrote: > So far, we have these modes of installation: > > 1) Direct installation using CPAN -> INSTALL > 2) Regular distribution (either from the Bioperl website or CPAN) using > 'make/nmake' ->INSTALL, INSTALL.WIN > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > 4) PPM (Windows-only) -> INSTALL.WIN > > Anything using make/nmake will need to be changed in docs. Do you want to > switch everything over to using 'perl Build.PL'? > > Also, since the 'manifying' problem is now fixed we can remove the blurb > about it from INSTALL and the wiki. I've already updated docs in CVS. The emails are just very slow to get through to guts. Do an update and let me know if I missed anything. I'll add the changes to the wiki when I get a chance. From n.haigh at sheffield.ac.uk Thu Nov 16 17:44:28 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 17:44:28 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> References: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: <455CA37C.3070704@sheffield.ac.uk> --snip-- >> Yes, it surely needs to happen before 1.6. As suggested here >> and originally in the other thread, 1.5.2 can be the >> transition release with old Makefile.PL and Build.PL as well >> (set up to not overwrite Makefile.PL). >> > > So far, we have these modes of installation: > > 1) Direct installation using CPAN -> INSTALL > 2) Regular distribution (either from the Bioperl website or CPAN) using > 'make/nmake' ->INSTALL, INSTALL.WIN > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > Chris, Do you ever have a problem with nmake when doing an install from a regular distribution or CVS? I'm sure I used to get an nmake problem which wouldn't let you proceed further - might have been "nmake test" and it might be a while back now. Nath From cjfields at uiuc.edu Thu Nov 16 17:58:14 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 11:58:14 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <455CA37C.3070704@sheffield.ac.uk> Message-ID: <000001c709a8$c9c1b760$15327e82@pyrimidine> > --snip-- > >> Yes, it surely needs to happen before 1.6. As suggested here and > >> originally in the other thread, 1.5.2 can be the > transition release > >> with old Makefile.PL and Build.PL as well (set up to not overwrite > >> Makefile.PL). > >> > > > > So far, we have these modes of installation: > > > > 1) Direct installation using CPAN -> INSTALL > > 2) Regular distribution (either from the Bioperl website or CPAN) > > using 'make/nmake' ->INSTALL, INSTALL.WIN > > 3) CVS (bioperl-live) using make/nmake -> INSTALL, INSTALL.WIN > > > > Chris, > > Do you ever have a problem with nmake when doing an install > from a regular distribution or CVS? I'm sure I used to get an > nmake problem which wouldn't let you proceed further - might > have been "nmake test" > and it might be a while back now. > > Nath I haven't had problems beyond the '-w' paranoia and 'Subroutine x redefined at' warnings, which is an ActivePerl issue. 'nmake test' works for me (that's what I have been using on all the RC's and using bioperl-live). I think 'Build test' also uses nmake, so if that works nmake should also work. I have used both an old version (1.5) and the recent VC++ nmake version (8.00.50727.42) w/o problems. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From pcantalupo at gmail.com Thu Nov 16 16:26:31 2006 From: pcantalupo at gmail.com (Paul Cantalupo) Date: Thu, 16 Nov 2006 11:26:31 -0500 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID Message-ID: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Hello, Is there a way with Bioperl (or some other tool - NCBI EUtils?) to convert a Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's that I need to convert to Mouse GeneIDs so that I can compare them to my Mouse microarray data. Thank you, Paul -- Paul Cantalupo Research Specialist/Systems Programmer 559 Crawford Hall Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Work: 412-624-4687 Fax: 412-624-4759 Ask me about Toastmasters: www.toastmasters.org Midday Club Treasurer From bosborne11 at verizon.net Thu Nov 16 18:09:01 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 16 Nov 2006 13:09:01 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <001901c709a0$0b6a6d50$15327e82@pyrimidine> Message-ID: Chris, So a package like bioperl-ext, normally requiring a C compiler and make/nmake, now no longer needs make/nmake? I don't recall this coming up in our discussions... Brian O. On 11/16/06 11:55 AM, "Chris Fields" wrote: > Anything using make/nmake will need to be changed in docs. From bix at sendu.me.uk Thu Nov 16 18:14:12 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 18:14:12 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: References: Message-ID: <455CAA74.60500@sendu.me.uk> Brian Osborne wrote: > Chris, > > So a package like bioperl-ext, normally requiring a C compiler and > make/nmake, now no longer needs make/nmake? I don't recall this coming up in > our discussions... I'm sure you'd still need compiler tools to do compilation. I wasn't sure what to say about bioperl-ext in the docs, so I didn't change anything. bioperl-ext isn't my concern (see the thread where I was deciding which packages needed a unified release), so I'll not be trying to change it over to Build.PL From bix at sendu.me.uk Thu Nov 16 18:16:48 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 16 Nov 2006 18:16:48 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: References: Message-ID: <455CAB10.1090703@sendu.me.uk> Brian Osborne wrote: > George, > > But the most recent versions of Module::Build do the installations > correctly? And it's as simple as specifying PREFIX or LIB? In Build.PL's case, it's --prefix or --lib, but yes. For both Module::Build and MakeMaker in recent versions, --install_base is recommended. From cjfields at uiuc.edu Thu Nov 16 18:41:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 12:41:56 -0600 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: Message-ID: <000101c709ae$e475bfb0$15327e82@pyrimidine> > Chris, > > So a package like bioperl-ext, normally requiring a C > compiler and make/nmake, now no longer needs make/nmake? I > don't recall this coming up in our discussions... > > Brian O. The makefile setup for bioperl-ext is much more complex than for the others, so I don't know how that would be handled using Module::Build. I tried it earlier on before the RCs on Mac OS X and it installed fine, but Inline complained when running other tests so I tossed it. I don't think it ever worked under Windows using nmake, unless you're using CygWin/GNU make. I believe the Build file must use make/nmake somehow, so there must be a way to compile C code included with the distribution. I just haven't had time to invesitgate yet. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Thu Nov 16 19:05:27 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 16 Nov 2006 19:05:27 +0000 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <000101c709ae$e475bfb0$15327e82@pyrimidine> References: <000101c709ae$e475bfb0$15327e82@pyrimidine> Message-ID: <455CB677.6080608@sheffield.ac.uk> Chris Fields wrote: >> Chris, >> >> So a package like bioperl-ext, normally requiring a C >> compiler and make/nmake, now no longer needs make/nmake? I >> don't recall this coming up in our discussions... >> >> Brian O. >> > > The makefile setup for bioperl-ext is much more complex than for the others, > so I don't know how that would be handled using Module::Build. I tried it > earlier on before the RCs on Mac OS X and it installed fine, but Inline > complained when running other tests so I tossed it. I don't think it ever > worked under Windows using nmake, unless you're using CygWin/GNU make. > > I believe the Build file must use make/nmake somehow, so there must be a way > to compile C code included with the distribution. I just haven't had time > to invesitgate yet. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > > I was under the impression that Module::Build is pure Perl and thus wouldn't use make/nmake. This page might help, look under "code" in this section: http://search.cpan.org/~kwilliams/Module-Build-0.2805/lib/Module/Build.pm#ACTIONS According to change logs they use ExtUtils::CBuilder to do all compiling of C code (since version 0.27_01) see: http://search.cpan.org/src/KWILLIAMS/Module-Build-0.27_03/Changes HTH Nathan From bosborne11 at verizon.net Thu Nov 16 18:05:15 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 16 Nov 2006 13:05:15 -0500 Subject: [Bioperl-l] "progress": useful changes vs. "shiny new thingie" In-Reply-To: <17756.36534.549232.263868@satchel.alerce.com> Message-ID: George, But the most recent versions of Module::Build do the installations correctly? And it's as simple as specifying PREFIX or LIB? Brian O. On 11/16/06 11:15 AM, "George Hartzell" wrote: > Module::Build can be a real pain-in-the_%$* if you're used to > installing perl modules in a specialized place using something like > this: > > perl Makefile.PL PREFIX=~/perl-stuff From er at xs4all.nl Thu Nov 16 21:01:12 2006 From: er at xs4all.nl (Erik) Date: Thu, 16 Nov 2006 22:01:12 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch Message-ID: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> Hi all, Using bioperl-live, I noticed a problem with the parsing in Bio/SeqIO/genbank.pm. It occurs in the DBSOURCE section, where the 'dblink' annotation gets its values. I got several values that had a double colon, like InterPro::IPR011000 etc. Not all 'dblink' values were affected. Here is a patch which seems to fix it / it works for me: ======= --- Bio/SeqIO/genbank.pm.orig 2006-11-16 18:33:30.060417520 +0100 +++ Bio/SeqIO/genbank.pm 2006-11-16 20:29:59.014934936 +0100 @@ -504,7 +504,7 @@ my $db; # this is because GenBank dropped the spaces!!! # I'm sure we're not going to get this right - if( $id =~ s/^(EchoBASE|IntAct|SWISS-2DPAGE|ECO2DBASE|ECOGENE|TIGRFAMs|TIGR|GO|InterPro|Pfam|PROSITE|SGD|GermOnline|HSSP|PhosSite)//i ) { + if( $id =~ s/^(EchoBASE|IntAct|SWISS-2DPAGE|ECO2DBASE|ECOGENE|TIGRFAMs|TIGR|GO|InterPro|Pfam|PROSITE|SGD|GermOnline|HSSP|PhosSite)://i ) { $db = $1; } $annotation->add_Annotation======= I also wrote a few tests for the problem, which also needed an extra file in t/data. I will attach the lot hth, Erik -------------- next part -------------- A non-text attachment was scrubbed... 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Name: genbank.pm.diff Type: application/octet-stream Size: 608 bytes Desc: not available URL: From jason at bioperl.org Thu Nov 16 19:45:24 2006 From: jason at bioperl.org (Jason Stajich) Date: Thu, 16 Nov 2006 11:45:24 -0800 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> References: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Message-ID: have you tried ensembl's biomart? http://www.ensembl.org/Multi/martview you will want the ortholog table. -jason On Nov 16, 2006, at 8:26 AM, Paul Cantalupo wrote: > Hello, > > Is there a way with Bioperl (or some other tool - NCBI EUtils?) to > convert a > Human NCBI GeneID to a Mouse GeneID. I have a list of Human > GeneID's that I > need to convert to Mouse GeneIDs so that I can compare them to my > Mouse > microarray data. > > Thank you, > > Paul > > -- > Paul Cantalupo > Research Specialist/Systems Programmer > 559 Crawford Hall > Department of Biological Sciences > University of Pittsburgh > Pittsburgh, PA 15260 > Work: 412-624-4687 > Fax: 412-624-4759 > > Ask me about Toastmasters: www.toastmasters.org > Midday Club Treasurer > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From allenday at ucla.edu Thu Nov 16 13:43:35 2006 From: allenday at ucla.edu (Allen Day) Date: Thu, 16 Nov 2006 05:43:35 -0800 Subject: [Bioperl-l] Status of Bio::Tools::WebBlat? In-Reply-To: <455C65D7.5060704@sendu.me.uk> References: <455C65D7.5060704@sendu.me.uk> Message-ID: <5c24dcc30611160543p79f4f375y339c5d3efdbb96c0@mail.gmail.com> Hi Sendu, Several years ago I was asked by Jim Kent to stop maintaining it. He was concerned it would overload the UCSC servers. It's not in the distribution for the same reason. -Allen On 11/16/06, Sendu Bala wrote: > Bio/Tools/WebBlat.pm was in the old MANIFEST.SKIP file, as if the intent > was that it not be included in any distribution. I've had a very quick > look at it and the docs seem a little out of date. More importantly, I > couldn't get it to return any results. > > I can't find any tests for it in the t/ directory either. Is there any > interest in developing this module to get it into a working and tested > state, or should I exclude it from the up-coming release of Bioperl? > > If no one wants to maintain it, should it be deprecated? > > > Thank you, > Sendu. > From torsten.seemann at infotech.monash.edu.au Fri Nov 17 00:42:41 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 17 Nov 2006 11:42:41 +1100 Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch In-Reply-To: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> References: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> Message-ID: <455D0581.4010805@infotech.monash.edu.au> Erik, > Using bioperl-live, I noticed a problem with the parsing in > Bio/SeqIO/genbank.pm. > It occurs in the DBSOURCE section, where the 'dblink' annotation gets its > values. I got several values that had a double colon, like > InterPro::IPR011000 etc. Not all 'dblink' values were affected. > Here is a patch which seems to fix it / it works for me: Thank you very much for your contribution of bug fix and patch and new tests, you have been very thorough. However, these contributions are best done via the Bugzilla tracking system: http://bugzilla.open-bio.org/ For more information see: http://www.bioperl.org/wiki/Bugs -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From cjfields at uiuc.edu Thu Nov 16 13:47:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 07:47:26 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455C5D5A.5020205@sheffield.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> Message-ID: On Nov 16, 2006, at 6:45 AM, Nathan S. Haigh wrote: > Sendu Bala wrote: >> Chris Fields wrote: >>> I see that there is a PPMMaker module with Module::Build, so we'll >>> have to >>> look into that for WinXP PPMs.. >> >> Nathan, does: >> >> perl Build.PL >> ./Build ppmdist >> >> create anything useful? For me it generates a tar.gz containing blib, >> and a ppd file (the contents of which can be adjusted by supplying >> "an >> optional argument codebase which is used in the generated ppd file to >> specify the (usually relative) URL of the distribution. By default, >> this value is the distribution name without any path information", >> eg. >> ./Build ppmdist --codebase "MSWin32-x86-multi-thread/ >> Bioperl....tar.gz"). >> >> Is this PPM4 format? What else needs to be done to it to make it >> suitable? I can easily extend the ppmdist action to do whatever you >> want, so let me know. > > Sorry, but i've been busy this last week etc so haven't be able to > test > RC3 on WinXP yet - hopefully Chris' tests have been sufficient. > > Essentially a PPM dist comprises of the .tar.gz file you described (of > the blib dir) and then the XML file (.ppd) which describes the package > and it's dependencies. The syntax of the XML has changed for PPM4 > (which > required me to do these changes by hand on the ppd that was previously > output by "make ppd". For PPM4 the XML in the ppd file can be copied > over to packages.xml file in our PPM repository. the codebase URL > can be > relative/absolute and it's exact value depends on the relative > position > of the XML (whether in the .ppd or package.xml file) and the .tar.gz > file. Thus, by default, they would have to reside in the same dir > on our > server. > > Without looking at the XML I couldn't say if it was PPM3 or PPM4 > compatible. Could you e-mail me the ppd file and I'll take a look. > > Cheers > Nath I'll also try making a PPM here. I noticed that Module::Build has a developer release; I may check with the developers about PPM compatibility. I hate to say it, but we might need to get a PPM3 rolled for this release if people ask for it. There has been some backlash about PPM4 so a lot of people are actually downgrading to an older ActivePerl installations for PPM3. We'll just make a barebones version if this pops up (and no Bundle). One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a developer release, but as the latest release (which implies it is stable): http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Not sure what's going on there, but I don't think that was intended, correct? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Nov 17 02:51:49 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 16 Nov 2006 20:51:49 -0600 Subject: [Bioperl-l] Parsing the CDS join or complement statements to get the sub-locations In-Reply-To: References: Message-ID: <277B1C9B-1719-47C5-9A34-9B4E179A78A0@uiuc.edu> On Nov 16, 2006, at 1:55 AM, Joanne Chen wrote: > Got the strand problem fixed. Thanks. =) No problem. Just as a heads up, we plan on making some changes to SplitLocations but nothing too dramatic (hopefully). chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From dmessina at wustl.edu Fri Nov 17 03:54:50 2006 From: dmessina at wustl.edu (David Messina) Date: Thu, 16 Nov 2006 21:54:50 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455B3F11.6070102@campus.iztacala.unam.mx> References: <4554514D.2020001@sendu.me.uk> <455B33C1.1010800@sendu.me.uk> <455B3F11.6070102@campus.iztacala.unam.mx> Message-ID: <450674EB-F9CA-4BBF-8EB9-D08423FD16FD@wustl.edu> Sorry, just seeing this now. > ignored, only run manually by people who want to install Deobfuscator? Thanks for asking. As Mauricio said, manual installation only is what I would suggest. Dave From torsten.seemann at infotech.monash.edu.au Fri Nov 17 00:19:42 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 17 Nov 2006 11:19:42 +1100 Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast and mpi-blast In-Reply-To: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> References: <000b01c708c1$c0f76ea0$15327e82@pyrimidine> Message-ID: <455D001E.4000409@infotech.monash.edu.au> Andrew, >> Anyone have any opinions as to how easy/difficult it would be >> to incorporate mpiblast into >> Bio::Tools::Run::StandAloneBlast? It runs essentially the >> same way as blastall, and its output is nearly identical. > I think plans were to rewrite StandAloneBlast and RemoteBlast to make them > more 'generic' (i.e. capable of running other BLAST-related programs), > though I'm not sure at what stage everything is. Chris is correct is saying there were plans to rewrite the Blast modules - at the time myself, Roger Hall, Chris? and Jason were involved, but unfortunately Roger fell ill in Feb 2006 and had to have urgent heart surgery. (And my wife had a baby :-) Here's some of the early discussion: http://portal.open-bio.org/pipermail/bioperl-l/2006-February/020745.html ANYWAY, I think it might be possible to incorporate mpiblast easily, even without changing Bioperl if we are lucky, via the ->executable() setter method. If not, I added rpsblast support last year which is similar to blastall, so it'd probably be achievable. How does the the output of mpiblast differ to NCBI blastall ? What command line options does mpiblast take? -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From bix at sendu.me.uk Fri Nov 17 07:38:30 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 07:38:30 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> Message-ID: <455D66F6.4070804@sendu.me.uk> Chris Fields wrote: > One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a > developer release, but as the latest release (which implies it is stable): > > http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ > > Not sure what's going on there, but I don't think that was intended, > correct? It wasn't intended. I've deleted the file and if you refresh you should find that page doesn't exist anymore? From bix at sendu.me.uk Fri Nov 17 10:20:11 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 10:20:11 +0000 Subject: [Bioperl-l] Testing with Build.PL Message-ID: <455D8CDB.1070100@sendu.me.uk> Developers, For those not familiar with Module::Build and Build.PL I thought I'd point out some useful testing-related things. To run the whole test suite (the same thing that happens during an install process), say: perl Build.PL (answer 'n' to the script installation question to reduce the amount of output you see later on) ./Build test To run a single test script you can of course continue to do: perl -I. -w t/script.t However to see what would really happen during the full "./Build test" you can say: ./Build test --test_files t/script.t To do the same but see the full test output say: ./Build test --test_files t/script.t --verbose If anyone else has tips, please post them. Cheers, Sendu. From sanges at biogem.it Fri Nov 17 10:14:03 2006 From: sanges at biogem.it (Remo Sanges) Date: Fri, 17 Nov 2006 10:14:03 +0000 Subject: [Bioperl-l] Fellowships for Junior Scientists Message-ID: <455D8B6B.1050108@biogem.it> Apologies for the off topic post... AREA Science Park (http://www.area.trieste.it/opencms/opencms/area/en/) and CBM (http://www.cbm.fvg.it/?lang=en_US) are launching a mobility initiative aimed at attracting international scientists to work with the biomedical research community of Trieste. Research areas: * Biostatistics * Systems Biology * Algorithm Development The fellowships are funded by AREA Science Park and the CBM - Consortium for Molecular Biomedicine as part of an international mobility programme run by AREA Science Park and the CBM. The programme aims at attracting young scientists to the Friuli Venezia Giulia Region and adding them to the community of researchers operating in Trieste in the field of biomedicine. CBM and AREA Science Park are two research institutes recognised by the Ministry of Education, Universities and Research. Here there are laboratories integrating dry and wet lab research and developing a wide research program encompassing functional and comparative genomics, bioinformatics database, software development and algorithm development. The laboratories are already integrated in international collaborative projects tackling non-coding RNA genes, regulatory elements, and bioinformatics workflow management systems. For further information: http://www.cbm.fvg.it/?page=mobility&lang=en_US&id=2 Regards Remo Sanges From er at xs4all.nl Fri Nov 17 10:57:43 2006 From: er at xs4all.nl (Erik) Date: Fri, 17 Nov 2006 11:57:43 +0100 (CET) Subject: [Bioperl-l] Bio/SeqIO/genbank.pm patch In-Reply-To: <455D0581.4010805@infotech.monash.edu.au> References: <8997.156.83.0.21.1163710872.squirrel@webmail.xs4all.nl> <455D0581.4010805@infotech.monash.edu.au> Message-ID: <16667.156.83.0.21.1163761063.squirrel@webmail.xs4all.nl> > However, these contributions are best done via the Bugzilla tracking > system: http://bugzilla.open-bio.org/ ok, I'll do that, but a little later today. Maybe just as well as I later thought of some, err.., imperfections in the tests anyway :) Erik From cjfields at uiuc.edu Fri Nov 17 13:43:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 07:43:38 -0600 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455D66F6.4070804@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> Message-ID: <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> On Nov 17, 2006, at 1:38 AM, Sendu Bala wrote: > Chris Fields wrote: >> One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a >> developer release, but as the latest release (which implies it is >> stable): >> >> http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ >> >> Not sure what's going on there, but I don't think that was intended, >> correct? > > It wasn't intended. I've deleted the file and if you refresh you > should > find that page doesn't exist anymore? The page is still there, but the distribution is gone (i.e. the 'Download' link is now dead). http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Fri Nov 17 13:51:03 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 13:51:03 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> Message-ID: <455DBE47.90501@sendu.me.uk> Chris Fields wrote: > > On Nov 17, 2006, at 1:38 AM, Sendu Bala wrote: > >> Chris Fields wrote: >>> One BioPerl CPAN issue: I noticed that 1.5.2-RC3 is not listed as a >>> developer release, but as the latest release (which implies it is >>> stable): >>> >>> http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ >>> >>> Not sure what's going on there, but I don't think that was intended, >>> correct? >> >> It wasn't intended. I've deleted the file and if you refresh you should >> find that page doesn't exist anymore? > > The page is still there, but the distribution is gone (i.e. the > 'Download' link is now dead). > > http://search.cpan.org/~sendu/bioperl-1.5.2-RC3/ Hmm, I see just a big 'Not found' message for a non-existing page. I think the old page is still stuck in a cache somewhere for you. In any case, don't whatever you do look in the super-sekrit http://search.cpan.org/~sendu/ because I'm testing out CPAN stuff and getting it horribly wrong. Multiple times. I'll make a post when CPAN stuff is ready to test. From cuiw at ncbi.nlm.nih.gov Fri Nov 17 14:59:15 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Fri, 17 Nov 2006 09:59:15 -0500 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <37bd06460611160826q7d39ff30i285142831196f4b1@mail.gmail.com> Message-ID: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> You can query HomoloGene DB using NCBI EUtils: ESearch like this: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=homologene& term=BRCA1[gene%20name]&retmode=text Once get HomoloGene id then Then Efetch: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=homologene&i d=5276 Just SOAP it to get the gi and acc via taxid. Good luck. Wenwu Cui -----Original Message----- From: Paul Cantalupo [mailto:pcantalupo at gmail.com] Sent: Thursday, November 16, 2006 11:27 AM To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID Hello, Is there a way with Bioperl (or some other tool - NCBI EUtils?) to convert a Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's that I need to convert to Mouse GeneIDs so that I can compare them to my Mouse microarray data. Thank you, Paul -- Paul Cantalupo Research Specialist/Systems Programmer 559 Crawford Hall Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Work: 412-624-4687 Fax: 412-624-4759 Ask me about Toastmasters: www.toastmasters.org Midday Club Treasurer _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Fri Nov 17 17:43:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 17:43:55 +0000 Subject: [Bioperl-l] No more Makefile.PL (MakeMaker -> Module::Build) In-Reply-To: <455DF2BC.9010601@sheffield.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> Message-ID: <455DF4DB.5000808@sendu.me.uk> Nathan S. Haigh wrote: > Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked up as > a developer release? I didn't try that variation, but have decided to go with bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a developer release. I've outlined the numbering scheme here: http://www.bioperl.org/wiki/Making_a_BioPerl_release#Making_the_distribution_directory From cjfields at uiuc.edu Fri Nov 17 18:30:20 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 12:30:20 -0600 Subject: [Bioperl-l] CPAN Versioning, was [something else] In-Reply-To: <455DF4DB.5000808@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> Message-ID: <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> On Nov 17, 2006, at 11:43 AM, Sendu Bala wrote: > Nathan S. Haigh wrote: >> Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked >> up as >> a developer release? > > I didn't try that variation, but have decided to go with > bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a > developer > release. > > I've outlined the numbering scheme here: > http://www.bioperl.org/wiki/ > Making_a_BioPerl_release#Making_the_distribution_directory I noticed that Module::Build now has a developer release that uses this: Module-Build-0.2805_01.tar.gz So the '_###' seems to be key. If so I see a versioning dilemma that depends on what we want to call rel 1.5.2. If we used 'bioperl-1.5.2_004' for the RCs, then logically the final dev release would be 'bioperl-1.5.2', which would not be designated a dev release on CPAN (if the underscore rule holds up, that is). If we plan on having CPAN designate it a developer release (which I think is the consensus among the developers, since 1.6 would be the stable release), then the final 1.5.2 version would be something like 'bioperl-1.5_02' or 'bioperl-1.5_002'. RCs would be '1.5_02-RC#'. Or maybe even '1.5_02_##', which a few modules seem to use. However, even that is tricky; what do we call rel 1.6.1, a point release in the stable series? 'bioperl-1.6_2' would then be a developer release! Argghhh! Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Nov 17 18:51:27 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 17 Nov 2006 12:51:27 -0600 Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID In-Reply-To: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> References: <18C407FD4FFB424292D769FBD68C1987018122D8@NIHCESMLBX8.nih.gov> Message-ID: <55142E31-33F7-442C-B358-E81FA57E9F9E@uiuc.edu> On Nov 17, 2006, at 8:59 AM, Cui, Wenwu ((NIH/NLM/NCBI)) [C] wrote: > You can query HomoloGene DB using NCBI EUtils: > > ESearch like this: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? > db=homologene& > term=BRCA1[gene%20name]&retmode=text > > Once get HomoloGene id then > Then Efetch: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? > db=homologene&i > d=5276 > > Just SOAP it to get the gi and acc via taxid. > > Good luck. > > Wenwu Cui > > > -----Original Message----- > From: Paul Cantalupo [mailto:pcantalupo at gmail.com] > Sent: Thursday, November 16, 2006 11:27 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID > > Hello, > > Is there a way with Bioperl (or some other tool - NCBI EUtils?) to > convert a > Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's > that I > need to convert to Mouse GeneIDs so that I can compare them to my > Mouse > microarray data. > > Thank you, > > Paul > ... You could also use esearch(homologene, using history)->elink (homologene_gene, using history)->esummary(elink 'cookie'). I have set up a (very) experimental BioPerl interface to NCBI eutils (Bio::DB::EUtilities). If you update from CVS (this won't be in the 1.5.2 release), you could do something like this: ------------------------------------------------------ use Bio::DB::EUtilities; my $term = 'BRCA1[gene name]'; # grab BRCA1 homologene UID my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => $term, -usehistory => 'y'); $esearch->get_response; my @h_genes = $esearch->get_ids; # what Gene UIDs are linked to the Homologene UID? my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', -db => 'gene', -cookie => $esearch->next_cookie, -cmd => 'neighbor_history'); $elink->get_response; # what taxids go with which GeneID? my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', -cookie => $elink->next_cookie); $esum->get_response; while (my $docsum = $esum->next_docsum) { print $docsum->esummary_id,"\n"; print "\t\tTaxID: ",$docsum->get_Content_by_name('TaxID'),"\n"; print "\t\tOrganism: ",$docsum->get_Content_by_name ('Orgname'),"\n"; } ------------------------------------------------------ A future bioperl SOAP interface for eutils is also not out of the question either, just haven't had time to play around with it. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Fri Nov 17 19:35:11 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 17 Nov 2006 19:35:11 +0000 Subject: [Bioperl-l] CPAN Versioning, was [something else] In-Reply-To: <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> Message-ID: <455E0EEF.4080806@sendu.me.uk> Chris Fields wrote: > > On Nov 17, 2006, at 11:43 AM, Sendu Bala wrote: > >> Nathan S. Haigh wrote: >>> Can you name the file bioperl-1.5.2-RC_4.tar.gz and have it picked up as >>> a developer release? >> >> I didn't try that variation, but have decided to go with >> bioperl-1.5.2_004-RC.tar.gz which certainly is picked up as a developer >> release. >> >> I've outlined the numbering scheme here: >> http://www.bioperl.org/wiki/Making_a_BioPerl_release#Making_the_distribution_directory >> > > I noticed that Module::Build now has a developer release that uses this: > > Module-Build-0.2805_01.tar.gz > > So the '_###' seems to be key. If so I see a versioning dilemma that > depends on what we want to call rel 1.5.2. [snip] See the page I linked above. It shows what the filenames will be for RCs , releases and point releases for developer and non-developer releases. From gwu at molbio.mgh.harvard.edu Sat Nov 18 06:39:46 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 01:39:46 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455E0EEF.4080806@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> Message-ID: <455EAAB2.4010004@molbio.mgh.harvard.edu> Hi everyone, I saw some problems when installing BioPerl 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could not solve all the dependency issues with one shot of 'install Bundle::BioPerl'. Some packages such as GD-2.35 just could not be installed. And it turned out that CPAN refused to install BioPerl with some test return value 255. Then I went to /root/.cpan/build to configure, test, rebuild those problematic packages. After several more runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl successfully. Below attached is the output of CPAN, which stills complains three packages have issues: Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel. I think the first two are typos somewhere in the Bundle::BioPerl. And the third module is not on the server and could be found on the CPAN site. So my question is : Is this the right way to install BioPerl? It took me two days to figure it out but still not 100% sure all packages are installed properly. Any feedback is appreciated. Gang ================================================= cpan> install Bundle::BioPerl Ace is up to date. Bio::ASN1::EntrezGene is up to date. Class::AutoClass is up to date. Clone is up to date. Convert::Binary::C is up to date. Running install for module Data::Stag::writer The module Data::Stag::writer isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i Data::Stag::writer'. DBD::mysql is up to date. GD::SVG is up to date. GD is up to date. Graph::Directed is up to date. HTML::Parser is up to date. Running install for module HTTP::Request::Common- The module HTTP::Request::Common- isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i HTTP::Request::Common-'. LWP::UserAgent is up to date. Set::Scalar is up to date. SOAP::Lite is up to date. Running install for module Spreadhseet::ParseExcel The module Spreadhseet::ParseExcel isn't available on CPAN. Either the module has not yet been uploaded to CPAN, or it is temporary unavailable. Please contact the author to find out more about the status. Try 'i Spreadhseet::ParseExcel'. Storable is up to date. SVG is up to date. SVG::Graph is up to date. Text::Shellwords is up to date. XML::DOM::XPath is up to date. XML::Parser::PerlSAX is up to date. XML::SAX is up to date. XML::SAX::Base is up to date. XML::SAX::Writer is up to date. XML::Simple is up to date. XML::Twig is up to date. XML::Writer is up to date. Bundle summary: The following items in bundle Bundle::BioPerl had installation problems: Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel ==================================================== From bix at sendu.me.uk Sat Nov 18 08:04:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 18 Nov 2006 08:04:14 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <455EBE7E.4060105@sendu.me.uk> gang wu wrote: > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. What problems did you run into specifically with GD? > And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. Do you remember what the other problematic packages were, and what you had to do to get them working? > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. All three are typos. We'll get those fixed. > So my question is : Is this the right way to install BioPerl? At the present moment, yes. For 1.5.2 I'll probably be recommending not using Bundle::BioPerl once I fix some other things. > It took me two days to figure it out but still not 100% sure all packages are > installed properly. I'm sorry for the troubles you ran into. We'll try and do better for the final release of 1.5.2. From gwu at molbio.mgh.harvard.edu Sat Nov 18 08:07:47 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:07:47 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <455EBF53.4010701@molbio.mgh.harvard.edu> It turned out that most of the modules of BioPerl were not installed at all. And none of the scripts were installed. I had to download and install bioperl-1.5.2-RC3.tar.gz again. A similar problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually copied all stuff under Bio folder to the corresponding Perl library folder. Is it Ok to do it in this way? Gang gang wu wrote: > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. > > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. > > So my question is : Is this the right way to install BioPerl? It took me > two days to figure it out but still not 100% sure all packages are > installed properly. > > Any feedback is appreciated. > > Gang > > ================================================= > cpan> install Bundle::BioPerl > Ace is up to date. > Bio::ASN1::EntrezGene is up to date. > Class::AutoClass is up to date. > Clone is up to date. > Convert::Binary::C is up to date. > Running install for module Data::Stag::writer > > The module Data::Stag::writer isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Data::Stag::writer'. > DBD::mysql is up to date. > GD::SVG is up to date. > GD is up to date. > Graph::Directed is up to date. > HTML::Parser is up to date. > Running install for module HTTP::Request::Common- > > The module HTTP::Request::Common- isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i HTTP::Request::Common-'. > LWP::UserAgent is up to date. > Set::Scalar is up to date. > SOAP::Lite is up to date. > Running install for module Spreadhseet::ParseExcel > > The module Spreadhseet::ParseExcel isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Spreadhseet::ParseExcel'. > Storable is up to date. > SVG is up to date. > SVG::Graph is up to date. > Text::Shellwords is up to date. > XML::DOM::XPath is up to date. > XML::Parser::PerlSAX is up to date. > XML::SAX is up to date. > XML::SAX::Base is up to date. > XML::SAX::Writer is up to date. > XML::Simple is up to date. > XML::Twig is up to date. > XML::Writer is up to date. > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > ==================================================== > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From N.Haigh at sheffield.ac.uk Sat Nov 18 08:22:00 2006 From: N.Haigh at sheffield.ac.uk (Nathan Haigh) Date: Sat, 18 Nov 2006 08:22:00 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EAAB2.4010004@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> Message-ID: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Hi Gang, At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - we are in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things wrong with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such that it may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 and CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as dependencies will fail to install. I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - these will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install process much easier to the users. Thanks Nathan Quoting gang wu : > Hi everyone, > > I saw some problems when installing BioPerl > 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > not solve all the dependency issues with one shot of 'install > Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > installed. And it turned out that CPAN refused to install BioPerl with > some test return value 255. Then I went to /root/.cpan/build to > configure, test, rebuild those problematic packages. After several more > runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > successfully. > > Below attached is the output of CPAN, which stills complains three > packages have issues: Data::Stag::writer HTTP::Request::Common- > Spreadhseet::ParseExcel. I think the first two are typos somewhere in > the Bundle::BioPerl. And the third module is not on the server and could > be found on the CPAN site. > > So my question is : Is this the right way to install BioPerl? It took me > two days to figure it out but still not 100% sure all packages are > installed properly. > > Any feedback is appreciated. > > Gang > > ================================================= > cpan> install Bundle::BioPerl > Ace is up to date. > Bio::ASN1::EntrezGene is up to date. > Class::AutoClass is up to date. > Clone is up to date. > Convert::Binary::C is up to date. > Running install for module Data::Stag::writer > > The module Data::Stag::writer isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Data::Stag::writer'. > DBD::mysql is up to date. > GD::SVG is up to date. > GD is up to date. > Graph::Directed is up to date. > HTML::Parser is up to date. > Running install for module HTTP::Request::Common- > > The module HTTP::Request::Common- isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i HTTP::Request::Common-'. > LWP::UserAgent is up to date. > Set::Scalar is up to date. > SOAP::Lite is up to date. > Running install for module Spreadhseet::ParseExcel > > The module Spreadhseet::ParseExcel isn't available on CPAN. > > Either the module has not yet been uploaded to CPAN, or it is > temporary unavailable. Please contact the author to find out > more about the status. Try 'i Spreadhseet::ParseExcel'. > Storable is up to date. > SVG is up to date. > SVG::Graph is up to date. > Text::Shellwords is up to date. > XML::DOM::XPath is up to date. > XML::Parser::PerlSAX is up to date. > XML::SAX is up to date. > XML::SAX::Base is up to date. > XML::SAX::Writer is up to date. > XML::Simple is up to date. > XML::Twig is up to date. > XML::Writer is up to date. > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > ==================================================== > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From gwu at molbio.mgh.harvard.edu Sat Nov 18 08:30:30 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:30:30 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EBE7E.4060105@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> Message-ID: <455EC4A6.4040103@molbio.mgh.harvard.edu> Sendu Bala wrote: > gang wu wrote: >> Hi everyone, >> >> I saw some problems when installing BioPerl >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could >> not solve all the dependency issues with one shot of 'install >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >> installed. > > What problems did you run into specifically with GD? If I enable JPEG, GIFS and XPM, none of the test could pass. Since I usually use only PNG for output, I can live without them. I am not sure if it's system related problem. All of them work fine with my 32 bit Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with newer libgd runnig Redhat AS4 AMD/EM64T does not work. > >> And it turned out that CPAN refused to install BioPerl with >> some test return value 255. Then I went to /root/.cpan/build to >> configure, test, rebuild those problematic packages. After several more >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >> successfully. > > Do you remember what the other problematic packages were, and what you > had to do to get them working? > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I guess it should be XML::DOM::XPath.pm. I could not recall what other packages had issues, but basically it's special package configuration issue. >> Below attached is the output of CPAN, which stills complains three >> packages have issues: Data::Stag::writer HTTP::Request::Common- >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in >> the Bundle::BioPerl. And the third module is not on the server and could >> be found on the CPAN site. > > All three are typos. We'll get those fixed. > > >> So my question is : Is this the right way to install BioPerl? > > At the present moment, yes. For 1.5.2 I'll probably be recommending > not using Bundle::BioPerl once I fix some other things. > See my another message for other issues. > >> It took me two days to figure it out but still not 100% sure all >> packages are >> installed properly. > > I'm sorry for the troubles you ran into. We'll try and do better for > the final release of 1.5.2. Actually your hard work is benifiting the whole community and we all owe you a Thank You. From gwu at molbio.mgh.harvard.edu Sat Nov 18 08:44:45 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:44:45 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Message-ID: <455EC7FD.5010707@molbio.mgh.harvard.edu> Hi Nathan, Thanks for your message. I saw the C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you use 'install Bundle::BioPerl', which will definitely frustrate a bunch of users. Can this release be held for a while before most of the bugs are cleared? Thanks again. Gang Gang Nathan Haigh wrote: > Hi Gang, > > At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - we are > in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things wrong > with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). > > I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such that it > may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 and > CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as > dependencies will fail to install. > > I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - these > will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. > > If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install process > much easier to the users. > > Thanks > Nathan > > > Quoting gang wu : > > >> Hi everyone, >> >> I saw some problems when installing BioPerl >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could >> not solve all the dependency issues with one shot of 'install >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >> installed. And it turned out that CPAN refused to install BioPerl with >> some test return value 255. Then I went to /root/.cpan/build to >> configure, test, rebuild those problematic packages. After several more >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >> successfully. >> >> Below attached is the output of CPAN, which stills complains three >> packages have issues: Data::Stag::writer HTTP::Request::Common- >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in >> the Bundle::BioPerl. And the third module is not on the server and could >> be found on the CPAN site. >> >> So my question is : Is this the right way to install BioPerl? It took me >> two days to figure it out but still not 100% sure all packages are >> installed properly. >> >> Any feedback is appreciated. >> >> Gang >> >> ================================================= >> cpan> install Bundle::BioPerl >> Ace is up to date. >> Bio::ASN1::EntrezGene is up to date. >> Class::AutoClass is up to date. >> Clone is up to date. >> Convert::Binary::C is up to date. >> Running install for module Data::Stag::writer >> >> The module Data::Stag::writer isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i Data::Stag::writer'. >> DBD::mysql is up to date. >> GD::SVG is up to date. >> GD is up to date. >> Graph::Directed is up to date. >> HTML::Parser is up to date. >> Running install for module HTTP::Request::Common- >> >> The module HTTP::Request::Common- isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i HTTP::Request::Common-'. >> LWP::UserAgent is up to date. >> Set::Scalar is up to date. >> SOAP::Lite is up to date. >> Running install for module Spreadhseet::ParseExcel >> >> The module Spreadhseet::ParseExcel isn't available on CPAN. >> >> Either the module has not yet been uploaded to CPAN, or it is >> temporary unavailable. Please contact the author to find out >> more about the status. Try 'i Spreadhseet::ParseExcel'. >> Storable is up to date. >> SVG is up to date. >> SVG::Graph is up to date. >> Text::Shellwords is up to date. >> XML::DOM::XPath is up to date. >> XML::Parser::PerlSAX is up to date. >> XML::SAX is up to date. >> XML::SAX::Base is up to date. >> XML::SAX::Writer is up to date. >> XML::Simple is up to date. >> XML::Twig is up to date. >> XML::Writer is up to date. >> Bundle summary: The following items in bundle Bundle::BioPerl had >> installation problems: >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >> ==================================================== >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 gwu at molbio.mgh.harvard.edu Sat Nov 18 08:57:49 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 03:57:49 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <455EC4A6.4040103@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> Message-ID: <455ECB0D.5090606@molbio.mgh.harvard.edu> Hi everyone, I used to use MySQL to host the BioSQL schema and load Genbank into it with the 'load_seqdatabase.pl' without problem(except extremely slow. It took about 12 hours to load Arabidopsis thaliana). I just loaded the BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database without problem. When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with MySQL while always saw an error with Oracle: Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. , where the code is $sth->bind_param(); Any idea what the problem is? Gang From N.Haigh at sheffield.ac.uk Sat Nov 18 09:56:57 2006 From: N.Haigh at sheffield.ac.uk (Nathan Haigh) Date: Sat, 18 Nov 2006 09:56:57 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EC7FD.5010707@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> Message-ID: <1163843817.455ed8e970075@webmail.shef.ac.uk> Hi Chris, Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it contains some errors. I think Sendu *may* have some further instructions regarding this package a bit closer to the 1.5.2 release. Cheers Nathan Quoting gang wu : > Hi Nathan, > > Thanks for your message. I saw the > C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you > use 'install Bundle::BioPerl', which will definitely frustrate a bunch > of users. Can this release be held for a while before most of the bugs > are cleared? > > Thanks again. > Gang > > > Gang > > Nathan Haigh wrote: > > Hi Gang, > > > > At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - > we are > > in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things > wrong > > with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before). > > > > I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such > that it > > may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 > and > > CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as > > dependencies will fail to install. > > > > I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - > these > > will definately be sorted out by the time of the 1.5.2 release in a matter of weeks. > > > > If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install > process > > much easier to the users. > > > > Thanks > > Nathan > > > > > > Quoting gang wu : > > > > > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > >> > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in > >> the Bundle::BioPerl. And the third module is not on the server and could > >> be found on the CPAN site. > >> > >> So my question is : Is this the right way to install BioPerl? It took me > >> two days to figure it out but still not 100% sure all packages are > >> installed properly. > >> > >> Any feedback is appreciated. > >> > >> Gang > >> > >> ================================================= > >> cpan> install Bundle::BioPerl > >> Ace is up to date. > >> Bio::ASN1::EntrezGene is up to date. > >> Class::AutoClass is up to date. > >> Clone is up to date. > >> Convert::Binary::C is up to date. > >> Running install for module Data::Stag::writer > >> > >> The module Data::Stag::writer isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i Data::Stag::writer'. > >> DBD::mysql is up to date. > >> GD::SVG is up to date. > >> GD is up to date. > >> Graph::Directed is up to date. > >> HTML::Parser is up to date. > >> Running install for module HTTP::Request::Common- > >> > >> The module HTTP::Request::Common- isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i HTTP::Request::Common-'. > >> LWP::UserAgent is up to date. > >> Set::Scalar is up to date. > >> SOAP::Lite is up to date. > >> Running install for module Spreadhseet::ParseExcel > >> > >> The module Spreadhseet::ParseExcel isn't available on CPAN. > >> > >> Either the module has not yet been uploaded to CPAN, or it is > >> temporary unavailable. Please contact the author to find out > >> more about the status. Try 'i Spreadhseet::ParseExcel'. > >> Storable is up to date. > >> SVG is up to date. > >> SVG::Graph is up to date. > >> Text::Shellwords is up to date. > >> XML::DOM::XPath is up to date. > >> XML::Parser::PerlSAX is up to date. > >> XML::SAX is up to date. > >> XML::SAX::Base is up to date. > >> XML::SAX::Writer is up to date. > >> XML::Simple is up to date. > >> XML::Twig is up to date. > >> XML::Writer is up to date. > >> Bundle summary: The following items in bundle Bundle::BioPerl had > >> installation problems: > >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > >> ==================================================== > >> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/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 uiuc.edu Sat Nov 18 14:35:38 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 18 Nov 2006 08:35:38 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163843817.455ed8e970075@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> Message-ID: It probably doesn't need to be pulled, just updated to fix errors, spelling, etc. The problems reported with GD are common and normally are due to libgd issues or C code compilation problems during the test run (the DEPENDENCIES doc and wiki page indicate this). DBI/ DBD::mysql is another one that sometimes requires finessing (I remember it giving problems on CygWin and Mac OS X). Chris D. probably just needs a list of issues that need fixing. You also have to realize we're heading into Thanksgiving so some people may be incommunicado for the time being. Spelling is the main problem. Beyond that there really isn't anything we can do about those requirements beside not requiring them (i.e. removing them then explaining that particular components won't work), but then it wouldn't be a proper Bundle package. It's a catch-22. If there isn't a place in the install docs yet some of these issues could use a bit more detail or explanation, or at least redirect to some proper installation instructions based on the platform. I think, now that this is on CPAN, you'll likely see many more questions popping up. Chris (F.) On Nov 18, 2006, at 3:56 AM, Nathan Haigh wrote: > Hi Chris, > > Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it > contains some errors. I think Sendu *may* have some further > instructions regarding > this package a bit closer to the 1.5.2 release. > > Cheers > Nathan > > > > Quoting gang wu : > >> Hi Nathan, >> >> Thanks for your message. I saw the >> C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you >> use 'install Bundle::BioPerl', which will definitely frustrate a >> bunch >> of users. Can this release be held for a while before most of the >> bugs >> are cleared? >> >> Thanks again. >> Gang >> >> >> Gang >> >> Nathan Haigh wrote: >>> Hi Gang, >>> >>> At the moment we are having a few teathing problems with CPAN >>> packages. I notice that you are trying to install the 1.5.2 >>> release candidate 3 - >> we are >>> in the final stages of getting out the official 1.5.2 developer >>> release (hopefully in the next couple of weeks). There are indeed >>> a few things >> wrong >>> with the latest Bundle::BioPerl package but we thought we'd hold >>> off updating it until the 1.5.2 release (or shortly before). >>> >>> I think that the problem with CPAN installing dependencies is >>> that it has no way to correctly ordering the installation of >>> dependencies, such >> that it >>> may be neccessary to run the install several time in order to get >>> everything installed. For example, if prerequisite 2 depends on >>> prerequisite 1 >> and >>> CPAN installs prerequisite 2 first, then it's test suite will >>> probably fail and thus the installation of the package siting >>> both these as >>> dependencies will fail to install. >>> >>> I believe you are correct in the way you are installing bioperl, >>> but we still have a few issues to sort out with regards to the >>> CPAN packages - >> these >>> will definately be sorted out by the time of the 1.5.2 release in >>> a matter of weeks. >>> >>> If anyone is aware of a way to force CPAN to install modules in a >>> specific order, please let Sendu know - we may be able to make >>> the install >> process >>> much easier to the users. >>> >>> Thanks >>> Nathan >>> >>> >>> Quoting gang wu : >>> >>> >>>> Hi everyone, >>>> >>>> I saw some problems when installing BioPerl >>>> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>>> CPAN could >>>> not solve all the dependency issues with one shot of 'install >>>> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>>> installed. And it turned out that CPAN refused to install >>>> BioPerl with >>>> some test return value 255. Then I went to /root/.cpan/build to >>>> configure, test, rebuild those problematic packages. After >>>> several more >>>> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>>> successfully. >>>> >>>> Below attached is the output of CPAN, which stills complains three >>>> packages have issues: Data::Stag::writer HTTP::Request::Common- >>>> Spreadhseet::ParseExcel. I think the first two are typos >>>> somewhere in >>>> the Bundle::BioPerl. And the third module is not on the server >>>> and could >>>> be found on the CPAN site. >>>> >>>> So my question is : Is this the right way to install BioPerl? It >>>> took me >>>> two days to figure it out but still not 100% sure all packages are >>>> installed properly. >>>> >>>> Any feedback is appreciated. >>>> >>>> Gang >>>> >>>> ================================================= >>>> cpan> install Bundle::BioPerl >>>> Ace is up to date. >>>> Bio::ASN1::EntrezGene is up to date. >>>> Class::AutoClass is up to date. >>>> Clone is up to date. >>>> Convert::Binary::C is up to date. >>>> Running install for module Data::Stag::writer >>>> >>>> The module Data::Stag::writer isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i Data::Stag::writer'. >>>> DBD::mysql is up to date. >>>> GD::SVG is up to date. >>>> GD is up to date. >>>> Graph::Directed is up to date. >>>> HTML::Parser is up to date. >>>> Running install for module HTTP::Request::Common- >>>> >>>> The module HTTP::Request::Common- isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i HTTP::Request::Common-'. >>>> LWP::UserAgent is up to date. >>>> Set::Scalar is up to date. >>>> SOAP::Lite is up to date. >>>> Running install for module Spreadhseet::ParseExcel >>>> >>>> The module Spreadhseet::ParseExcel isn't available on CPAN. >>>> >>>> Either the module has not yet been uploaded to CPAN, or it is >>>> temporary unavailable. Please contact the author to find out >>>> more about the status. Try 'i Spreadhseet::ParseExcel'. >>>> Storable is up to date. >>>> SVG is up to date. >>>> SVG::Graph is up to date. >>>> Text::Shellwords is up to date. >>>> XML::DOM::XPath is up to date. >>>> XML::Parser::PerlSAX is up to date. >>>> XML::SAX is up to date. >>>> XML::SAX::Base is up to date. >>>> XML::SAX::Writer is up to date. >>>> XML::Simple is up to date. >>>> XML::Twig is up to date. >>>> XML::Writer is up to date. >>>> Bundle summary: The following items in bundle Bundle::BioPerl had >>>> installation problems: >>>> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >>>> ==================================================== >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Sat Nov 18 17:13:10 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sat, 18 Nov 2006 12:13:10 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EC4A6.4040103@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> Message-ID: <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> What version of libgd do you have installed? With recent versions of libgd (more recent than two years old) you will not be given the chance to select whether to compile JPEG, GIF and XPM support, since these options are selected automatically by running libgd-config. Lincoln On 11/18/06, gang wu wrote: > > > Sendu Bala wrote: > > gang wu wrote: > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN > could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. > > > > What problems did you run into specifically with GD? > If I enable JPEG, GIFS and XPM, none of the test could pass. Since I > usually use only PNG for output, I can live without them. I am not sure > if it's system related problem. All of them work fine with my 32 bit > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with newer > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > >> And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > > > > Do you remember what the other problematic packages were, and what you > > had to do to get them working? > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > guess it should be XML::DOM::XPath.pm. I could not recall what other > packages had issues, but basically it's special package configuration > issue. > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos somewhere in > >> the Bundle::BioPerl. And the third module is not on the server and > could > >> be found on the CPAN site. > > > > All three are typos. We'll get those fixed. > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > At the present moment, yes. For 1.5.2 I'll probably be recommending > > not using Bundle::BioPerl once I fix some other things. > > > See my another message for other issues. > > > >> It took me two days to figure it out but still not 100% sure all > >> packages are > >> installed properly. > > > > I'm sorry for the troubles you ran into. We'll try and do better for > > the final release of 1.5.2. > Actually your hard work is benifiting the whole community and we all owe > you a Thank You. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From dag at sonsorol.org Sat Nov 18 17:47:07 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Sat, 18 Nov 2006 12:47:07 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> Message-ID: <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> Hi folks, On November 17th, Victor de Jager filed a bug report with CPAN (thanks Victor!) covering the following issues with the 2.1.6 bundle: > Bundle summary: The following items in bundle Bundle::BioPerl had > installation problems: > Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel > > This should be Spreadsheet::ParseExcel of course. > Data::Stag::writer does not exist in CPAN, should be > Data::Stag::Writer > > Hope it helps, meanwhile I got around using the CVS version. > Best regards I immediately fixed the errors and uploaded version 2.1.7 on the same day, by now it has probably propagated through the CPAN mirror system but you can find it directly here: http://search.cpan.org/~craffi/ Please let me know directly (email: dag at sonsorol.org) if there are *other* things that need to be added or updated. Sorry for the problems with 2.1.6 -- the contents of that Bundle were given to me by someone else on Oct 17th :) and I think I was sitting on a plane at the time and did not have time to do a local CPAN test with it. My apologies. Regards, Chris On Nov 18, 2006, at 9:35 AM, Chris Fields wrote: > It probably doesn't need to be pulled, just updated to fix errors, > spelling, etc. The problems reported with GD are common and > normally are due to libgd issues or C code compilation problems > during the test run (the DEPENDENCIES doc and wiki page indicate > this). DBI/DBD::mysql is another one that sometimes requires > finessing (I remember it giving problems on CygWin and Mac OS X). > Chris D. probably just needs a list of issues that need fixing. > You also have to realize we're heading into Thanksgiving so some > people may be incommunicado for the time being. > > Spelling is the main problem. Beyond that there really isn't > anything we can do about those requirements beside not requiring > them (i.e. removing them then explaining that particular components > won't work), but then it wouldn't be a proper Bundle package. It's > a catch-22. If there isn't a place in the install docs yet some of > these issues could use a bit more detail or explanation, or at > least redirect to some proper installation instructions based on > the platform. > > I think, now that this is on CPAN, you'll likely see many more > questions popping up. > > Chris (F.) > > On Nov 18, 2006, at 3:56 AM, Nathan Haigh wrote: > >> Hi Chris, >> >> Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it >> contains some errors. I think Sendu *may* have some further >> instructions regarding >> this package a bit closer to the 1.5.2 release. >> >> Cheers >> Nathan >> >> >> >> Quoting gang wu : >> >>> Hi Nathan, >>> >>> Thanks for your message. I saw the >>> C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if >>> you >>> use 'install Bundle::BioPerl', which will definitely frustrate a >>> bunch >>> of users. Can this release be held for a while before most of the >>> bugs >>> are cleared? >>> >>> Thanks again. >>> Gang >>> >>> >>> Gang >>> >>> Nathan Haigh wrote: >>>> Hi Gang, >>>> >>>> At the moment we are having a few teathing problems with CPAN >>>> packages. I notice that you are trying to install the 1.5.2 >>>> release candidate 3 - >>> we are >>>> in the final stages of getting out the official 1.5.2 developer >>>> release (hopefully in the next couple of weeks). There are >>>> indeed a few things >>> wrong >>>> with the latest Bundle::BioPerl package but we thought we'd hold >>>> off updating it until the 1.5.2 release (or shortly before). >>>> >>>> I think that the problem with CPAN installing dependencies is >>>> that it has no way to correctly ordering the installation of >>>> dependencies, such >>> that it >>>> may be neccessary to run the install several time in order to >>>> get everything installed. For example, if prerequisite 2 depends >>>> on prerequisite 1 >>> and >>>> CPAN installs prerequisite 2 first, then it's test suite will >>>> probably fail and thus the installation of the package siting >>>> both these as >>>> dependencies will fail to install. >>>> >>>> I believe you are correct in the way you are installing bioperl, >>>> but we still have a few issues to sort out with regards to the >>>> CPAN packages - >>> these >>>> will definately be sorted out by the time of the 1.5.2 release >>>> in a matter of weeks. >>>> >>>> If anyone is aware of a way to force CPAN to install modules in >>>> a specific order, please let Sendu know - we may be able to make >>>> the install >>> process >>>> much easier to the users. >>>> >>>> Thanks >>>> Nathan >>>> >>>> >>>> Quoting gang wu : >>>> >>>> >>>>> Hi everyone, >>>>> >>>>> I saw some problems when installing BioPerl >>>>> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>>>> CPAN could >>>>> not solve all the dependency issues with one shot of 'install >>>>> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>>>> installed. And it turned out that CPAN refused to install >>>>> BioPerl with >>>>> some test return value 255. Then I went to /root/.cpan/build to >>>>> configure, test, rebuild those problematic packages. After >>>>> several more >>>>> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>>>> successfully. >>>>> >>>>> Below attached is the output of CPAN, which stills complains three >>>>> packages have issues: Data::Stag::writer HTTP::Request::Common- >>>>> Spreadhseet::ParseExcel. I think the first two are typos >>>>> somewhere in >>>>> the Bundle::BioPerl. And the third module is not on the server >>>>> and could >>>>> be found on the CPAN site. >>>>> >>>>> So my question is : Is this the right way to install BioPerl? >>>>> It took me >>>>> two days to figure it out but still not 100% sure all packages are >>>>> installed properly. >>>>> >>>>> Any feedback is appreciated. >>>>> >>>>> Gang >>>>> >>>>> ================================================= >>>>> cpan> install Bundle::BioPerl >>>>> Ace is up to date. >>>>> Bio::ASN1::EntrezGene is up to date. >>>>> Class::AutoClass is up to date. >>>>> Clone is up to date. >>>>> Convert::Binary::C is up to date. >>>>> Running install for module Data::Stag::writer >>>>> >>>>> The module Data::Stag::writer isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i Data::Stag::writer'. >>>>> DBD::mysql is up to date. >>>>> GD::SVG is up to date. >>>>> GD is up to date. >>>>> Graph::Directed is up to date. >>>>> HTML::Parser is up to date. >>>>> Running install for module HTTP::Request::Common- >>>>> >>>>> The module HTTP::Request::Common- isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i HTTP::Request::Common-'. >>>>> LWP::UserAgent is up to date. >>>>> Set::Scalar is up to date. >>>>> SOAP::Lite is up to date. >>>>> Running install for module Spreadhseet::ParseExcel >>>>> >>>>> The module Spreadhseet::ParseExcel isn't available on CPAN. >>>>> >>>>> Either the module has not yet been uploaded to CPAN, or it is >>>>> temporary unavailable. Please contact the author to find out >>>>> more about the status. Try 'i Spreadhseet::ParseExcel'. >>>>> Storable is up to date. >>>>> SVG is up to date. >>>>> SVG::Graph is up to date. >>>>> Text::Shellwords is up to date. >>>>> XML::DOM::XPath is up to date. >>>>> XML::Parser::PerlSAX is up to date. >>>>> XML::SAX is up to date. >>>>> XML::SAX::Base is up to date. >>>>> XML::SAX::Writer is up to date. >>>>> XML::Simple is up to date. >>>>> XML::Twig is up to date. >>>>> XML::Writer is up to date. >>>>> Bundle summary: The following items in bundle Bundle::BioPerl had >>>>> installation problems: >>>>> Data::Stag::writer HTTP::Request::Common- >>>>> Spreadhseet::ParseExcel >>>>> ==================================================== >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/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 > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > From n.haigh at sheffield.ac.uk Sat Nov 18 18:32:17 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Sat, 18 Nov 2006 18:32:17 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> <455EC7FD.5010707@molbio.mgh.harvard.edu> <1163843817.455ed8e970075@webmail.shef.ac.uk> <1417791E-A9C0-4F76-BEF6-6EA485D2B981@sonsorol.org> Message-ID: <455F51B1.6000301@sheffield.ac.uk> Chris Dagdigian wrote: > > Hi folks, > > On November 17th, Victor de Jager filed a bug report with CPAN (thanks > Victor!) covering the following issues with the 2.1.6 bundle: > >> Bundle summary: The following items in bundle Bundle::BioPerl had >> installation problems: >> Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel >> >> This should be Spreadsheet::ParseExcel of course. >> Data::Stag::writer does not exist in CPAN, should be Data::Stag::Writer >> >> Hope it helps, meanwhile I got around using the CVS version. >> Best regards > > I immediately fixed the errors and uploaded version 2.1.7 on the same > day, by now it has probably propagated through the CPAN mirror system > but you can find it directly here: > > http://search.cpan.org/~craffi/ > > Please let me know directly (email: dag at sonsorol.org) if there are > *other* things that need to be added or updated. > > Sorry for the problems with 2.1.6 -- the contents of that Bundle were > given to me by someone else on Oct 17th :) and I think I was sitting > on a plane at the time and did not have time to do a local CPAN test > with it. My apologies. > > Regards, > Chris > > That was me - my bad! :-[ Nath From hlapp at gmx.net Sun Nov 19 03:08:00 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 18 Nov 2006 22:08:00 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <455ECB0D.5090606@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> Message-ID: <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> This is very odd. I would mean that preparing the statement failed, i.e., that the generated SQL was not accepted by the server (or the Oracle client library). Which test does this happen with? Could you run the test alone in which it happens with TEST_VERBOSE turned on? E.g., $ make test_03simpleseq TEST_VERBOSE=1 if it's the simpleseq test that's causing the failure. Capture the output in a file and send it to me. -hilmar On Nov 18, 2006, at 3:57 AM, gang wu wrote: > Hi everyone, > > I used to use MySQL to host the BioSQL schema and load Genbank into it > with the 'load_seqdatabase.pl' without problem(except extremely > slow. It > took about 12 hours to load Arabidopsis thaliana). I just loaded the > BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database > without > problem. > > When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with > MySQL while always saw an error with Oracle: > Can't call method "bind_param" on an undefined value at > /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm > line 939. > > , where the code is $sth->bind_param(); > > Any idea what the problem is? > > Gang > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From gwu at molbio.mgh.harvard.edu Sun Nov 19 03:09:08 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Sat, 18 Nov 2006 22:09:08 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> Message-ID: <455FCAD4.7050709@molbio.mgh.harvard.edu> Lincoln, Thanks for your message. I have gd-2.0.28-4.4E.1 and gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. Attached is the output. Gang ================================================== [root at elegans GD-2.35]# perl Makefile.PL NOTICE: This module requires libgd 2.0.28 or higher. If you are using Math::Trig 1.01 or lower, it has a bug that causes a "prerequisite not found" warning to be issued. You may safely ignore this warning. Type perl Makefile.PL -h for command-line option summary Where is libgd installed? [/usr/lib] Please choose the features that match how libgd was built: Build JPEG support? [y] Build PNG support? [y] Build FreeType support? [y] Build GIF support? [y] Build support for animated GIFs? [y] Build XPM support? [y] If you experience compile problems, please check the @INC, @LIBPATH and @LIBS arrays defined in Makefile.PL and manually adjust, if necessary. Checking if your kit is complete... Looks good Writing Makefile for GD [root at elegans GD-2.35]# make cp GD/Polyline.pm blib/lib/GD/Polyline.pm cp qd.pl blib/lib/qd.pl cp GD/Image.pm blib/lib/GD/Image.pm cp GD.pm blib/lib/GD.pm AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) cp GD/Simple.pm blib/lib/GD/Simple.pm cp GD/Polygon.pm blib/lib/GD/Polygon.pm /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc && mv GD.xsc GD.c gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c GD.xs: In function `XS_GD__Image_STORABLE_thaw': GD.xs:923: warning: cast from pointer to integer of different size GD.xs: In function `XS_GD__Image_gifanimbegin': GD.xs:990: warning: cast to pointer from integer of different size GD.xs: In function `XS_GD__Image_gifanimadd': GD.xs:1015: warning: cast to pointer from integer of different size GD.xs: In function `XS_GD__Image_gifanimend': GD.xs:1034: warning: cast to pointer from integer of different size Running Mkbootstrap for GD () chmod 644 GD.bs rm -f blib/arch/auto/GD/GD.so gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11 /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11 /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when searching for -lXpm /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when searching for -lXpm /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc chmod 755 blib/arch/auto/GD/GD.so cp GD.bs blib/arch/auto/GD/GD.bs chmod 644 blib/arch/auto/GD/GD.bs cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bdf2gdfont.pl Manifying blib/man1/bdf2gdfont.pl.1 Manifying blib/man3/GD::Polyline.3pm Manifying blib/man3/GD::Image.3pm Manifying blib/man3/GD::Simple.3pm Manifying blib/man3/GD.3pm Manifying blib/man3/GD::Polygon.3pm [root at elegans GD-2.35]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. at t/GD.t line 14 Compilation failed in require at t/GD.t line 14. BEGIN failed--compilation aborted at t/GD.t line 14. t/GD..........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-12 Failed 12/12 tests, 0.00% okay t/Polyline....Can't load '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 Compilation failed in require at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. BEGIN failed--compilation aborted at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. Compilation failed in require at t/Polyline.t line 10. BEGIN failed--compilation aborted at t/Polyline.t line 10. t/Polyline....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED test 1 Failed 1/1 tests, 0.00% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/GD.t 255 65280 12 23 191.67% 1-12 t/Polyline.t 255 65280 1 2 200.00% 1 Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. make: *** [test_dynamic] Error 255 [root at elegans GD-2.35]# =========================================================== Lincoln Stein wrote: > What version of libgd do you have installed? With recent versions of > libgd (more recent than two years old) you will not be given the > chance to select whether to compile JPEG, GIF and XPM support, since > these options are selected automatically by running libgd-config. > > Lincoln > > On 11/18/06, *gang wu* > wrote: > > > Sendu Bala wrote: > > gang wu wrote: > >> Hi everyone, > >> > >> I saw some problems when installing BioPerl > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously > CPAN could > >> not solve all the dependency issues with one shot of 'install > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > >> installed. > > > > What problems did you run into specifically with GD? > If I enable JPEG, GIFS and XPM, none of the test could pass. Since I > usually use only PNG for output, I can live without them. I am not > sure > if it's system related problem. All of them work fine with my 32 bit > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with > newer > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > >> And it turned out that CPAN refused to install BioPerl with > >> some test return value 255. Then I went to /root/.cpan/build to > >> configure, test, rebuild those problematic packages. After > several more > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > >> successfully. > > > > Do you remember what the other problematic packages were, and > what you > > had to do to get them working? > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > guess it should be XML::DOM::XPath.pm. I could not recall what other > packages had issues, but basically it's special package > configuration issue. > >> Below attached is the output of CPAN, which stills complains three > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > >> Spreadhseet::ParseExcel. I think the first two are typos > somewhere in > >> the Bundle::BioPerl. And the third module is not on the server > and could > >> be found on the CPAN site. > > > > All three are typos. We'll get those fixed. > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > At the present moment, yes. For 1.5.2 I'll probably be recommending > > not using Bundle::BioPerl once I fix some other things. > > > See my another message for other issues. > > > >> It took me two days to figure it out but still not 100% sure all > >> packages are > >> installed properly. > > > > I'm sorry for the troubles you ran into. We'll try and do better for > > the final release of 1.5.2. > Actually your hard work is benifiting the whole community and we > all owe > you a Thank You. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu From bix at sendu.me.uk Sun Nov 19 15:51:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 19 Nov 2006 15:51:55 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455EBF53.4010701@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> Message-ID: <45607D9B.4010703@sendu.me.uk> gang wu wrote: > It turned out that most of the modules of BioPerl were not installed at > all. And none of the scripts were installed. I had to download and > install bioperl-1.5.2-RC3.tar.gz > again. A similar > problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually > copied all stuff under Bio folder to the corresponding Perl library > folder. Is it Ok to do it in this way? It will work, but is hardly good enough from our point of view (you shouldn't have to do that). Can you tell me exactly what you mean by 'were not installed'? What did you do to try and install? How did you determine that installation had failed? With CPAN, if you were still getting errors during testing, what were those remaining errors, and did you do a forced install to ignore the errors? If a forced install didn't actually install anything, what message did CPAN give you about that, if any? With the manual download, after doing "perl Makefile.PL", what is your output of "make install"? Thank you, Sendu. From lincoln.stein at gmail.com Sun Nov 19 15:54:11 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sun, 19 Nov 2006 10:54:11 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <455FCAD4.7050709@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> <455FCAD4.7050709@molbio.mgh.harvard.edu> Message-ID: <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> That's very odd. gd.0.28 should install gdlib-config, and the existence of this executable should inhibit the interactive questions. Could you see if there's a gdlib-config executable installed on your system? Lincoln On 11/18/06, gang wu wrote: > > Lincoln, > Thanks for your message. I have gd-2.0.28-4.4E.1 and > gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. > Attached is the output. > > Gang > > ================================================== > [root at elegans GD-2.35]# perl Makefile.PL > NOTICE: This module requires libgd 2.0.28 or higher. > > If you are using Math::Trig 1.01 or lower, it has a bug that > causes a "prerequisite not found" warning to be issued. You may > safely ignore this warning. > > Type perl Makefile.PL -h for command-line option summary > > > Where is libgd installed? [/usr/lib] > > Please choose the features that match how libgd was built: > Build JPEG support? [y] > Build PNG support? [y] > Build FreeType support? [y] > Build GIF support? [y] > Build support for animated GIFs? [y] > Build XPM support? [y] > > If you experience compile problems, please check the @INC, @LIBPATH and > @LIBS > arrays defined in Makefile.PL and manually adjust, if necessary. > > Checking if your kit is complete... > Looks good > Writing Makefile for GD > [root at elegans GD-2.35]# make > cp GD/Polyline.pm blib/lib/GD/Polyline.pm > cp qd.pl blib/lib/qd.pl > cp GD/Image.pm blib/lib/GD/Image.pm > cp GD.pm blib/lib/GD.pm > AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) > cp GD/Simple.pm blib/lib/GD/Simple.pm > cp GD/Polygon.pm blib/lib/GD/Polygon.pm > /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap > /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc > && mv GD.xsc GD.c > gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE > -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g > -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC > "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG > -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c > GD.xs: In function `XS_GD__Image_STORABLE_thaw': > GD.xs:923: warning: cast from pointer to integer of different size > GD.xs: In function `XS_GD__Image_gifanimbegin': > GD.xs:990: warning: cast to pointer from integer of different size > GD.xs: In function `XS_GD__Image_gifanimadd': > GD.xs:1015: warning: cast to pointer from integer of different size > GD.xs: In function `XS_GD__Image_gifanimend': > GD.xs:1034: warning: cast to pointer from integer of different size > Running Mkbootstrap for GD () > chmod 644 GD.bs > rm -f blib/arch/auto/GD/GD.so > gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 > -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 > -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm > /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz > /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz > /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm > /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when > searching for -lX11 > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when > searching for -lX11 > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when > searching for -lXpm > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when > searching for -lXpm > /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc > /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc > chmod 755 blib/arch/auto/GD/GD.so > cp GD.bs blib/arch/auto/GD/GD.bs > chmod 644 blib/arch/auto/GD/GD.bs > cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" > blib/script/bdf2gdfont.pl > Manifying blib/man1/bdf2gdfont.pl.1 > Manifying blib/man3/GD::Polyline.3pm > Manifying blib/man3/GD::Image.3pm > Manifying blib/man3/GD::Simple.3pm > Manifying blib/man3/GD.3pm > Manifying blib/man3/GD::Polygon.3pm > [root at elegans GD-2.35]# make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: > ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at > /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. > at t/GD.t line 14 > Compilation failed in require at t/GD.t line 14. > BEGIN failed--compilation aborted at t/GD.t line 14. > t/GD..........dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-12 > Failed 12/12 tests, 0.00% okay > t/Polyline....Can't load > '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: > /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: > gdImageGifAnimAddPtr at > /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. > at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 > Compilation failed in require at > /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. > BEGIN failed--compilation aborted at > /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. > Compilation failed in require at t/Polyline.t line 10. > BEGIN failed--compilation aborted at t/Polyline.t line 10. > t/Polyline....dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED test 1 > Failed 1/1 tests, 0.00% okay > Failed Test Stat Wstat Total Fail Failed List of Failed > > ------------------------------------------------------------------------------- > t/GD.t 255 65280 12 23 191.67% 1-12 > t/Polyline.t 255 65280 1 2 200.00% 1 > Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. > make: *** [test_dynamic] Error 255 > [root at elegans GD-2.35]# > =========================================================== > > Lincoln Stein wrote: > > What version of libgd do you have installed? With recent versions of > > libgd (more recent than two years old) you will not be given the > > chance to select whether to compile JPEG, GIF and XPM support, since > > these options are selected automatically by running libgd-config. > > > > Lincoln > > > > On 11/18/06, *gang wu* > > wrote: > > > > > > Sendu Bala wrote: > > > gang wu wrote: > > >> Hi everyone, > > >> > > >> I saw some problems when installing BioPerl > > >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously > > CPAN could > > >> not solve all the dependency issues with one shot of 'install > > >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be > > >> installed. > > > > > > What problems did you run into specifically with GD? > > If I enable JPEG, GIFS and XPM, none of the test could pass. Since > I > > usually use only PNG for output, I can live without them. I am not > > sure > > if it's system related problem. All of them work fine with my 32 bit > > Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with > > newer > > libgd runnig Redhat AS4 AMD/EM64T does not work. > > > > > >> And it turned out that CPAN refused to install BioPerl with > > >> some test return value 255. Then I went to /root/.cpan/build to > > >> configure, test, rebuild those problematic packages. After > > several more > > >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl > > >> successfully. > > > > > > Do you remember what the other problematic packages were, and > > what you > > > had to do to get them working? > > > > > XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I > > guess it should be XML::DOM::XPath.pm. I could not recall what other > > packages had issues, but basically it's special package > > configuration issue. > > >> Below attached is the output of CPAN, which stills complains > three > > >> packages have issues: Data::Stag::writer HTTP::Request::Common- > > >> Spreadhseet::ParseExcel. I think the first two are typos > > somewhere in > > >> the Bundle::BioPerl. And the third module is not on the server > > and could > > >> be found on the CPAN site. > > > > > > All three are typos. We'll get those fixed. > > > > > > > > >> So my question is : Is this the right way to install BioPerl? > > > > > > At the present moment, yes. For 1.5.2 I'll probably be > recommending > > > not using Bundle::BioPerl once I fix some other things. > > > > > See my another message for other issues. > > > > > >> It took me two days to figure it out but still not 100% sure all > > >> packages are > > >> installed properly. > > > > > > I'm sorry for the troubles you ran into. We'll try and do better > for > > > the final release of 1.5.2. > > Actually your hard work is benifiting the whole community and we > > all owe > > you a Thank You. > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From lincoln.stein at gmail.com Sun Nov 19 17:22:25 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sun, 19 Nov 2006 12:22:25 -0500 Subject: [Bioperl-l] [Gmod-gbrowse] aggregators issue? In-Reply-To: <455CE3CE.4060305@mail.med.upenn.edu> References: <455CE3CE.4060305@mail.med.upenn.edu> Message-ID: <6dce9a0b0611190922h7eb79928y46104c17266eccce@mail.gmail.com> Hi, What you want to do is what the heterogeneous_segments glyph does. The redgreen_box glyph originally only operated on the top level feature and not with aggregated features. However, since what you want to do is reasonable I've added a new color_subparts option, so that you will get the right effect with this modified stanza: [Linkage2] feature = qtl color_subparts = 1 glyph = redgreen_box key = Linkage2 You'll need to update bioperl to get this fix. The xyplot issue that you reported was a real bug in bioperl. This has now been fixed in both the release candidate and HEAD CVS repositories. Lincoln On 11/16/06, mmorley wrote: > > Hello All, > > Not sure where the problem lies but I'm trying to display results from a > Linkage analysis (many really).. > Perhaps my logic on the data structure is wrong but I have a peak > (locus,QTL,etc) that exceeds some defined significance that I have > predefined. > Within each peak there are markers (SNPs in this case) each with a level > of significance(score). Instead of displaying each SNP value as say in > XY plot... I have a score for the SNP to SNP interval.. The idea being > is I'd like to display the data using the redgreen_box glyph. > > To make it easier I created a little small test set which can be placed > on the Volvox tutorial ctgA > > Here is the gff data: > ---------------------------------------- > ctgA test peak 0 40000 . . . peak 3 ; Note > "EIF4G2" > ctgA test signal 0 1 0.4 . . peak 3 ; > ctgA test signal 2 25000 0.7 . . peak 3 ; > ctgA test signal 25000 35000 0.6 . . peak 3 ; > ctgA test signal 35000 40000 0.5 . . peak 3 ; > ctgA test peak 0 40000 . . . peak 10 ; Note "LRAP" > ctgA test signal 0 1 0.3 . . peak 10 ; > ctgA test signal 2 25000 0.4 . . peak 10 ; > ctgA test signal 25000 35000 0.7 . . peak 10 ; > ctgA test signal 35000 40000 0.5 . . peak 10 ; > --------------------------------------------------- > > here is my aggregator: > -------------------------------------- > qtl{signal/peak} > ----------------------------------------- > and my track: > --------------------------------------------- > [Linkage2] > feature = qtl > glyph = redgreen_box > key = Linkage2 > ------------------------------------------- > > right now very basic... the problem is well nothing is displayed using > that track... I do however get the label for each printed.. but no > graphic. If I change the feature to "signal" I do get data plotted but > each signal is on a different line,which is expected but not what I want. > > Also as a side note if I decide to plot the data as an xy_plot using the > following track stanza: > [Linkage] > feature = qtl > glyph = xyplot > graph_type = line > height = 50 > min_score = 0 > max_score = 1 > scale = right > key = Linkage > > I get both peaks plotted but within the same plot... However a second > plot is created it is just empty. > > Hopefully I'm convening this well... and if not hopefully fairly easy to > test... > > > -Mike > > > -- > Michael Morley > Bioinformatics Specialist > University of Pennsylvania > Department of Pediatrics > 3516 Civic Center Blvd., > 510B Abramson Pediatric Research Center, > Philadelphia, PA 19104-4318. > Phone: (215) 590-7673 > FAX: (215) 590-3709 > > > > > > > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From pmiguel at purdue.edu Mon Nov 20 00:58:42 2006 From: pmiguel at purdue.edu (Phillip SanMiguel) Date: Sun, 19 Nov 2006 19:58:42 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <45607D9B.4010703@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> Message-ID: <4560FDC2.4000309@purdue.edu> Sendu Bala wrote: > gang wu wrote: > >> It turned out that most of the modules of BioPerl were not installed at >> all. And none of the scripts were installed. I had to download and >> install bioperl-1.5.2-RC3.tar.gz >> again. A similar >> problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually >> copied all stuff under Bio folder to the corresponding Perl library >> folder. Is it Ok to do it in this way? >> > > It will work, but is hardly good enough from our point of view (you > shouldn't have to do that). > > Can you tell me exactly what you mean by 'were not installed'? What did > you do to try and install? How did you determine that installation had > failed? > > [...] My guess is that he thought that bioperl bundle installed the dependencies *and* bioperl itself. That was my presumption the first time I saw it on CPAN. -- Phillip From bikash_lohia2000 at yahoo.com Mon Nov 20 12:45:38 2006 From: bikash_lohia2000 at yahoo.com (bikash lohia) Date: Mon, 20 Nov 2006 04:45:38 -0800 (PST) Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi Message-ID: <20061120124538.40740.qmail@web54205.mail.yahoo.com> hello group, I am new to this group and want a help.i have list of accesion id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to manually search gene database of NCBI for converting this accession no. of cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i want to do it through perl programming where the program directly takes the list of id ( such as AK105331,Ak070197) from notepad file and searches in gene database of ncbi. to give results in accession id starting with OS****** .i want only the accession id of corresponding Ak***** id. for example - AK070197 of nucleotide databse = Os02g0669100 of gene database. i want to convert all this AK***** ids to OS***** ids through programming in perl/bioperl as manually not possible for long list. please help. i have no idea how can the code be. with thanks in advance from Bikash --------------------------------- Everyone is raving about the all-new Yahoo! Mail beta. From sdavis2 at mail.nih.gov Mon Nov 20 13:31:48 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 08:31:48 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi In-Reply-To: <20061120124538.40740.qmail@web54205.mail.yahoo.com> References: <20061120124538.40740.qmail@web54205.mail.yahoo.com> Message-ID: <200611200831.49098.sdavis2@mail.nih.gov> On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean From sdavis2 at mail.nih.gov Mon Nov 20 13:31:48 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 08:31:48 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to gene acc.id of gene database of ncbi In-Reply-To: <20061120124538.40740.qmail@web54205.mail.yahoo.com> References: <20061120124538.40740.qmail@web54205.mail.yahoo.com> Message-ID: <200611200831.49098.sdavis2@mail.nih.gov> On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean From avilella at gmail.com Mon Nov 20 14:53:08 2006 From: avilella at gmail.com (Albert Vilella) Date: Mon, 20 Nov 2006 14:53:08 +0000 Subject: [Bioperl-l] mmap perl Message-ID: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> Hi all, A bit of an off-topic: Has anyone ever investigated with libcache-mmap-perl or libcache-fastmmap-perl? Cheers, Albert. From cuiw at ncbi.nlm.nih.gov Mon Nov 20 15:45:13 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 10:45:13 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812330@NIHCESMLBX8.nih.gov> This script only works for 1 ACC to 1 Gene ID. perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 15:45:13 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 10:45:13 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812330@NIHCESMLBX8.nih.gov> This script only works for 1 ACC to 1 Gene ID. perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 16:03:44 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 11:03:44 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812332@NIHCESMLBX8.nih.gov> Correction: perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id")' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Mon Nov 20 16:03:44 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Mon, 20 Nov 2006 11:03:44 -0500 Subject: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi In-Reply-To: <200611200831.49098.sdavis2@mail.nih.gov> Message-ID: <18C407FD4FFB424292D769FBD68C198701812332@NIHCESMLBX8.nih.gov> Correction: perl -MLWP::Simple -e '($id = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&t erm=AK070197[acc]")) =~ s/(\A.*)|(<\/Id>.*\Z)//gxms; getprint ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id= $id")' Wenwu Cui -----Original Message----- From: Davis, Sean (NIH/NCI) [E] Sent: Monday, November 20, 2006 8:32 AM To: bioperl-l at lists.open-bio.org Cc: bikash lohia; bioperl1 Subject: Re: [Bioperl-l] to convert cDNA id of nucleotide database to geneacc.id of gene database of ncbi On Monday 20 November 2006 07:45, bikash lohia wrote: > hello group, I am new to this group and want a help.i have list of accesion > id of rice (oryza sativa)such as AK070197 , AK105331 etc i have to > manually search gene database of NCBI for converting this accession no. of > cDNA(eg.AK070197) to gene id of oryza sativa to get os******* gene id . i > want to do it through perl programming where the program directly takes the > list of id ( such as AK105331,Ak070197) from notepad file and searches in > gene database of ncbi. to give results in accession id starting with > OS****** .i want only the accession id of corresponding Ak***** id. for > example - AK070197 of nucleotide databse = Os02g0669100 of gene database. > i want to convert all this AK***** ids to OS***** ids through programming > in perl/bioperl as manually not possible for long list. please help. i > have no idea how can the code be. with thanks in advance from Bikash There is some useful data at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA The README file contains details of each file. The gene2accession.gz file contains genbank accession numbers and maps them back to Entrez Gene ID. The gene_info.gz file contains the Entrez Gene summary information for all Entrez Genes. With these two files (loaded into appropriate perl hashes), your task can be complete relatively easily. Alternatively, you could use the eUtils modules, which I think are available only via CVS. Sean _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From gwu at molbio.mgh.harvard.edu Mon Nov 20 15:57:48 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 10:57:48 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> Message-ID: <4561D07C.4060800@molbio.mgh.harvard.edu> Hi Hilmar, Thanks for your message. Below are several tests for Oracle and MySQL. MySQL actually also has two tests with failed items which may be related to data in BioSQL database. Could it be my Oracle installation/configuration has some issues? Thanks. Gang Output of 'make test' for Oracle ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....ok 14/19Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. t/01dbadaptor.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-19 Failed 5/19 tests, 73.68% okay t/02species.......ok 5/65Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. t/02species.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-65 Failed 60/65 tests, 7.69% okay t/03simpleseq.....ok 5/59Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/03simpleseq.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-59 Failed 54/59 tests, 8.47% okay t/04swiss.........ok 5/52Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 78. t/04swiss.........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-52 Failed 47/52 tests, 9.62% okay t/05seqfeature....ok 3/48Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/05seqfeature....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 4-48 Failed 45/48 tests, 6.25% okay t/06comment.......ok 2/11Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/06comment.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-11 Failed 9/11 tests, 18.18% okay t/07dblink........ok 2/18Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/07dblink........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/08genbank.......ok 2/18Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/08genbank.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/09fuzzy2........ok 2/21Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 64. t/09fuzzy2........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-21 Failed 19/21 tests, 9.52% okay t/10ensembl.......ok 2/15Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1420. t/10ensembl.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-15 Failed 13/15 tests, 13.33% okay t/11locuslink.....ok 4/110Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/11locuslink.....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-110 Failed 106/110 tests, 3.64% okay t/12ontology......ok 4/738Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 98. t/12ontology......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-738 Failed 734/738 tests, 0.54% okay t/13remove........ok 1/59Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. t/13remove........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-59 Failed 58/59 tests, 1.69% okay t/14query.........ok t/15cluster.......ok 5/160Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. t/15cluster.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-160 Failed 155/160 tests, 3.12% okay t/16obda..........ok 2/12Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. t/16obda..........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-12 Failed 10/12 tests, 16.67% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 t/02species.t 255 65280 65 120 184.62% 6-65 t/03simpleseq.t 255 65280 59 108 183.05% 6-59 t/04swiss.t 255 65280 52 94 180.77% 6-52 t/05seqfeature.t 255 65280 48 90 187.50% 4-48 t/06comment.t 255 65280 11 18 163.64% 3-11 t/07dblink.t 255 65280 18 32 177.78% 3-18 t/08genbank.t 255 65280 18 32 177.78% 3-18 t/09fuzzy2.t 255 65280 21 38 180.95% 3-21 t/10ensembl.t 255 65280 15 26 173.33% 3-15 t/11locuslink.t 255 65280 110 212 192.73% 5-110 t/12ontology.t 255 65280 738 1468 198.92% 5-738 t/13remove.t 255 65280 59 116 196.61% 2-59 t/15cluster.t 255 65280 160 310 193.75% 6-160 t/16obda.t 255 65280 12 20 166.67% 3-12 Failed 15/16 test scripts, 6.25% okay. 1347/1423 subtests failed, 5.34% okay. make: *** [test_dynamic] Error 255 ======================================================= Output of 'make test TEST_VERBOSE=1' for Oracle ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....1..19 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-19 Failed 5/19 tests, 73.68% okay t/02species.......1..65 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-65 Failed 60/65 tests, 7.69% okay t/03simpleseq.....1..59 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-59 Failed 54/59 tests, 8.47% okay t/04swiss.........1..52 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 78. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-52 Failed 47/52 tests, 9.62% okay t/05seqfeature....1..48 ok 1 ok 2 ok 3 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 4-48 Failed 45/48 tests, 6.25% okay t/06comment.......1..11 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-11 Failed 9/11 tests, 18.18% okay t/07dblink........1..18 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/08genbank.......1..18 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-18 Failed 16/18 tests, 11.11% okay t/09fuzzy2........1..21 todo 17; ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 64. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-21 Failed 19/21 tests, 9.52% okay t/10ensembl.......1..15 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1420. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-15 Failed 13/15 tests, 13.33% okay t/11locuslink.....1..110 ok 1 ok 2 ok 3 ok 4 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-110 Failed 106/110 tests, 3.64% okay t/12ontology......1..738 ok 1 ok 2 ok 3 ok 4 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 98. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-738 Failed 734/738 tests, 0.54% okay t/13remove........1..59 ok 1 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 41. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-59 Failed 58/59 tests, 1.69% okay t/14query.........1..18 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok t/15cluster.......1..160 ok 1 ok 2 ok 3 ok 4 ok 5 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 1. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-160 Failed 155/160 tests, 3.12% okay t/16obda..........1..12 ok 1 ok 2 Can't call method "bind_param" on an undefined value at /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939, line 72. dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-12 Failed 10/12 tests, 16.67% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 t/02species.t 255 65280 65 120 184.62% 6-65 t/03simpleseq.t 255 65280 59 108 183.05% 6-59 t/04swiss.t 255 65280 52 94 180.77% 6-52 t/05seqfeature.t 255 65280 48 90 187.50% 4-48 t/06comment.t 255 65280 11 18 163.64% 3-11 t/07dblink.t 255 65280 18 32 177.78% 3-18 t/08genbank.t 255 65280 18 32 177.78% 3-18 t/09fuzzy2.t 255 65280 21 38 180.95% 3-21 t/10ensembl.t 255 65280 15 26 173.33% 3-15 t/11locuslink.t 255 65280 110 212 192.73% 5-110 t/12ontology.t 255 65280 738 1468 198.92% 5-738 t/13remove.t 255 65280 59 116 196.61% 2-59 t/15cluster.t 255 65280 160 310 193.75% 6-160 t/16obda.t 255 65280 12 20 166.67% 3-12 Failed 15/16 test scripts, 6.25% okay. 1347/1423 subtests failed, 5.34% okay. make: *** [test_dynamic] Error 255 ======================================================= Output of 'make test' for MySQL =================================================== [root at elegans bioperl-db-1.5.2-RC3]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/01dbadaptor.....ok t/02species.......FAILED tests 11, 14-40, 49-119 Failed 99/65 tests, -52.31% okay t/03simpleseq.....ok t/04swiss.........ok t/05seqfeature....ok t/06comment.......ok t/07dblink........ok t/08genbank.......ok t/09fuzzy2........ok t/10ensembl.......ok t/11locuslink.....ok t/12ontology......ok t/13remove........ok t/14query.........ok t/15cluster.......ok 155/160 -------------------- WARNING --------------------- MSG: failed to store one or more child objects for an instance of class Bio::Cluster::UniGene (PK=168) --------------------------------------------------- t/15cluster.......ok t/16obda..........ok Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/02species.t 65 136 209.23% 11 14-40 49-119 Failed 1/16 test scripts, 93.75% okay. 28/1423 subtests failed, 98.03% okay. make: *** [test_dynamic] Error 255 ====================================================== Output of 'make test_02species TEST_VERBOSE=1' for MySQL ====================================================== [root at elegans bioperl-db-1.5.2-RC3]# make test_02species TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests @ARGV;' t/02species.t t/02species....1..65 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 not ok 11 # Test 11 got: '29' (t/02species.t at line 45) # Expected: '11' ok 12 ok 13 not ok 14 # Test 14 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 49 fail #3) # Expected: 'Hominidae' not ok 15 # Test 15 got: 'Hominidae' (t/02species.t at line 49 fail #4) # Expected: 'Catarrhini' not ok 16 # Test 16 got: 'Hominoidea' (t/02species.t at line 49 fail #5) # Expected: 'Primates' not ok 17 # Test 17 got: 'Catarrhini' (t/02species.t at line 49 fail #6) # Expected: 'Eutheria' not ok 18 # Test 18 got: 'Simiiformes' (t/02species.t at line 49 fail #7) # Expected: 'Mammalia' not ok 19 # Test 19 got: 'Haplorrhini' (t/02species.t at line 49 fail #8) # Expected: 'Vertebrata' not ok 20 # Test 20 got: 'Primates' (t/02species.t at line 49 fail #9) # Expected: 'Chordata' not ok 21 # Test 21 got: 'Euarchontoglires' (t/02species.t at line 49 fail #10) # Expected: 'Metazoa' not ok 22 # Test 22 got: 'Eutheria' (t/02species.t at line 49 fail #11) # Expected: 'Eukaryota' not ok 23 # Failed test 23 in t/02species.t at line 49 fail #12 not ok 24 # Failed test 24 in t/02species.t at line 49 fail #13 not ok 25 # Failed test 25 in t/02species.t at line 49 fail #14 not ok 26 # Failed test 26 in t/02species.t at line 49 fail #15 not ok 27 # Failed test 27 in t/02species.t at line 49 fail #16 not ok 28 # Failed test 28 in t/02species.t at line 49 fail #17 not ok 29 # Failed test 29 in t/02species.t at line 49 fail #18 not ok 30 # Failed test 30 in t/02species.t at line 49 fail #19 not ok 31 # Failed test 31 in t/02species.t at line 49 fail #20 not ok 32 # Failed test 32 in t/02species.t at line 49 fail #21 not ok 33 # Failed test 33 in t/02species.t at line 49 fail #22 not ok 34 # Failed test 34 in t/02species.t at line 49 fail #23 not ok 35 # Failed test 35 in t/02species.t at line 49 fail #24 not ok 36 # Failed test 36 in t/02species.t at line 49 fail #25 not ok 37 # Failed test 37 in t/02species.t at line 49 fail #26 not ok 38 # Failed test 38 in t/02species.t at line 49 fail #27 not ok 39 # Failed test 39 in t/02species.t at line 49 fail #28 not ok 40 # Failed test 40 in t/02species.t at line 49 fail #29 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 not ok 49 # Test 49 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 63 fail #3) # Expected: 'Hominidae' not ok 50 # Test 50 got: 'Hominidae' (t/02species.t at line 63 fail #4) # Expected: 'Catarrhini' not ok 51 # Test 51 got: 'Hominoidea' (t/02species.t at line 63 fail #5) # Expected: 'Primates' not ok 52 # Test 52 got: 'Catarrhini' (t/02species.t at line 63 fail #6) # Expected: 'Eutheria' not ok 53 # Test 53 got: 'Simiiformes' (t/02species.t at line 63 fail #7) # Expected: 'Mammalia' not ok 54 # Test 54 got: 'Haplorrhini' (t/02species.t at line 63 fail #8) # Expected: 'Vertebrata' not ok 55 # Test 55 got: 'Primates' (t/02species.t at line 63 fail #9) # Expected: 'Chordata' not ok 56 # Test 56 got: 'Euarchontoglires' (t/02species.t at line 63 fail #10) # Expected: 'Metazoa' not ok 57 # Test 57 got: 'Eutheria' (t/02species.t at line 63 fail #11) # Expected: 'Eukaryota' not ok 58 # Failed test 58 in t/02species.t at line 63 fail #12 not ok 59 # Failed test 59 in t/02species.t at line 63 fail #13 not ok 60 # Failed test 60 in t/02species.t at line 63 fail #14 not ok 61 # Failed test 61 in t/02species.t at line 63 fail #15 not ok 62 # Failed test 62 in t/02species.t at line 63 fail #16 not ok 63 # Failed test 63 in t/02species.t at line 63 fail #17 not ok 64 # Failed test 64 in t/02species.t at line 63 fail #18 not ok 65 # Failed test 65 in t/02species.t at line 63 fail #19 not ok 66 # Failed test 66 in t/02species.t at line 63 fail #20 not ok 67 # Failed test 67 in t/02species.t at line 63 fail #21 not ok 68 # Failed test 68 in t/02species.t at line 63 fail #22 not ok 69 # Failed test 69 in t/02species.t at line 63 fail #23 not ok 70 # Failed test 70 in t/02species.t at line 63 fail #24 not ok 71 # Failed test 71 in t/02species.t at line 63 fail #25 not ok 72 # Failed test 72 in t/02species.t at line 63 fail #26 not ok 73 # Failed test 73 in t/02species.t at line 63 fail #27 not ok 74 # Failed test 74 in t/02species.t at line 63 fail #28 not ok 75 # Failed test 75 in t/02species.t at line 63 fail #29 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 not ok 90 # Test 90 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 91 fail #3) # Expected: 'Hominidae' not ok 91 # Test 91 got: 'Hominidae' (t/02species.t at line 91 fail #4) # Expected: 'Catarrhini' not ok 92 # Test 92 got: 'Hominoidea' (t/02species.t at line 91 fail #5) # Expected: 'Primates' not ok 93 # Test 93 got: 'Catarrhini' (t/02species.t at line 91 fail #6) # Expected: 'Eutheria' not ok 94 # Test 94 got: 'Simiiformes' (t/02species.t at line 91 fail #7) # Expected: 'Mammalia' not ok 95 # Test 95 got: 'Haplorrhini' (t/02species.t at line 91 fail #8) # Expected: 'Vertebrata' not ok 96 # Test 96 got: 'Primates' (t/02species.t at line 91 fail #9) # Expected: 'Chordata' not ok 97 # Test 97 got: 'Euarchontoglires' (t/02species.t at line 91 fail #10) # Expected: 'Metazoa' not ok 98 # Test 98 got: 'Eutheria' (t/02species.t at line 91 fail #11) # Expected: 'Eukaryota' not ok 99 # Failed test 99 in t/02species.t at line 91 fail #12 not ok 100 # Failed test 100 in t/02species.t at line 91 fail #13 not ok 101 # Failed test 101 in t/02species.t at line 91 fail #14 not ok 102 # Failed test 102 in t/02species.t at line 91 fail #15 not ok 103 # Failed test 103 in t/02species.t at line 91 fail #16 not ok 104 # Failed test 104 in t/02species.t at line 91 fail #17 not ok 105 # Failed test 105 in t/02species.t at line 91 fail #18 not ok 106 # Failed test 106 in t/02species.t at line 91 fail #19 not ok 107 # Failed test 107 in t/02species.t at line 91 fail #20 not ok 108 # Failed test 108 in t/02species.t at line 91 fail #21 not ok 109 # Failed test 109 in t/02species.t at line 91 fail #22 not ok 110 # Failed test 110 in t/02species.t at line 91 fail #23 not ok 111 # Failed test 111 in t/02species.t at line 91 fail #24 not ok 112 # Failed test 112 in t/02species.t at line 91 fail #25 not ok 113 # Failed test 113 in t/02species.t at line 91 fail #26 not ok 114 # Failed test 114 in t/02species.t at line 91 fail #27 not ok 115 # Failed test 115 in t/02species.t at line 91 fail #28 not ok 116 # Failed test 116 in t/02species.t at line 91 fail #29 ok 117 ok 118 ok 119 FAILED tests 11, 14-40, 49-119 Failed 99/65 tests, -52.31% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/02species.t 65 136 209.23% 11 14-40 49-119 Failed 1/1 test scripts, 0.00% okay. 28/65 subtests failed, 56.92% okay. make: *** [test_02species] Error 255 ======================================================= Output of 'make test_15cluster TEST_VERBOSE=1' for MySQL ======================================================= [root at elegans bioperl-db-1.5.2-RC3]# make test_15cluster TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests @ARGV;' t/15cluster.t t/15cluster....1..160 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 -------------------- WARNING --------------------- MSG: failed to store one or more child objects for an instance of class Bio::Cluster::UniGene (PK=201) --------------------------------------------------- ok 156 ok 157 ok 158 ok 159 ok 160 ok All tests successful. Files=1, Tests=160, 18 wallclock secs ( 4.39 cusr + 0.37 csys = 4.76 CPU) ======================================================= Hilmar Lapp wrote: > This is very odd. I would mean that preparing the statement failed, > i.e., that the generated SQL was not accepted by the server (or the > Oracle client library). > > Which test does this happen with? > > Could you run the test alone in which it happens with TEST_VERBOSE > turned on? E.g., > > $ make test_03simpleseq TEST_VERBOSE=1 > > if it's the simpleseq test that's causing the failure. Capture the > output in a file and send it to me. > > -hilmar > > On Nov 18, 2006, at 3:57 AM, gang wu wrote: > >> Hi everyone, >> >> I used to use MySQL to host the BioSQL schema and load Genbank into it >> with the 'load_seqdatabase.pl' without problem(except extremely slow. It >> took about 12 hours to load Arabidopsis thaliana). I just loaded the >> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database without >> problem. >> >> When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with >> MySQL while always saw an error with Oracle: >> Can't call method "bind_param" on an undefined value at >> /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm >> >> line 939. >> >> , where the code is $sth->bind_param(); >> >> Any idea what the problem is? >> >> Gang >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > --=========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > > From dmessina at wustl.edu Mon Nov 20 16:31:55 2006 From: dmessina at wustl.edu (David Messina) Date: Mon, 20 Nov 2006 10:31:55 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4560FDC2.4000309@purdue.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> Message-ID: On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: > [...] > My guess is that he thought that bioperl bundle installed the > dependencies *and* bioperl itself. That was my presumption the first > time I saw it on CPAN. Me too, actually. Perhaps there could be a big, bold warning displayed when using CPAN to install Bundle::BioPerl, saying something like "you will still need to install BioPerl separately by doing ..." ? Likewise, I think the INSTALL document that comes with the BioPerl distribution (and on the wiki) implies the difference between BioPerl and Bundle::BioPerl but doesn't say so explicitly. I'd be happy to add this to INSTALL if there are no objections... Dave From sdavis2 at mail.nih.gov Mon Nov 20 17:23:33 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 20 Nov 2006 12:23:33 -0500 Subject: [Bioperl-l] mmap perl In-Reply-To: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> References: <358f4d650611200653v6263279bu6d3a432233ef022a@mail.gmail.com> Message-ID: <200611201223.33703.sdavis2@mail.nih.gov> On Monday 20 November 2006 09:53, Albert Vilella wrote: > Hi all, > > A bit of an off-topic: > > Has anyone ever investigated with libcache-mmap-perl or > libcache-fastmmap-perl? Hi, Albert. You will probably need to be more specific here. Yes, there are perl implementations of MANY caching schemes. Sean From cjfields at uiuc.edu Mon Nov 20 17:36:41 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 11:36:41 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: Message-ID: <000301c70cca$70f8d030$15327e82@pyrimidine> > On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: > > [...] > > My guess is that he thought that bioperl bundle installed the > > dependencies *and* bioperl itself. That was my presumption > the first > > time I saw it on CPAN. > > Me too, actually. > > Perhaps there could be a big, bold warning displayed when > using CPAN to install Bundle::BioPerl, saying something like > "you will still need to install BioPerl separately by doing ..." ? > > Likewise, I think the INSTALL document that comes with the > BioPerl distribution (and on the wiki) implies the difference > between BioPerl and Bundle::BioPerl but doesn't say so explicitly. > > I'd be happy to add this to INSTALL if there are no objections... > > Dave Dave, Go ahead. We need to also make the change on the wiki in the relevant pages. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Mon Nov 20 17:46:02 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 20 Nov 2006 17:46:02 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> Message-ID: <4561E9DA.3020002@sendu.me.uk> David Messina wrote: > On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: >> [...] >> My guess is that he thought that bioperl bundle installed the >> dependencies *and* bioperl itself. That was my presumption the first >> time I saw it on CPAN. > > Me too, actually. > > Perhaps there could be a big, bold warning displayed when using CPAN > to install Bundle::BioPerl, saying something like "you will still > need to install BioPerl separately by doing ..." ? > > Likewise, I think the INSTALL document that comes with the BioPerl > distribution (and on the wiki) implies the difference between BioPerl > and Bundle::BioPerl but doesn't say so explicitly. The description for Bundle::BioPerl (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) says: "NOTE: This Bundle does not install BioPerl" > I'd be happy to add this to INSTALL if there are no objections... I'll be changing the INSTALL docs to say not to use Bundle::BioPerl when installing with CPAN (you don't need it). Bundle::BioPerl is only for convenience when installing manually from archives or CVS. From cjfields at uiuc.edu Mon Nov 20 17:52:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 11:52:12 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4561D07C.4060800@molbio.mgh.harvard.edu> Message-ID: <000701c70ccc$9b9c9360$15327e82@pyrimidine> > Hi Hilmar, > > Thanks for your message. Below are several tests for Oracle > and MySQL. > MySQL actually also has two tests with failed items which may > be related to data in BioSQL database. > > Could it be my Oracle installation/configuration has some issues? > > Thanks. > > Gang ... You stated in a previous post that you had preloaded taxonomy; the various species test fails may be from that. Hilmar pointed out in a previous thread that tests require a BioSQL database without NCBI taxonomy loaded (i.e. just the schema). The INSTALL doc should now state that. As for the rest, could it be the DBharness.biosql.conf file setup, which assumes MySQL by default? If you switch to Oracle you have to indicate the proper DBD driver in the conf file: ... # DBD driver to use - mandatory 'driver' => 'oracle', ... Chris > Hilmar Lapp wrote: > > This is very odd. I would mean that preparing the statement failed, > > i.e., that the generated SQL was not accepted by the server (or the > > Oracle client library). > > > > Which test does this happen with? > > > > Could you run the test alone in which it happens with TEST_VERBOSE > > turned on? E.g., > > > > $ make test_03simpleseq TEST_VERBOSE=1 > > > > if it's the simpleseq test that's causing the failure. Capture the > > output in a file and send it to me. > > > > -hilmar > > > > On Nov 18, 2006, at 3:57 AM, gang wu wrote: > > > >> Hi everyone, > >> > >> I used to use MySQL to host the BioSQL schema and load > Genbank into it > >> with the 'load_seqdatabase.pl' without problem(except > extremely slow. It > >> took about 12 hours to load Arabidopsis thaliana). I just > loaded the > >> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy > database without > >> problem. > >> > >> When I 'make test' with bioperl-db-1.5.2.R3, all tests can > pass with > >> MySQL while always saw an error with Oracle: > >> Can't call method "bind_param" on an undefined value at > >> > /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ BasePersistenceAdaptor.pm > >> > >> line 939. > >> > >> , where the code is $sth->bind_param(); > >> > >> Any idea what the problem is? > >> > >> Gang > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > --=========================================================== > > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > > =========================================================== > > > > > > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From dmessina at wustl.edu Mon Nov 20 18:34:27 2006 From: dmessina at wustl.edu (David Messina) Date: Mon, 20 Nov 2006 12:34:27 -0600 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4561E9DA.3020002@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> <4561E9DA.3020002@sendu.me.uk> Message-ID: <911B53D4-1E95-4B52-A604-DA3C776EB71A@wustl.edu> On Nov 20, 2006, at 11:46 AM, Sendu Bala wrote: > The description for Bundle::BioPerl > (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) > > says: > "NOTE: This Bundle does not install BioPerl" Right, but if you are in the CPAN shell, you won't see that: cpan[2]> b Bundle::BioPerl CPAN_USERID CRAFFI (Chris Dagdigian ) CPAN_VERSION 2.001008 CPAN_FILE C/CR/CRAFFI/Bundle-BioPerl-2.1.8.tar.gz UPLOAD_DATE 2006-11-18 MANPAGE Bundle::BioPerl - A bundle to install external CPAN modules used by BioPerl 1.5.2 CONTAINS Ace Bio::ASN1::EntrezGene Class::AutoClass Clone Convert::Binary::C Data::Stag::Writer DBD::mysql GD::SVG GD Graph::Directed HTML::Parser HTTP::Request::Common LWP::UserAgent Set::Scalar SOAP::Lite Spreadsheet::ParseExcel Storable SVG SVG::Graph Text::Shellwords XML::DOM::XPath XML::Parser::PerlSAX XML::SAX XML::SAX::Base XML::SAX::Writer XML::Simple XML::Twig XML::Writer INST_FILE /Users/davemessina/.cpan/Bundle/BioPerl.pm INST_VERSION 2.1.8 Nor if you type: cpan[6]> readme Bundle::BioPerl Not to make too much of this (some will miss it no matter how many warnings there are), but I am suggesting that it could be a little more noticeable, that's all. > I'll be changing the INSTALL docs to say not to use Bundle::BioPerl > when installing with CPAN (you don't need it). Bundle::BioPerl is > only for convenience when installing manually from archives or CVS. Ah, okay, great, Sendu. I didn't know that. ;) I'll leave it to you, then. Dave From gwu at molbio.mgh.harvard.edu Mon Nov 20 18:31:34 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:31:34 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <45607D9B.4010703@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> Message-ID: <4561F486.9050601@molbio.mgh.harvard.edu> Hi Sendu, I think the package was not installed at all. The only thing I saw in the Bio folder is ANS1 which was another package(I mistakenly thought it's the only package installed by Bundle-BioPerl 2.1.16). I did not force install with CPAN. So is it possible that the three typos forbid bioperl be installed? Thanks. Gang Sendu Bala wrote: > gang wu wrote: >> It turned out that most of the modules of BioPerl were not installed >> at all. And none of the scripts were installed. I had to download and >> install bioperl-1.5.2-RC3.tar.gz >> again. A similar >> problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually >> copied all stuff under Bio folder to the corresponding Perl library >> folder. Is it Ok to do it in this way? > > It will work, but is hardly good enough from our point of view (you > shouldn't have to do that). > > Can you tell me exactly what you mean by 'were not installed'? What > did you do to try and install? How did you determine that installation > had failed? > > With CPAN, if you were still getting errors during testing, what were > those remaining errors, and did you do a forced install to ignore the > errors? If a forced install didn't actually install anything, what > message did CPAN give you about that, if any? > > With the manual download, after doing "perl Makefile.PL", what is your > output of "make install"? > > > Thank you, > Sendu. From gwu at molbio.mgh.harvard.edu Mon Nov 20 18:39:55 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:39:55 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <6dce9a0b0611180913k59660f60nd5b16b8784959130@mail.gmail.com> <455FCAD4.7050709@molbio.mgh.harvard.edu> <6dce9a0b0611190754t6d43ab04xaa178d62d822ad3a@mail.gmail.com> Message-ID: <4561F67B.7070401@molbio.mgh.harvard.edu> No gdlib-config was found on my system. The rpm is the newest version from Redhat AS 4 channel for AMD/EM64T. Do you think I need to update the package myself? Thanks Gang Lincoln Stein wrote: > That's very odd. gd.0.28 should install gdlib-config, and the existence of > this executable should inhibit the interactive questions. Could you see if > there's a gdlib-config executable installed on your system? > > Lincoln > > On 11/18/06, gang wu wrote: > >> Lincoln, >> Thanks for your message. I have gd-2.0.28-4.4E.1 and >> gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T. >> Attached is the output. >> >> Gang >> >> ================================================== >> [root at elegans GD-2.35]# perl Makefile.PL >> NOTICE: This module requires libgd 2.0.28 or higher. >> >> If you are using Math::Trig 1.01 or lower, it has a bug that >> causes a "prerequisite not found" warning to be issued. You may >> safely ignore this warning. >> >> Type perl Makefile.PL -h for command-line option summary >> >> >> Where is libgd installed? [/usr/lib] >> >> Please choose the features that match how libgd was built: >> Build JPEG support? [y] >> Build PNG support? [y] >> Build FreeType support? [y] >> Build GIF support? [y] >> Build support for animated GIFs? [y] >> Build XPM support? [y] >> >> If you experience compile problems, please check the @INC, @LIBPATH and >> @LIBS >> arrays defined in Makefile.PL and manually adjust, if necessary. >> >> Checking if your kit is complete... >> Looks good >> Writing Makefile for GD >> [root at elegans GD-2.35]# make >> cp GD/Polyline.pm blib/lib/GD/Polyline.pm >> cp qd.pl blib/lib/qd.pl >> cp GD/Image.pm blib/lib/GD/Image.pm >> cp GD.pm blib/lib/GD.pm >> AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD) >> cp GD/Simple.pm blib/lib/GD/Simple.pm >> cp GD/Polygon.pm blib/lib/GD/Polygon.pm >> /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap >> /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap GD.xs > GD.xsc >> && mv GD.xsc GD.c >> gcc -c -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE >> -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include >> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g >> -pipe -m64 -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC >> "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" -DHAVE_JPEG >> -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c >> GD.xs: In function `XS_GD__Image_STORABLE_thaw': >> GD.xs:923: warning: cast from pointer to integer of different size >> GD.xs: In function `XS_GD__Image_gifanimbegin': >> GD.xs:990: warning: cast to pointer from integer of different size >> GD.xs: In function `XS_GD__Image_gifanimadd': >> GD.xs:1015: warning: cast to pointer from integer of different size >> GD.xs: In function `XS_GD__Image_gifanimend': >> GD.xs:1034: warning: cast to pointer from integer of different size >> Running Mkbootstrap for GD () >> chmod 644 GD.bs >> rm -f blib/arch/auto/GD/GD.so >> gcc -shared GD.o -o blib/arch/auto/GD/GD.so -L/usr/lib/X11 >> -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64 >> -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm >> /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz >> /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz >> /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm >> /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when >> searching for -lX11 >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when >> searching for -lX11 >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when >> searching for -lXpm >> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when >> searching for -lXpm >> /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc >> /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc >> chmod 755 blib/arch/auto/GD/GD.so >> cp GD.bs blib/arch/auto/GD/GD.bs >> chmod 644 blib/arch/auto/GD/GD.bs >> cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" >> blib/script/bdf2gdfont.pl >> Manifying blib/man1/bdf2gdfont.pl.1 >> Manifying blib/man3/GD::Polyline.3pm >> Manifying blib/man3/GD::Image.3pm >> Manifying blib/man3/GD::Simple.3pm >> Manifying blib/man3/GD.3pm >> Manifying blib/man3/GD::Polygon.3pm >> [root at elegans GD-2.35]# make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: >> ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at >> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. >> at t/GD.t line 14 >> Compilation failed in require at t/GD.t line 14. >> BEGIN failed--compilation aborted at t/GD.t line 14. >> t/GD..........dubious >> >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-12 >> Failed 12/12 tests, 0.00% okay >> t/Polyline....Can't load >> '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD: >> /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol: >> gdImageGifAnimAddPtr at >> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230. >> at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45 >> Compilation failed in require at >> /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. >> BEGIN failed--compilation aborted at >> /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45. >> Compilation failed in require at t/Polyline.t line 10. >> BEGIN failed--compilation aborted at t/Polyline.t line 10. >> t/Polyline....dubious >> >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED test 1 >> Failed 1/1 tests, 0.00% okay >> Failed Test Stat Wstat Total Fail Failed List of Failed >> >> ------------------------------------------------------------------------------- >> t/GD.t 255 65280 12 23 191.67% 1-12 >> t/Polyline.t 255 65280 1 2 200.00% 1 >> Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay. >> make: *** [test_dynamic] Error 255 >> [root at elegans GD-2.35]# >> =========================================================== >> >> Lincoln Stein wrote: >> >>> What version of libgd do you have installed? With recent versions of >>> libgd (more recent than two years old) you will not be given the >>> chance to select whether to compile JPEG, GIF and XPM support, since >>> these options are selected automatically by running libgd-config. >>> >>> Lincoln >>> >>> On 11/18/06, *gang wu* >> > wrote: >>> >>> >>> Sendu Bala wrote: >>> > gang wu wrote: >>> >> Hi everyone, >>> >> >>> >> I saw some problems when installing BioPerl >>> >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously >>> CPAN could >>> >> not solve all the dependency issues with one shot of 'install >>> >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be >>> >> installed. >>> > >>> > What problems did you run into specifically with GD? >>> If I enable JPEG, GIFS and XPM, none of the test could pass. Since >>> >> I >> >>> usually use only PNG for output, I can live without them. I am not >>> sure >>> if it's system related problem. All of them work fine with my 32 bit >>> Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with >>> newer >>> libgd runnig Redhat AS4 AMD/EM64T does not work. >>> > >>> >> And it turned out that CPAN refused to install BioPerl with >>> >> some test return value 255. Then I went to /root/.cpan/build to >>> >> configure, test, rebuild those problematic packages. After >>> several more >>> >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl >>> >> successfully. >>> > >>> > Do you remember what the other problematic packages were, and >>> what you >>> > had to do to get them working? >>> > >>> XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I >>> guess it should be XML::DOM::XPath.pm. I could not recall what other >>> packages had issues, but basically it's special package >>> configuration issue. >>> >> Below attached is the output of CPAN, which stills complains >>> >> three >> >>> >> packages have issues: Data::Stag::writer HTTP::Request::Common- >>> >> Spreadhseet::ParseExcel. I think the first two are typos >>> somewhere in >>> >> the Bundle::BioPerl. And the third module is not on the server >>> and could >>> >> be found on the CPAN site. >>> > >>> > All three are typos. We'll get those fixed. >>> > >>> > >>> >> So my question is : Is this the right way to install BioPerl? >>> > >>> > At the present moment, yes. For 1.5.2 I'll probably be >>> >> recommending >> >>> > not using Bundle::BioPerl once I fix some other things. >>> > >>> See my another message for other issues. >>> > >>> >> It took me two days to figure it out but still not 100% sure all >>> >> packages are >>> >> installed properly. >>> > >>> > I'm sorry for the troubles you ran into. We'll try and do better >>> >> for >> >>> > the final release of 1.5.2. >>> Actually your hard work is benifiting the whole community and we >>> all owe >>> you a Thank You. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 >>> (516) 367-8380 (voice) >>> (516) 367-8389 (fax) >>> FOR URGENT MESSAGES & SCHEDULING, >>> PLEASE CONTACT MY ASSISTANT, >>> SANDRA MICHELSEN, AT michelse at cshl.edu >>> >> > > > From gwu at molbio.mgh.harvard.edu Mon Nov 20 18:54:46 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 13:54:46 -0500 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <4561E9DA.3020002@sendu.me.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBF53.4010701@molbio.mgh.harvard.edu> <45607D9B.4010703@sendu.me.uk> <4560FDC2.4000309@purdue.edu> <4561E9DA.3020002@sendu.me.uk> Message-ID: <4561F9F6.5020700@molbio.mgh.harvard.edu> Sendu Bala wrote: > David Messina wrote: > >> On Nov 19, 2006, at 6:58 PM, Phillip SanMiguel wrote: >> >>> [...] >>> My guess is that he thought that bioperl bundle installed the >>> dependencies *and* bioperl itself. That was my presumption the first >>> time I saw it on CPAN. >>> >> Me too, actually. >> >> Perhaps there could be a big, bold warning displayed when using CPAN >> to install Bundle::BioPerl, saying something like "you will still >> need to install BioPerl separately by doing ..." ? >> >> Likewise, I think the INSTALL document that comes with the BioPerl >> distribution (and on the wiki) implies the difference between BioPerl >> and Bundle::BioPerl but doesn't say so explicitly. >> > > The description for Bundle::BioPerl > (http://search.cpan.org/~craffi/Bundle-BioPerl-2.1.7/BioPerl.pm) > > says: > "NOTE: This Bundle does not install BioPerl" > > > >> I'd be happy to add this to INSTALL if there are no objections... >> > > I'll be changing the INSTALL docs to say not to use Bundle::BioPerl when > installing with CPAN (you don't need it). Bundle::BioPerl is only for > convenience when installing manually from archives or CVS. > This can save a lot of time and confusion. But why can't BioPerl be installed with Bundle::BioPerl when using CPAN? It sounds convenient. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From gwu at molbio.mgh.harvard.edu Mon Nov 20 19:40:56 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 14:40:56 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000701c70ccc$9b9c9360$15327e82@pyrimidine> References: <000701c70ccc$9b9c9360$15327e82@pyrimidine> Message-ID: <456204C8.8000404@molbio.mgh.harvard.edu> Chris Fields wrote: >> Hi Hilmar, >> >> Thanks for your message. Below are several tests for Oracle >> and MySQL. >> MySQL actually also has two tests with failed items which may >> be related to data in BioSQL database. >> >> Could it be my Oracle installation/configuration has some issues? >> >> Thanks. >> >> Gang >> > > ... > > You stated in a previous post that you had preloaded taxonomy; the various > species test fails may be from that. Hilmar pointed out in a previous > thread that tests require a BioSQL database without NCBI taxonomy loaded > (i.e. just the schema). The INSTALL doc should now state that. > You are right, all tests can pass for MySQL after unloading NCBI Taxonomy data. But output for Oracle tests were not affected. Thanks. > As for the rest, could it be the DBharness.biosql.conf file setup, which > assumes MySQL by default? If you switch to Oracle you have to indicate the > proper DBD driver in the conf file: > > ... > > # DBD driver to use - mandatory > 'driver' => 'oracle', > > ... > > I did change the configuration, or it can not pass the DBI connection tests. Below is part of my parameters: 'driver' => 'Oracle', 'host' => 'elegans', 'user' => 'biosqldb_sgowner', 'port' => '1521', 'password' => 'pass', 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], 'dbname' => 'oracle_sid', 'database' => 'biosql', > Chris > > > >> Hilmar Lapp wrote: >> >>> This is very odd. I would mean that preparing the statement failed, >>> i.e., that the generated SQL was not accepted by the server (or the >>> Oracle client library). >>> >>> Which test does this happen with? >>> >>> Could you run the test alone in which it happens with TEST_VERBOSE >>> turned on? E.g., >>> >>> $ make test_03simpleseq TEST_VERBOSE=1 >>> >>> if it's the simpleseq test that's causing the failure. Capture the >>> output in a file and send it to me. >>> >>> -hilmar >>> >>> On Nov 18, 2006, at 3:57 AM, gang wu wrote: >>> >>> >>>> Hi everyone, >>>> >>>> I used to use MySQL to host the BioSQL schema and load >>>> >> Genbank into it >> >>>> with the 'load_seqdatabase.pl' without problem(except >>>> >> extremely slow. It >> >>>> took about 12 hours to load Arabidopsis thaliana). I just >>>> >> loaded the >> >>>> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy >>>> >> database without >> >>>> problem. >>>> >>>> When I 'make test' with bioperl-db-1.5.2.R3, all tests can >>>> >> pass with >> >>>> MySQL while always saw an error with Oracle: >>>> Can't call method "bind_param" on an undefined value at >>>> >>>> >> /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/ >> > BasePersistenceAdaptor.pm > >>>> line 939. >>>> >>>> , where the code is $sth->bind_param(); >>>> >>>> Any idea what the problem is? >>>> >>>> Gang >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> --=========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >>> >>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > From cjfields at uiuc.edu Mon Nov 20 20:19:56 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 14:19:56 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <456204C8.8000404@molbio.mgh.harvard.edu> Message-ID: <000301c70ce1$3ee70190$15327e82@pyrimidine> ... > You are right, all tests can pass for MySQL after unloading > NCBI Taxonomy data. But output for Oracle tests were not > affected. Thanks. Yes, the oracle tests were by far the worst, which suggests something in the driver/configuration. > > As for the rest, could it be the DBharness.biosql.conf file setup, > > which assumes MySQL by default? If you switch to Oracle > you have to > > indicate the proper DBD driver in the conf file: > > > > ... > > > > # DBD driver to use - mandatory > > 'driver' => 'oracle', > > > > ... > > > > > I did change the configuration, or it can not pass the DBI > connection tests. Below is part of my parameters: > 'driver' => 'Oracle', > 'host' => 'elegans', > 'user' => 'biosqldb_sgowner', > 'port' => '1521', > 'password' => 'pass', > 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], > 'dbname' => 'oracle_sid', > 'database' => 'biosql', Try changing the driver to all lower case (i.e. from 'Oracle' to 'oracle'). Also, the schema_sql is still set to the mysql schema (not oracle). That shouldn't make a difference, but you never know. Hopefully that isn't your real password! Chris From gwu at molbio.mgh.harvard.edu Mon Nov 20 20:34:07 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Mon, 20 Nov 2006 15:34:07 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000301c70ce1$3ee70190$15327e82@pyrimidine> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> Message-ID: <4562113F.6040306@molbio.mgh.harvard.edu> Chris Fields wrote: > ... > >> You are right, all tests can pass for MySQL after unloading >> NCBI Taxonomy data. But output for Oracle tests were not >> affected. Thanks. >> > > Yes, the oracle tests were by far the worst, which suggests something in the > driver/configuration. > > >>> As for the rest, could it be the DBharness.biosql.conf file setup, >>> which assumes MySQL by default? If you switch to Oracle >>> >> you have to >> >>> indicate the proper DBD driver in the conf file: >>> >>> ... >>> >>> # DBD driver to use - mandatory >>> 'driver' => 'oracle', >>> >>> ... >>> >>> >>> >> I did change the configuration, or it can not pass the DBI >> connection tests. Below is part of my parameters: >> 'driver' => 'Oracle', >> 'host' => 'elegans', >> 'user' => 'biosqldb_sgowner', >> 'port' => '1521', >> 'password' => 'pass', >> 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], >> 'dbname' => 'oracle_sid', >> 'database' => 'biosql', >> > > Try changing the driver to all lower case (i.e. from 'Oracle' to 'oracle'). > Also, the schema_sql is still set to the mysql schema (not oracle). That > shouldn't make a difference, but you never know. > Can not change 'Oracle' to 'oracle', the DBD driver name is DBD::Oracle. It's an odd naming inconsistence. MySQL DBD driver name is DBD::mysql. How about PostgreSQL DBD driver naming? > Hopefully that isn't your real password! > > Chris > > From ryanx07 at hotmail.com Mon Nov 20 20:42:47 2006 From: ryanx07 at hotmail.com (L Xu) Date: Mon, 20 Nov 2006 15:42:47 -0500 Subject: [Bioperl-l] Error message for installation Message-ID: I got an error message when I installed Bioperl through ActivePerl following the online instruction about window installation: ERROR: Installing File-Spec-0.82 would downgrade File::Spec from version 3.12 to 0.82 and File::Spec::Functions from version 1.3 to 1.1 and File::Spec::Mac from version 1.4 to 1.2 and File::Spec::OS2 from version 1.2 to 1.1 and File::Spec::Unix from version 1.5 to 1.2 and File::Spec::VMS from version 1.4 to 1.1 and File::Spec::Win32 from version 1.6 to 1.2 It looks like the Bioperl 1.4 using some old version files compared to ActivePerl. I wonder if these old version files can cause some problems and how to fix them. Thanks and happy thanksgiving. L _________________________________________________________________ Get FREE company branded e-mail accounts and business Web site from Microsoft Office Live http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ From hlapp at gmx.net Mon Nov 20 21:28:29 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:28:29 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4561F0F4.3060106@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> Message-ID: <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> It looks like you are using the MySQL schema under Oracle. There are different DDL scripts for each supported RDBMS. The ones for Oracle are in the sql/biosql-ora subdirectory. Note the INSTALL document in that directory. -hilmar On Nov 20, 2006, at 1:16 PM, gang wu wrote: > Hi Hilmar, > > Below is the output. Thanks. > > Gang > ========================================================== > [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 > [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor > TEST_VERBOSE=1 > PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ > perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e > 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests > @ARGV;' t/01dbadaptor.t > t/01dbadaptor....1..19 > ok 1 > ok 2 > ok 3 > ok 4 > ok 5 > ok 6 > ok 7 > ok 8 > ok 9 > ok 10 > ok 11 > attempting to load adaptor class for BioNamespace > ok 12 > attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor > instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor > ok 13 > ok 14 > attempting to load driver for adaptor class > Bio::DB::BioSQL::BioNamespaceAdaptor > attempting to load driver for adaptor class > Bio::DB::BioSQL::BasePersistenceAdaptor > Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as > driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor > preparing UK select statement: SELECT biodatabase.oid, > biodatabase.name, biodatabase.authority FROM biodatabase WHERE name > = ? > DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": > invalid identifier (DBD ERROR: error possibly near <*> indicator at > char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = :p1') [for > Statement "SELECT biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ > Bio/DB/BioSQL/BaseDriver.pm line 1800. > BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) > Can't call method "bind_param" on an undefined value at blib/lib/ > Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. > dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-19 > Failed 5/19 tests, 73.68% okay > Failed Test Stat Wstat Total Fail Failed List of Failed > ---------------------------------------------------------------------- > --------- > t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 > Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% > okay. > make: *** [test_01dbadaptor] Error 2 > ========================================================= > > > Hilmar Lapp wrote: >> Hi Gang, >> >> what I wanted to get at was the error message from the driver when >> it fails to generate the prepared statement, but this is not in >> the output. >> >> I believe you need set the HARNESS_VERBOSE environment variable to >> 1 before testing to get what I need: >> >> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >> csh/tcsh >> $ make test_01dbadaptor TEST_VERBOSE=1 >> >> This will lead to _a lot_ of debugging output. Do not run this for >> the entire test suite. >> >> The errors for mysql I believe are related to the fact that have >> loaded the NCBI taxonomy before testing? Run the tests on a fresh >> (completely empty) instance of BioSQL. >> >> Let me know what you get for the Oracle test above. >> >> -hilmar >> >> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >> >>> Hi Hilmar, >>> >>> Thanks for your message. Below are several tests for Oracle and >>> MySQL. MySQL actually also has two tests with failed items which >>> may be related to data in BioSQL database. >>> >>> Could it be my Oracle installation/configuration has some issues? >>> >>> Thanks. >>> >>> Gang >> >> --=========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> >> -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Nov 20 21:33:50 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:33:50 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <000301c70ce1$3ee70190$15327e82@pyrimidine> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> Message-ID: <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> On Nov 20, 2006, at 3:19 PM, Chris Fields wrote: > Try changing the driver to all lower case (i.e. from 'Oracle' to > 'oracle'). This can in fact be harmful. The driver-specific code is loaded from files or directories named after the driver. On case-sensitive file systems, changing the case will render those files inaccessible. > Also, the schema_sql is still set to the mysql schema (not > oracle). That > shouldn't make a difference, but you never know. It doesn't make a difference if the schema instance exists already (and I wouldn't recommend anything else). -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Nov 20 21:34:30 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 20 Nov 2006 16:34:30 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4562113F.6040306@molbio.mgh.harvard.edu> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> <4562113F.6040306@molbio.mgh.harvard.edu> Message-ID: <24789A58-9A86-4B83-9CBB-CE2597B1DA60@gmx.net> On Nov 20, 2006, at 3:34 PM, gang wu wrote: > How about PostgreSQL DBD driver naming? DBD::Pg -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From Kevin.M.Brown at asu.edu Mon Nov 20 21:44:22 2006 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Mon, 20 Nov 2006 14:44:22 -0700 Subject: [Bioperl-l] Budle::BioPerl dependency issues Message-ID: <1A4207F8295607498283FE9E93B775B4024C58D3@EX02.asurite.ad.asu.edu> Redhat tends to have two different packages. GD and GD-devel. The first is for runtime applications to use, the other is needed to be able to build code against GD. They do this for almost all the libraries (e.g. glibc & glibc-devel, x11 and x11-devel, etc...). > No gdlib-config was found on my system. The rpm is the newest version > from Redhat AS 4 channel for AMD/EM64T. Do you think I need to update > the package myself? Thanks From n.haigh at sheffield.ac.uk Mon Nov 20 22:45:24 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 20 Nov 2006 22:45:24 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <45623004.1010807@sheffield.ac.uk> Could you answer the following questions, so that we know your setup and are better able to respond: 1) Can you confirm what version of ActivePerl you are running. 2) Can you confirm what PPM repositories you have enabled. 3) Can you confirm what version of Bioperl you tried to install. This issue has cropped up before, but I can't remember off hand exactly what the problem was, or how it was solved. I think it might be a problem with using the new PPM4 GUI to install bioperl 1.4 from the old style PPD. I'll await your response before making further comments. Thanks Nath L Xu wrote: > I got an error message when I installed Bioperl through ActivePerl following > the online instruction about window installation: > > ERROR: Installing File-Spec-0.82 would downgrade File::Spec from version > 3.12 to 0.82 and File::Spec::Functions from version 1.3 to 1.1 and > File::Spec::Mac from version 1.4 to 1.2 and File::Spec::OS2 from version 1.2 > to 1.1 and File::Spec::Unix from version 1.5 to 1.2 and File::Spec::VMS from > version 1.4 to 1.1 and File::Spec::Win32 from version 1.6 to 1.2 > > It looks like the Bioperl 1.4 using some old version files compared to > ActivePerl. I wonder if these old version files can cause some problems and > how to fix them. > > Thanks and happy thanksgiving. > > > L > > _________________________________________________________________ > Get FREE company branded e-mail accounts and business Web site from > Microsoft Office Live > http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From n.haigh at sheffield.ac.uk Mon Nov 20 22:49:51 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Mon, 20 Nov 2006 22:49:51 +0000 Subject: [Bioperl-l] Bioperl 1.4 on Windows Message-ID: <4562310F.8080403@sheffield.ac.uk> There have been at least a coupl eof posts recently about users having problems installing bioperl 1.4 using the PPM GUI shipped with ActivePerl 5.8.8.819. I think this is because the Bioperl 1.4 ppd is built for PPM3 and not PPM4. Would it make sense to update the Bioperl 1.4 PPD since it is the official "stable" release? Nath From cjfields at uiuc.edu Mon Nov 20 23:07:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 17:07:12 -0600 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> References: <000301c70ce1$3ee70190$15327e82@pyrimidine> <22E63A42-020D-4DCA-BBC9-754A682AE141@gmx.net> Message-ID: On Nov 20, 2006, at 3:33 PM, Hilmar Lapp wrote: > > On Nov 20, 2006, at 3:19 PM, Chris Fields wrote: > >> Try changing the driver to all lower case (i.e. from 'Oracle' to >> 'oracle'). > > This can in fact be harmful. The driver-specific code is loaded > from files or directories named after the driver. On case-sensitive > file systems, changing the case will render those files inaccessible. Yeah, just noticed that the driver is DBD::Oracle. I thought it might be lowercase, like DBD::mysql. >> Also, the schema_sql is still set to the mysql schema (not >> oracle). That >> shouldn't make a difference, but you never know. > > It doesn't make a difference if the schema instance exists already > (and I wouldn't recommend anything else). > > -hilmar The conf file indicates that as well. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Mon Nov 20 23:33:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 20 Nov 2006 17:33:48 -0600 Subject: [Bioperl-l] Bioperl 1.4 on Windows In-Reply-To: <4562310F.8080403@sheffield.ac.uk> References: <4562310F.8080403@sheffield.ac.uk> Message-ID: On Nov 20, 2006, at 4:49 PM, Nathan S. Haigh wrote: > There have been at least a coupl eof posts recently about users having > problems installing bioperl 1.4 using the PPM GUI shipped with > ActivePerl 5.8.8.819. I think this is because the Bioperl 1.4 ppd is > built for PPM3 and not PPM4. Would it make sense to update the Bioperl > 1.4 PPD since it is the official "stable" release? > > Nath We could change the PPD to remove any versioning requirements. It's possible that PPM4 treats them as explicit version requirements, so instead of installing rel. X or greater, it only tries to install rel. X, which then has version requirements of it's own that PPM4 misreads. Not sure if this is a common problem with PPM4 but it's definitely bad. The best course of action for Windows users will be to update to 1.5.2 when the final version is released. The vast majority will be using it for parsing BLAST reports and retrieving sequences, both of which have undergone major revisions since 1.4 (in fact, I don't think BLAST report parsing will work if they run a BLAST version before 2.2.13). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jcv128 at psu.edu Tue Nov 21 00:52:47 2006 From: jcv128 at psu.edu (Juan Cristobal Vera) Date: Mon, 20 Nov 2006 19:52:47 -0500 Subject: [Bioperl-l] GO terms not present in Swiss annotation object Message-ID: <1164070364l.1106082l.0l@psu.edu> Hi, I'm writing a simple application to extract various fields from swissprot objects and I can't access the GO terms found in "dblink" part of the swiss format flat files. I'm not a professional programmer and I can't figure out why this is occuring. All the other "dblink" keys are being generated as far as I can tell (e.g. embl, pfam, etc). The GO terms are just skipped over and it's driving me crazy. Not sure if this is a bug or a deliberate strategy I'm unfamiliar with. I apologize if this is not the correct forum to ask for this sort of help and would ask to be directed to the proper one. Juan Cristobal Vera Graduate Student Department of Biology Penn State University 208 Mueller Laboratory University Park, PA 16802 (814)863-2957 From cjfields at uiuc.edu Tue Nov 21 06:19:59 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 00:19:59 -0600 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164070364l.1106082l.0l@psu.edu> References: <1164070364l.1106082l.0l@psu.edu> Message-ID: Juan, The DBLink objects should be generated. You'll need to give us a bit more information to go on, though. We need an example sequence, your local version of Bioperl, maybe a test script, etc. This is the right forum for this, yes, if you are using BioPerl. Chris On Nov 20, 2006, at 6:52 PM, Juan Cristobal Vera wrote: > > > Hi, > I'm writing a simple application to extract various fields from > swissprot objects and I can't access the GO terms found in > "dblink" part of the swiss format flat files. I'm not a > professional programmer and I can't figure out why this is > occuring. All the other "dblink" keys are being > generated as far as I can tell (e.g. embl, pfam, etc). The GO > terms are just skipped over and it's driving me crazy. Not sure if > this is a bug or a deliberate strategy I'm unfamiliar with. I > apologize if this is not the correct forum to ask for this sort of > help and would ask to be directed to the proper one. > > > > Juan Cristobal Vera > > Graduate Student > > Department of Biology > > Penn State University > > 208 Mueller Laboratory > > University Park, PA 16802 > > (814)863-2957 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From gwu at molbio.mgh.harvard.edu Tue Nov 21 08:11:03 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 03:11:03 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> Message-ID: <4562B497.6080805@molbio.mgh.harvard.edu> Can you show me where it indicates I am actually using the MySQL schema. I am pretty sure that I used the sql script files from sql/biosql-ora(Has anyone actually tried to install MySQL schema on Oracle?). I can reinstall the schema if you think that's the way to solve the problem. Thanks very much. Gang Hilmar Lapp wrote: > It looks like you are using the MySQL schema under Oracle. There are > different DDL scripts for each supported RDBMS. The ones for Oracle > are in the sql/biosql-ora subdirectory. Note the INSTALL document in > that directory. > > -hilmar > > > On Nov 20, 2006, at 1:16 PM, gang wu wrote: > > >> Hi Hilmar, >> >> Below is the output. Thanks. >> >> Gang >> ========================================================== >> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >> TEST_VERBOSE=1 >> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >> @ARGV;' t/01dbadaptor.t >> t/01dbadaptor....1..19 >> ok 1 >> ok 2 >> ok 3 >> ok 4 >> ok 5 >> ok 6 >> ok 7 >> ok 8 >> ok 9 >> ok 10 >> ok 11 >> attempting to load adaptor class for BioNamespace >> ok 12 >> attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor >> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >> ok 13 >> ok 14 >> attempting to load driver for adaptor class >> Bio::DB::BioSQL::BioNamespaceAdaptor >> attempting to load driver for adaptor class >> Bio::DB::BioSQL::BasePersistenceAdaptor >> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >> preparing UK select statement: SELECT biodatabase.oid, >> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >> = ? >> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >> invalid identifier (DBD ERROR: error possibly near <*> indicator at >> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >> Statement "SELECT biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >> Bio/DB/BioSQL/BaseDriver.pm line 1800. >> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >> Can't call method "bind_param" on an undefined value at blib/lib/ >> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >> dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 15-19 >> Failed 5/19 tests, 73.68% okay >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ---------------------------------------------------------------------- >> --------- >> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >> okay. >> make: *** [test_01dbadaptor] Error 2 >> ========================================================= >> >> >> Hilmar Lapp wrote: >> >>> Hi Gang, >>> >>> what I wanted to get at was the error message from the driver when >>> it fails to generate the prepared statement, but this is not in >>> the output. >>> >>> I believe you need set the HARNESS_VERBOSE environment variable to >>> 1 before testing to get what I need: >>> >>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>> csh/tcsh >>> $ make test_01dbadaptor TEST_VERBOSE=1 >>> >>> This will lead to _a lot_ of debugging output. Do not run this for >>> the entire test suite. >>> >>> The errors for mysql I believe are related to the fact that have >>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>> (completely empty) instance of BioSQL. >>> >>> Let me know what you get for the Oracle test above. >>> >>> -hilmar >>> >>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>> >>> >>>> Hi Hilmar, >>>> >>>> Thanks for your message. Below are several tests for Oracle and >>>> MySQL. MySQL actually also has two tests with failed items which >>>> may be related to data in BioSQL database. >>>> >>>> Could it be my Oracle installation/configuration has some issues? >>>> >>>> Thanks. >>>> >>>> Gang >>>> >>> --=========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >>> >>> >>> > > From n.haigh at sheffield.ac.uk Tue Nov 21 08:47:40 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 21 Nov 2006 08:47:40 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <4562BD2C.4000906@sheffield.ac.uk> L Xu wrote: > Thank you for the prompt response. Here is the information you needed: > (1)ActivePerl version 5.8.8.819 and PPM version 4.00 > (2)http://ppm4.activestate.com/MsWin32-x86/5.8/819/package.xml > http://bioperl.org/DIST/RC > http://bioperl.org/DIST > http://theoryx5.uwinnipeg.ca/ppms > http://www.Bribes.org/perl/ppm > (3)bioperl-1.4 > > Once again, thank you very much. > > L When you do a search for Bioperl, do you also get listing for Bioperl 1.5.2 RC2. If you do, try to install that and let us know how you get on. If you don't see a 1.5.2 RC2 let me know and I'll try to find out what the problem is. The PPM package is a little behind since there is an RC4 - I'll try to get the RC4 packaged today if I have time. We are hoping that RC4 is the last release candidate before the official 1.5.2 release, so if you do install the RC2 remember to upgrade the package in a week or two. Cheers Nath From er at xs4all.nl Tue Nov 21 12:16:53 2006 From: er at xs4all.nl (Erik) Date: Tue, 21 Nov 2006 13:16:53 +0100 (CET) Subject: [Bioperl-l] double-colon bug Message-ID: <6661.156.83.1.251.1164111413.squirrel@webmail.xs4all.nl> Hi all, Could one of the committers apply the fix as proposed for bug 2146 ? It's a small change: added a ':' to the regex at line 507. I did add a 'show the bug' snippet, albeit somewhat belatedly. It passes all 135 genbank tests with that change. Also, it fixes my application :) Thanks, Erik http://bugzilla.open-bio.org/show_bug.cgi?id=2146 From cjfields at uiuc.edu Tue Nov 21 13:21:35 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 07:21:35 -0600 Subject: [Bioperl-l] Error message for installation In-Reply-To: <4562BD2C.4000906@sheffield.ac.uk> References: <4562BD2C.4000906@sheffield.ac.uk> Message-ID: <67BD6F52-A994-4FC7-8E4F-375F21D1E1F9@uiuc.edu> All of the RCs are in their own directory; http://www.bioperl.org/DIST/RC I couldn't install 1.5.2 myself unless I set the repository to that directory. I think that's fine as long as we set the final release to the regular installation directory (http://www.bioperl.org/DIST) and use package.xml to point to the other required packages in the RC directory. Chris On Nov 21, 2006, at 2:47 AM, Nathan S. Haigh wrote: > L Xu wrote: >> Thank you for the prompt response. Here is the information you >> needed: >> (1)ActivePerl version 5.8.8.819 and PPM version 4.00 >> (2)http://ppm4.activestate.com/MsWin32-x86/5.8/819/package.xml >> http://bioperl.org/DIST/RC >> http://bioperl.org/DIST >> http://theoryx5.uwinnipeg.ca/ppms >> http://www.Bribes.org/perl/ppm >> (3)bioperl-1.4 >> >> Once again, thank you very much. >> >> L > > When you do a search for Bioperl, do you also get listing for Bioperl > 1.5.2 RC2. If you do, try to install that and let us know how you get > on. If you don't see a 1.5.2 RC2 let me know and I'll try to find out > what the problem is. > > The PPM package is a little behind since there is an RC4 - I'll try to > get the RC4 packaged today if I have time. We are hoping that RC4 > is the > last release candidate before the official 1.5.2 release, so if you do > install the RC2 remember to upgrade the package in a week or two. > > Cheers > Nath > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From n.haigh at sheffield.ac.uk Tue Nov 21 14:56:29 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 21 Nov 2006 14:56:29 +0000 Subject: [Bioperl-l] Error message for installation In-Reply-To: References: Message-ID: <4563139D.2040108@sheffield.ac.uk> L Xu wrote: > I tried to install 1,5,2RC2, but got the following error message: > ################### > ...... > Generating HTML for Heap-0.71 ... DONE > Generating HTML for Error-0.17008 ... DONE > Generating HTML for XML-RegExp-0.03 ... DONE > Installing to site area ... failed > > ERROR: File conflict; package Bioperl-1.4 already provide > C:/Perl/html/bin/bp_aacomp.html > ########################## > Should I first uninstall Bioperl-1.4, if so how to do it? Thanks. > > > L > I'll have a look at this a bit later this afternoon. If you are using the PPM4 GUI, you should be able to right click an installed package and click remove (or something to that effect) and you will then have to apply the changes (like when you install a package). Once it's uninstalled, try installing 1.5.2 RC2 and let me know how you go. Cheers Nath From akarger at CGR.Harvard.edu Tue Nov 21 15:21:18 2006 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 21 Nov 2006 10:21:18 -0500 Subject: [Bioperl-l] Translating alternate start codons Message-ID: I think this is more a Bio question than a Bioperl question. I did this: ######### #!/usr/local/bin/perl use strict; use warnings; use Bio::Seq; use Bio::Tools::CodonTable; my $seqobj = Bio::PrimarySeq->new ( -seq => 'ATATGATAA', -id => 'GeneFragment-12', -accession_number => 'X78121', -alphabet => 'dna', ); $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; print "ATA $is a valid start codon\n"; print "Table 4: ", $seqobj->translate("-codontable_id" => 4)->seq,"\n"; print "Table 1: ", $seqobj->translate("-codontable_id" => 1)->seq,"\n"; ########### I got this: ATA is a valid start codon Table 4: IW* Table 1: I** But EMBL tells me that EMBLCDS:AAT64955 starts with an M: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[EMBLCDS:'A AT64955']+-qnum+1+-enum+3 So, does Bioperl purposely not translate start codons to M, while EMBL does? Am I supposed to just change the I to M explicitly in my code? I didn't see an obvious option to translate() to do it. Thanks, - Amir Karger Research Computing Life Sciences Division Harvard University 617-496-0626 From bix at sendu.me.uk Tue Nov 21 15:21:34 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 15:21:34 +0000 Subject: [Bioperl-l] Budle::BioPerl dependency issues In-Reply-To: <1163838120.455ec2a8d2224@webmail.shef.ac.uk> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <1163838120.455ec2a8d2224@webmail.shef.ac.uk> Message-ID: <4563197E.7010909@sendu.me.uk> Nathan Haigh wrote: > > If anyone is aware of a way to force CPAN to install modules in a > specific order, please let Sendu know - we may be able to make the > install process much easier to the users. As regards the Bundle, you just have to specify the modules in the desired order. The question is, what order of installation, if any, results in no first-time failures? From akarger at CGR.Harvard.edu Tue Nov 21 16:16:01 2006 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 21 Nov 2006 11:16:01 -0500 Subject: [Bioperl-l] Translating alternate start codons Message-ID: > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > Amir, > > The best documentation for translate() is in the online > Bioperl Tutorial, > have you checked that? > > Brian O. Thanks for the quick response. The tutorial is quite informative. It seems to me that the POD needs to document -complete more thoroughly, though: Or if you expect a complete coding sequence (CDS) translation, with inititator at the beginning and terminator at the end: $protein_seq_obj = $cds_seq_obj->translate(-complete => 1); This doesn't really explain what it does. I guess -complete was chosen as a compromise between having too many options and having lots of functionality. In my case, I want to keep the *, and I don't want warnings about terminators in the middle, because I've got a bunch of pseudogenes. So I'll just translate the M myself. I'm sure you've had many "the documentation is spread out in too many places" discussions before, and I know keeping docs up to date is Hard. Oh well. -Amir > > > On 11/21/06 10:21 AM, "Amir Karger" wrote: > > > I think this is more a Bio question than a Bioperl question. > > > > I did this: > > > > ######### > > #!/usr/local/bin/perl > > > > use strict; > > use warnings; > > > > use Bio::Seq; > > use Bio::Tools::CodonTable; > > > > my $seqobj = Bio::PrimarySeq->new ( > > -seq => 'ATATGATAA', > > -id => 'GeneFragment-12', > > -accession_number => 'X78121', > > -alphabet => 'dna', > > ); > > > > $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); > > my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; > > print "ATA $is a valid start codon\n"; > > print "Table 4: ", $seqobj->translate("-codontable_id" => > 4)->seq,"\n"; > > print "Table 1: ", $seqobj->translate("-codontable_id" => > 1)->seq,"\n"; > > ########### > > > > I got this: > > ATA is a valid start codon > > Table 4: IW* > > Table 1: I** > > > > But EMBL tells me that EMBLCDS:AAT64955 starts with an M: > > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ > EMBLCDS:'A > > AT64955']+-qnum+1+-enum+3 > > > > So, does Bioperl purposely not translate start codons to M, > while EMBL > > does? Am I supposed to just change the I to M explicitly in > my code? I > > didn't see an obvious option to translate() to do it. > > > > Thanks, > > > > - Amir Karger > > Research Computing > > Life Sciences Division > > Harvard University > > 617-496-0626 > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From gwu at molbio.mgh.harvard.edu Tue Nov 21 17:00:55 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 12:00:55 -0500 Subject: [Bioperl-l] Two BioPerl-1.5.2-RC3 installation issues Message-ID: <456330C7.1020801@molbio.mgh.harvard.edu> When installing bioperl-1.5.2RC3, I chose to run the BioDBGFF tests with MySQL database. Below is the warning message. =============================================== Checking if your kit is complete... Warning: the following files are missing in your kit: t/BioDBSeqFeature_mysql.t Please inform the author. Writing Makefile for Bio =============================================== Another thins is the installation of Bio-ASN1-EntrezGene-1.09, the 'make test' requires bioperl be preinstalled(Bio::Index::...) while bioperl requires it be preinstalled. Is this a circle reference issue? Gang Gang From bix at sendu.me.uk Tue Nov 21 17:31:37 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:31:37 +0000 Subject: [Bioperl-l] Two BioPerl-1.5.2-RC3 installation issues In-Reply-To: <456330C7.1020801@molbio.mgh.harvard.edu> References: <456330C7.1020801@molbio.mgh.harvard.edu> Message-ID: <456337F9.6090001@sendu.me.uk> gang wu wrote: > When installing bioperl-1.5.2RC3, I chose to run the BioDBGFF tests with > MySQL database. Below is the warning message. > =============================================== > Checking if your kit is complete... > Warning: the following files are missing in your kit: > t/BioDBSeqFeature_mysql.t > Please inform the author. > Writing Makefile for Bio > =============================================== That should get resolved in RC4. > Another thins is the installation of Bio-ASN1-EntrezGene-1.09, the 'make > test' requires bioperl be preinstalled(Bio::Index::...) while bioperl > requires it be preinstalled. Is this a circle reference issue? Yes it is. You'll have to force install one of them. Again, it should get resolved in RC4 (Bio::ASN1::EntrezGene won't be a requirement). Thank you for your feedback, Sendu. From bix at sendu.me.uk Tue Nov 21 17:41:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:41:04 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read Message-ID: <45633A30.7060009@sendu.me.uk> With the new Build.PL, when it does its check to see if optional external modules are installed or not, for each module that isn't installed I can print out details of what Bioperl modules need it and why and then ask if you'd like to install that module before proceeding. This is obviously very useful for people doing one-off installations from CPAN, giving them informed choices and letting them avoid any problems with particular external modules (vs. having all or nothing by installing Bundle::BioPerl). But for developers, if you choose not to install a module, you'll keep getting asked if you want to install it every time you run Build.PL. So the question is, would this be too annoying? How often do you run Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I run it all the time because I'm developing the thing and trying to sort out installation issues, but would it bother anyone else? Cheers, Sendu. From bix at sendu.me.uk Tue Nov 21 17:45:46 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 17:45:46 +0000 Subject: [Bioperl-l] Changing default reply-to on this list Message-ID: <45633B4A.6060804@sendu.me.uk> Hi, I'd like to propose changing the default reply-to for posts on this list from the current 'reply to the poster' to 'reply to the mailing list'. That way people can just hit 'reply' instead of 'reply to all' in order to get a reply back to the list. If people then changed the current habit of 'reply to all' to just 'reply' it would avoid people being replied to getting multiple copies of the reply - one direct, a second from the mailing list. Cheers, Sendu. From stefan.kirov at bms.com Tue Nov 21 18:08:02 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 13:08:02 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: <45634082.6040001@bms.com> Sendu, This is not a problem - see prerequisites_policy ask/follow options for CPAN config. Hope this helps. Stefan Sendu Bala wrote: > With the new Build.PL, when it does its check to see if optional > external modules are installed or not, for each module that isn't > installed I can print out details of what Bioperl modules need it and > why and then ask if you'd like to install that module before proceeding. > > This is obviously very useful for people doing one-off installations > from CPAN, giving them informed choices and letting them avoid any > problems with particular external modules (vs. having all or nothing by > installing Bundle::BioPerl). > > But for developers, if you choose not to install a module, you'll keep > getting asked if you want to install it every time you run Build.PL. > > So the question is, would this be too annoying? How often do you run > Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I > run it all the time because I'm developing the thing and trying to sort > out installation issues, but would it bother anyone else? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bix at sendu.me.uk Tue Nov 21 18:17:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 18:17:10 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45634082.6040001@bms.com> References: <45633A30.7060009@sendu.me.uk> <45634082.6040001@bms.com> Message-ID: <456342A6.4060000@sendu.me.uk> Stefan Kirov wrote: > Sendu, > This is not a problem - see > prerequisites_policy ask/follow > options for CPAN config. That does not apply to the situation I describe. The follow policy applies to required modules when installing with CPAN. I am talking about installing modules that are /not/ required when using CPAN and even when /not/ using CPAN to do an installation. From n.haigh at sheffield.ac.uk Tue Nov 21 18:20:15 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Tue, 21 Nov 2006 18:20:15 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <4563435F.5010400@sheffield.ac.uk> Sendu Bala wrote: > Hi, > > I'd like to propose changing the default reply-to for posts on this list > from the current 'reply to the poster' to 'reply to the mailing list'. > That way people can just hit 'reply' instead of 'reply to all' in order > to get a reply back to the list. > > If people then changed the current habit of 'reply to all' to just > 'reply' it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > I don't seem to get multiple copies! However, the first reason (to just hit replay) is reason enough to change the default behaviour! :-) Nath From stefan.kirov at bms.com Tue Nov 21 18:24:39 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 13:24:39 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <456342A6.4060000@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> <45634082.6040001@bms.com> <456342A6.4060000@sendu.me.uk> Message-ID: <45634467.5010300@bms.com> Sendu Bala wrote: > Stefan Kirov wrote: >> Sendu, >> This is not a problem - see >> prerequisites_policy ask/follow >> options for CPAN config. > > That does not apply to the situation I describe. The follow policy > applies to required modules when installing with CPAN. I am talking > about installing modules that are /not/ required when using CPAN and > even when /not/ using CPAN to do an installation. > Sorry, I did not get that.... I personally do not run make often and would guess this to be case for most people as well. Stefan From stefan.kirov at bms.com Tue Nov 21 17:20:34 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 12:20:34 -0500 Subject: [Bioperl-l] Performance of Bio::Species Message-ID: <45633562.2030107@bms.com> New Bio::Species implementation seems to degrade significantly performance. It seems this happens when the Bio::Tree::Tree is constructed. See the stats bellow (based on simple Bio::Species object construction, script and test sequence file attached): 10000 iterrations new implementation: Constructor: 115 wallclock secs (113.50 usr + 0.67 sys = 114.17 CPU) Accessor: 0 wallclock secs ( 0.17 usr + 0.00 sys = 0.17 CPU) old implementation (bioperl-1.4 Constructor: 1 wallclock secs ( 0.84 usr + 0.10 sys = 0.94 CPU) Accessor: 0 wallclock secs ( 0.13 usr + 0.01 sys = 0.14 CPU) You can see that when reading a genbank file you would double the time necessary to construct the Bio::Seq object (100 iterations): old implementation (bioperl-1.4 Constructor: 0 wallclock secs ( 0.01 usr + 0.00 sys = 0.01 CPU) Accessor: 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU) Constructor(seqio)/reading seq: 3 wallclock secs ( 2.51 usr + 0.31 sys = 2.83 CPU) new implementation: Constructor: 2 wallclock secs ( 1.14 usr + 0.01 sys = 1.15 CPU) Accessor: 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU) Constructor(seqio)/reading seq: 5 wallclock secs ( 5.10 usr + 0.20 sys = 5.30 CPU) This may not pose a problem to people who read few sequences or files with no lineage data, but it could be a significant headache otherwise. I saw from CVS that Sendu knows there are memory leaks (I find cycles). If the classification is supplied incorrectly (includes a reference to an array in the classification array) things get really messy (~17 GB of RAM for a Bio::Species object), though weird enough the cycle is not indefinite. If I have more time I will try to debug this further and submit a formal bug report/patch, but I am not sure if I will anytime soon. I am sure there are people who understand Bio::Taxon/Bio::Tree::Tree better than me and might have better idea how to fix this. Stefan /// use Bio::Species; use Benchmark; use Bio::SeqIO; my @classification=qw( sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota ); my $species; my $t1 = new Benchmark; for my $i (1..100) { $species = Bio::Species->new(-classification => [@classification]); } my $t2 = new Benchmark; for my $i (1..100) { my $bin = $species->binomial; } my $t3 = new Benchmark; print "Constructor: ", timestr(timediff($t2, $t1)),"\n"; print "Accessor: ", timestr(timediff($t3, $t2)),"\n"; my $f=shift; my $t4= new Benchmark; for my $i (1..100) { my $sio=new Bio::SeqIO(-file=>$f,-format=>'genbank'); my $seq=$sio->next_seq; } my $t5= new Benchmark; print "Constructor(seqio)/reading seq: ", timestr(timediff($t5, $t4)),"\n"; -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: NM_000161.genbank URL: From dmessina at wustl.edu Tue Nov 21 19:06:38 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:06:38 -0600 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> > it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. This behavior can be changed by going to http://lists.open-bio.org/mailman/listinfo/bioperl-l entering your subscribed email address in the last field on the page, clicking the "unsubscribe or edit options" button to the right of that field. On the next page, enter your password in the password field and click "Log in". On the options page that you see next, the last option, called "Avoid duplicate copies of messages?", should be set to "Yes" if you don't want multiple copies. Dave From dmessina at wustl.edu Tue Nov 21 19:11:06 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:11:06 -0600 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> Would it be possible to set it up such that when the user is asked whether to install an unrequired module, the possible answers are "yes", "no", "skip all"? The latter being to skip all subsequent questions about unrequired modules. Dave From bix at sendu.me.uk Tue Nov 21 19:30:52 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:30:52 +0000 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> References: <45633A30.7060009@sendu.me.uk> <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> Message-ID: <456353EC.9030304@sendu.me.uk> David Messina wrote: > Would it be possible to set it up such that when the user is asked > whether to install an unrequired module, the possible answers are "yes", > "no", "skip all"? The latter being to skip all subsequent questions > about unrequired modules. Yes, thanks, that's a good idea. I currently (in my private copy) have the default as 'no', but if changed as above, should the default be to 'skip all'? Or, perhaps have an initial question 'do you want to be asked to install optional modules you don't have' would be better? From hlapp at gmx.net Tue Nov 21 19:33:11 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:33:11 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <4562B497.6080805@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> Message-ID: The Oracle error is ORA-00904: "BIODATABASE"."OID": invalid identifier and if you look at the accompanying statement, it's the UK select statement: SELECT <*>biodatabase.oid, biodatabase.name, biodatabase.authority FROM biodatabase WHERE name = :p1 The column OID must exist in the Biodatabase table (which actually is a synonym to the SG_BIODATABASE table), if it is the Oracle schema. This actually prompts another suggestion, sorry for not asking that first: did you actually install the BioSQL-API on top of the schema by running the script BS-create-Biosql-API.sql? (It seems that the statement it chokes on is also the first statement being prepared, so this may well be the reason) -hilmar On Nov 21, 2006, at 3:11 AM, gang wu wrote: > Can you show me where it indicates I am actually using the MySQL > schema. > I am pretty sure that I used the sql script files from > sql/biosql-ora(Has anyone actually tried to install MySQL schema on > Oracle?). I can reinstall the schema if you think that's the way to > solve the problem. Thanks very much. > > Gang > > Hilmar Lapp wrote: >> It looks like you are using the MySQL schema under Oracle. There are >> different DDL scripts for each supported RDBMS. The ones for Oracle >> are in the sql/biosql-ora subdirectory. Note the INSTALL document in >> that directory. >> >> -hilmar >> >> >> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >> >> >>> Hi Hilmar, >>> >>> Below is the output. Thanks. >>> >>> Gang >>> ========================================================== >>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>> TEST_VERBOSE=1 >>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>> @ARGV;' t/01dbadaptor.t >>> t/01dbadaptor....1..19 >>> ok 1 >>> ok 2 >>> ok 3 >>> ok 4 >>> ok 5 >>> ok 6 >>> ok 7 >>> ok 8 >>> ok 9 >>> ok 10 >>> ok 11 >>> attempting to load adaptor class for BioNamespace >>> ok 12 >>> attempting to load module >>> Bio::DB::BioSQL::BioNamespaceAdaptor >>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>> ok 13 >>> ok 14 >>> attempting to load driver for adaptor class >>> Bio::DB::BioSQL::BioNamespaceAdaptor >>> attempting to load driver for adaptor class >>> Bio::DB::BioSQL::BasePersistenceAdaptor >>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>> preparing UK select statement: SELECT biodatabase.oid, >>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >>> = ? >>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>> invalid identifier (DBD ERROR: error possibly near <*> indicator at >>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>> Statement "SELECT biodatabase.oid, biodatabase.name, >>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >>> Can't call method "bind_param" on an undefined value at blib/lib/ >>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>> dubious >>> Test returned status 255 (wstat 65280, 0xff00) >>> DIED. FAILED tests 15-19 >>> Failed 5/19 tests, 73.68% okay >>> Failed Test Stat Wstat Total Fail Failed List of Failed >>> -------------------------------------------------------------------- >>> -- >>> --------- >>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>> okay. >>> make: *** [test_01dbadaptor] Error 2 >>> ========================================================= >>> >>> >>> Hilmar Lapp wrote: >>> >>>> Hi Gang, >>>> >>>> what I wanted to get at was the error message from the driver when >>>> it fails to generate the prepared statement, but this is not in >>>> the output. >>>> >>>> I believe you need set the HARNESS_VERBOSE environment variable to >>>> 1 before testing to get what I need: >>>> >>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>> csh/tcsh >>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>> >>>> This will lead to _a lot_ of debugging output. Do not run this for >>>> the entire test suite. >>>> >>>> The errors for mysql I believe are related to the fact that have >>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>> (completely empty) instance of BioSQL. >>>> >>>> Let me know what you get for the Oracle test above. >>>> >>>> -hilmar >>>> >>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>> >>>> >>>>> Hi Hilmar, >>>>> >>>>> Thanks for your message. Below are several tests for Oracle and >>>>> MySQL. MySQL actually also has two tests with failed items which >>>>> may be related to data in BioSQL database. >>>>> >>>>> Could it be my Oracle installation/configuration has some issues? >>>>> >>>>> Thanks. >>>>> >>>>> Gang >>>>> >>>> --=========================================================== >>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>> =========================================================== >>>> >>>> >>>> >>>> >>>> >>>> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From dmessina at wustl.edu Tue Nov 21 19:36:10 2006 From: dmessina at wustl.edu (David Messina) Date: Tue, 21 Nov 2006 13:36:10 -0600 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <456353EC.9030304@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> <0F113B7B-0CB9-487A-9DB0-7C14EF8D100C@wustl.edu> <456353EC.9030304@sendu.me.uk> Message-ID: <5DF4D1D9-754F-443F-ADDE-4127C579BF82@wustl.edu> On Nov 21, 2006, at 1:30 PM, Sendu Bala wrote: > Yes, thanks, that's a good idea. I currently (in my private copy) > have the default as 'no', but if changed as above, should the > default be to 'skip all'? Yeah, that makes sense to me. > Or, perhaps have an initial question 'do you want to be asked to > install optional modules you don't have' would be better? I think that would work fine, too -- whichever is easiest for you... Dave From bix at sendu.me.uk Tue Nov 21 19:37:14 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:37:14 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45633562.2030107@bms.com> References: <45633562.2030107@bms.com> Message-ID: <4563556A.1050101@sendu.me.uk> Stefan Kirov wrote: > New Bio::Species implementation seems to degrade significantly > performance. It seems this happens when the Bio::Tree::Tree is constructed. > See the stats bellow (based on simple Bio::Species object construction, > script and test sequence file attached): [snip] Thanks. If you come up with anything, please file that bug report. I certainly regard this as an important thing that must be fixed, though I don't know if I should hold up release of 1.5.2 for it. Now that you've reported on it I'm leaning toward yes, since the new Bio::Species implementation is one of the major new features of 1.5.2 and it ought to work well. Anyway, for the memory leak I have some ideas I haven't tried yet; I don't know if my efforts will solve the speed issue though. If anyone can spare the time to look at the problem, please do. Cheers, Sendu. From hlapp at gmx.net Tue Nov 21 19:46:45 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:46:45 -0500 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <93D5ABA0-290A-4087-8999-4FFBA6CFD918@gmx.net> I don't think that's a good idea. First, it is really hard to reply to someone off-list that way. Second, it is especially annoying given that reply-to-poster is generally considered best-practice and so therefore almost all lists reply off-list if you just hit reply. In fact I had this set to reply-to-list on one of our (NESCent's) own listserves to help the less computer-savvy but it was so annoying that I set it back to reply-to-sender within days. Compared to that, hitting the delete key on the duplicate takes about 0.2 seconds for me and hasn't bothered me much ever. Bottom line is, if you suggest people to change their habits then it is close impossible if it is only a single place that likes to do it the other way. -hilmar On Nov 21, 2006, at 12:45 PM, Sendu Bala wrote: > Hi, > > I'd like to propose changing the default reply-to for posts on this > list >> from the current 'reply to the poster' to 'reply to the mailing >> list'. > That way people can just hit 'reply' instead of 'reply to all' in > order > to get a reply back to the list. > > If people then changed the current habit of 'reply to all' to just > 'reply' it would avoid people being replied to getting multiple copies > of the reply - one direct, a second from the mailing list. > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Nov 21 19:41:25 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:41:25 -0500 Subject: [Bioperl-l] Optional dependency handling, devs please read In-Reply-To: <45633A30.7060009@sendu.me.uk> References: <45633A30.7060009@sendu.me.uk> Message-ID: I typically run (ran) perl Makefile.PL when I'm forced to, i.e., if someone changed Makefile.PL in the repository and I cvs update. Or if something is just going weird, as a last resort before rebooting ;) On Nov 21, 2006, at 12:41 PM, Sendu Bala wrote: > With the new Build.PL, when it does its check to see if optional > external modules are installed or not, for each module that isn't > installed I can print out details of what Bioperl modules need it and > why and then ask if you'd like to install that module before > proceeding. > > This is obviously very useful for people doing one-off installations >> from CPAN, giving them informed choices and letting them avoid any > problems with particular external modules (vs. having all or > nothing by > installing Bundle::BioPerl). > > But for developers, if you choose not to install a module, you'll keep > getting asked if you want to install it every time you run Build.PL. > > So the question is, would this be too annoying? How often do you run > Build.PL? (Or, how often did you do 'perl Makefile.PL' previously?) I > run it all the time because I'm developing the thing and trying to > sort > out installation issues, but would it bother anyone else? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Nov 21 19:56:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 14:56:18 -0500 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4563556A.1050101@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > I don't know if I should hold up release of 1.5.2 for it. Now that > you've > reported on it I'm leaning toward yes, since the new Bio::Species > implementation is one of the major new features of 1.5.2 and it > ought to > work well. I disagree to some extent. This is a developer release, so not everything is expected to work perfectly. What's not desirable is if fixing this required another entire redesign of the API, so that every dev release introduces different API. The thing is, you'll really only get trouble reports once you put it out and people start using it in anger. Don't expect to make it perfect before. > > Anyway, for the memory leak I have some ideas I haven't tried yet; I > don't know if my efforts will solve the speed issue though. The memory leak sounds more concerning to me. Under which circumstances would it crash a script or blow throuhg all of say 1-2GB when it should have taken only a tenth of that. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Tue Nov 21 19:58:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 19:58:58 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> References: <45633B4A.6060804@sendu.me.uk> <5DC94CCC-0A04-4765-A90E-10DD91C8A32D@wustl.edu> Message-ID: <45635A82.6070209@sendu.me.uk> David Messina wrote: >> it would avoid people being replied to getting multiple copies >> of the reply - one direct, a second from the mailing list. > > This behavior can be changed by going to > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > entering your subscribed email address in the last field on the page, > clicking the "unsubscribe or edit options" button to the right of > that field. > > On the next page, enter your password in the password field and click > "Log in". On the options page that you see next, the last option, > called "Avoid duplicate copies of messages?", should be set to "Yes" > if you don't want multiple copies. Ah, thanks for that. Given Hilmar's reply, forget the proposal. I'll just live in misery :( From bosborne11 at verizon.net Tue Nov 21 19:58:00 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 21 Nov 2006 14:58:00 -0500 Subject: [Bioperl-l] Translating alternate start codons In-Reply-To: Message-ID: Amir, I think I understand your question, perhaps not, and I think the recommended solution is to create your own "custom" codon table. See t/CodonTable.t for an example. Brian O. On 11/21/06 11:16 AM, "Amir Karger" wrote: >> From: Brian Osborne [mailto:bosborne11 at verizon.net] >> >> Amir, >> >> The best documentation for translate() is in the online >> Bioperl Tutorial, >> have you checked that? >> >> Brian O. > > Thanks for the quick response. The tutorial is quite informative. > It seems to me that the POD needs to document -complete more thoroughly, > though: > > Or if you expect a complete coding sequence (CDS) > translation, > with inititator at the beginning and terminator at the > end: > > $protein_seq_obj = $cds_seq_obj->translate(-complete > => 1); > > This doesn't really explain what it does. > > I guess -complete was chosen as a compromise between having too many > options and having lots of functionality. In my case, I want to keep the > *, and I don't want warnings about terminators in the middle, because > I've got a bunch of pseudogenes. So I'll just translate the M myself. > > I'm sure you've had many "the documentation is spread out in too many > places" discussions before, and I know keeping docs up to date is Hard. > Oh well. > > -Amir > >> >> >> On 11/21/06 10:21 AM, "Amir Karger" wrote: >> >>> I think this is more a Bio question than a Bioperl question. >>> >>> I did this: >>> >>> ######### >>> #!/usr/local/bin/perl >>> >>> use strict; >>> use warnings; >>> >>> use Bio::Seq; >>> use Bio::Tools::CodonTable; >>> >>> my $seqobj = Bio::PrimarySeq->new ( >>> -seq => 'ATATGATAA', >>> -id => 'GeneFragment-12', >>> -accession_number => 'X78121', >>> -alphabet => 'dna', >>> ); >>> >>> $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); >>> my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; >>> print "ATA $is a valid start codon\n"; >>> print "Table 4: ", $seqobj->translate("-codontable_id" => >> 4)->seq,"\n"; >>> print "Table 1: ", $seqobj->translate("-codontable_id" => >> 1)->seq,"\n"; >>> ########### >>> >>> I got this: >>> ATA is a valid start codon >>> Table 4: IW* >>> Table 1: I** >>> >>> But EMBL tells me that EMBLCDS:AAT64955 starts with an M: >>> >> http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ >> EMBLCDS:'A >>> AT64955']+-qnum+1+-enum+3 >>> >>> So, does Bioperl purposely not translate start codons to M, >> while EMBL >>> does? Am I supposed to just change the I to M explicitly in >> my code? I >>> didn't see an obvious option to translate() to do it. >>> >>> Thanks, >>> >>> - Amir Karger >>> Research Computing >>> Life Sciences Division >>> Harvard University >>> 617-496-0626 >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Tue Nov 21 20:16:18 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 20:16:18 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: <45635E92.7080000@sendu.me.uk> Hilmar Lapp wrote: > > On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > >> Anyway, for the memory leak I have some ideas I haven't tried yet; I >> don't know if my efforts will solve the speed issue though. > > The memory leak sounds more concerning to me. Under which circumstances > would it crash a script or blow throuhg all of say 1-2GB when it should > have taken only a tenth of that. Its been reported as causing problems if you do something like parse a large embl file with many (10s of thousands) sequences in it. So basically any situation that you make lots of Bio::Species objects. IIRC the reporter ran out of memory on a ~40000 sequence embl file. Neither the memory leak fix or speed fix ought to require any API change. I'm fairly certain that the memory leak, at least, is confined to a problem with (as suggested) Bio::Tree* stuff failing to clean up on destruction. There was in fact already an unnoticed problem with Bio::Tree::Node not getting cleaned up (see my #*** comment in the code), but my Bio::Species-related changes exacerbated the problem and also made them noticeable, since you're more likely to create thousands of Bio::Species than you were Bio::Tree::Node. From jason at bioperl.org Tue Nov 21 05:57:54 2006 From: jason at bioperl.org (Jason Stajich) Date: Mon, 20 Nov 2006 21:57:54 -0800 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164070364l.1106082l.0l@psu.edu> References: <1164070364l.1106082l.0l@psu.edu> Message-ID: a specific accession and example code will make it easier for someone to reproduce (and debug) your problem. On Nov 20, 2006, at 4:52 PM, Juan Cristobal Vera wrote: > > > Hi, > I'm writing a simple application to extract various fields from > swissprot objects and I can't access the GO terms found in > "dblink" part of the swiss format flat files. I'm not a > professional programmer and I can't figure out why this is > occuring. All the other "dblink" keys are being > generated as far as I can tell (e.g. embl, pfam, etc). The GO > terms are just skipped over and it's driving me crazy. Not sure if > this is a bug or a deliberate strategy I'm unfamiliar with. I > apologize if this is not the correct forum to ask for this sort of > help and would ask to be directed to the proper one. > > > > Juan Cristobal Vera > > Graduate Student > > Department of Biology > > Penn State University > > 208 Mueller Laboratory > > University Park, PA 16802 > > (814)863-2957 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason at bioperl.org http://jason.open-bio.org/ From stefan.kirov at bms.com Tue Nov 21 20:20:40 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Tue, 21 Nov 2006 15:20:40 -0500 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> Message-ID: <45635F98.8030901@bms.com> Hilmar Lapp wrote: > On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: > > >> I don't know if I should hold up release of 1.5.2 for it. Now that >> you've >> reported on it I'm leaning toward yes, since the new Bio::Species >> implementation is one of the major new features of 1.5.2 and it >> ought to >> work well. >> > > I disagree to some extent. This is a developer release, so not > everything is expected to work perfectly. > > What's not desirable is if fixing this required another entire > redesign of the API, so that every dev release introduces different API. > > The thing is, you'll really only get trouble reports once you put it > out and people start using it in anger. Don't expect to make it > perfect before. > > >> Anyway, for the memory leak I have some ideas I haven't tried yet; I >> don't know if my efforts will solve the speed issue though. >> > > The memory leak sounds more concerning to me. Under which > circumstances would it crash a script or blow throuhg all of say > 1-2GB when it should have taken only a tenth of that. > > As I was saying, I did pass ref to an array in the classification (wrong parsing): push @classification,'sapiens', 'Homo', 'Hominidae', $arrayref; and my script took 17-18 GB. I am really surprised it stopped getting more RAM and finished successfully. I did not explore further. Stefan > -hilmar > > From gwu at molbio.mgh.harvard.edu Tue Nov 21 20:33:10 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 21 Nov 2006 15:33:10 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> Message-ID: <45636286.6040504@molbio.mgh.harvard.edu> Hi Hilmar, I just rebuilt the Oracle BioSQL database by strictly following the INSTALL doc. You are right that BS-create-Biosql-API.sql must be run to make bioperl-db work with it(the oid columns). But my installation problem was caused by running BS-create-Biosql-API2.sql after it, which rendered the database not compatible with bioperl-db. If I ran only BS-create-Biosql-API.sql, ll bioperl-db tests could pass. Does this mean that the Oracle version is not interoperable between the Bio- projects at this point? Did I miss anything in the INSTALL or README? I only saw a line "-- all others (Biojava, etc)" but did not realize I could not run both BS-create-Biosql-API.sql and BS-create-Biosql-API2.sql. I this is the case, can you please add it to the docs? Thanks very much for your help. Gang Hilmar Lapp wrote: > The Oracle error is > > ORA-00904: "BIODATABASE"."OID": invalid identifier > > and if you look at the accompanying statement, it's the UK select > statement: > > SELECT <*>biodatabase.oid, biodatabase.name, > biodatabase.authority FROM biodatabase WHERE name = :p1 > > The column OID must exist in the Biodatabase table (which actually is > a synonym to the SG_BIODATABASE table), if it is the Oracle schema. > > This actually prompts another suggestion, sorry for not asking that > first: did you actually install the BioSQL-API on top of the schema by > running the script BS-create-Biosql-API.sql? (It seems that the > statement it chokes on is also the first statement being prepared, so > this may well be the reason) > > -hilmar > > On Nov 21, 2006, at 3:11 AM, gang wu wrote: > >> Can you show me where it indicates I am actually using the MySQL schema. >> I am pretty sure that I used the sql script files from >> sql/biosql-ora(Has anyone actually tried to install MySQL schema on >> Oracle?). I can reinstall the schema if you think that's the way to >> solve the problem. Thanks very much. >> >> Gang >> >> Hilmar Lapp wrote: >>> It looks like you are using the MySQL schema under Oracle. There are >>> different DDL scripts for each supported RDBMS. The ones for Oracle >>> are in the sql/biosql-ora subdirectory. Note the INSTALL document in >>> that directory. >>> >>> -hilmar >>> >>> >>> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >>> >>> >>>> Hi Hilmar, >>>> >>>> Below is the output. Thanks. >>>> >>>> Gang >>>> ========================================================== >>>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>>> TEST_VERBOSE=1 >>>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ >>>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>>> @ARGV;' t/01dbadaptor.t >>>> t/01dbadaptor....1..19 >>>> ok 1 >>>> ok 2 >>>> ok 3 >>>> ok 4 >>>> ok 5 >>>> ok 6 >>>> ok 7 >>>> ok 8 >>>> ok 9 >>>> ok 10 >>>> ok 11 >>>> attempting to load adaptor class for BioNamespace >>>> ok 12 >>>> attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor >>>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>>> ok 13 >>>> ok 14 >>>> attempting to load driver for adaptor class >>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>> attempting to load driver for adaptor class >>>> Bio::DB::BioSQL::BasePersistenceAdaptor >>>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>>> preparing UK select statement: SELECT biodatabase.oid, >>>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name >>>> = ? >>>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>>> invalid identifier (DBD ERROR: error possibly near <*> indicator at >>>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>>> Statement "SELECT biodatabase.oid, biodatabase.name, >>>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ >>>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>>> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace) >>>> Can't call method "bind_param" on an undefined value at blib/lib/ >>>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>>> dubious >>>> Test returned status 255 (wstat 65280, 0xff00) >>>> DIED. FAILED tests 15-19 >>>> Failed 5/19 tests, 73.68% okay >>>> Failed Test Stat Wstat Total Fail Failed List of Failed >>>> ---------------------------------------------------------------------- >>>> --------- >>>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>>> okay. >>>> make: *** [test_01dbadaptor] Error 2 >>>> ========================================================= >>>> >>>> >>>> Hilmar Lapp wrote: >>>> >>>>> Hi Gang, >>>>> >>>>> what I wanted to get at was the error message from the driver when >>>>> it fails to generate the prepared statement, but this is not in >>>>> the output. >>>>> >>>>> I believe you need set the HARNESS_VERBOSE environment variable to >>>>> 1 before testing to get what I need: >>>>> >>>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>>> csh/tcsh >>>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>>> >>>>> This will lead to _a lot_ of debugging output. Do not run this for >>>>> the entire test suite. >>>>> >>>>> The errors for mysql I believe are related to the fact that have >>>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>>> (completely empty) instance of BioSQL. >>>>> >>>>> Let me know what you get for the Oracle test above. >>>>> >>>>> -hilmar >>>>> >>>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>>> >>>>> >>>>>> Hi Hilmar, >>>>>> >>>>>> Thanks for your message. Below are several tests for Oracle and >>>>>> MySQL. MySQL actually also has two tests with failed items which >>>>>> may be related to data in BioSQL database. >>>>>> >>>>>> Could it be my Oracle installation/configuration has some issues? >>>>>> >>>>>> Thanks. >>>>>> >>>>>> Gang >>>>>> >>>>> --=========================================================== >>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>>> =========================================================== >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > --=========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > > From jason at bioperl.org Tue Nov 21 16:47:37 2006 From: jason at bioperl.org (Jason Stajich) Date: Tue, 21 Nov 2006 08:47:37 -0800 Subject: [Bioperl-l] Translating alternate start codons In-Reply-To: References: Message-ID: <8273f6c20611210847q7178025bm8e5367a5ae2138d4@mail.gmail.com> It seem then you don't want to use 'complete' since you don't always expect complete CDSes. Shouldn't you just translate to generate the peptide and then operate on the initial and terminal residues to achieve what you want. substr($peptide,0,1,'M'); chop($peptide) if substr($peptide,-1,1) eq $TERMINATOR; This is a community project so any help in improving apparent deficiencies in documentation are gladly welcomed - the wiki is designed to let everyone contribute. I think that clarifications and better descriptions for modules should reside there so please add your input on the webpages. A dev with write access can migrate updated documentation to the module's POD where appropriate. -jason On 11/21/06, Amir Karger wrote: > > > From: Brian Osborne [mailto:bosborne11 at verizon.net] > > > > Amir, > > > > The best documentation for translate() is in the online > > Bioperl Tutorial, > > have you checked that? > > > > Brian O. > > Thanks for the quick response. The tutorial is quite informative. > It seems to me that the POD needs to document -complete more thoroughly, > though: > > Or if you expect a complete coding sequence (CDS) > translation, > with inititator at the beginning and terminator at the > end: > > $protein_seq_obj = $cds_seq_obj->translate(-complete > => 1); > > This doesn't really explain what it does. > > I guess -complete was chosen as a compromise between having too many > options and having lots of functionality. In my case, I want to keep the > *, and I don't want warnings about terminators in the middle, because > I've got a bunch of pseudogenes. So I'll just translate the M myself. > > I'm sure you've had many "the documentation is spread out in too many > places" discussions before, and I know keeping docs up to date is Hard. > Oh well. > > -Amir > > > > > > > On 11/21/06 10:21 AM, "Amir Karger" wrote: > > > > > I think this is more a Bio question than a Bioperl question. > > > > > > I did this: > > > > > > ######### > > > #!/usr/local/bin/perl > > > > > > use strict; > > > use warnings; > > > > > > use Bio::Seq; > > > use Bio::Tools::CodonTable; > > > > > > my $seqobj = Bio::PrimarySeq->new ( > > > -seq => 'ATATGATAA', > > > -id => 'GeneFragment-12', > > > -accession_number => 'X78121', > > > -alphabet => 'dna', > > > ); > > > > > > $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 4 ); > > > my $is = $myCodonTable->is_start_codon('ATA') ? "is" : "is not"; > > > print "ATA $is a valid start codon\n"; > > > print "Table 4: ", $seqobj->translate("-codontable_id" => > > 4)->seq,"\n"; > > > print "Table 1: ", $seqobj->translate("-codontable_id" => > > 1)->seq,"\n"; > > > ########### > > > > > > I got this: > > > ATA is a valid start codon > > > Table 4: IW* > > > Table 1: I** > > > > > > But EMBL tells me that EMBLCDS:AAT64955 starts with an M: > > > > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+3b6PL1TmQt3+-e+[ > > EMBLCDS:'A > > > AT64955']+-qnum+1+-enum+3 > > > > > > So, does Bioperl purposely not translate start codons to M, > > while EMBL > > > does? Am I supposed to just change the I to M explicitly in > > my code? I > > > didn't see an obvious option to translate() to do it. > > > > > > Thanks, > > > > > > - Amir Karger > > > Research Computing > > > Life Sciences Division > > > Harvard University > > > 617-496-0626 > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich jason at bioperl.org http://www.duke.edu/~jes12/ From bosborne11 at verizon.net Tue Nov 21 20:53:39 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 21 Nov 2006 15:53:39 -0500 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: <200611211032.kALAWahR014137@dev.open-bio.org> Message-ID: Bioperl-l, INSTALL has changed in CVS but the Wiki's version has not - you always have to change both versions of the INSTALL instructions, this is how Chris has elected to do it. Brian O. Date: Tue, 21 Nov 2006 10:32:36 +0000 To: Subject: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 Update of /home/repository/bioperl/bioperl-live In directory dev.open-bio.org:/tmp/cvs-serv14112 Modified Files: DEPENDENCIES INSTALL INSTALL.WIN Log Message: clarification for Bundle::BioPerl, updates for Build.PL Index: DEPENDENCIES =================================================================== RCS file: /home/repository/bioperl/bioperl-live/DEPENDENCIES,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** DEPENDENCIES 14 Nov 2006 15:13:24 -0000 1.1 --- DEPENDENCIES 21 Nov 2006 10:32:34 -0000 1.2 *************** *** 5,10 **** The following packages are used by Bioperl. Not all are required for Bioperl to operate properly, however some functionality will be missing ! without them. You can easily install all of these, except srsperl.pm, ! using the Bundle::BioPerl CPAN bundle. The DBD::mysql, DB_File and XML::Parser modules require other applications --- 5,11 ---- The following packages are used by Bioperl. Not all are required for Bioperl to operate properly, however some functionality will be missing ! without them. You can easily install all of these by using CPAN to install ! Bioperl, or if you have installed Bioperl manually (from archive or CVS), ! by using the Bundle::BioPerl CPAN bundle. The DBD::mysql, DB_File and XML::Parser modules require other applications Index: INSTALL =================================================================== RCS file: /home/repository/bioperl/bioperl-live/INSTALL,v retrieving revision 1.57 retrieving revision 1.58 diff -C2 -d -r1.57 -r1.58 *** INSTALL 16 Nov 2006 16:27:49 -0000 1.57 --- INSTALL 21 Nov 2006 10:32:34 -0000 1.58 *************** *** 1,24 **** # $Id$ ! Installing Bioperl for Unix ! * BIOPERL INSTALLATION ! * SYSTEM REQUIREMENTS ! * OPTIONAL ! * ADDITIONAL INSTALLATION INFORMATION ! * THE BIOPERL BUNDLE ! * INSTALLING BIOPERL THE EASY WAY USING CPAN ! * INSTALLING BIOPERL THE EASY WAY USING GNU 'make' ! * WHERE ARE THE MAN PAGES? ! * EXTERNAL PROGRAMS ! * Environment Variables ! * INSTALLING BIOPERL SCRIPTS ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA ! * INSTALLING BIOPERL MODULES THE HARD WAY ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION ! * THE TEST SYSTEM ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE ! * CONFIGURING for BSD and Solaris boxes ! * INSTALLATION BIOPERL INSTALLATION --- 1,24 ---- # $Id$ ! Installing Bioperl for Unix ! * BIOPERL INSTALLATION ! * SYSTEM REQUIREMENTS ! * OPTIONAL ! * ADDITIONAL INSTALLATION INFORMATION ! * THE BIOPERL BUNDLE ! * INSTALLING BIOPERL THE EASY WAY USING CPAN ! * INSTALLING BIOPERL THE EASY WAY USING Build.PL ! * WHERE ARE THE MAN PAGES? ! * EXTERNAL PROGRAMS ! * Environment Variables ! * INSTALLING BIOPERL SCRIPTS ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA ! * INSTALLING BIOPERL MODULES THE HARD WAY ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION ! * THE TEST SYSTEM ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE ! * CONFIGURING for BSD and Solaris boxes ! * INSTALLATION BIOPERL INSTALLATION *************** *** 41,48 **** modules is included in the DEPENDENCIES file. ! The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation of these ! external modules easy. Simply install the bundle using your CPAN shell and ! all necessary modules will be installed. See THE BIOPERL BUNDLE, ! below. OPTIONAL --- 41,49 ---- modules is included in the DEPENDENCIES file. ! When not using CPAN to install Bioperl itself, the CPAN Bioperl Bundle ! (Bundle::BioPerl) makes installation of these external modules easy. Simply ! install the bundle using your CPAN shell and many optional modules will be ! installed. See THE BIOPERL BUNDLE, below. However, it is recommended you use ! CPAN to install Bioperl and not use Bundle::BioPerl. OPTIONAL *************** *** 61,64 **** --- 62,72 ---- THE BIOPERL BUNDLE + You do not need to install Bundle::BioPerl if you will install Bioperl + using CPAN. This is for users manually installing Bioperl from archives + or CVS, who also want an easy way to install the optional external + modules that Bioperl makes use of. + + Bundle::BioPerl does *not* install Bioperl. + You typically need root privileges to install using CPAN. If you don't have these privileges please see INSTALLING BIOPERL IN A PERSONAL *************** *** 86,96 **** CPAN: Storable loaded ok Going to read /home/bosborne/.cpan/Metadata ! Database was generated on Tue, 24 Feb 2004 23:55:23 GMT ! DistributionB/BI/BIRNEY/bioperl-1.2.tar.gz ! DistributionB/BI/BIRNEY/bioperl-1.4.tar.gz Now install: ! cpan>install B/BI/BIRNEY/bioperl-1.4.tar.gz If you've installed everything perfectly and all the network connections --- 94,105 ---- CPAN: Storable loaded ok Going to read /home/bosborne/.cpan/Metadata ! Database was generated on Mon, 20 Nov 2006 05:24:36 GMT ! Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz ! Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz ! Distribution S/SE/SENDU/bioperl-1.5.2_100.tar.gz Now install: ! cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz If you've installed everything perfectly and all the network connections *************** *** 100,105 **** undetected bug in Bioperl, flawed test script, problems with CGI script used for sequence retrieval at public database, and so on. Remember ! that there are over 700 modules in Bioperl and the test suite is running ! more than 9000 individual tests, a few failed tests may not affect your usage of Bioperl. --- 109,114 ---- undetected bug in Bioperl, flawed test script, problems with CGI script used for sequence retrieval at public database, and so on. Remember ! that there are over 800 modules in Bioperl and the test suite is running ! more than 12000 individual tests, a few failed tests may not affect your usage of Bioperl. *************** *** 107,111 **** Bioperl and you'd like to install anyway do: ! cpan>force install B/BI/BIRNEY/bioperl-1.4.tar.gz This is what most experienced Bioperl users would do. However, if you're --- 116,120 ---- Bioperl and you'd like to install anyway do: ! cpan>force install S/SE/SENDU/bioperl-1.5.2_100.tar.gz This is what most experienced Bioperl users would do. However, if you're *************** *** 113,117 **** bioperl-l at bioperl.org. ! INSTALLING BIOPERL THE EASY WAY USING GNU 'make' The advantage of this approach is it's stepwise, so it's easy to stop and --- 122,126 ---- bioperl-l at bioperl.org. ! INSTALLING BIOPERL THE EASY WAY USING Build.PL The advantage of this approach is it's stepwise, so it's easy to stop and *************** *** 120,126 **** Download, then unpack the tar file. For example: ! >gunzip bioperl-1.5.2.tar.gz ! >tar xvf bioperl-1.5.2.tar ! >cd bioperl-1.5.2 Now issue the make commands: --- 129,135 ---- Download, then unpack the tar file. For example: ! >gunzip bioperl-1.5.2_100.tar.gz ! >tar xvf bioperl-1.5.2_100.tar ! >cd bioperl-1.5.2_100 Now issue the make commands: *************** *** 135,141 **** undetected bug in Bioperl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that ! there are over 700 modules in Bioperl and the test suite is running almost ! 9000 individual tests, a few failed tests may not affect your usage of ! Bioperl. If you decide that the failed tests will not affect how you intend to use --- 144,150 ---- undetected bug in Bioperl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that ! there are over 800 modules in Bioperl and the test suite is running more ! than 12000 individual tests, a few failed tests may not affect your usage ! of Bioperl. If you decide that the failed tests will not affect how you intend to use *************** *** 148,154 **** bioperl-l at bioperl.org. ! To 'make install' you need write permission in the perl5/site_perl/source ! area. Usually this will require you becoming root, so you will want to ! talk to your systems manager if you don't have the necessary privileges. It is also straightforward to install the package outside of the this --- 157,164 ---- bioperl-l at bioperl.org. ! To './Build install' you need write permission in the perl5/site_perl/source ! area (or similar, depending on your environment). Usually this will require ! you becoming root, so you will want to talk to your systems manager if you ! don't have the necessary privileges. It is also straightforward to install the package outside of the this *************** *** 158,165 **** WHERE ARE THE MAN PAGES? ! When using Makefile.PL, we had to disable the automatic creation of man ! pages because this step was triggering a "line too long" error on some ! OSs due to shell constraints. If you want man pages installed use the ! Build.PL installation process. EXTERNAL PROGRAMS --- 168,176 ---- WHERE ARE THE MAN PAGES? ! When using Makefile.PL (no longer covered in this documentation), we had ! to disable the automatic creation of man pages because this step was ! triggering a "line too long" error on some OSs due to shell constraints. ! If you want man pages installed use the Build.PL installation process ! discussed above. EXTERNAL PROGRAMS *************** *** 229,234 **** like, simply answer the questions on 'perl Build.PL'. The installation directory can be specified by ! perl Build.PL ! ./Build install --install_path script=/foo/scripts By default they install to /usr/bin or similar, depending on platform. --- 240,245 ---- like, simply answer the questions on 'perl Build.PL'. The installation directory can be specified by ! perl Build.PL ! ./Build install --install_path script=/foo/scripts By default they install to /usr/bin or similar, depending on platform. *************** *** 297,301 **** execute the make commands from the Compile/SW directory. ! If all else fails or are unable to access the perl distribution directories, ask your system administrator to place the files there for you. You can always execute perl scripts in the same directory as the --- 308,312 ---- execute the make commands from the Compile/SW directory. ! If all else fails and you are unable to access the perl distribution directories, ask your system administrator to place the files there for you. You can always execute perl scripts in the same directory as the *************** *** 312,316 **** #!/usr/bin/perl use lib "/home/users/dag/lib/perl5/"; ! use Bio::Seq; #<...insert whizzy perl code here...> --- 323,327 ---- #!/usr/bin/perl use lib "/home/users/dag/lib/perl5/"; ! use Bio::Perl; #<...insert whizzy perl code here...> *************** *** 319,341 **** csh or tcsh: ! setenv PERL5LIB /home/users/dag/lib/perl5// bash or sh: ! export PERL5LIB=/home/users/dag/lib/perl5// THE TEST SYSTEM The Bioperl test system is located in the t/ directory and is ! automatically run whenever you execute the 'make test' command. Alternatively if you want to investigate the behavior of a specific test ! such as the SeqIO test you would type: ! >perl -I. -w t/SeqIO.t ! The -I. tells Perl to use the current directory as the include path - this ! makes sure you are testing the modules in this directory not ones ! installed elsewhere in your PERL5LIB path. The -w tells Perl to print all ! warnings. If you are trying to learn how to use a module, often the test suite is a --- 330,357 ---- csh or tcsh: ! setenv PERL5LIB /home/users/dag/lib/perl5/ bash or sh: ! export PERL5LIB=/home/users/dag/lib/perl5/ THE TEST SYSTEM The Bioperl test system is located in the t/ directory and is ! automatically run whenever you execute the './Build test' command ! (having previously run 'Perl Build.PL'; if you have already installed ! Bioperl answer 'no' to script installation to get nicer test output ! later). Alternatively if you want to investigate the behavior of a specific test ! such as the Seq test you would type: ! >./Build test --test_files t/Seq.t --verbose ! The ./ ensures you are using the Build script in the current directory to ! make sure you are testing the modules in this directory not ones ! installed elsewhere. The --test_files arguement can be used multiple times ! to try a set of test scripts in one go. The --verbose arguement outputs ! the detailed test results, instead of just the summary you see during ! './Build test'. If you are trying to learn how to use a module, often the test suite is a *************** *** 385,388 **** This should install the compiled extension. The Bio::Tools::pSW module will work cleanly now. - - \ No newline at end of file --- 401,402 ---- Index: INSTALL.WIN =================================================================== RCS file: /home/repository/bioperl/bioperl-live/INSTALL.WIN,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -d -r1.23 -r1.24 *** INSTALL.WIN 14 Nov 2006 15:13:24 -0000 1.23 --- INSTALL.WIN 21 Nov 2006 10:32:34 -0000 1.24 *************** *** 80,89 **** 7) Right click the latest version of Bioperl available and choose ! install. ! ! 7a) This package will be sufficient for the main ! functionality of Bioperl. However, if you require ! full functionality, you should also install the ! latest Bundle-BioPerl package. 8) Click the green arrow (Run marked actions) to complete the --- 80,85 ---- 7) Right click the latest version of Bioperl available and choose ! install. (Note for users of previous Bioperl releases: you should ! not have to use the Bundle-BioPerl package anymore.) 8) Click the green arrow (Run marked actions) to complete the _______________________________________________ Bioperl-guts-l mailing list Bioperl-guts-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l ------ End of Forwarded Message From bix at sendu.me.uk Tue Nov 21 21:32:02 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 21 Nov 2006 21:32:02 +0000 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: References: Message-ID: <45637052.4040003@sendu.me.uk> Brian Osborne wrote: > Bioperl-l, > > INSTALL has changed in CVS but the Wiki's version has not - you always have > to change both versions of the INSTALL instructions, this is how Chris has > elected to do it. Yes, I will edit the wiki when I've finished with the INSTALL docs. (I may be changing them further, please don't consider the current information gospel.) From hlapp at gmx.net Tue Nov 21 21:44:50 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 21 Nov 2006 16:44:50 -0500 Subject: [Bioperl-l] bioperl-db question In-Reply-To: <45636286.6040504@molbio.mgh.harvard.edu> References: <001801c70905$dbdd7a40$15327e82@pyrimidine> <455C4CFD.5080005@sendu.me.uk> <455C5D5A.5020205@sheffield.ac.uk> <455D66F6.4070804@sendu.me.uk> <86812533-7577-4349-8A5C-118E488007DB@uiuc.edu> <455DBE47.90501@sendu.me.uk> <455DF2BC.9010601@sheffield.ac.uk> <455DF4DB.5000808@sendu.me.uk> <58B3B961-C21B-4C4C-A578-B54BF0FCCE2F@uiuc.edu> <455E0EEF.4080806@sendu.me.uk> <455EAAB2.4010004@molbio.mgh.harvard.edu> <455EBE7E.4060105@sendu.me.uk> <455EC4A6.4040103@molbio.mgh.harvard.edu> <455ECB0D.5090606@molbio.mgh.harvard.edu> <0676078B-8A15-493D-ADDB-C38FFAD37E05@gmx.net> <4561D07C.4060800@molbio.mgh.harvard.edu> <4561F0F4.3060106@molbio.mgh.harvard.edu> <3F9E5236-7EC1-4053-911C-440C1FE49343@gmx.net> <4562B497.6080805@molbio.mgh.harvard.edu> <45636286.6040504@molbio.mgh.harvard.edu> Message-ID: <064D0938-C753-40BD-8A0D-C900985193B8@gmx.net> Yes this needs to be better documented. Note that you can use both APIs if you install them under different users (= schema in Oracle). I'm not 100% sure whether both variants are fully prepared for this; you may have to create synonyms for the schema-owner tables first, i.e., SQL> CREATE SYNONYM sg_biodatabase FOR biosqlowner.sg_biodatabase; etc, assuming that are logged on as the user under which you want to create the API, and biosqlowner is the schema-owner of the BioSQL instance. Did you want to use BioSQL with both bioperl and biojava? -hilmar On Nov 21, 2006, at 3:33 PM, gang wu wrote: > Hi Hilmar, > > I just rebuilt the Oracle BioSQL database by strictly following the > INSTALL doc. You are right that BS-create-Biosql-API.sql must be > run to make bioperl-db work with it(the oid columns). But my > installation problem was caused by running BS-create-Biosql- > API2.sql after it, which rendered the database not compatible with > bioperl-db. If I ran only BS-create-Biosql-API.sql, ll bioperl-db > tests could pass. Does this mean that the Oracle version is not > interoperable between the Bio- projects at this point? > > Did I miss anything in the INSTALL or README? I only saw a line "-- > all others (Biojava, etc)" but did not realize I could not run both > BS-create-Biosql-API.sql and BS-create-Biosql-API2.sql. I this is > the case, can you please add it to the docs? > > Thanks very much for your help. > > Gang > > Hilmar Lapp wrote: >> The Oracle error is >> >> ORA-00904: "BIODATABASE"."OID": invalid identifier >> >> and if you look at the accompanying statement, it's the UK select >> statement: >> >> SELECT <*>biodatabase.oid, biodatabase.name, >> biodatabase.authority FROM biodatabase WHERE name = :p1 >> >> The column OID must exist in the Biodatabase table (which actually >> is a synonym to the SG_BIODATABASE table), if it is the Oracle >> schema. >> >> This actually prompts another suggestion, sorry for not asking >> that first: did you actually install the BioSQL-API on top of the >> schema by running the script BS-create-Biosql-API.sql? (It seems >> that the statement it chokes on is also the first statement being >> prepared, so this may well be the reason) >> >> -hilmar >> >> On Nov 21, 2006, at 3:11 AM, gang wu wrote: >> >>> Can you show me where it indicates I am actually using the MySQL >>> schema. >>> I am pretty sure that I used the sql script files from >>> sql/biosql-ora(Has anyone actually tried to install MySQL schema on >>> Oracle?). I can reinstall the schema if you think that's the way to >>> solve the problem. Thanks very much. >>> >>> Gang >>> >>> Hilmar Lapp wrote: >>>> It looks like you are using the MySQL schema under Oracle. There >>>> are >>>> different DDL scripts for each supported RDBMS. The ones for Oracle >>>> are in the sql/biosql-ora subdirectory. Note the INSTALL >>>> document in >>>> that directory. >>>> >>>> -hilmar >>>> >>>> >>>> On Nov 20, 2006, at 1:16 PM, gang wu wrote: >>>> >>>> >>>>> Hi Hilmar, >>>>> >>>>> Below is the output. Thanks. >>>>> >>>>> Gang >>>>> ========================================================== >>>>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1 >>>>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor >>>>> TEST_VERBOSE=1 >>>>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/ >>>>> lib64/ >>>>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e >>>>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests >>>>> @ARGV;' t/01dbadaptor.t >>>>> t/01dbadaptor....1..19 >>>>> ok 1 >>>>> ok 2 >>>>> ok 3 >>>>> ok 4 >>>>> ok 5 >>>>> ok 6 >>>>> ok 7 >>>>> ok 8 >>>>> ok 9 >>>>> ok 10 >>>>> ok 11 >>>>> attempting to load adaptor class for BioNamespace >>>>> ok 12 >>>>> attempting to load module >>>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> ok 13 >>>>> ok 14 >>>>> attempting to load driver for adaptor class >>>>> Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> attempting to load driver for adaptor class >>>>> Bio::DB::BioSQL::BasePersistenceAdaptor >>>>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as >>>>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor >>>>> preparing UK select statement: SELECT biodatabase.oid, >>>>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE >>>>> name >>>>> = ? >>>>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID": >>>>> invalid identifier (DBD ERROR: error possibly near <*> >>>>> indicator at >>>>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name, >>>>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for >>>>> Statement "SELECT biodatabase.oid, biodatabase.name, >>>>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/ >>>>> lib/ >>>>> Bio/DB/BioSQL/BaseDriver.pm line 1800. >>>>> BioNamespaceAdaptor: binding UK column 1 to >>>>> "__dummy__" (namespace) >>>>> Can't call method "bind_param" on an undefined value at blib/lib/ >>>>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939. >>>>> dubious >>>>> Test returned status 255 (wstat 65280, 0xff00) >>>>> DIED. FAILED tests 15-19 >>>>> Failed 5/19 tests, 73.68% okay >>>>> Failed Test Stat Wstat Total Fail Failed List of Failed >>>>> ------------------------------------------------------------------ >>>>> ---- >>>>> --------- >>>>> t/01dbadaptor.t 255 65280 19 10 52.63% 15-19 >>>>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68% >>>>> okay. >>>>> make: *** [test_01dbadaptor] Error 2 >>>>> ========================================================= >>>>> >>>>> >>>>> Hilmar Lapp wrote: >>>>> >>>>>> Hi Gang, >>>>>> >>>>>> what I wanted to get at was the error message from the driver >>>>>> when >>>>>> it fails to generate the prepared statement, but this is not in >>>>>> the output. >>>>>> >>>>>> I believe you need set the HARNESS_VERBOSE environment >>>>>> variable to >>>>>> 1 before testing to get what I need: >>>>>> >>>>>> $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for >>>>>> csh/tcsh >>>>>> $ make test_01dbadaptor TEST_VERBOSE=1 >>>>>> >>>>>> This will lead to _a lot_ of debugging output. Do not run this >>>>>> for >>>>>> the entire test suite. >>>>>> >>>>>> The errors for mysql I believe are related to the fact that have >>>>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh >>>>>> (completely empty) instance of BioSQL. >>>>>> >>>>>> Let me know what you get for the Oracle test above. >>>>>> >>>>>> -hilmar >>>>>> >>>>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote: >>>>>> >>>>>> >>>>>>> Hi Hilmar, >>>>>>> >>>>>>> Thanks for your message. Below are several tests for Oracle and >>>>>>> MySQL. MySQL actually also has two tests with failed items which >>>>>>> may be related to data in BioSQL database. >>>>>>> >>>>>>> Could it be my Oracle installation/configuration has some >>>>>>> issues? >>>>>>> >>>>>>> Thanks. >>>>>>> >>>>>>> Gang >>>>>>> >>>>>> --=========================================================== >>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>>>>> =========================================================== >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> --=========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> >> -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Tue Nov 21 23:54:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 17:54:32 -0600 Subject: [Bioperl-l] GO terms not present in Swiss annotation object In-Reply-To: <1164141156l.712786l.0l@psu.edu> References: <1164141156l.712786l.0l@psu.edu> Message-ID: <101BBBA4-391D-4F87-8181-F754A2357DA8@uiuc.edu> You'll want to always reply to the list as well. I would say update to a newer version; many changes have been made to parsing GenBank/ SwissProt/EMBL since rel 1.4, including dblinks. If you're using windows you'll need to follow the instructions on the website for the latest release candidate: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Note that the release candidates are located in a different repository, so you'll need to set that up to find them. chris On Nov 21, 2006, at 2:32 PM, Juan Cristobal Vera wrote: > ok, thanks for responding! > I'm using ActivePerl 5.8.8 build 819 on a windows machine (sorry) > and the bioperl 1.4 PPM3 package. Perhaps this is too old? > Here's part of my code (mostly derived from bioperl docs): > ......................... > #cut > > $seqInObj = $indexObj->get_Seq_by_id($line); #get sequence and > create seq object > > #cut > > if (defined $seqInObj->annotation){ > $annotObj = $seqInObj->annotation; #create annotation object > foreach $key ($annotObj->get_all_annotation_keys){ > @values = $annotObj->get_Annotations($key); > foreach $value (@values){ > if (lc($key) eq "dblink"){ > print $outfh "Annotation: $key\n"; > print $outfh $value->as_text,"\n"; > $dbhash_ref = $value->hash_tree; > for $dbKey (keys %{$dbhash_ref}) { > print $outfh $dbKey,": ",$dbhash_ref-> > {$dbKey},"\n"; #none of these prints produce GO terms > } > } > } > } > } > ......................... > My program searches an indexed database on my machine, creates the > objects, and prints out relevant annotations. > Here are some of the accessions I used for testing: > P19351 TNNT_DROME > P36188 TNNI_DROME > P11147 HSP7D_DROME > .......................................... > the relevant output looks something like this (for debugging) for > P19351: > ...................................................................... > Direct database link to X58188 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: X58188 > optional_id: CAA41171.1 > Annotation: dblink > Direct database link to X59376 in database EMBL > database: EMBL > comment: -; mRNA. > primary_id: X59376 > optional_id: CAA42020.1 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48802.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48803.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48804.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAF48805.2 > Annotation: dblink > Direct database link to AE003507 in database EMBL > database: EMBL > comment: -; Genomic_DNA. > primary_id: AE003507 > optional_id: AAN09458.1 > Annotation: dblink > Direct database link to AY122145 in database EMBL > database: EMBL > comment: -; mRNA. > primary_id: AY122145 > optional_id: AAM52657.1 > Annotation: dblink > Direct database link to A40547 in database PIR > database: PIR > primary_id: A40547 > optional_id: A40547 > Annotation: dblink > Direct database link to B38594 in database PIR > database: PIR > primary_id: B38594 > optional_id: B38594 > Annotation: dblink > Direct database link to Dm.1717 in database UniGene > database: UniGene > primary_id: Dm.1717 > optional_id: - > Annotation: dblink > Direct database link to P45379 in database HSSP > database: HSSP > primary_id: P45379 > optional_id: 1J1E > Annotation: dblink > Direct database link to P36188 in database IntAct > database: IntAct > primary_id: P36188 > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PA in database KEGG > database: KEGG > primary_id: dme:CG7178-PA > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PB in database KEGG > database: KEGG > primary_id: dme:CG7178-PB > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PC in database KEGG > database: KEGG > primary_id: dme:CG7178-PC > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PD in database KEGG > database: KEGG > primary_id: dme:CG7178-PD > optional_id: - > Annotation: dblink > Direct database link to dme:CG7178-PG in database KEGG > database: KEGG > primary_id: dme:CG7178-PG > optional_id: - > Annotation: dblink > Direct database link to FBgn0004028 in database FlyBase > database: FlyBase > primary_id: FBgn0004028 > optional_id: wupA > Annotation: dblink > Direct database link to IPR001978 in database InterPro > database: InterPro > primary_id: IPR001978 > optional_id: Troponin > Annotation: dblink > Direct database link to PF00992 in database Pfam > database: Pfam > comment: 1 > primary_id: PF00992 > optional_id: Troponin > .............................................. > as you can see, no GO terms above > ...................................................... > Vs. the actual content of the flat file from for the dblinks from > P19351: > DR EMBL; X54504; CAA38366.1; -; mRNA. > DR EMBL; AY439172; AAR24583.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24584.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24585.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24586.1; -; Genomic_DNA. > DR EMBL; AY439172; AAR24587.1; -; Genomic_DNA. > DR EMBL; AY665838; AAU09446.1; -; mRNA. > DR EMBL; AE014298; AAF48288.2; -; Genomic_DNA. > DR EMBL; AE014298; AAF48289.2; -; Genomic_DNA. > DR EMBL; AE014298; AAF48290.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52491.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52492.1; -; Genomic_DNA. > DR EMBL; AE014298; AAX52493.1; -; Genomic_DNA. > DR EMBL; AY051989; AAK93413.1; -; mRNA. > DR EMBL; AY070875; AAL48497.1; ALT_SEQ; mRNA. > DR PIR; S13251; S13251. > DR UniGene; Dm.20472; -. > DR HSSP; P45379; 1J1E. > DR Ensembl; CG7107; Drosophila melanogaster. > DR KEGG; dme:CG7107-PE; -. > DR KEGG; dme:CG7107-PF; -. > DR KEGG; dme:CG7107-PG; -. > DR FlyBase; FBgn0004169; up. > DR GO; GO:0007498; P:mesoderm development; IEP:FlyBase. ...... > where the GO term is last entry in dblink section above. > Any help you could provide would be most welcome. Let me know if > this is insufficient information or if you need a working script. > > > On Tue, 21 Nov 2006 00:19:59 -0600 Chris Fields wrote: > Juan, The DBLink objects should be generated. You'll need to give > us a bit more information to go on, though. We need an example > sequence, your local version of Bioperl, maybe a test script, etc. > This is the right forum for this, yes, if you are using BioPerl. > Chris On Nov 20, 2006, at 6:52 PM, Juan Cristobal Vera wrote: > > > > Hi, > I'm writing a simple application to extract various fields > from > swissprot objects and I can't access the GO terms found in > > "dblink" part of the swiss format flat files. I'm not a > > professional programmer and I can't figure out why this is > > occuring. All the other "dblink" keys are being > > generated as far as I can tell (e.g. embl, pfam, etc). The GO > > terms are just skipped over and it's driving me crazy. Not sure if > > this is a bug or a deliberate strategy I'm unfamiliar with. I > > apologize if this is not the correct forum to ask for this sort of > > help and would ask to be directed to the proper one. > > > > Juan > Cristobal Vera > > Graduate Student > > Department of Biology > > > Penn State University > > 208 Mueller Laboratory > > University > Park, PA 16802 > > (814)863-2957 > > > _______________________________________________ > Bioperl-l mailing > list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/ > mailman/listinfo/bioperl-l Christopher Fields Postdoctoral > Researcher Lab of Dr. Robert Switzer Dept of Biochemistry > University of Illinois Urbana-Champaign > > Juan Cristobal Vera > Graduate Student > Department of Biology > Penn State University > 208 Mueller Laboratory > University Park, PA 16802 > (814)863-2957 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Nov 21 23:56:48 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 21 Nov 2006 17:56:48 -0600 Subject: [Bioperl-l] FW: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 INSTALL, 1.57, 1.58 INSTALL.WIN, 1.23, 1.24 In-Reply-To: References: Message-ID: On Nov 21, 2006, at 2:53 PM, Brian Osborne wrote: > Bioperl-l, > > INSTALL has changed in CVS but the Wiki's version has not - you > always have > to change both versions of the INSTALL instructions, this is how > Chris has > elected to do it. > > Brian O. Agreed (thanks Brian for pointing that out). I have to update these by hand until I can find a more automated way (which will be hard considering the meta content in the wiki). Chris > > > > Date: Tue, 21 Nov 2006 10:32:36 +0000 > To: > Subject: [Bioperl-guts-l] bioperl-live DEPENDENCIES, 1.1, 1.2 > INSTALL, 1.57, > 1.58 INSTALL.WIN, 1.23, 1.24 > > Update of /home/repository/bioperl/bioperl-live > In directory dev.open-bio.org:/tmp/cvs-serv14112 > > Modified Files: > DEPENDENCIES INSTALL INSTALL.WIN > Log Message: > clarification for Bundle::BioPerl, updates for Build.PL > > Index: DEPENDENCIES > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/DEPENDENCIES,v > retrieving revision 1.1 > retrieving revision 1.2 > diff -C2 -d -r1.1 -r1.2 > *** DEPENDENCIES 14 Nov 2006 15:13:24 -0000 1.1 > --- DEPENDENCIES 21 Nov 2006 10:32:34 -0000 1.2 > *************** > *** 5,10 **** > The following packages are used by Bioperl. Not all are required for > Bioperl to operate properly, however some functionality will be > missing > ! without them. You can easily install all of these, except > srsperl.pm, > ! using the Bundle::BioPerl CPAN bundle. > > The DBD::mysql, DB_File and XML::Parser modules require other > applications > --- 5,11 ---- > The following packages are used by Bioperl. Not all are required for > Bioperl to operate properly, however some functionality will be > missing > ! without them. You can easily install all of these by using CPAN > to install > ! Bioperl, or if you have installed Bioperl manually (from archive > or CVS), > ! by using the Bundle::BioPerl CPAN bundle. > > The DBD::mysql, DB_File and XML::Parser modules require other > applications > > Index: INSTALL > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/INSTALL,v > retrieving revision 1.57 > retrieving revision 1.58 > diff -C2 -d -r1.57 -r1.58 > *** INSTALL 16 Nov 2006 16:27:49 -0000 1.57 > --- INSTALL 21 Nov 2006 10:32:34 -0000 1.58 > *************** > *** 1,24 **** > # $Id$ > > ! Installing Bioperl for Unix > > ! * BIOPERL INSTALLATION > ! * SYSTEM REQUIREMENTS > ! * OPTIONAL > ! * ADDITIONAL INSTALLATION INFORMATION > ! * THE BIOPERL BUNDLE > ! * INSTALLING BIOPERL THE EASY WAY USING CPAN > ! * INSTALLING BIOPERL THE EASY WAY USING GNU 'make' > ! * WHERE ARE THE MAN PAGES? > ! * EXTERNAL PROGRAMS > ! * Environment Variables > ! * INSTALLING BIOPERL SCRIPTS > ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA > ! * INSTALLING BIOPERL MODULES THE HARD WAY > ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION > ! * THE TEST SYSTEM > ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE > ! * CONFIGURING for BSD and Solaris boxes > ! * INSTALLATION > > BIOPERL INSTALLATION > --- 1,24 ---- > # $Id$ > > ! Installing Bioperl for Unix > > ! * BIOPERL INSTALLATION > ! * SYSTEM REQUIREMENTS > ! * OPTIONAL > ! * ADDITIONAL INSTALLATION INFORMATION > ! * THE BIOPERL BUNDLE > ! * INSTALLING BIOPERL THE EASY WAY USING CPAN > ! * INSTALLING BIOPERL THE EASY WAY USING Build.PL > ! * WHERE ARE THE MAN PAGES? > ! * EXTERNAL PROGRAMS > ! * Environment Variables > ! * INSTALLING BIOPERL SCRIPTS > ! * INSTALLING BIOPERL IN A PERSONAL MODULE AREA > ! * INSTALLING BIOPERL MODULES THE HARD WAY > ! * USING MODULES NOT INSTALLED IN THE STANDARD LOCATION > ! * THE TEST SYSTEM > ! * BUILDING THE OPTIONAL bioperl-ext PACKAGE > ! * CONFIGURING for BSD and Solaris boxes > ! * INSTALLATION > > BIOPERL INSTALLATION > *************** > *** 41,48 **** > modules is included in the DEPENDENCIES file. > > ! The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation of > these > ! external modules easy. Simply install the bundle using your CPAN > shell and > ! all necessary modules will be installed. See THE BIOPERL BUNDLE, > ! below. > > OPTIONAL > --- 41,49 ---- > modules is included in the DEPENDENCIES file. > > ! When not using CPAN to install Bioperl itself, the CPAN Bioperl > Bundle > ! (Bundle::BioPerl) makes installation of these external modules easy. > Simply > ! install the bundle using your CPAN shell and many optional > modules will be > ! installed. See THE BIOPERL BUNDLE, below. However, it is > recommended you > use > ! CPAN to install Bioperl and not use Bundle::BioPerl. > > OPTIONAL > *************** > *** 61,64 **** > --- 62,72 ---- > THE BIOPERL BUNDLE > > + You do not need to install Bundle::BioPerl if you will install > Bioperl > + using CPAN. This is for users manually installing Bioperl from > archives > + or CVS, who also want an easy way to install the optional external > + modules that Bioperl makes use of. > + > + Bundle::BioPerl does *not* install Bioperl. > + > You typically need root privileges to install using CPAN. If you > don't > have these privileges please see INSTALLING BIOPERL IN A PERSONAL > *************** > *** 86,96 **** > CPAN: Storable loaded ok > Going to read /home/bosborne/.cpan/Metadata > ! Database was generated on Tue, 24 Feb 2004 23:55:23 GMT > ! DistributionB/BI/BIRNEY/bioperl-1.2.tar.gz > ! DistributionB/BI/BIRNEY/bioperl-1.4.tar.gz > > Now install: > > ! cpan>install B/BI/BIRNEY/bioperl-1.4.tar.gz > > If you've installed everything perfectly and all the network > connections > --- 94,105 ---- > CPAN: Storable loaded ok > Going to read /home/bosborne/.cpan/Metadata > ! Database was generated on Mon, 20 Nov 2006 05:24:36 GMT > ! Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz > ! Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz > ! Distribution S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > Now install: > > ! cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > If you've installed everything perfectly and all the network > connections > *************** > *** 100,105 **** > undetected bug in Bioperl, flawed test script, problems with CGI > script used for sequence retrieval at public database, and so on. > Remember > ! that there are over 700 modules in Bioperl and the test suite is > running > ! more than 9000 individual tests, a few failed tests may not > affect your > usage of Bioperl. > > --- 109,114 ---- > undetected bug in Bioperl, flawed test script, problems with CGI > script used for sequence retrieval at public database, and so on. > Remember > ! that there are over 800 modules in Bioperl and the test suite is > running > ! more than 12000 individual tests, a few failed tests may not > affect your > usage of Bioperl. > > *************** > *** 107,111 **** > Bioperl and you'd like to install anyway do: > > ! cpan>force install B/BI/BIRNEY/bioperl-1.4.tar.gz > > This is what most experienced Bioperl users would do. However, if > you're > --- 116,120 ---- > Bioperl and you'd like to install anyway do: > > ! cpan>force install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > > This is what most experienced Bioperl users would do. However, if > you're > *************** > *** 113,117 **** > bioperl-l at bioperl.org. > > ! INSTALLING BIOPERL THE EASY WAY USING GNU 'make' > > The advantage of this approach is it's stepwise, so it's easy to > stop and > --- 122,126 ---- > bioperl-l at bioperl.org. > > ! INSTALLING BIOPERL THE EASY WAY USING Build.PL > > The advantage of this approach is it's stepwise, so it's easy to > stop and > *************** > *** 120,126 **** > Download, then unpack the tar file. For example: > > ! >gunzip bioperl-1.5.2.tar.gz > ! >tar xvf bioperl-1.5.2.tar > ! >cd bioperl-1.5.2 > > Now issue the make commands: > --- 129,135 ---- > Download, then unpack the tar file. For example: > > ! >gunzip bioperl-1.5.2_100.tar.gz > ! >tar xvf bioperl-1.5.2_100.tar > ! >cd bioperl-1.5.2_100 > > Now issue the make commands: > *************** > *** 135,141 **** > undetected bug in Bioperl, flawed test script, problems with CGI > script > using for sequence retrieval at public database, and so on. > Remember that > ! there are over 700 modules in Bioperl and the test suite is > running almost > ! 9000 individual tests, a few failed tests may not affect your > usage of > ! Bioperl. > > If you decide that the failed tests will not affect how you > intend to use > --- 144,150 ---- > undetected bug in Bioperl, flawed test script, problems with CGI > script > using for sequence retrieval at public database, and so on. > Remember that > ! there are over 800 modules in Bioperl and the test suite is > running more > ! than 12000 individual tests, a few failed tests may not affect > your usage > ! of Bioperl. > > If you decide that the failed tests will not affect how you > intend to use > *************** > *** 148,154 **** > bioperl-l at bioperl.org. > > ! To 'make install' you need write permission in the perl5/ > site_perl/source > ! area. Usually this will require you becoming root, so you will > want to > ! talk to your systems manager if you don't have the necessary > privileges. > > It is also straightforward to install the package outside of the > this > --- 157,164 ---- > bioperl-l at bioperl.org. > > ! To './Build install' you need write permission in the > perl5/site_perl/source > ! area (or similar, depending on your environment). Usually this will > require > ! you becoming root, so you will want to talk to your systems > manager if you > ! don't have the necessary privileges. > > It is also straightforward to install the package outside of the > this > *************** > *** 158,165 **** > WHERE ARE THE MAN PAGES? > > ! When using Makefile.PL, we had to disable the automatic creation > of man > ! pages because this step was triggering a "line too long" error on > some > ! OSs due to shell constraints. If you want man pages installed use > the > ! Build.PL installation process. > > EXTERNAL PROGRAMS > --- 168,176 ---- > WHERE ARE THE MAN PAGES? > > ! When using Makefile.PL (no longer covered in this documentation), > we had > ! to disable the automatic creation of man pages because this step was > ! triggering a "line too long" error on some OSs due to shell > constraints. > ! If you want man pages installed use the Build.PL installation > process > ! discussed above. > > EXTERNAL PROGRAMS > *************** > *** 229,234 **** > like, simply answer the questions on 'perl Build.PL'. > The installation directory can be specified by > ! perl Build.PL > ! ./Build install --install_path script=/foo/scripts > By default they install to /usr/bin or similar, depending on > platform. > > --- 240,245 ---- > like, simply answer the questions on 'perl Build.PL'. > The installation directory can be specified by > ! perl Build.PL > ! ./Build install --install_path script=/foo/scripts > By default they install to /usr/bin or similar, depending on > platform. > > *************** > *** 297,301 **** > execute the make commands from the Compile/SW directory. > > ! If all else fails or are unable to access the perl distribution > directories, ask your system administrator to place the files > there for > you. You can always execute perl scripts in the same directory as > the > --- 308,312 ---- > execute the make commands from the Compile/SW directory. > > ! If all else fails and you are unable to access the perl distribution > directories, ask your system administrator to place the files > there for > you. You can always execute perl scripts in the same directory as > the > *************** > *** 312,316 **** > #!/usr/bin/perl > use lib "/home/users/dag/lib/perl5/"; > ! use Bio::Seq; > #<...insert whizzy perl code here...> > > --- 323,327 ---- > #!/usr/bin/perl > use lib "/home/users/dag/lib/perl5/"; > ! use Bio::Perl; > #<...insert whizzy perl code here...> > > *************** > *** 319,341 **** > csh or tcsh: > > ! setenv PERL5LIB /home/users/dag/lib/perl5// > > bash or sh: > > ! export PERL5LIB=/home/users/dag/lib/perl5// > > THE TEST SYSTEM > > The Bioperl test system is located in the t/ directory and is > ! automatically run whenever you execute the 'make test' command. > Alternatively if you want to investigate the behavior of a > specific test > ! such as the SeqIO test you would type: > > ! >perl -I. -w t/SeqIO.t > > ! The -I. tells Perl to use the current directory as the include > path - this > ! makes sure you are testing the modules in this directory not ones > ! installed elsewhere in your PERL5LIB path. The -w tells Perl to > print all > ! warnings. > > If you are trying to learn how to use a module, often the test > suite is a > --- 330,357 ---- > csh or tcsh: > > ! setenv PERL5LIB /home/users/dag/lib/perl5/ > > bash or sh: > > ! export PERL5LIB=/home/users/dag/lib/perl5/ > > THE TEST SYSTEM > > The Bioperl test system is located in the t/ directory and is > ! automatically run whenever you execute the './Build test' command > ! (having previously run 'Perl Build.PL'; if you have already > installed > ! Bioperl answer 'no' to script installation to get nicer test output > ! later). > Alternatively if you want to investigate the behavior of a > specific test > ! such as the Seq test you would type: > > ! >./Build test --test_files t/Seq.t --verbose > > ! The ./ ensures you are using the Build script in the current > directory to > ! make sure you are testing the modules in this directory not ones > ! installed elsewhere. The --test_files arguement can be used > multiple times > ! to try a set of test scripts in one go. The --verbose arguement > outputs > ! the detailed test results, instead of just the summary you see > during > ! './Build test'. > > If you are trying to learn how to use a module, often the test > suite is a > *************** > *** 385,388 **** > This should install the compiled extension. The Bio::Tools::pSW > module will work cleanly now. > - > - > \ No newline at end of file > --- 401,402 ---- > > Index: INSTALL.WIN > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/INSTALL.WIN,v > retrieving revision 1.23 > retrieving revision 1.24 > diff -C2 -d -r1.23 -r1.24 > *** INSTALL.WIN 14 Nov 2006 15:13:24 -0000 1.23 > --- INSTALL.WIN 21 Nov 2006 10:32:34 -0000 1.24 > *************** > *** 80,89 **** > > 7) Right click the latest version of Bioperl available > and > choose > ! install. > ! > ! 7a) This package will be sufficient for > the main > ! functionality of Bioperl. However, if you > require > ! full functionality, you should also > install the > ! latest Bundle-BioPerl package. > > 8) Click the green arrow (Run marked actions) to > complete the > --- 80,85 ---- > > 7) Right click the latest version of Bioperl available > and > choose > ! install. (Note for users of previous Bioperl releases: > you > should > ! not have to use the Bundle-BioPerl package anymore.) > > 8) Click the green arrow (Run marked actions) to > complete the > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l > > ------ End of Forwarded Message > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jcv128 at psu.edu Tue Nov 21 20:53:07 2006 From: jcv128 at psu.edu (Juan Cristobal Vera) Date: Tue, 21 Nov 2006 15:53:07 -0500 Subject: [Bioperl-l] GO terms not present in Swiss annotation object-more details Message-ID: <1164142374l.1118292l.0l@psu.edu> Hi, I'm writing a simple application to extract various fields from swissprot objects and I can't access the GO terms found in dblink part of the swiss format flat files. I'm not a professional programmer and I can't figure out why this is occuring. All the other dblink keys are being generated as far as I can tell (e.g. embl, pfam, etc). The GO terms are just skipped over and it's driving me crazy. Not sure if this is a bug or a deliberate strategy I'm unfamiliar with. I'm using ActivePerl 5.8.8 build 819 on a windows machine (sorry) and the bioperl 1.4 PPM3 package. Perhaps this is too old? Here's part of my code (mostly derived from bioperl docs): ......................... #cut $seqInObj = $indexObj->get_Seq_by_id($line); #get sequence and create seq object #cut if (defined $seqInObj->annotation){ $annotObj = $seqInObj->annotation; #create annotation object foreach $key ($annotObj->get_all_annotation_keys){ @values =$annotObj->get_Annotations($key); foreach $value (@values){ if (lc($key) eq "dblink"){ print $outfh "Annotation: $key\n"; print $outfh $value->as_text,"\n"; $dbhash_ref = $value->hash_tree; for $dbKey (keys %{$dbhash_ref}) { print $outfh $dbKey,":",$dbhash_ref->{$dbKey},"\n"; #none of these prints produce GO terms } } } } } ......................... My program searches an indexed database on my machine, creates the objects, and prints out relevant annotations. Here are some of the accessions I used for testing: P19351 TNNT_DROME P36188 TNNI_DROME P11147 HSP7D_DROME .......................................... the relevant output looks something like this (for debugging) for P19351: ...................................................................... Direct database link to X58188 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: X58188 optional_id: CAA41171.1 Annotation: dblink Direct database link to X59376 in database EMBL database: EMBL comment: -; mRNA. primary_id: X59376 optional_id: CAA42020.1 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48802.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48803.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48804.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAF48805.2 Annotation: dblink Direct database link to AE003507 in database EMBL database: EMBL comment: -; Genomic_DNA. primary_id: AE003507 optional_id: AAN09458.1 Annotation: dblink Direct database link to AY122145 in database EMBL database: EMBL comment: -; mRNA. primary_id: AY122145 optional_id: AAM52657.1 Annotation: dblink Direct database link to A40547 in database PIR database: PIR primary_id: A40547 optional_id: A40547 Annotation: dblink Direct database link to B38594 in database PIR database: PIR primary_id: B38594 optional_id: B38594 Annotation: dblink Direct database link to Dm.1717 in database UniGene database: UniGene primary_id: Dm.1717 optional_id: - Annotation: dblink Direct database link to P45379 in database HSSP database: HSSP primary_id: P45379 optional_id: 1J1E Annotation: dblink Direct database link to P36188 in database IntAct database: IntAct primary_id: P36188 optional_id: - Annotation: dblink Direct database link to dme:CG7178-PA in database KEGG database: KEGG primary_id: dme:CG7178-PA optional_id: - Annotation: dblink Direct database link to dme:CG7178-PB in database KEGG database: KEGG primary_id: dme:CG7178-PB optional_id: - Annotation: dblink Direct database link to dme:CG7178-PC in database KEGG database: KEGG primary_id: dme:CG7178-PC optional_id: - Annotation: dblink Direct database link to dme:CG7178-PD in database KEGG database: KEGG primary_id: dme:CG7178-PD optional_id: - Annotation: dblink Direct database link to dme:CG7178-PG in database KEGG database: KEGG primary_id: dme:CG7178-PG optional_id: - Annotation: dblink Direct database link to FBgn0004028 in database FlyBase database: FlyBase primary_id: FBgn0004028 optional_id: wupA Annotation: dblink Direct database link to IPR001978 in database InterPro database: InterPro primary_id: IPR001978 optional_id: Troponin Annotation: dblink Direct database link to PF00992 in database Pfam database: Pfam comment: 1 primary_id: PF00992 optional_id: Troponin .............................................. as you can see, no GO terms above ...................................................... Vs. the actual content of the flat file from for the dblinks from P19351: DR EMBL; X54504; CAA38366.1; -; mRNA. DR EMBL; AY439172; AAR24583.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24584.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24585.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24586.1; -; Genomic_DNA. DR EMBL; AY439172; AAR24587.1; -; Genomic_DNA. DR EMBL; AY665838; AAU09446.1; -; mRNA. DR EMBL; AE014298; AAF48288.2; -; Genomic_DNA. DR EMBL; AE014298; AAF48289.2; -; Genomic_DNA. DR EMBL; AE014298; AAF48290.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52491.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52492.1; -; Genomic_DNA. DR EMBL; AE014298; AAX52493.1; -; Genomic_DNA. DR EMBL; AY051989; AAK93413.1; -; mRNA. DR EMBL; AY070875; AAL48497.1; ALT_SEQ; mRNA. DR PIR; S13251; S13251. DR UniGene; Dm.20472; -. DR HSSP; P45379; 1J1E. DR Ensembl; CG7107; Drosophila melanogaster. DR KEGG; dme:CG7107-PE; -. DR KEGG; dme:CG7107-PF; -. DR KEGG; dme:CG7107-PG; -. DR FlyBase; FBgn0004169; up. DR GO; GO:0007498; P:mesoderm development; IEP:FlyBase. ...... where the GO term is last entry in dblink section above. Any help you could provide would be most welcome. Let me know if this is insufficient information or if you need a working script. Juan Cristobal Vera Graduate Student Department of Biology Penn State University 208 Mueller Laboratory University Park, PA 16802 (814)863-2957 From s.bulashevska at dkfz-heidelberg.de Wed Nov 22 11:20:32 2006 From: s.bulashevska at dkfz-heidelberg.de (Svetlana Bulashevska) Date: Wed, 22 Nov 2006 12:20:32 +0100 Subject: [Bioperl-l] a question on gene retrieval Message-ID: <45643280.3000001@dkfz.de> Dear Sirs, I am very new to bioperl and I would highly appreciate if you could advise me on the following. I have the locations of the sequences (like chr5|-1|102826728|102828399) in the human genome and I would like to retrieve what known genes lay in the close proximity to the sequences (they can also overlap with the sequence). What bioperl modules and classes should I use? Thank you very much, Svetlana Bulashevska. From bosborne11 at verizon.net Wed Nov 22 14:04:35 2006 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 22 Nov 2006 09:04:35 -0500 Subject: [Bioperl-l] a question on gene retrieval In-Reply-To: <45643280.3000001@dkfz.de> Message-ID: Svetlana, There's a page discussing these sorts of questions at the Bioperl Wiki: http://www.bioperl.org/wiki/Getting_Genomic_Sequences It sounds like you just want to compare pairs of coordinates initially, not retrieve sequence, yes? Brian O. On 11/22/06 6:20 AM, "Svetlana Bulashevska" wrote: > Dear Sirs, > I am very new to bioperl and I would highly appreciate if you could > advise me on the following. > I have the locations of the sequences (like chr5|-1|102826728|102828399) > in the human genome > and I would like to retrieve what known genes lay in the close proximity > to the sequences (they can also overlap with the sequence). What bioperl > modules and classes should I use? > Thank you very much, > Svetlana Bulashevska. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cuiw at ncbi.nlm.nih.gov Wed Nov 22 16:50:07 2006 From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C]) Date: Wed, 22 Nov 2006 11:50:07 -0500 Subject: [Bioperl-l] a question on gene retrieval In-Reply-To: <45643280.3000001@dkfz.de> Message-ID: <18C407FD4FFB424292D769FBD68C1987018123A1@NIHCESMLBX8.nih.gov> You can use LWP to retrieve the following URL http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=5&maps=genes [102826728:104828399]-r&cmd=txt and then parse the HTML. Good luck! Wenwu Cui -----Original Message----- From: Svetlana Bulashevska [mailto:s.bulashevska at dkfz-heidelberg.de] Sent: Wednesday, November 22, 2006 6:21 AM To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] a question on gene retrieval Dear Sirs, I am very new to bioperl and I would highly appreciate if you could advise me on the following. I have the locations of the sequences (like chr5|-1|102826728|102828399) in the human genome and I would like to retrieve what known genes lay in the close proximity to the sequences (they can also overlap with the sequence). What bioperl modules and classes should I use? Thank you very much, Svetlana Bulashevska. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cain at cshl.edu Wed Nov 22 19:09:13 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 14:09:13 -0500 (EST) Subject: [Bioperl-l] Unable to build Module::Build on CentOS Message-ID: Hello, I don't want to throw too much fuel on the Module::Build fire, but I have just discovered that I can't get Module::Build to install on CentOS 4.4. It appears that the developers of MB are aware of the problem, but the currently release ---------------------------------------------------------------------- Scott Cain, Ph. D. cain at cshl.org GMOD Coordinator, http://www.gmod.org/ (216)392-3087 ---------------------------------------------------------------------- From cain at cshl.edu Wed Nov 22 19:59:53 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 14:59:53 -0500 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: References: Message-ID: <1164225594.2639.2.camel@localhost.localdomain> Whoops! That was a half composed message that I thought I canceled. \me blushes Oh well, I was going to write a short note to indicate that in fact, I could not get Module::Build to pass tests on CentOS 4.4 and the authors appear to be aware of the problem, but I have no idea if it is likely to be fixed any time soon. So, if anyone wants to install BioPerl 1.5.2 on any CentOS boxes, they have to force install Module::Build. :-/ Scott On Wed, 2006-11-22 at 14:09 -0500, Scott Cain wrote: > Hello, > > I don't want to throw too much fuel on the Module::Build fire, but I have > just discovered that I can't get Module::Build to install on CentOS 4.4. > It appears that the developers of MB are aware of the problem, but the > currently release > > ---------------------------------------------------------------------- > Scott Cain, Ph. D. cain at cshl.org > GMOD Coordinator, http://www.gmod.org/ (216)392-3087 > ---------------------------------------------------------------------- > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From cain at cshl.edu Wed Nov 22 20:04:25 2006 From: cain at cshl.edu (Scott Cain) Date: Wed, 22 Nov 2006 15:04:25 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows Message-ID: <1164225865.2639.8.camel@localhost.localdomain> Hello, I just wanted to mention that I made a few minor changes to Build.PL so that I could get `perl Build.PL` to complete successfully. I am using ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't present either. The main thing I did was to have the BioDBGFF test subroutine quit without asking any questions if Build.PL detected that it was running on Windows. There may be a more elegant way of fixing the problem, but I just wanted it to work (as I am also working a release candidate of GBrowse that depends on the release candidate of bioperl). Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From bix at sendu.me.uk Wed Nov 22 23:16:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 22 Nov 2006 23:16:10 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <1164225594.2639.2.camel@localhost.localdomain> References: <1164225594.2639.2.camel@localhost.localdomain> Message-ID: <4564DA3A.1000601@sendu.me.uk> Scott Cain wrote: > Whoops! That was a half composed message that I thought I canceled. > > \me blushes > > Oh well, I was going to write a short note to indicate that in fact, I > could not get Module::Build to pass tests on CentOS 4.4 and the authors > appear to be aware of the problem, but I have no idea if it is likely to > be fixed any time soon. So, if anyone wants to install BioPerl 1.5.2 on > any CentOS boxes, they have to force install Module::Build. :-/ Thanks for the info. 1.5.2 will come with the old ExtUtils::MakeMaker-based Makefile.PL so it should still be possible to install without a force. From bix at sendu.me.uk Wed Nov 22 23:30:07 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 22 Nov 2006 23:30:07 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164225865.2639.8.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> Message-ID: <4564DD7F.8090301@sendu.me.uk> Scott Cain wrote: > Hello, > > I just wanted to mention that I made a few minor changes to Build.PL so > that I could get `perl Build.PL` to complete successfully. I am using > ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > present either. The main thing I did was to have the BioDBGFF test > subroutine quit without asking any questions if Build.PL detected that > it was running on Windows. Is it completely impossible for it to pass under Windows? I find that quite a shame! I'm surprised it was necessary to make your changes, because it already had to return true from: DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0}) Can Windows pass that test without DBD::mysql installed, and having passed it why does it then fail the actual BioDBSeqFeature_mysql.t script? The cleanest way to do your change would be to make some change to the test_db() sub, eg: sub test_db { eval {require DBI;}; if ($^O =~ /mswin/i) { return "Windows isn't supported"; } unless (DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0})) { return "Could not connect to test database"; } return; } From cjfields at uiuc.edu Thu Nov 23 03:32:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 22 Nov 2006 21:32:34 -0600 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <4564DD7F.8090301@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> Message-ID: On Nov 22, 2006, at 5:30 PM, Sendu Bala wrote: > Scott Cain wrote: >> Hello, >> >> I just wanted to mention that I made a few minor changes to >> Build.PL so >> that I could get `perl Build.PL` to complete successfully. I am >> using >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't >> present either. The main thing I did was to have the BioDBGFF test >> subroutine quit without asking any questions if Build.PL detected >> that >> it was running on Windows. > > Is it completely impossible for it to pass under Windows? I find that > quite a shame! > > I'm surprised it was necessary to make your changes, because it > already > had to return true from: > > DBI->connect('dbi:mysql:test',undef,undef, > {RaiseError=>0,PrintError=>0}) > > Can Windows pass that test without DBD::mysql installed, and having > passed it why does it then fail the actual BioDBSeqFeature_mysql.t > script? I think he means the BioDBGFF.t tests, not BioDBSeqFeature_mysql.t. Myself, I can't get the Build script to detect my local MySQL on WinXP, though the BioDBGFF.t tests passed. I haven't been back to work since last Friday so I can't run updated WinXP tests myself. ... chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From roy at colibase.bham.ac.uk Tue Nov 21 18:51:30 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Tue, 21 Nov 2006 18:51:30 +0000 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45633B4A.6060804@sendu.me.uk> References: <45633B4A.6060804@sendu.me.uk> Message-ID: <45634AB2.1020701@colibase.bham.ac.uk> > I'd like to propose changing the default reply-to for posts on this list > from the current 'reply to the poster' to 'reply to the mailing list'. > That way people can just hit 'reply' instead of 'reply to all' in order > to get a reply back to the list. We did this on our mailing list, and found it to be problematic if the messages still appear to come from an individual rather than the list- people may not realise they are replying to the whole list. This can lead to all sorts of issues- my boss and a collaborator once had a discussion (fortunately nothing too sensitive) that was accidentally copied to everyone in their field. The alternative is to overwrite the from: field as well as reply-to:, but then you rely on people having suitably informative signatures should anyone want to contact them off-list, and it makes the archives less useful. See also this: http://www.unicom.com/pw/reply-to-harmful.html Maybe you could tag a reminder to reply-all on every list message? Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From torsten.seemann at infotech.monash.edu.au Thu Nov 23 02:09:42 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Thu, 23 Nov 2006 13:09:42 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: References: Message-ID: <456502E6.8030409@infotech.monash.edu.au> > I don't want to throw too much fuel on the Module::Build fire, but I have > just discovered that I can't get Module::Build to install on CentOS 4.4. I concur with this problem :-( Most of the errors seem to be due to the large number of environmental variables I have set: "Couldn't run Build.PL: Argument list too long at /root/.cpan/build/Module-Build-0.2805/blib/lib/Module/Build/Compat.pm line 200." I had to "force install" the latest Module::Build to get bioperl-live tested and installed via Build.PL. -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From bix at sendu.me.uk Thu Nov 23 07:44:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 07:44:16 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <456502E6.8030409@infotech.monash.edu.au> References: <456502E6.8030409@infotech.monash.edu.au> Message-ID: <45655150.7090300@sendu.me.uk> Torsten Seemann wrote: >> I don't want to throw too much fuel on the Module::Build fire, but I have >> just discovered that I can't get Module::Build to install on CentOS 4.4. > > I concur with this problem :-( > > Most of the errors seem to be due to the large number of environmental > variables I have set: > > "Couldn't run Build.PL: Argument list too long at > /root/.cpan/build/Module-Build-0.2805/blib/lib/Module/Build/Compat.pm > line 200." > > I had to "force install" the latest Module::Build to get bioperl-live > tested and installed via Build.PL. Did everything with the Bioperl Build.PL script work fine after that? From bix at sendu.me.uk Thu Nov 23 10:48:05 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 10:48:05 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <4564DD7F.8090301@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> Message-ID: <45657C65.50200@sendu.me.uk> Sendu Bala wrote: > Scott Cain wrote: >> Hello, >> >> I just wanted to mention that I made a few minor changes to Build.PL so >> that I could get `perl Build.PL` to complete successfully. I am using >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't >> present either. The main thing I did was to have the BioDBGFF test >> subroutine quit without asking any questions if Build.PL detected that >> it was running on Windows. > > Is it completely impossible for it to pass under Windows? I find that > quite a shame! > > I'm surprised it was necessary to make your changes, because it already > had to return true from: [snip] Sorry, that all made no sense because I didn't pay attention to what changes you actually made. Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if being on mswin still causes a problem, or can the excludes_os restriction on line 78 of Build.PL be lifted now? Cheers, Sendu. From Squig at web.de Thu Nov 23 10:46:30 2006 From: Squig at web.de (Squig at web.de) Date: Thu, 23 Nov 2006 11:46:30 +0100 Subject: [Bioperl-l] Bioperl-ext and Staden Package Message-ID: <914558313@web.de> Hello, I have a short question concerning bioperl-ext and the io_lib from the staden package. Are there plans to fix bioperl-ext so it could be used with the actual version of io_lib (at the moment 1.10.1)? Myself has no experience in evoking externally written c - code from perl. But I think the changes to the io_lib - api are very well documented so a fix shouldn't be to hard for somebody with experience in this field. Please correct me if I'm totally wrong. Here you find the changes, you have to scroll a little bit down to "Changes". https://sourceforge.net/project/shownotes.php?release_id=340318&group_id=100316 If you think I could give a helping hand, please let me know. With kind regards, Stefan _______________________________________________________________________ Viren-Scan f?r Ihren PC! Jetzt f?r jeden. Sofort, online und kostenlos. Gleich testen! http://www.pc-sicherheit.web.de/freescan/?mc=022222 From cjfields at uiuc.edu Thu Nov 23 14:12:20 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 08:12:20 -0600 Subject: [Bioperl-l] Bioperl-ext and Staden Package In-Reply-To: <914558313@web.de> References: <914558313@web.de> Message-ID: On Nov 23, 2006, at 4:46 AM, Squig at web.de wrote: > Hello, > > I have a short question concerning bioperl-ext and the io_lib from > the staden package. > > Are there plans to fix bioperl-ext so it could be used with the > actual version of io_lib (at the moment 1.10.1)? This is one of the things tentatively planned but there have been no volunteers for it. > Myself has no experience in evoking externally written c - code > from perl. But I think the changes to the io_lib - api are very > well documented so a fix shouldn't be to hard for somebody with > experience in this field. Please correct me if I'm totally wrong. > > Here you find the changes, you have to scroll a little bit down to > "Changes". > https://sourceforge.net/project/shownotes.php? > release_id=340318&group_id=100316 > > If you think I could give a helping hand, please let me know. > > > With kind regards, > > Stefan > Any help would be greatly appreciated! There are tests included with bioperl-ext which you can add to or modify if needed. You can post patches for any changed code to bugzilla. Here's a HOWTO: http://www.bioperl.org/wiki/HOWTO:SubmitPatch Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sdavis2 at mail.nih.gov Thu Nov 23 15:43:37 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu, 23 Nov 2006 10:43:37 -0500 Subject: [Bioperl-l] Changing default reply-to on this list In-Reply-To: <45634AB2.1020701@colibase.bham.ac.uk> References: <45633B4A.6060804@sendu.me.uk> <45634AB2.1020701@colibase.bham.ac.uk> Message-ID: <4565C1A9.4080605@mail.nih.gov> Roy Chaudhuri wrote: >> I'd like to propose changing the default reply-to for posts on this list >> from the current 'reply to the poster' to 'reply to the mailing list'. >> That way people can just hit 'reply' instead of 'reply to all' in order >> to get a reply back to the list. >> > > We did this on our mailing list, and found it to be problematic if the > messages still appear to come from an individual rather than the list- > people may not realise they are replying to the whole list. This can > lead to all sorts of issues- my boss and a collaborator once had a > discussion (fortunately nothing too sensitive) that was accidentally > copied to everyone in their field. The alternative is to overwrite the > from: field as well as reply-to:, but then you rely on people having > suitably informative signatures should anyone want to contact them > off-list, and it makes the archives less useful. > > See also this: > http://www.unicom.com/pw/reply-to-harmful.html > I tend to agree here. I have seen some pretty significant accidents due to this feature. I think less harm is done by simply putting the thread back on list, if appropriate, if the sender happens to send to the original sender and not the entire list. Sean From bix at sendu.me.uk Thu Nov 23 21:18:01 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 21:18:01 +0000 Subject: [Bioperl-l] Please do not commit without testing Message-ID: <45661009.8040303@sendu.me.uk> Developers, Please do not commit changes without testing the test suite first, especially to branches! Note that: perl -I. -w t/test.t is NOT a good enough test, especially for test scripts that still use Test and not Test::More. (The above doesn't capture an incorrect number of tests in the plan.) Always initially do: ./Build test --test_files t/test.t --verbose Then run the entire test suite: ./Build test Thank you, Sendu. From The_Polymorph at rocketmail.com Thu Nov 23 21:30:42 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 23 Nov 2006 13:30:42 -0800 (PST) Subject: [Bioperl-l] Bioperl install question. Message-ID: <541373.13923.qm@web50815.mail.yahoo.com> Hi all. My set-up: WinXP (SP2) ActiveState Perl 5.8.8 I used the perl package manager to download BioPerl 1.2.3 but since that is rather old, I downloaded BioPerl-1.4.zip. Can anyone help me from this point? Where should I unzip the file to? Thanks, ~Katie ____________________________________________________________________________________ Want to start your own business? Learn how on Yahoo! Small Business. http://smallbusiness.yahoo.com/r-index From cjfields at uiuc.edu Thu Nov 23 21:43:30 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 15:43:30 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661009.8040303@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> Message-ID: On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: > Developers, > > Please do not commit changes without testing the test suite first, > especially to branches! > > Note that: > > perl -I. -w t/test.t > > is NOT a good enough test, especially for test scripts that still use > Test and not Test::More. (The above doesn't capture an incorrect > number > of tests in the plan.) > > Always initially do: > > ./Build test --test_files t/test.t --verbose > > Then run the entire test suite: > > ./Build test My bad. As a lousy excuse I have been extremely busy with family this holiday. However, the various changes using Module::Build need to be well-documented both in CVS docs and on the wiki. Your latter example ('./Build test --test_files t/test.t --verbose') is nowhere to be found. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 23 22:07:06 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 22:07:06 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> Message-ID: <45661B8A.9060405@sendu.me.uk> Chris Fields wrote: > > On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: > >> Developers, >> >> Please do not commit changes without testing the test suite first, >> especially to branches! >> >> Note that: >> >> perl -I. -w t/test.t >> >> is NOT a good enough test, especially for test scripts that still use >> Test and not Test::More. (The above doesn't capture an incorrect number >> of tests in the plan.) >> >> Always initially do: >> >> ./Build test --test_files t/test.t --verbose >> >> Then run the entire test suite: >> >> ./Build test [snip] > However, the various changes using Module::Build need to be > well-documented both in CVS docs and on the wiki. Your latter example > ('./Build test --test_files t/test.t --verbose') is nowhere to be found. I posted to the list about it on the 17th in thread 'Testing with Build.PL'. Where would you suggest a good place on the wiki would be to mention something like that? From cjfields at uiuc.edu Thu Nov 23 22:23:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 16:23:12 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> On Nov 23, 2006, at 4:07 PM, Sendu Bala wrote: > Chris Fields wrote: >> ... > [snip] >> However, the various changes using Module::Build need to be well- >> documented both in CVS docs and on the wiki. Your latter example >> ('./Build test --test_files t/test.t --verbose') is nowhere to be >> found. > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would > be to mention something like that? The mail list isn't the best place to document this; very few people (including developers) will take the time to go back digging through old posts except as a last resort. Hence these need to be well- documented AND easily accessible. Relevant changes need to be made everywhere that testing or using make/nmake is mentioned in CVS or the wiki. For the testing case I raised, maybe adding something to the various INSTALL docs and the FAQ would be a good start. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 23 22:36:47 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 22:36:47 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> Message-ID: <4566227F.4060102@sendu.me.uk> Chris Fields wrote: > On Nov 23, 2006, at 4:07 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> ... >> [snip] >>> However, the various changes using Module::Build need to be >>> well-documented both in CVS docs and on the wiki. Your latter >>> example ('./Build test --test_files t/test.t --verbose') is nowhere >>> to be found. >> >> I posted to the list about it on the 17th in thread 'Testing with >> Build.PL'. Where would you suggest a good place on the wiki would be >> to mention something like that? > > The mail list isn't the best place to document this; very few people > (including developers) will take the time to go back digging through old > posts except as a last resort. Hence these need to be well-documented > AND easily accessible. Relevant changes need to be made everywhere that > testing or using make/nmake is mentioned in CVS or the wiki. For the > testing case I raised, maybe adding something to the various INSTALL > docs and the FAQ would be a good start. It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's also on the wiki version of same.) I'm not sure that a developer would think to look in the installation documentation for that kind of information, so I've added the info to http://www.bioperl.org/wiki/Bioperl_Best_Practices#Testing as well. From n.haigh at sheffield.ac.uk Thu Nov 23 22:39:17 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 23 Nov 2006 22:39:17 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <45662315.5090600@sheffield.ac.uk> Sendu Bala wrote: > Chris Fields wrote: > >> On Nov 23, 2006, at 3:18 PM, Sendu Bala wrote: >> >> >>> Developers, >>> >>> Please do not commit changes without testing the test suite first, >>> especially to branches! >>> >>> Note that: >>> >>> perl -I. -w t/test.t >>> >>> is NOT a good enough test, especially for test scripts that still use >>> Test and not Test::More. (The above doesn't capture an incorrect number >>> of tests in the plan.) >>> >>> Always initially do: >>> >>> ./Build test --test_files t/test.t --verbose >>> >>> Then run the entire test suite: >>> >>> ./Build test >>> > [snip] > >> However, the various changes using Module::Build need to be >> well-documented both in CVS docs and on the wiki. Your latter example >> ('./Build test --test_files t/test.t --verbose') is nowhere to be found. >> > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would be to > mention something like that? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > I'd possibly put it somewhere like: http://www.bioperl.org/wiki/Developer_Information If there's enough stuff to create a new page? If so, how about a page called "testing" or "test suite" or "running tests"?? Just ensure it's given the "Developer resources" Category to make it that bit easier to locate. Nath From n.haigh at sheffield.ac.uk Thu Nov 23 22:31:58 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 23 Nov 2006 22:31:58 +0000 Subject: [Bioperl-l] Bioperl install question. In-Reply-To: <541373.13923.qm@web50815.mail.yahoo.com> References: <541373.13923.qm@web50815.mail.yahoo.com> Message-ID: <4566215E.9090409@sheffield.ac.uk> Caitlin wrote: > Hi all. > > My set-up: > > WinXP (SP2) > ActiveState Perl 5.8.8 > > > I used the perl package manager to download BioPerl 1.2.3 but since > that is rather old, I downloaded BioPerl-1.4.zip. Can anyone help me > from this point? Where should I unzip the file to? > > Thanks, > > ~Katie > > > Hi Katie, First of all try installing Bioperl 1.5.2 RC2 by following the installation instructions for windows at: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows#Installation_Guide See how you get on with that and let us know if you have troubles, or indeed if you manage to install successfully! Thanks Nathan From bix at sendu.me.uk Thu Nov 23 23:31:59 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 23 Nov 2006 23:31:59 +0000 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45662909.3010101@infotech.monash.edu.au> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> <45662909.3010101@infotech.monash.edu.au> Message-ID: <45662F6F.2090700@sendu.me.uk> Torsten Seemann wrote: >>> I had to "force install" the latest Module::Build to get bioperl-live >>> tested and installed via Build.PL. >> >> Did everything with the Bioperl Build.PL script work fine after that? > > Yes. > > However it was much "slower" to install, it initially pauses for a long > time, then eventually does the install. I'm guessing you're describing the period of time that it manifies the documentation? Don't you see lots of output detailing what is going on at each moment in time? From torsten.seemann at infotech.monash.edu.au Thu Nov 23 23:50:30 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 24 Nov 2006 10:50:30 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45662F6F.2090700@sendu.me.uk> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> <45662909.3010101@infotech.monash.edu.au> <45662F6F.2090700@sendu.me.uk> Message-ID: <456633C6.5080109@infotech.monash.edu.au> >>>> I had to "force install" the latest Module::Build to get >>>> bioperl-live tested and installed via Build.PL. >>> >>> Did everything with the Bioperl Build.PL script work fine after that? >> >> Yes. >> >> However it was much "slower" to install, it initially pauses for a >> long time, then eventually does the install. > > I'm guessing you're describing the period of time that it manifies the > documentation? Don't you see lots of output detailing what is going on > at each moment in time? Yes I see all the usual output. The pause is between the following two events:. ... ... Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 . # (no output for 15+ seconds on unloaded server) . Installing /usr/share/man/man1/bp_chaos_plot.pl.1" ... ... -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From torsten.seemann at infotech.monash.edu.au Thu Nov 23 23:04:41 2006 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri, 24 Nov 2006 10:04:41 +1100 Subject: [Bioperl-l] Unable to build Module::Build on CentOS In-Reply-To: <45655150.7090300@sendu.me.uk> References: <456502E6.8030409@infotech.monash.edu.au> <45655150.7090300@sendu.me.uk> Message-ID: <45662909.3010101@infotech.monash.edu.au> >> I had to "force install" the latest Module::Build to get bioperl-live >> tested and installed via Build.PL. > > Did everything with the Bioperl Build.PL script work fine after that? Yes. However it was much "slower" to install, it initially pauses for a long time, then eventually does the install. -- Dr Torsten Seemann http://www.vicbioinformatics.com Victorian Bioinformatics Consortium, Monash University, Australia From cjfields at uiuc.edu Fri Nov 24 04:04:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 22:04:58 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <4566227F.4060102@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> Message-ID: On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: ... > It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's > also on the wiki version of same.) Okay, but I find the Windows page hasn't been updated (still shows nmake). Everything needs to be changed, not just the UNIX pages > I'm not sure that a developer would think to look in the installation > documentation for that kind of information, so I've added the info to > http://www.bioperl.org/wiki/Bioperl_Best_Practices#Testing as well. Sounds good. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Nov 24 04:09:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 23 Nov 2006 22:09:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45662315.5090600@sheffield.ac.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45662315.5090600@sheffield.ac.uk> Message-ID: On Nov 23, 2006, at 4:39 PM, Nathan S. Haigh wrote: > Sendu Bala wrote: >> >> I posted to the list about it on the 17th in thread 'Testing with >> Build.PL'. Where would you suggest a good place on the wiki would >> be to >> mention something like that? >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > I'd possibly put it somewhere like: > http://www.bioperl.org/wiki/Developer_Information > > If there's enough stuff to create a new page? If so, how about a page > called "testing" or "test suite" or "running tests"?? > > Just ensure it's given the "Developer resources" Category to make it > that bit easier to locate. > > Nath ... I think we need to gear some docs not just towards users but also towards potential developers, so maybe a HOWTO for writing and running tests might be the best way to go. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From The_Polymorph at rocketmail.com Fri Nov 24 04:29:18 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 23 Nov 2006 20:29:18 -0800 (PST) Subject: [Bioperl-l] BioPerl install question (update). Message-ID: <20061124042918.5392.qmail@web50801.mail.yahoo.com> Hi all. Ok. I upgraded my ActiveState perl install from build 817 to build 819 and followed the directions located at the site below to install BioPerl 1.5.2 RC2: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Thanks for the help Nathan! ~Katie ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited From bix at sendu.me.uk Fri Nov 24 07:54:19 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 07:54:19 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> Message-ID: <4566A52B.80304@sendu.me.uk> Chris Fields wrote: > On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: > ... > >> It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. (It's >> also on the wiki version of same.) > > Okay, but I find the Windows page hasn't been updated (still shows > nmake). Everything needs to be changed, not just the UNIX pages I don't know what to say for the windows docs. I can't even get perl -V to work on my Windows machine: &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. The Build.PL scripts fails similarly: &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/Config.pm line 72. Can't locate the perl binary used to run this script in (C:\Perl\bin C:\Perl\bin C:\Perl\bin . C:\Program Files\ActiveState Komodo 3.5 C:\Perl\bin C:\WINDOWS\sy stem32 C:\WINDOWS C:\WINDOWS\System32\Wbem C:\Program Files\ATI Technologies\ATI .ACE) I took it that you had no problems? Should I just make the Windows docs similar to the Unix ones? (Or can you do the appropriate update?) From bix at sendu.me.uk Fri Nov 24 08:56:15 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 08:56:15 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 Message-ID: <4566B3AF.2050305@sendu.me.uk> Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. See http://www.bioperl.org/wiki/Release_1.5.2 for instructions on getting and testing this RC. Everyone: Even though 1.5.2 is a 'developer' release, we consider it the most stable and capable version of Bioperl, and recommend that you use it in all but the most critical production environments. Please try it out and let us know of any problems or difficulties you run into. Please try the new Build.PL installation script and report back how you get on. Also try installing using CPAN. Your CPAN mirrors may not be current enough, so you may have delete all entries in your urllist first. Developers: Please experiment with installation, especially via CPAN. If you already have all/most prerequisite external modules installed, try uninstalling some and report how effective the system is at reinstalling them for you. RC5 may form the final release for some of the packages (probably all except for bioperl-run), so any further commits made, even to branch-1-5-2, may not make final release. If you think you've committed an important bug fix that should be part of final release, let me know. Thank you, Sendu. PS. What happened to RC4? I didn't announce it, but it was available on CPAN where I did some testing on it. From n.haigh at sheffield.ac.uk Fri Nov 24 09:35:01 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Fri, 24 Nov 2006 09:35:01 +0000 Subject: [Bioperl-l] Bioperl install question. In-Reply-To: <20061124012953.66815.qmail@web50812.mail.yahoo.com> References: <20061124012953.66815.qmail@web50812.mail.yahoo.com> Message-ID: <4566BCC5.7050003@sheffield.ac.uk> Caitlin wrote: > Hi Nathan, > > Thanks for the quick reply. I wasn't able to locate a Perl Package > Manager GUI from the Start menu. The only options displayed are: > > Documentation > OLE Browser > Perl Package Manager > > Clicking on 'Perl Package Manager' loads ppm in a console window (i.e. > non-GUI environment). Should I re-install ActivePerl? If so, that would > eliminate my installed modules wouldn't it? > > Thanks, > > ~Katie > > It sounds like you probably have a version of ActivePerl < 5.8.8.819. If this is the case, download and install the latest ActivePerl version >= 5.8.8.819. If you do a reinstall into the same location as your current ActivePerl installation you will probably maintain all the currently installed modules - but I can't say for definate. Once you have ActivePerl >= 5.8.8.819 installed, you should be able to follow the instructions in the link I provided previously. Nath From n.haigh at sheffield.ac.uk Fri Nov 24 09:38:54 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Fri, 24 Nov 2006 09:38:54 +0000 Subject: [Bioperl-l] BioPerl install question (update). In-Reply-To: <20061124042918.5392.qmail@web50801.mail.yahoo.com> References: <20061124042918.5392.qmail@web50801.mail.yahoo.com> Message-ID: <4566BDAE.50105@sheffield.ac.uk> Caitlin wrote: > Hi all. > > Ok. I upgraded my ActiveState perl install from build 817 to build 819 > and followed the directions located at the site below to install > BioPerl 1.5.2 RC2: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Thanks for the help Nathan! > > ~Katie > > Ah - have just sent an e-mail to say update to build 819! We should be releasing the proper 1.5.2 release quite soon (hopefully in a week or two) At that stage, you should update the bioperl package. It nice to hear it when things work! Nath From cjfields at uiuc.edu Fri Nov 24 12:15:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 24 Nov 2006 06:15:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <4566A52B.80304@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <6AD44379-BAD1-425D-9703-90EC5C1DD661@uiuc.edu> <4566227F.4060102@sendu.me.uk> <4566A52B.80304@sendu.me.uk> Message-ID: On Nov 24, 2006, at 1:54 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 23, 2006, at 4:36 PM, Sendu Bala wrote: >> ... >>> It /is/ in the INSTALL docs. See the 'THE TEST SYSTEM' section. >>> (It's >>> also on the wiki version of same.) >> Okay, but I find the Windows page hasn't been updated (still shows >> nmake). Everything needs to be changed, not just the UNIX pages > > I don't know what to say for the windows docs. I can't even get > > perl -V > > to work on my Windows machine: > > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > > The Build.PL scripts fails similarly: > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > &Config::AUTOLOAD failed on Config::launcher at C:/Perl/lib/ > Config.pm line 72. > Can't locate the perl binary used to run this script in (C:\Perl > \bin C:\Perl\bin > C:\Perl\bin . C:\Program Files\ActiveState Komodo 3.5 C:\Perl\bin > C:\WINDOWS\sy > stem32 C:\WINDOWS C:\WINDOWS\System32\Wbem C:\Program Files\ATI > Technologies\ATI > .ACE) > > I took it that you had no problems? Should I just make the Windows > docs similar to the Unix ones? (Or can you do the appropriate update?) No, everything worked on my machine. I'll try making the necessary changes as soon as I can, but it won't be today. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Fri Nov 24 21:38:07 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 16:38:07 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45661B8A.9060405@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: Is it possible to add a file to the repository (at least temporarily) called README.Build or something that would contain those examples? I find myself saving your emails which I don't think is the most efficient way for me to have those bits handy when I'll need them. -hilmar On Nov 23, 2006, at 5:07 PM, Sendu Bala wrote: > > I posted to the list about it on the 17th in thread 'Testing with > Build.PL'. Where would you suggest a good place on the wiki would > be to > mention something like that? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Fri Nov 24 22:08:37 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 22:08:37 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> Message-ID: <45676D65.6000409@sendu.me.uk> Hilmar Lapp wrote: > Is it possible to add a file to the repository (at least temporarily) > called README.Build or something that would contain those examples? > > I find myself saving your emails which I don't think is the most > efficient way for me to have those bits handy when I'll need them. Given that Makefile.PL is just a stub that prints a message about Build.PL, I can just extend the message to include more tips? From hlapp at gmx.net Fri Nov 24 22:27:43 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 17:27:43 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45676D65.6000409@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> Message-ID: On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: > Hilmar Lapp wrote: >> Is it possible to add a file to the repository (at least temporarily) >> called README.Build or something that would contain those examples? >> >> I find myself saving your emails which I don't think is the most >> efficient way for me to have those bits handy when I'll need them. > > Given that Makefile.PL is just a stub that prints a message about > Build.PL, I can just extend the message to include more tips? You could but that wouldn't substitute. Typing ./Build instead of make is not too hard of a change to make; however, you don't want me to go back and run perl Makefile.PL to get a quick refresher every time I want to use a more advanced feature of the generated Build file, do you? -hilmar > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Fri Nov 24 22:46:49 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 24 Nov 2006 22:46:49 +0000 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> Message-ID: <45677659.404@sendu.me.uk> Hilmar Lapp wrote: > > On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: > >> Hilmar Lapp wrote: >>> Is it possible to add a file to the repository (at least temporarily) >>> called README.Build or something that would contain those examples? >>> >>> I find myself saving your emails which I don't think is the most >>> efficient way for me to have those bits handy when I'll need them. >> >> Given that Makefile.PL is just a stub that prints a message about >> Build.PL, I can just extend the message to include more tips? > > You could but that wouldn't substitute. Typing ./Build instead of make > is not too hard of a change to make; however, you don't want me to go > back and run perl Makefile.PL to get a quick refresher every time I want > to use a more advanced feature of the generated Build file, do you? If you can remember at least that it is ./Build you need to do something with, it has lovely in-built help. It's entirely standard stuff so nothing to learn - just remember its there! > ./Build -h No action '-h' defined, try running the 'help' action. ./Build help ./Build help test From hlapp at gmx.net Sat Nov 25 00:08:18 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 24 Nov 2006 19:08:18 -0500 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45677659.404@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> <45677659.404@sendu.me.uk> Message-ID: <965EC1D8-AC7D-491A-BCFE-82776D724161@gmx.net> On Nov 24, 2006, at 5:46 PM, Sendu Bala wrote: > If you can remember at least that it is ./Build you need to do > something > with, it has lovely in-built help. It's entirely standard stuff so > nothing to learn - just remember its there! > >> ./Build -h > No action '-h' defined, try running the 'help' action. > > > > ./Build help > > > > ./Build help test > > Sounds nice & will surely be helpful. I guess what I was trying to say is that you could make the value of the examples you typed up in emails already (including the above) much more lasting by copy&pasting them into a document that's within easy reach of a developer who is losing his/her nerves because somebody from the extended family spilled cranberry sauce across his/her new laptop over Thanksgiving. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Sat Nov 25 00:13:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 24 Nov 2006 18:13:44 -0600 Subject: [Bioperl-l] Please do not commit without testing In-Reply-To: <45677659.404@sendu.me.uk> References: <45661009.8040303@sendu.me.uk> <45661B8A.9060405@sendu.me.uk> <45676D65.6000409@sendu.me.uk> <45677659.404@sendu.me.uk> Message-ID: <9AF9038D-71FD-46AD-A486-5B9472BC29AA@uiuc.edu> On Nov 24, 2006, at 4:46 PM, Sendu Bala wrote: > Hilmar Lapp wrote: >> >> On Nov 24, 2006, at 5:08 PM, Sendu Bala wrote: >> >>> Hilmar Lapp wrote: >>>> Is it possible to add a file to the repository (at least >>>> temporarily) >>>> called README.Build or something that would contain those examples? >>>> >>>> I find myself saving your emails which I don't think is the most >>>> efficient way for me to have those bits handy when I'll need them. >>> >>> Given that Makefile.PL is just a stub that prints a message about >>> Build.PL, I can just extend the message to include more tips? >> >> You could but that wouldn't substitute. Typing ./Build instead of >> make >> is not too hard of a change to make; however, you don't want me to go >> back and run perl Makefile.PL to get a quick refresher every time >> I want >> to use a more advanced feature of the generated Build file, do you? > > If you can remember at least that it is ./Build you need to do > something > with, it has lovely in-built help. It's entirely standard stuff so > nothing to learn - just remember its there! > >> ./Build -h > No action '-h' defined, try running the 'help' action. > > > > ./Build help > > > > ./Build help test > > Hilmar's suggestion of collecting these snippets of Build-related commands in a single place seems like a good start, since it doesn't really pertain to installation but is of use for developers and future release pumpkins. As for the help example above, as helpful as it is, I don't think most would know it was even there unless it was pointed out. A few blurbs in the FAQ, maybe in the 'BioPerl in General' or a new developer section, might also help. 'How do I run tests using Module::Build?' or 'Where can I find out more about Module::Build?', for instance. It's also much easier (at least to me) to point out to new users or developers that any relevant information is found in 'document x' vs. 'this post on the mail list, found in the mail archives at this link, just follow the thread...'. chris (still recovering after being dragged out on Black Friday). Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Fri Nov 24 23:16:47 2006 From: jason at bioperl.org (Jason Stajich) Date: Fri, 24 Nov 2006 15:16:47 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45635F98.8030901@bms.com> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> Message-ID: <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> Can we just weaken the references with Scalar::Util? This should solve the problem for circular refs. Is Scalar::Util part of the core distro in the min perl we are supporting? I can add this in Bio::Tree::Node and look around to see where else it is a problem. We just need a simple script to verify it is having an effect (i.e. a bug report with this). -jason On Nov 21, 2006, at 12:20 PM, Stefan Kirov wrote: > Hilmar Lapp wrote: >> On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote: >> >> >>> I don't know if I should hold up release of 1.5.2 for it. Now that >>> you've >>> reported on it I'm leaning toward yes, since the new Bio::Species >>> implementation is one of the major new features of 1.5.2 and it >>> ought to >>> work well. >>> >> >> I disagree to some extent. This is a developer release, so not >> everything is expected to work perfectly. >> >> What's not desirable is if fixing this required another entire >> redesign of the API, so that every dev release introduces >> different API. >> >> The thing is, you'll really only get trouble reports once you put it >> out and people start using it in anger. Don't expect to make it >> perfect before. >> >> >>> Anyway, for the memory leak I have some ideas I haven't tried yet; I >>> don't know if my efforts will solve the speed issue though. >>> >> >> The memory leak sounds more concerning to me. Under which >> circumstances would it crash a script or blow throuhg all of say >> 1-2GB when it should have taken only a tenth of that. >> >> > As I was saying, I did pass ref to an array in the classification > (wrong > parsing): > push @classification,'sapiens', 'Homo', 'Hominidae', $arrayref; > and my script took 17-18 GB. I am really surprised it stopped getting > more RAM and finished successfully. I did not explore further. > Stefan >> -hilmar >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Sat Nov 25 12:47:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 12:47:28 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> Message-ID: <45683B60.9090402@sendu.me.uk> Jason Stajich wrote: > Can we just weaken the references with Scalar::Util? This should solve > the problem for circular refs. I don't know about Stefan's problem, but I tried weakening refs - it fixed the memory leak I was seeing, but caused other problems. > Is Scalar::Util part of the core distro in the min perl we are supporting? Yes. > I can add this in Bio::Tree::Node and look around to see where else it > is a problem. We just need a simple script to verify it is having an > effect (i.e. a bug report with this). perl -w -MBio::SeqIO -e '$si = new Bio::SeqIO(-file => "5UTR.Pln_nr.dat", -format => "embl"); while ($seq = $si->next_seq) { $seq->id; }' Where 5UTR.Pln_nr.dat is a large embl file with ~50000 sequences. For me this takes ~11mins to parse and ~2GB memory. Once I weakened refs in all the places I could find in Bio::Tree::Node and Bio::Tree::Tree it used a constant 0.3% of memory but still took around 11mins. However lots of the tests in the test suite then fail, because Nodes are often made purely to add into a Tree, with the requirement that the Tree keeps hard refs to them all (else the Tree would fall apart). I think the Tree actually only keeps a ref to its root Node, which means Nodes in general must keep hard refs to their Descendants. With that constraint, I haven't been able to break the deadlock and get these things to clean up. Hopefully I'm missing something obvious; please look into it. From cjfields at uiuc.edu Sat Nov 25 13:32:43 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sat, 25 Nov 2006 07:32:43 -0600 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45683B60.9090402@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> Message-ID: <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: ... > I think the Tree actually only keeps a ref to its root Node, which > means > Nodes in general must keep hard refs to their Descendants. With that > constraint, I haven't been able to break the deadlock and get these > things to clean up. > > Hopefully I'm missing something obvious; please look into it. I'm curious to see if this affects sequence parsing (i.e. SwissProt DB parsing). Does anyone know? It sounds pretty serious. Sendu, could you commit a bug report for this? I don't think this should hold up rel 1.5.2 (it's a dev release) but it would be nice to get it fixed. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Sat Nov 25 13:57:53 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 13:57:53 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> Message-ID: <45684BE1.8010902@sendu.me.uk> Chris Fields wrote: > > On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: > ... > >> I think the Tree actually only keeps a ref to its root Node, which means >> Nodes in general must keep hard refs to their Descendants. With that >> constraint, I haven't been able to break the deadlock and get these >> things to clean up. >> >> Hopefully I'm missing something obvious; please look into it. > > I'm curious to see if this affects sequence parsing (i.e. SwissProt DB > parsing). Does anyone know? It sounds pretty serious. Any time you create lots of Bio::Species objects the memory leak ought to arise. > Sendu, could you commit a bug report for this? I don't think this > should hold up rel 1.5.2 (it's a dev release) but it would be nice to > get it fixed. http://bugzilla.open-bio.org/show_bug.cgi?id=2149 From bix at sendu.me.uk Sat Nov 25 22:08:59 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 25 Nov 2006 22:08:59 +0000 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> Message-ID: <4568BEFB.4070201@sendu.me.uk> Jason Stajich wrote: > > The circular ref is from Bio::Species when you have > $self->{tree} = Bio::Tree::Tree->new(-root => $self); > > I added a weaken call in Bio::Species code explicitly -- we can't > generally weaken the ref to the root node in Bio::Tree::Tree as that > breaks some other things as you saw. Thanks. Though there's still the issue with Bio::Tree::Node::node_cleanup not doing anything. > I'm not sure I am digging what you've done with Bio::Tree::Tree. Why > didn't you make a specialized Tree object for Taxonomy stuff so that you > can add methods like lineage_node, etc? http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because it's a Tree function. It goes hand in hand with get_lca(), which was already there. I suppose you're saying it would have been more appropriate to have a new Tree-based object that only differed in its new() instead of adding an option to Tree's new()? My thinking was that both the -node option and get_lineage_nodes() are useful for trees in general, not just Bio::Taxon. From jason at bioperl.org Sat Nov 25 21:20:41 2006 From: jason at bioperl.org (Jason Stajich) Date: Sat, 25 Nov 2006 13:20:41 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <45684BE1.8010902@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> Message-ID: The circular ref is from Bio::Species when you have $self->{tree} = Bio::Tree::Tree->new(-root => $self); I added a weaken call in Bio::Species code explicitly -- we can't generally weaken the ref to the root node in Bio::Tree::Tree as that breaks some other things as you saw. I'm not sure I am digging what you've done with Bio::Tree::Tree. Why didn't you make a specialized Tree object for Taxonomy stuff so that you can add methods like lineage_node, etc? We'll talk about it in more detail in Dec I guess to see if we can clean up some of the things here. -jason On Nov 25, 2006, at 5:57 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote: >> ... >>> I think the Tree actually only keeps a ref to its root Node, >>> which means >>> Nodes in general must keep hard refs to their Descendants. With that >>> constraint, I haven't been able to break the deadlock and get these >>> things to clean up. >>> >>> Hopefully I'm missing something obvious; please look into it. >> I'm curious to see if this affects sequence parsing (i.e. >> SwissProt DB parsing). Does anyone know? It sounds pretty serious. > > Any time you create lots of Bio::Species objects the memory leak > ought to arise. > > >> Sendu, could you commit a bug report for this? I don't think this >> should hold up rel 1.5.2 (it's a dev release) but it would be nice >> to get it fixed. > > http://bugzilla.open-bio.org/show_bug.cgi?id=2149 -- Jason Stajich, PhD Miller Research Fellow University of California, Berkeley lab: 510.642.8441 http://pmb.berkeley.edu/~taylor/people/js.html From biology0046 at hotmail.com Sun Nov 26 13:19:45 2006 From: biology0046 at hotmail.com (=?gb2312?B?va0gzsTi/Q==?=) Date: Sun, 26 Nov 2006 13:19:45 +0000 Subject: [Bioperl-l] PAML problem Message-ID: I use scripts at PAML Howto page to caculate M7 or M8 model. but it always report errors: ------------------------------------------------- Error: err: incorrect model for pairwise comparison.check NSsites, alpha, aaDist.. ------------------------------------------------- Can't call method "next_result" on an undefined value at pamtest.txt line 65. ---------------------------------------------------------- use Bio::Tools::Run::Phylo::PAML::Codeml; use Bio::Tools::Run::Alignment::Clustalw; # for projecting alignments from protein to R/DNA space use Bio::Align::Utilities qw(aa_to_dna_aln); # for input of the sequence data use Bio::SeqIO; use Bio::AlignIO; my $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new; #my $seqdata = shift || 'cds.fa'; my $seqio = new Bio::SeqIO(-file =>"CG4686.cds", -format => 'fasta'); my %seqs; my @prots; # process each sequence while ( my $seq = $seqio->next_seq ) { $seqs{$seq->display_id} = $seq; # translate them into protein my $protein = $seq->translate(); my $pseq = $protein->seq(); if( $pseq =~ /\*/ && $pseq !~ /\*$/ ) { warn("provided a CDS sequence with a stop codon, PAML will choke!"); #exit(0); } # Tcoffee can't handle '*' even if it is trailing $pseq =~ s/\*//g; $protein->seq($pseq); push @prots, $protein; } if( @prots < 2 ) { warn("Need at least 2 CDS sequences to proceed"); exit(0); } open(OUT, ">align_output.txt") || die("cannot open output align_output for writing"); # Align the sequences with clustalw my $aa_aln = $aln_factory->align(\@prots); # project the protein alignment back to CDS coordinates my $dna_aln = aa_to_dna_aln($aa_aln, \%seqs); my @each = $dna_aln->each_seq(); my $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new ( -params => { 'NSsites' => 7, 'ncatG'=>10, 'seqtype' => 1, } ); #I change the parameters here # set the alignment object $kaks_factory->alignment($dna_aln); # run the KaKs analysis my ($rc,$parser) = $kaks_factory->run(); my $result = $parser->next_result; Seqfile:>D_pseudoobscuraATGATGGACACATTGGACTACATCACCCTCAGCAATCCCGTGAGCAAGGCGGTTATATATTCGGGATCGGCTATCTTCCGAGCCCTTGGGCTGCGTCCGAAACAGTTGGTTCCGAAGGAGACCCAGACAGTGCGTCCGGTAATGACTCAGTACATGTCGCCGGGTGCTGGCTCGCTGCATAATTTGGCCGGCCGGTACTATCATTTCGTGCGACTGGCTGGCCTAGGCGGCGCTTCGGCTATTTTCATGGGAGCCTACTGCAAATACGTCCTGAAGGAGATCAAGAACGAAAAGGAGCAGCTGGACTCGCAGGCCTTTGCCGATGTCGCCAATCGCATACACTTTTTGCATTCGTTTGCACTGATGGCCATGCCACTGGCCCACTATCCCATAATCACGGGCTCTTTGATGACCACTGGCACACTGCTCTTCAGCGGCTGCATGTACTATCGTGCATTGACGGGCGAGAAGCGCTTCCAGCCGTTTGCCACCGTTGGAGGCTTCTGTCTGATAGCCGCTTGGCTGACGCTGATATTT >D_willistoniATGTCAATAGTTGATACATTGGACTATATAACCCTGGGTAATCCAGTGAGTCGCTTGGTCATATCTTCAACATCGGCATTAATGCGTACAATTGGTCTGCGCCCCAAGCAGGTGCCTATAAAGGATACAGAAATAGCTGGATTGCCACAGCAGGTCCATCATTTCGGAAATCCAAATGGCCCATCCTTATATACAATTGCCGGCTCTCATTATAACTTTATTCGTCTAGCTGGAATTGGCGGAGCATCGGCTATATTTATGGGAGCGTATTGTAAATATTTTCTTAAGGATATCAATGATCCCAAGGAACAGTTGGATTCACAAGCCTTTGCCGATGTGGCCAATCGTATACATTTTCTCCACTCATTTGCATTAATGGCGATGCCCTTGGCTCATTATCCAGTTTTTACTGGCGCCCTTATGACCACCGGCACATTACTTTTCAGTGGGTGTATGTACTATCGCGCTTTAACCGGTGATAAGAGACTTCAACATTATGCCACAATTGGTGGCTTCTGTCTAATGGCTGCTTGGTTATCCTTGGTTTTG >D_melanogasterATGTCAGTCGCTGACACCATTGAATACGTGACCCTGGGCAATCCTGTCAGCAAGATGGTAGCCTCGTCCGCATCCGCCCTGCTCCGCACGCTTGGTCTGCGTCCCAAGAAGGTGCCGGTGCAGGAGACGAGTATGGCGGTGCTCCCTGCCGCCCACAGCTACGCGCATTCACACGGATCACTCTATCGACTGGCCGGCTGCCATTACCACTTCATTCGGCTGGCCGGGATCGTCGGCGCGTCGGCCATCTTTATGGGCGCCTACTGCAAGTACGTCCTGAAGGACGTCAGCGATCCCAAGGAGCAGGTGGACTCGCAGGCCTTTGCTGATGTGGCCAATCGCATCCACTTTCTGCACTCCTTTGCCATGATGGCCATGCCTCTGGCCCACTATCCCGTATTCACTGGCACTTTGATGATTACGGGCATGATGCTTTTCAGCGGCTGCATGTACTACCGCGCTTTGACTGGCGAGAAGCGTCTGCAACCGTACGCGACCGTCGGAGGATTCTGCCTGATGGCCGCGTGGCTGTCGCTGGTCCTG _________________________________________________________________ ?????????????? MSN Messenger: http://messenger.msn.com/cn From chhalling at verizon.net Sun Nov 26 21:00:18 2006 From: chhalling at verizon.net (Conrad Halling) Date: Sun, 26 Nov 2006 16:00:18 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456A0062.6080103@verizon.net> I attempted to use CPAN to install BioPerl 1.5.2 RC5 into a fresh installation of Perl 5.8.8 under Mac OS X 10.4.8 with all dependencies installed. The tests fail for t/SearchIO. An edited record of the output is shown below. cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz [*snip*] *** Optional dependencies section *** All dependencies are installed [*snip*] Running make test PERL_DL_NONLAZY=1 /test/perl/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t [*snip*] t/SearchIO...................ok 1/1340 -------------------- WARNING --------------------- MSG: XML::SAX::Expat not currently supported; must have local copies of NCBI DTD docs! --------------------------------------------------- -------------------- WARNING --------------------- MSG: error in parsing a report: 404 File `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/NCBI_BlastOutput.dtd' does not exist file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/NCBI_BlastOutput.dtd Handler couldn't resolve external entity at line 2, column 82, byte 104 error in processing external entity reference at line 2, column 82, byte 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm line 187 --------------------------------------------------- t/SearchIO...................NOK 5/1340 # Failed test 'The object isa Bio::Search::Result::ResultI' # in t/SearchIO.t at line 65. # The object isn't defined Can't call method "database_name" on an undefined value at t/SearchIO.t line 66. # Looks like you planned 1340 tests but only ran 5. # Looks like you failed 1 test of 5 run. # Looks like your test died just after 5. t/SearchIO...................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-1340 Failed 1336/1340 tests, 0.30% okay [*snip*] Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/SearchIO.t 255 65280 1340 2671 5-1340 2 tests and 126 subtests skipped. Failed 1/235 test scripts. 1336/11940 subtests failed. Files=235, Tests=11940, 321 wallclock secs (154.44 cusr + 24.28 csys = 178.72 CPU) Failed 1/235 test programs. 1336/11940 subtests failed. make: *** [test_dynamic] Error 255 /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > > Everyone: > Even though 1.5.2 is a 'developer' release, we consider it the most > stable and capable version of Bioperl, and recommend that you use > it in all but the most critical production environments. Please > try it out and let us know of any problems or difficulties you run > into. > > Please try the new Build.PL installation script and report back how > you get on. Also try installing using CPAN. Your CPAN mirrors may > not be current enough, so you may have delete all entries in your > urllist first. > > > Developers: > Please experiment with installation, especially via CPAN. If you > already have all/most prerequisite external modules installed, > try uninstalling some and report how effective the system is at > reinstalling them for you. > > RC5 may form the final release for some of the packages (probably > all except for bioperl-run), so any further commits made, even to > branch-1-5-2, may not make final release. If you think you've > committed an important bug fix that should be part of final release, > let me know. > > > Thank you, > Sendu. > > > PS. What happened to RC4? I didn't announce it, but it was available on > CPAN where I did some testing on it. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Conrad Halling chhalling at verizon.net From cjfields at uiuc.edu Sun Nov 26 22:04:59 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 16:04:59 -0600 Subject: [Bioperl-l] EntrezGene test failures Message-ID: I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ Build test --test_files t/entrezgene.t --verbose': .. ok 1367 ok 1368 - correct number of loops for T18 # Looks like you planned 1417 tests but only ran 1368. # Looks like you failed 22 tests of 1368 run. dubious Test returned status 22 (wstat 5632, 0x1600) DIED. FAILED tests 56, 162, 182, 184, 367, 512, 603, 631, 667, 711, 766, 920, 998, 1107, 1140, 1192, 1225, 1248, 1270, 1297, 1320, 1345, 1369-1417 Failed 71/1417 tests, 94.99% okay Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------ ------- t/entrezgene.t 22 5632 1417 120 56 162 182 184 367 512 603 631 667 711 766 920 998 1107 1140 1192 1225 1248 1270 1297 1320 1345 1369-1417 Failed 1/1 test scripts. 71/1417 subtests failed. Files=1, Tests=1417, 3 wallclock secs ( 3.06 cusr + 0.09 csys = 3.15 CPU) Failed 1/1 test programs. 71/1417 subtests failed. Looks like not all tests are run. Of the tests that fail, all are from unmatched values. A few examples: # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '14' # expected: '16' not ok 56 - correct number of loops for T15 ... # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '28' # expected: '30' ... not ok 162 - correct number of loops for T15 # Failed test in t/entrezgene.t at line 456. # got: '0' # expected: '1' # Failed test 'correct number of loops for T15' # in t/entrezgene.t at line 495. # got: '6' # expected: '5' chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Sun Nov 26 22:17:30 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 16:17:30 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456A0062.6080103@verizon.net> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> Message-ID: <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: > I attempted to use CPAN to install BioPerl 1.5.2 RC5 into a fresh > installation of Perl 5.8.8 under Mac OS X 10.4.8 with all dependencies > installed. > > The tests fail for t/SearchIO. An edited record of the output is shown > below. > > > cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz > > [*snip*] > > *** Optional dependencies section *** > All dependencies are installed > > [*snip*] > > Running make test > PERL_DL_NONLAZY=1 /test/perl/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > > [*snip*] > > t/SearchIO...................ok > 1/1340 > -------------------- WARNING --------------------- > MSG: XML::SAX::Expat not currently supported; must have local > copies of > NCBI DTD docs! > --------------------------------------------------- > > -------------------- WARNING --------------------- > MSG: error in parsing a report: > > 404 File > `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ > NCBI_BlastOutput.dtd' > does not exist > file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ > NCBI_BlastOutput.dtd > Handler couldn't resolve external entity at line 2, column 82, byte > 104 > error in processing external entity reference at line 2, column 82, > byte > 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm > line 187 > > --------------------------------------------------- > t/SearchIO...................NOK > 5/1340 > # Failed test 'The object isa Bio::Search::Result::ResultI' > # in t/SearchIO.t at line 65. > # The object isn't defined > Can't call method "database_name" on an undefined value at t/ > SearchIO.t > line 66. > # Looks like you planned 1340 tests but only ran 5. > # Looks like you failed 1 test of 5 run. > # Looks like your test died just after 5. > t/SearchIO...................dubious > > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-1340 > Failed 1336/1340 tests, 0.30% okay > > [*snip*] > > Failed Test Stat Wstat Total Fail List of Failed > ---------------------------------------------------------------------- > --------- > t/SearchIO.t 255 65280 1340 2671 5-1340 > 2 tests and 126 subtests skipped. > Failed 1/235 test scripts. 1336/11940 subtests failed. > Files=235, Tests=11940, 321 wallclock secs (154.44 cusr + 24.28 csys = > 178.72 CPU) > Failed 1/235 test programs. 1336/11940 subtests failed. > make: *** [test_dynamic] Error 255 > /usr/bin/make test -- NOT OK > Running make install > make test had returned bad status, won't install without force > ... There is an eval{} block set up to catch that error but apparently it doesn't work. I'll have a look at it. Like the warning states, XML::SAX::Expat is not supported for BLASTXML parsing unless you have the NCBI DTDs installed as well (blame this on NCBI since their BLAST DTDs don't have the explicit web address). Saying that I don't recommend using XML::SAX::Expat at all (it is no longer actively maintained). Pretty much any other XML::SAX backend works; I recommend using XML::SAX::ExpatXS or XML::LibXML for speedier parsing, though XML::SAX::PurePerl also works. Chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Sun Nov 26 22:56:28 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 26 Nov 2006 22:56:28 +0000 Subject: [Bioperl-l] EntrezGene test failures In-Reply-To: References: Message-ID: <456A1B9C.5000105@sendu.me.uk> Chris Fields wrote: > I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ > Build test --test_files t/entrezgene.t --verbose': Yes, Stefan is in the middle of bug fixing/ improvements. I changed the test script recently to highlight the problems. From cjfields at uiuc.edu Sun Nov 26 23:48:23 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 17:48:23 -0600 Subject: [Bioperl-l] EntrezGene test failures In-Reply-To: <2ac232dd4a.2dd4a2ac23@bms.com> References: <2ac232dd4a.2dd4a2ac23@bms.com> Message-ID: On Nov 26, 2006, at 5:44 PM, Stefan Kirov wrote: > I thought Sendu rolled back some changes I've made. I was planning to > commit changes both to the module and the tests, but I am not done > yet. > Stefan Not a problem, just wanted to check. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From stefan.kirov at bms.com Sun Nov 26 23:44:29 2006 From: stefan.kirov at bms.com (Stefan Kirov) Date: Sun, 26 Nov 2006 18:44:29 -0500 Subject: [Bioperl-l] EntrezGene test failures Message-ID: <2ac232dd4a.2dd4a2ac23@bms.com> I thought Sendu rolled back some changes I've made. I was planning to commit changes both to the module and the tests, but I am not done yet. Stefan ----- Original Message ----- From: Chris Fields Date: Sunday, November 26, 2006 5:04 pm Subject: [Bioperl-l] EntrezGene test failures > I'm getting failed tests from entrezgene.t off CVS HEAD. Using './ > Build test --test_files t/entrezgene.t --verbose': > > .. > ok 1367 > ok 1368 - correct number of loops for T18 > # Looks like you planned 1417 tests but only ran 1368. > # Looks like you failed 22 tests of 1368 run. > dubious > Test returned status 22 (wstat 5632, 0x1600) > DIED. FAILED tests 56, 162, 182, 184, 367, 512, 603, 631, 667, 711, > > 766, 920, 998, 1107, 1140, 1192, 1225, 1248, 1270, 1297, 1320, > 1345, > 1369-1417 > Failed 71/1417 tests, 94.99% okay > Failed Test Stat Wstat Total Fail List of Failed > -------------------------------------------------------------------- > ---- > ------- > t/entrezgene.t 22 5632 1417 120 56 162 182 184 367 512 603 > 631 > 667 711 > 766 920 998 1107 1140 1192 > 1225 1248 1270 > 1297 1320 1345 1369-1417 > Failed 1/1 test scripts. 71/1417 subtests failed. > Files=1, Tests=1417, 3 wallclock secs ( 3.06 cusr + 0.09 csys = > 3.15 CPU) > Failed 1/1 test programs. 71/1417 subtests failed. > > > > Looks like not all tests are run. Of the tests that fail, all are > from unmatched values. A few examples: > > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '14' > # expected: '16' > not ok 56 - correct number of loops for T15 > > ... > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '28' > # expected: '30' > > ... > > not ok 162 - correct number of loops for T15 > > # Failed test in t/entrezgene.t at line 456. > # got: '0' > # expected: '1' > > # Failed test 'correct number of loops for T15' > # in t/entrezgene.t at line 495. > # got: '6' > # expected: '5' > > > > chris > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at uiuc.edu Mon Nov 27 04:14:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 26 Nov 2006 22:14:32 -0600 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4568BEFB.4070201@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> <4568BEFB.4070201@sendu.me.uk> Message-ID: <34BAD635-8C9F-4A22-B114-B3EFB5B544DD@uiuc.edu> On Nov 25, 2006, at 4:08 PM, Sendu Bala wrote: > Jason Stajich wrote: >> >> The circular ref is from Bio::Species when you have >> $self->{tree} = Bio::Tree::Tree->new(-root => $self); >> >> I added a weaken call in Bio::Species code explicitly -- we can't >> generally weaken the ref to the root node in Bio::Tree::Tree as that >> breaks some other things as you saw. > > Thanks. Though there's still the issue with > Bio::Tree::Node::node_cleanup not doing anything. > > >> I'm not sure I am digging what you've done with Bio::Tree::Tree. Why >> didn't you make a specialized Tree object for Taxonomy stuff so >> that you >> can add methods like lineage_node, etc? > > http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree > > get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because > it's > a Tree function. It goes hand in hand with get_lca(), which was > already > there. > > I suppose you're saying it would have been more appropriate to have a > new Tree-based object that only differed in its new() instead of > adding > an option to Tree's new()? > > My thinking was that both the -node option and get_lineage_nodes() are > useful for trees in general, not just Bio::Taxon. Jason's fixes seem to fix the problem (I tested on Mac OS X). However, does Scalar::Utils come as core with perl 5.6.1? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Mon Nov 27 04:58:14 2006 From: jason at bioperl.org (Jason Stajich) Date: Sun, 26 Nov 2006 20:58:14 -0800 Subject: [Bioperl-l] Performance of Bio::Species In-Reply-To: <4568BEFB.4070201@sendu.me.uk> References: <45633562.2030107@bms.com> <4563556A.1050101@sendu.me.uk> <45635F98.8030901@bms.com> <08253F93-77E9-4605-8944-D862FCD6EC4A@bioperl.org> <45683B60.9090402@sendu.me.uk> <805163C1-52F2-4012-858E-10B01E0D46ED@uiuc.edu> <45684BE1.8010902@sendu.me.uk> <4568BEFB.4070201@sendu.me.uk> Message-ID: On Nov 25, 2006, at 2:08 PM, Sendu Bala wrote: > Jason Stajich wrote: >> The circular ref is from Bio::Species when you have >> $self->{tree} = Bio::Tree::Tree->new(-root => $self); >> I added a weaken call in Bio::Species code explicitly -- we can't >> generally weaken the ref to the root node in Bio::Tree::Tree as >> that breaks some other things as you saw. > > Thanks. Though there's still the issue with > Bio::Tree::Node::node_cleanup not doing anything. > right - well I am not sure that it is going to get called if you have to remove the cleanup_methods from the object (or does this mean at all?). I don't have any time to debug it any more so we'll just have to wait till later to figure it out. I'd really like to re-visit the tree bjects to see about making them faster anyways so maybe the memory cycle issue can be revisited as well. > >> I'm not sure I am digging what you've done with Bio::Tree::Tree. >> Why didn't you make a specialized Tree object for Taxonomy stuff >> so that you can add methods like lineage_node, etc? > > http://www.bioperl.org/wiki/Change_log#Bio::Tree::Tree > > get_lineage_nodes() was added to Bio::Tree::TreeFunctionsI because > it's a Tree function. It goes hand in hand with get_lca(), which > was already there. > > I suppose you're saying it would have been more appropriate to have > a new Tree-based object that only differed in its new() instead of > adding an option to Tree's new()? > > My thinking was that both the -node option and get_lineage_nodes() > are useful for trees in general, not just Bio::Taxon. > I guess I was talking about this code in new() - seems like a Tree::Taxon object could have been made to deal with the special case, but probably I am just not seeing the whole picture so no worries. # to stop us pulling in entire database of a Bio::Taxon when we later do # get_nodes() or similar, specifically set ancestor() for each node if ($node->isa('Bio::Taxon')) { push(@lineage, $node) unless $node eq $root; my $ancestor = $root; foreach my $lineage_node (@lineage) { $lineage_node->ancestor($ancestor); } continue { $ancestor = $lineage_node; } } -- Jason Stajich jason at bioperl.org http://jason.open-bio.org/ From anhthu.tieu at gsf.de Mon Nov 27 08:38:36 2006 From: anhthu.tieu at gsf.de (Anh-Thu Tieu) Date: Mon, 27 Nov 2006 09:38:36 +0100 Subject: [Bioperl-l] exention files for bioperl1.5.2 Message-ID: <456AA40C.3050207@gsf.de> Hi, I noticed there has been a new release for bioperl1.5.2 and I wondered whether there is/ will also be an extension file for this version also (as for version 1.4 or 1.5.1). Until now I have only found the core, network, db and the run files. Is it sufficient to install those four packages (+ various additional perl modules) to make bioperl1.5.2 run or do I need any exention files. Thank you. Best regards, Anh Thu From n.haigh at sheffield.ac.uk Mon Nov 27 09:52:39 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 09:52:39 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456AB567.2010601@sheffield.ac.uk> I just checked out RC5 and ran "perl Build.PL" I get: Can't locate object method "new" via package "Module::Build::Notes" (perhaps you forgot to load "Module::Build::Notes"?) at /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. Nath From bix at sendu.me.uk Mon Nov 27 14:50:08 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 14:50:08 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456AB567.2010601@sheffield.ac.uk> References: <4566B3AF.2050305@sendu.me.uk> <456AB567.2010601@sheffield.ac.uk> Message-ID: <456AFB20.4050102@sendu.me.uk> Nathan Haigh wrote: > I just checked out RC5 and ran "perl Build.PL" I get: > > Can't locate object method "new" via package "Module::Build::Notes" > (perhaps you forgot to load "Module::Build::Notes"?) at > /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. What version of Module::Build do you have installed? Does your Module/Build/Base.pm not 'use Modules::Build::Notes' somewhere near the top? Try upgrading to v0.2805 of Module::Build and let me know if that solves the problem. (If you don't have Module::Build installed at all, didn't you get some kind of prompt to install it?) Thank you, Sendu. From bix at sendu.me.uk Mon Nov 27 16:01:16 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 16:01:16 +0000 Subject: [Bioperl-l] exention files for bioperl1.5.2 In-Reply-To: <456AA40C.3050207@gsf.de> References: <456AA40C.3050207@gsf.de> Message-ID: <456B0BCC.2020202@sendu.me.uk> Anh-Thu Tieu wrote: > Hi, > > I noticed there has been a new release for bioperl1.5.2 and I wondered > whether there is/ will also be an extension file for this version also > (as for version 1.4 or 1.5.1). Until now I have only found the core, > network, db and the run files. Is it sufficient to install those four > packages (+ various additional perl modules) to make bioperl1.5.2 run or > do I need any exention files. What do you mean by 'extension' file? If you mean the bioperl-ext package then hopefully whatever old version you have will still work. It hasn't been tested, nor will it be updated for 1.5.2 From n.haigh at sheffield.ac.uk Mon Nov 27 16:05:40 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 16:05:40 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456AFB20.4050102@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456AB567.2010601@sheffield.ac.uk> <456AFB20.4050102@sendu.me.uk> Message-ID: <456B0CD4.1060602@sheffield.ac.uk> Sendu Bala wrote: > Nathan Haigh wrote: >> I just checked out RC5 and ran "perl Build.PL" I get: >> >> Can't locate object method "new" via package "Module::Build::Notes" >> (perhaps you forgot to load "Module::Build::Notes"?) at >> /home/bo1nsh/cvswc/bioperl-1-5-2/ModuleBuildBioperl.pm line 633. > > What version of Module::Build do you have installed? Does your > Module/Build/Base.pm not 'use Modules::Build::Notes' somewhere near > the top? > > Try upgrading to v0.2805 of Module::Build and let me know if that > solves the problem. > > (If you don't have Module::Build installed at all, didn't you get some > kind of prompt to install it?) > > > Thank you, > Sendu. I have v0.2612 installed. Upgrading to Module::Build 0.2805 fixed the problem. Nath From bix at sendu.me.uk Mon Nov 27 16:18:35 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 16:18:35 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> Message-ID: <456B0FDB.9020208@sendu.me.uk> Chris Fields wrote: > On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: [snip] >> t/SearchIO...................ok >> 1/1340 >> -------------------- WARNING --------------------- >> MSG: XML::SAX::Expat not currently supported; must have local >> copies of >> NCBI DTD docs! >> --------------------------------------------------- >> >> -------------------- WARNING --------------------- >> MSG: error in parsing a report: >> >> 404 File >> `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >> NCBI_BlastOutput.dtd' >> does not exist >> file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >> NCBI_BlastOutput.dtd >> Handler couldn't resolve external entity at line 2, column 82, byte >> 104 >> error in processing external entity reference at line 2, column 82, >> byte >> 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm >> line 187 [snip] > There is an eval{} block set up to catch that error but apparently it > doesn't work. I'll have a look at it. The test script has nothing to catch in the eval because blastxml.pm catches the error and emits a warning. You'll either have to make blastxml.pm throw (instead of returning undef + warn), or figure something else out. It's a behaviour change, but would anyone care if it threw thanks to this problem? From cjfields at uiuc.edu Mon Nov 27 16:41:53 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 27 Nov 2006 10:41:53 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B0FDB.9020208@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456A0062.6080103@verizon.net> <83047C5D-BA52-429A-A46C-EBBE64549598@uiuc.edu> <456B0FDB.9020208@sendu.me.uk> Message-ID: On Nov 27, 2006, at 10:18 AM, Sendu Bala wrote: > Chris Fields wrote: >> On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote: > [snip] >>> t/SearchIO...................ok >>> 1/1340 >>> -------------------- WARNING --------------------- >>> MSG: XML::SAX::Expat not currently supported; must have local >>> copies of >>> NCBI DTD docs! >>> --------------------------------------------------- >>> >>> -------------------- WARNING --------------------- >>> MSG: error in parsing a report: >>> >>> 404 File >>> `/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >>> NCBI_BlastOutput.dtd' >>> does not exist >>> file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/ >>> NCBI_BlastOutput.dtd >>> Handler couldn't resolve external entity at line 2, column 82, >>> byte 104 >>> error in processing external entity reference at line 2, column >>> 82, byte >>> 104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/ >>> Parser.pm line 187 > > [snip] > >> There is an eval{} block set up to catch that error but apparently >> it doesn't work. I'll have a look at it. > > The test script has nothing to catch in the eval because > blastxml.pm catches the error and emits a warning. You'll either > have to make blastxml.pm throw (instead of returning undef + warn), > or figure something else out. > > It's a behaviour change, but would anyone care if it threw thanks > to this problem? Ah, that's my fault. I had changed that to a throw but didn't commit it. In a nutshell, we can't/won't support XML::SAX::Expat for a number of reasons. One is the problem with the BLAST DTDs (no explicit web address, so XML validation fails). There may be a way to turn validation off. However, the other, more serious issue is that it is no longer maintained (it hasn't been updated in three years). There were plans a year ago for XML::SAX::ExpatXS to take over the XML::SAX::Expat namespace but no one has bothered to make the changeover, apparently. I have committed the change from warn to throw and made the error message more explicit. You can look it over and merge to 1.5.2 at your discretion. chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cain.cshl at gmail.com Mon Nov 27 17:39:09 2006 From: cain.cshl at gmail.com (Scott Cain) Date: Mon, 27 Nov 2006 12:39:09 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <45657C65.50200@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> Message-ID: <1164649150.2575.57.camel@localhost.localdomain> Hi Sendu, I won't have time to do testing on Windows until much later in the day, but I at least want to throw out a little more information. In ActivePerl 819, DBI appears to be installed by default, but the method 'available_drivers' doesn't appear to be available (not implemented? returns something invalid when there are none? not sure at the moment). Anyway, as a result, when I run perl Build.PL and there are no drivers installed, it crashes. I'll try to tease out what is going on later tonight. Scott On Thu, 2006-11-23 at 10:48 +0000, Sendu Bala wrote: > Sendu Bala wrote: > > Scott Cain wrote: > >> Hello, > >> > >> I just wanted to mention that I made a few minor changes to Build.PL so > >> that I could get `perl Build.PL` to complete successfully. I am using > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > >> present either. The main thing I did was to have the BioDBGFF test > >> subroutine quit without asking any questions if Build.PL detected that > >> it was running on Windows. > > > > Is it completely impossible for it to pass under Windows? I find that > > quite a shame! > > > > I'm surprised it was necessary to make your changes, because it already > > had to return true from: > [snip] > > Sorry, that all made no sense because I didn't pay attention to what > changes you actually made. > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > being on mswin still causes a problem, or can the excludes_os > restriction on line 78 of Build.PL be lifted now? > > > Cheers, > Sendu. -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain.cshl at gmail.com GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From n.haigh at sheffield.ac.uk Mon Nov 27 17:48:59 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 17:48:59 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456B250B.4050607@sheffield.ac.uk> When running ./Build test for bioperl-run, the tests for DrawGram and DrawTree require me to manually close the window that is opened and press return in the console in order for the test to complete. Nath From bix at sendu.me.uk Mon Nov 27 17:54:58 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 27 Nov 2006 17:54:58 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B250B.4050607@sheffield.ac.uk> References: <4566B3AF.2050305@sendu.me.uk> <456B250B.4050607@sheffield.ac.uk> Message-ID: <456B2672.5030405@sendu.me.uk> Nathan Haigh wrote: > When running ./Build test for bioperl-run, the tests for DrawGram and > DrawTree require me to manually close the window that is opened and > press return in the console in order for the test to complete. Hasn't that always been the case in the past? Or did you only recently install some optional pre-req? Does anyone know a way around this? From n.haigh at sheffield.ac.uk Mon Nov 27 18:31:18 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Mon, 27 Nov 2006 18:31:18 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <456B2672.5030405@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> <456B250B.4050607@sheffield.ac.uk> <456B2672.5030405@sendu.me.uk> Message-ID: <456B2EF6.10808@sheffield.ac.uk> Sendu Bala wrote: > Nathan Haigh wrote: >> When running ./Build test for bioperl-run, the tests for DrawGram and >> DrawTree require me to manually close the window that is opened and >> press return in the console in order for the test to complete. > > Hasn't that always been the case in the past? Or did you only recently > install some optional pre-req? > > Does anyone know a way around this? I've always had Phylip installed, and I know I've run the tests remotely without X11 forwarding - which obviously wouldn't allow the windows to appear (tests were still successful). I'm also sure I've run the test locally previously - but I've not noticed it before - starting to think I'm going mad! :-P Nath From cjfields at uiuc.edu Mon Nov 27 21:47:12 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 27 Nov 2006 15:47:12 -0600 Subject: [Bioperl-l] DBSOURCE parsing Message-ID: Jason, I am working on stockholm and GenPept format parsing, both which have DBLink objects. I have a couple of questions. First, (not a huge issue really, more like a curiosity), is it possible to pass a callback to Annotation objects for the overloaded operators? I'm just thinking of situations where the data is displayed differently in other formats (like Stockholm). Also, would it be feasible to have DBLink objects also contain annotations (comments, other DBLink objects, etc) for more complex data? In particular this regards GenPept stuff, like the following examples: DBSOURCE swissprot: locus BRCA1_HUMAN, accession P38398; class: standard. created: Oct 1, 1994. sequence updated: Feb 1, 1995. annotation updated: Nov 14, 2006. xrefs: U14680.1, AAA73985.1, L78833.1, AAC37594.1, AY273801.1, AAP12647.1, A58881, 1JM7A, 1JNXX, 1N5OX, 1OQAA, 1T15A, 1T29A, 1T2UA, 1T2VA, 1T2VB, 1T2VC, 1T2VD, 1T2VE, 1Y98A xrefs (non-sequence databases): UniGene:Hs.194143, IntAct:P38398, TRANSFAC:T04074, Ensembl:ENSG00000012048, KEGG:hsa:672, HGNC:1100, MIM:113705, MIM:114480, Reactome:P38398, ArrayExpress:P38398, GO:0031436, GO:0008274, GO:0005634, GO:0000151, GO:0050681, GO:0003677, GO:0019899, GO:0003713, GO:0015631, GO:0008270, GO:0030521, GO:0007059, GO:0006978, GO:0008630, GO:0042759, GO:0046600, GO:0016481, GO:0045739, GO:0031398, GO:0045893, GO:0016567, GO:0042981, GO:0042127, GO:0006357, GO:0006359, InterPro:IPR011364, InterPro:IPR001357, InterPro:IPR002378, InterPro:IPR001841, PANTHER:PTHR13763, Pfam:PF00533, Pfam:PF00097, PIRSF:PIRSF001734, PRINTS:PR00493, SMART:SM00292, SMART:SM00184, PROSITE:PS50172, PROSITE:PS00518, PROSITE:PS50089 ... DBSOURCE pdb: molecule 1T2U, chain 65, release Apr 22, 2004; deposition: Apr 22, 2004; class: Antitumor Protein; source: Mol_id: 1; Organism_scientific: Homo Sapiens; Organism_common: Human; Gene: Brca1; Expression_system: Escherichia Coli; Expression_system_common: Bacteria; Exp. method: X-Ray Diffraction. ... DBSOURCE pir: locus I49350; summary: #length 1812 #molecular-weight 198788 #checksum 8813 ; genetic: #gene Brca1 ; superfamily: transcriptional regulator, BRCA1 type; RING finger homology ; PIR dates: 02-Jul-1996 #sequence_revision 02-Jul-1996 #text_change 09-May-2004 . ... DBSOURCE prf: locus 2202221A; state: hepatoma/colonic tumor; taxonomy: Mammalia. My thought is, the first line would be the main DBLink object data, with all subsequent lines as annotation objects (comments, DBLinks, etc) in an annotation collection contained within the main DBLink object. I don't think there would be any danger of circular references if handled correctly. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From chhalling at verizon.net Tue Nov 28 03:25:00 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:25:00 -0500 Subject: [Bioperl-l] A procedure for efficient testing of the installation of BioPerl Message-ID: <456BAC0C.10503@verizon.net> I have devised the following procedure that lets me repeatedly install BioPerl release candidates for testing the installation process. I am performing these tests under Mac OS X 10.4.8. I thought it would be useful to document this process for anyone else who is testing the installation process. I downloaded the tarball for Perl 5.8.8 and ran the following commands to set up the code for installation: cd /Volumes/CHHalling/Perl/Perl-5.8.8 tar -xzf perl-5.8.8.tgz cd perl-5.8.8 sh Configure -Dprefix=/test/perl -Dcc=gcc -des make make test For each round of testing, I run the following commands to install a fresh copy of Perl 5.8.8 and then initialize the cpan utility: cd /Volumes/CHHalling/Perl/Perl-5.8.8/perl-5.8.8 sudo rm -rf /test sudo mkdir /test sudo make install sudo rm -rf ~/.cpan export PATH=/test/perl/bin:$PATH sudo cpan Then I run my cpan commands. For installing BioPerl without having installed the dependencies, I enter the command: cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz For installing the dependencies, then installing BioPerl, I enter the commands: cpan> install Bundle::BioPerl cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz For testing modifications to Bundle::BioPerl (the subject of my next post), I execute the following commands (which exit the cpan utility after I have initialized it, create the Bundle subdirectory, copy the BioPerl.pm file that contains the Bundle::BioPerl package to the .cpan/Bundle directory, start the cpan utility, and install Bundle::BioPerl and BioPerl 1.5.2 RC5): cpan> exit $ sudo mkdir ~/.cpan/Bundle $ sudo cp /Volumes/CHHalling/Perl/BioPerl/BioPerl.pm ~/.cpan/Bundle/ $ sudo cpan cpan> install Bundle::BioPerl cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz When I have finished testing the installation, I loop back to step 2, where I remove the /test directory and reinstall Perl 5.8.8. A note: I was going to use the same procedure to test installing BioPerl 1.5.2 under Perl 5.6.1, but I discovered that Perl 5.6.1 is *so old* that there is no Makefile for Mac OS X. -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Tue Nov 28 03:02:59 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:02:59 -0500 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 In-Reply-To: <4566B3AF.2050305@sendu.me.uk> References: <4566B3AF.2050305@sendu.me.uk> Message-ID: <456BA6E3.3010908@verizon.net> I compiled and installed Perl 5.8.8 under Mac OS X 10.4.8 into a directory named /test/perl. Then I used the cpan utility to attempt to install BioPerl 1.5.2 RC5 without having installed any of its dependencies. The installation failed because of the following test failures: t/SeqFeature t/SeqHound_DB t/SeqVersion Here are the pertinent details: t/SeqFeature.................IO::String or LWP::UserAgent or HTTP::Request not installed - skipping DB tests... Can't locate URI/Escape.pm in @INC (@INC contains: t /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/arch /test/perl/lib/5.8.8/darwin-2level /test/perl/lib/5.8.8 /test/perl/lib/site_perl/5.8.8/darwin-2level /test/perl/lib/site_perl/5.8.8 /test/perl/lib/site_perl .) at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/SeqFeature/Annotated.pm line 86. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/SeqFeature/Annotated.pm line 86. Compilation failed in require at t/SeqFeature.t line 52. BEGIN failed--compilation aborted at t/SeqFeature.t line 52. t/SeqFeature.................dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/SeqHound_DB................ok 1/14Can't locate LWP/UserAgent.pm in @INC (@INC contains: /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/arch /test/perl/lib/5.8.8/darwin-2level /test/perl/lib/5.8.8 /test/perl/lib/site_perl/5.8.8/darwin-2level /test/perl/lib/site_perl/5.8.8 /test/perl/lib/site_perl .) at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/WebDBSeqI.pm line 78. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/WebDBSeqI.pm line 78. Compilation failed in require at (eval 19) line 3. ...propagated at /test/perl/lib/5.8.8/base.pm line 85. BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/SeqHound.pm line 88. Compilation failed in require at t/SeqHound_DB.t line 41. BEGIN failed--compilation aborted at t/SeqHound_DB.t line 41. Use of uninitialized value in -f at t/SeqHound_DB.t line 34. t/SeqHound_DB................dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/SeqVersion.................NOK 1 # Failed test 'use Bio::DB::SeqVersion;' # in t/SeqVersion.t at line 21. # Tried to use 'Bio::DB::SeqVersion'. # Error: Base class package "LWP::UserAgent" is empty. # (Perhaps you need to 'use' the module which defines that package first.) # at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/WebAgent.pm line 90 # BEGIN failed--compilation aborted at t/SeqVersion.t line 21. # Compilation failed in require at (eval 4) line 3. # ...propagated at /test/perl/lib/5.8.8/base.pm line 85. # BEGIN failed--compilation aborted at /Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/SeqVersion.pm line 71. # Compilation failed in require at (eval 3) line 2. # BEGIN failed--compilation aborted at (eval 3) line 2. Can't locate object method "new" via package "Bio::DB::SeqVersion" at t/SeqVersion.t line 23. # Looks like you planned 10 tests but only ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test died just after 1. t/SeqVersion.................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-10 Failed 10/10 tests, 0.00% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/SeqFeature.t 2 512 211 0 0.00% ?? t/SeqHound_DB.t 2 512 14 0 0.00% ?? t/SeqVersion.t 255 65280 10 19 190.00% 1-10 9 tests and 228 subtests skipped. Failed 3/235 test scripts, 98.72% okay. 10/11535 subtests failed, 99.91% okay. make: *** [test_dynamic] Error 255 /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force Sendu Bala wrote: > Bioperl 1.5.2 Release Candidate 5 is ready and available for testing. > See http://www.bioperl.org/wiki/Release_1.5.2 for > instructions on getting and testing this RC. > [*snip*] > Thank you, > Sendu. -- Conrad Halling chhalling at verizon.net From chhalling at verizon.net Tue Nov 28 03:51:14 2006 From: chhalling at verizon.net (Conrad Halling) Date: Mon, 27 Nov 2006 22:51:14 -0500 Subject: [Bioperl-l] A new Bundle::BioPerl Message-ID: <456BB232.4020808@verizon.net> After experimenting with the existing Bundle::BioPerl version 2.1.8 under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install all of the BioPerl dependencies unless run multiple times. I edited the the order that the dependencies were listed so I could get all the dependencies to install on the first try. Then I got carried away and ran some grep commands on the bioperl-live source code to identify all of the dependencies that are use'd or require'd, and I added these dependencies to the Bundle::BioPerl package. Many of these dependencies are core Perl modules, which it doesn't hurt to update. After a few rounds of testing during Thanksgiving weekend festivities, I have completed a new Bundle::BioPerl package that installs virtually all of the dependencies on the first try. There are two modules that won't install. The first is Bio::ASN1::EntrezGene, and the second is CORBA::ORBit. Bio::ASN1::EntrezGene won't install because it is dependent on Bio::Index::AbstractSeq, which is part of BioPerl. CORBA::ORBit won't install because its tarball appears to be corrupted. The cpan utility also reports that Math::Trig and Text::Balanced didn't install, but this is an error, because they are installed correctly. The cpan commands for installing the BioPerl dependencies, Bio::ASN1::EntrezGene, and BioPerl 1.5.2 RC5, will become: cpan> install Bundle::BioPerl cpan> force install Bio::ASN1::EntrezGene cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz I have filed a Bugzilla bug report (bug #2153) and attached my Bundle::BioPerl package (attachment #508) to it for consideration. -- Conrad Halling chhalling at verizon.net From DGroskreutz at twt.com Tue Nov 28 07:00:40 2006 From: DGroskreutz at twt.com (DGroskreutz at twt.com) Date: Tue, 28 Nov 2006 01:00:40 -0600 Subject: [Bioperl-l] CN=Deb Groskreutz/OU=MSN/O=TWT is out of the office. Message-ID: I will be out of the office starting 11/27/2006 and will not return until 12/04/2006. NOTICE OF CONFIDENTIALITY: The information contained in this communication, including attachments, is intended for the specific delivery to and use by the individual(s) to whom it is addressed. This email includes confidential information that may be attorney-client privileged. Any review, retransmission, dissemination, or unauthorized use of this communication is strictly prohibited and may be unlawful. If you have received this communication in error, please reply to the sender immediately and delete the original communication and any copy of it from your computer system, including all attachments. From bix at sendu.me.uk Tue Nov 28 10:53:10 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 10:53:10 +0000 Subject: [Bioperl-l] A new Bundle::BioPerl In-Reply-To: <456BB232.4020808@verizon.net> References: <456BB232.4020808@verizon.net> Message-ID: <456C1516.5050900@sendu.me.uk> Conrad Halling wrote: > After experimenting with the existing Bundle::BioPerl version 2.1.8 > under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install > all of the BioPerl dependencies unless run multiple times. > > I edited the the order that the dependencies were listed so I could get > all the dependencies to install on the first try. Thank you so much for all your hard work. Its extremely valuable. That said, I'm no longer recommending the usage of Bundle::BioPerl. Instead what I'll do is apply your discovered order to the new Build.PL installation system. You're welcome of course to contact Chris Dagdigian to make sure he knows about your new version of Bundle::BioPerl. He can then upload it to CPAN if he's happy with it, and people who choose to still use the Makefile.PL installation process will surely appreciate the new version of Bundle::BioPerl. Thanks again, Sendu. From st537 at york.ac.uk Tue Nov 28 11:02:07 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Tue, 28 Nov 2006 11:02:07 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... Message-ID: <456C172F.4060008@york.ac.uk> Hi, I am trying to learn bioperl and I'm attempting a few basic thing! I seem to be ok with reading in and outputting sequences and files now I am trying to do a simple BLAST search using a sequence (a sequence object in fact). The code I am attempting to run is at the bottom of the message... I am probably making a dumb mistake and don't understand the capabilities of the objects well enough, but the info for the remoteblast->submit_blast function says that it can take sequences as an argument, I've also tried sending the fasta file name containing my sequence as an argument to submit_blast, with the same result.... I have also tried sending $seqio_obj->next_seq........... i.e the following error message displayed on my terminal: Can't call method "submit_blast" on an undefined value at bioptest2.pl line 22, line 1. I haven't got around to figuring out how to process the returned data from this yet, just trying to get the function to run first! Thanks for any help that anyone can offer me with this... Samantha Thompson #******************************** use Bio::Seq; use Bio::SeqIO; use Bio::Tools::Run::RemoteBlast; use Bio::SearchIO; #seq bit $seq_obj = Bio::Seq->new(-format => 'fasta'); $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); $seq_obj = $seqio_obj->next_seq; #blast bit $remote_blast = Bio::Tools::Run::RemoteBlast->new ( -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); #end From bix at sendu.me.uk Tue Nov 28 12:39:29 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 12:39:29 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C172F.4060008@york.ac.uk> References: <456C172F.4060008@york.ac.uk> Message-ID: <456C2E01.5070805@sendu.me.uk> Samantha Thompson wrote: > Hi, > I am trying to learn bioperl and I'm attempting a few basic thing! I > seem to be ok with reading in and outputting sequences and files now I > am trying to do a simple BLAST search using a sequence (a sequence > object in fact). The code I am attempting to run is at the bottom of the > message... > I am probably making a dumb mistake and don't understand the > capabilities of the objects well enough, but the info for the > remoteblast->submit_blast function says that it can take sequences as an > argument, I've also tried sending the fasta file name containing my > sequence as an argument to submit_blast, with the same result.... I > have also tried sending $seqio_obj->next_seq........... i.e the > following error message displayed on my terminal: > > Can't call method "submit_blast" on an undefined value at bioptest2.pl > line 22, line 1. Always start your perl scripts with 'use strict;'. This will help you find and fix the main problem with your script, that you made a RemoteBlast object and stored it as $remote_blast, but then tried to use submit_blast() on $remoteBlast which doesn't exist. I've rewritten your code below: use strict; > use Bio::Seq; > use Bio::SeqIO; > > use Bio::Tools::Run::RemoteBlast; > use Bio::SearchIO; > > #seq bit > # $seq_obj = Bio::Seq->new(-format => 'fasta'); # above line doesn't do anything, $seq_obj gets overwritten below > my $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > my $seq_obj = $seqio_obj->next_seq; > > > > #blast bit > my $remote_blast = Bio::Tools::Run::RemoteBlast->new(-prog => 'blastp', -db => 'nr', -expect => '1e-15' ); # submit_blast takes the sequence object, not the sequence string my $blastreturn_obj = $remote_blast->submit_blast($seq_obj); From n.haigh at sheffield.ac.uk Tue Nov 28 13:10:45 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 28 Nov 2006 13:10:45 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C172F.4060008@york.ac.uk> References: <456C172F.4060008@york.ac.uk> Message-ID: <456C3555.3040807@sheffield.ac.uk> Samantha Thompson wrote: > Hi, > I am trying to learn bioperl and I'm attempting a few basic thing! I > seem to be ok with reading in and outputting sequences and files now I > am trying to do a simple BLAST search using a sequence (a sequence > object in fact). The code I am attempting to run is at the bottom of the > message... > I am probably making a dumb mistake and don't understand the > capabilities of the objects well enough, but the info for the > remoteblast->submit_blast function says that it can take sequences as an > argument, I've also tried sending the fasta file name containing my > sequence as an argument to submit_blast, with the same result.... I > have also tried sending $seqio_obj->next_seq........... i.e the > following error message displayed on my terminal: > > Can't call method "submit_blast" on an undefined value at bioptest2.pl > line 22, line 1. > > I haven't got around to figuring out how to process the returned data > from this yet, just trying to get the function to run first! > Thanks for any help that anyone can offer me with this... > > Samantha Thompson > > #******************************** > > > use Bio::Seq; > use Bio::SeqIO; > > use Bio::Tools::Run::RemoteBlast; > use Bio::SearchIO; > > #seq bit > > $seq_obj = Bio::Seq->new(-format => 'fasta'); > > $seqio_obj = Bio::SeqIO->new(-file => > "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > > $seq_obj = $seqio_obj->next_seq; > > > > #blast bit > > $remote_blast = Bio::Tools::Run::RemoteBlast->new ( > -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); > > $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); > > > > > #end > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > Hi Samantha, At first glance and without running any code, the first thing I can see that is incorrect is: $blastreturn_obj = $remoteBlast->submit_blast($seq_obj->seq); I believe that submit_blast() would be likely to take the actual sequence object ($seq_obj) as the argument and not the actual sequence string itself (e.g. "ACTGCTG") that you get by calling $seq_obj->seq. So swap this line for: $blastreturn_obj = $remoteBlast->submit_blast($seq_obj); And see how you get on. Nath From hlapp at gmx.net Tue Nov 28 16:20:59 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 28 Nov 2006 11:20:59 -0500 Subject: [Bioperl-l] load_seqdatabase.pl question In-Reply-To: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> Message-ID: <53C6D534-6E36-4061-B955-E74537839265@gmx.net> Hi Derek, first off, I'd recommend to always post such questions to the mailing list; sometimes I may not have a chance to check my email for a while or respond right away but someone else may know the answer too. In your case it looks like you didn't install bioperl-db. You need to install bioperl-db from CVS (using the main trunk). Instructions for how to do this are on the bioperl web site. Let me (and the list) know if you have trouble finding those. Let me know if you did install bioperl-db. (If you did, did you also set PERL5LIB if you installed it in non-standard place, such as your home directory?) -hilmar On Nov 27, 2006, at 12:07 PM, Derek Buchfink wrote: > Hi, I am new to BioSQL and I am looking to use the > load_seqdatabase.pl script to load some data into a PostgreSQL > 8.1.4 database. I am using version 1.24 of the script. However, I > am getting the following error: > > Can't locate Bio/DB/BioDB.pm in @INC (@INC contains: /usr/lib/ > perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/ > perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/ > site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/ > 5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386- > linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread- > multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/ > lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/ > perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/ > site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/ > site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi / > usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/ > perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/ > vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/ > vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/ > vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/ > vendor_perl .) at load_seqdatabase.pl line 337. > BEGIN failed--compilation aborted at load_seqdatabase.pl line 337. > > Do you know how to solve this issue or do you have any helpful > suggestions? Thank you very much. > > Derek Buchfink -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cain at cshl.edu Tue Nov 28 16:42:23 2006 From: cain at cshl.edu (Scott Cain) Date: Tue, 28 Nov 2006 11:42:23 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164649150.2575.57.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> Message-ID: <1164732143.2584.33.camel@localhost.localdomain> Hi Sendu, It looks like what you've done did the trick--bioperl installed on both ActivePerl 817 and 819 using Module::Build (though I must admit I didn't look at the tests--I just wanted `perl Build.PL` to work). Nice work! Scott On Mon, 2006-11-27 at 12:39 -0500, Scott Cain wrote: > Hi Sendu, > > I won't have time to do testing on Windows until much later in the day, > but I at least want to throw out a little more information. In > ActivePerl 819, DBI appears to be installed by default, but the method > 'available_drivers' doesn't appear to be available (not implemented? > returns something invalid when there are none? not sure at the moment). > Anyway, as a result, when I run perl Build.PL and there are no drivers > installed, it crashes. I'll try to tease out what is going on later > tonight. > > Scott > > > On Thu, 2006-11-23 at 10:48 +0000, Sendu Bala wrote: > > Sendu Bala wrote: > > > Scott Cain wrote: > > >> Hello, > > >> > > >> I just wanted to mention that I made a few minor changes to Build.PL so > > >> that I could get `perl Build.PL` to complete successfully. I am using > > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > > >> present either. The main thing I did was to have the BioDBGFF test > > >> subroutine quit without asking any questions if Build.PL detected that > > >> it was running on Windows. > > > > > > Is it completely impossible for it to pass under Windows? I find that > > > quite a shame! > > > > > > I'm surprised it was necessary to make your changes, because it already > > > had to return true from: > > [snip] > > > > Sorry, that all made no sense because I didn't pay attention to what > > changes you actually made. > > > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > > being on mswin still causes a problem, or can the excludes_os > > restriction on line 78 of Build.PL be lifted now? > > > > > > Cheers, > > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain at cshl.edu GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From bix at sendu.me.uk Tue Nov 28 16:56:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 28 Nov 2006 16:56:04 +0000 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <1164732143.2584.33.camel@localhost.localdomain> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> <1164732143.2584.33.camel@localhost.localdomain> Message-ID: <456C6A24.5090105@sendu.me.uk> Scott Cain wrote: > Hi Sendu, > > It looks like what you've done did the trick--bioperl installed on both > ActivePerl 817 and 819 using Module::Build (though I must admit I didn't > look at the tests--I just wanted `perl Build.PL` to work). Nice work! ... I didn't do anything yet :O Can you check on an export of bioperl-release-1-5-2-rc5 and compare to an export of branch-1-5-2 and let me know if you see the bug in the former and no bug in the latter? From gwu at molbio.mgh.harvard.edu Tue Nov 28 21:13:11 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Tue, 28 Nov 2006 16:13:11 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <53C6D534-6E36-4061-B955-E74537839265@gmx.net> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> Message-ID: <456CA667.6010609@molbio.mgh.harvard.edu> Hi everyone, I'm using load_seqdatabase.pl to upload some Genbank genome sequences to my Oracle BioSQL database. I saw some errors(See attached warning message) related to seqfeature_qualifier_value (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data type of maximum 4000 bytes. Did anybody mention this issue before? Should I just modify the column to a type being able store more data such as LONG or CLOB? Thanks. Gang Log information: ============================================ load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank /genomeseq/arabidopsis//NC_003070.gbk Loading /genomeseq/arabidopsis//NC_003070.gbk ... -------------------- WARNING --------------------- MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement execution: ORA-01461: can bind a LONG value only for insert into a LONG column (DBD ERROR: error possibly near <*> indicator at char 12 in 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, rank) VALUES (:p1, :p2, :p3, :p4)') name: INSERT ASSOC [2] Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue values: FK[Bio::SeqFeature::Generic]:14898, FK[Bio::Annotation::SimpleValue]:800, value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFVGTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADRGTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEILASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFPWEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERASVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRYIQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEAEDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDINQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDWRLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFALDIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDNQGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRYMRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYTFESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGLVQATYQASAPLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKVHLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAYTDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFVSVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSEKETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLGNFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEVTAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQLEVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTLSVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVTILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRLMLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAVPDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEYTYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVDISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLRVKLDFNFMYASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQSQVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSNTYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCLSIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWDILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSEIAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASVTRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGLHGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSSKPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDFQTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGLHIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVARLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCLLISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRNGRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVENSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPLWLSVGADASVLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVYLTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITNDSYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQESAGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTSDRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSVFSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESWQFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIVRISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMSVQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRVYPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAMSPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDILGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAKSSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLRPYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMGQRKFIPAKDACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQAINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", rank:"1" -------------------------------------------------- ============================================= From cain.cshl at gmail.com Tue Nov 28 20:18:02 2006 From: cain.cshl at gmail.com (Scott Cain) Date: Tue, 28 Nov 2006 15:18:02 -0500 Subject: [Bioperl-l] Minor changes to Build.PL for Windows In-Reply-To: <456C6A24.5090105@sendu.me.uk> References: <1164225865.2639.8.camel@localhost.localdomain> <4564DD7F.8090301@sendu.me.uk> <45657C65.50200@sendu.me.uk> <1164649150.2575.57.camel@localhost.localdomain> <1164732143.2584.33.camel@localhost.localdomain> <456C6A24.5090105@sendu.me.uk> Message-ID: <536f21b00611281218v3e6fd7a1ia2c9e81ef7ad678c@mail.gmail.com> Sendu, I've tried exports of both branches and they both work. Scott On 11/28/06, Sendu Bala wrote: > > Scott Cain wrote: > > Hi Sendu, > > > > It looks like what you've done did the trick--bioperl installed on both > > ActivePerl 817 and 819 using Module::Build (though I must admit I didn't > > look at the tests--I just wanted `perl Build.PL` to work). Nice work! > > ... > > I didn't do anything yet :O > > Can you check on an export of bioperl-release-1-5-2-rc5 and compare to > an export of branch-1-5-2 and let me know if you see the bug in the > former and no bug in the latter? > > From lincoln.stein at gmail.com Wed Nov 29 02:15:38 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 28 Nov 2006 21:15:38 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph Message-ID: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> Hi, I had to back out a change I made to Bio/Graphics/Glyph recently (on both live and 1.52 branches). It caused a bizarre problem in which some features had twice the expected height. Lincoln On 11/23/06, Sendu Bala wrote: > > Sendu Bala wrote: > > Scott Cain wrote: > >> Hello, > >> > >> I just wanted to mention that I made a few minor changes to Build.PL so > >> that I could get `perl Build.PL` to complete successfully. I am using > >> ActivePerl 819 and don't have MySQL installed (so DBD::mysql isn't > >> present either. The main thing I did was to have the BioDBGFF test > >> subroutine quit without asking any questions if Build.PL detected that > >> it was running on Windows. > > > > Is it completely impossible for it to pass under Windows? I find that > > quite a shame! > > > > I'm surprised it was necessary to make your changes, because it already > > had to return true from: > [snip] > > Sorry, that all made no sense because I didn't pay attention to what > changes you actually made. > > Anyway, I've re-done the BioDBGFF auto-feature testing. Can you say if > being on mswin still causes a problem, or can the excludes_os > restriction on line 78 of Build.PL be lifted now? > > > Cheers, > Sendu. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From hlapp at gmx.net Wed Nov 29 04:54:53 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 28 Nov 2006 23:54:53 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <456CA667.6010609@molbio.mgh.harvard.edu> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> Message-ID: These are the protein translations stored in the feature table as tags of features, right? You can change the type of the column (although there may be some issues when you update the column because the NVL() clause won't work if I recall that correctly), but doing so will deprive you of any 'normal' searches against that column. (You can still use functions from the DBMS_LOB package, but they will be much slower and are completely non-standard.) It is up to you whether that is too big of a price to pay for having some redundant protein translations (translating the feature's DNA sequence should give you the same) in the database. I always trimmed those feature tags off (using a custom SeqProcessor). An alternative is to convert these feature tags into actual bioentries (i.e., Bio::Seq objects; again, a custom SeqProcessor will allow you to do that). -hilmar On Nov 28, 2006, at 4:13 PM, gang wu wrote: > Hi everyone, > > I'm using load_seqdatabase.pl to upload some Genbank genome > sequences to > my Oracle BioSQL database. I saw some errors(See attached warning > message) related to seqfeature_qualifier_value > (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data > type of maximum 4000 bytes. Did anybody mention this issue before? > Should I just modify the column to a type being able store more data > such as LONG or CLOB? > > Thanks. > > Gang > > > Log information: > ============================================ > > load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser > biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank > /genomeseq/arabidopsis//NC_003070.gbk > > > Loading /genomeseq/arabidopsis//NC_003070.gbk ... > > > -------------------- WARNING --------------------- > MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement > execution: ORA-01461: can bind a LONG value only for insert into a > LONG > column (DBD ERROR: error possibly near <*> indicator at char 12 in > 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, > rank) VALUES (:p1, :p2, :p3, :p4)') > name: INSERT ASSOC [2] > Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue > values: FK[Bio::SeqFeature::Generic]:14898, > FK[Bio::Annotation::SimpleValue]:800, > value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFV > GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADR > GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEI > LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFP > WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERA > SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRY > IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEA > EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDI > NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDW > RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFAL > DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDN > QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRY > MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYT > FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGL > VQATYQASA! > > PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKV > HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAY > TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFV > SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSE > KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLG > NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEV > TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQL > EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTL > SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVT > ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRL > MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAV > PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEY > TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVD > ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLR > VKLDFNFM! > > YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQS > QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSN > TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCL > SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWD > ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSE > IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASV > TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGL > HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSS > KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDF > QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGL > HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVA > RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCL > LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRN > GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVE > NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPL > WLSVGADAS! > > VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVY > LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITND > SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQES > AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTS > DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSV > FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESW > QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIV > RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMS > VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRV > YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAM > SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDI > LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAK > SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLR > PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMG > QRKFIPAK! > > DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQ > AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", > rank:"1" > -------------------------------------------------- > > > ============================================= > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Wed Nov 29 09:32:24 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 09:32:24 +0000 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> Message-ID: <456D53A8.80800@sendu.me.uk> Lincoln Stein wrote: > Hi, > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > both live and 1.52 branches). It caused a bizarre problem in which some > features had twice the expected height. Exactly which recent commits are the necessary reversion? Just 'fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height'? I'm confused by 'removed debugging warning' since you did different things during that named commit in HEAD (you removed a warn()) vs branch-1-5-2 (you added a bunch of non-warn related stuff). From lincoln.stein at gmail.com Wed Nov 29 14:41:25 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 29 Nov 2006 09:41:25 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <456D53A8.80800@sendu.me.uk> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> Message-ID: <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> There were two branch-1-5-2 commits last night. Both are needed to back out the changes. Lincoln On 11/29/06, Sendu Bala wrote: > > Lincoln Stein wrote: > > Hi, > > > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > > both live and 1.52 branches). It caused a bizarre problem in which some > > features had twice the expected height. > > Exactly which recent commits are the necessary reversion? Just 'fixed > minor bug which caused some features drawn with the "box" glyph to have > an unexpected height'? > > I'm confused by 'removed debugging warning' since you did different > things during that named commit in HEAD (you removed a warn()) vs > branch-1-5-2 (you added a bunch of non-warn related stuff). > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From lincoln.stein at gmail.com Wed Nov 29 14:38:18 2006 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 29 Nov 2006 09:38:18 -0500 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <456D53A8.80800@sendu.me.uk> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> Message-ID: <6dce9a0b0611290638h46dc7d95o7ce5f7977fddfc81@mail.gmail.com> Uh oh. Perhaps I made a mistake during the commits. I will check what's up. Lincoln On 11/29/06, Sendu Bala wrote: > > Lincoln Stein wrote: > > Hi, > > > > I had to back out a change I made to Bio/Graphics/Glyph recently (on > > both live and 1.52 branches). It caused a bizarre problem in which some > > features had twice the expected height. > > Exactly which recent commits are the necessary reversion? Just 'fixed > minor bug which caused some features drawn with the "box" glyph to have > an unexpected height'? > > I'm confused by 'removed debugging warning' since you did different > things during that named commit in HEAD (you removed a warn()) vs > branch-1-5-2 (you added a bunch of non-warn related stuff). > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bix at sendu.me.uk Wed Nov 29 15:53:04 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 15:53:04 +0000 Subject: [Bioperl-l] Fix to Bio::Graphics::Glyph In-Reply-To: <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> References: <6dce9a0b0611281815q600b5549pc93815a92c43eb7b@mail.gmail.com> <456D53A8.80800@sendu.me.uk> <6dce9a0b0611290641n654c8583n3a10726119471417@mail.gmail.com> Message-ID: <456DACE0.5060401@sendu.me.uk> Lincoln Stein wrote: > There were two branch-1-5-2 commits last night. Both are needed to back > out the changes. I'm not seeing the changes as a true revert. cvs diff -r 1.113.4.6 Bio/Graphics/Glyph.pm Index: Bio/Graphics/Glyph.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph.pm,v retrieving revision 1.113.4.6 retrieving revision 1.113.4.9 diff -r1.113.4.6 -r1.113.4.9 3c3 < # $Id: Glyph.pm,v 1.113.4.6 2006/11/19 17:18:45 lstein Exp $ --- > # $Id: Glyph.pm,v 1.113.4.9 2006/11/29 02:38:33 lstein Exp $ 126a127,128 > my $feature = $self->feature; > return 1 if $feature->can('compound') && $feature->compound; 1636a1639 > cvs diff -r 1.40.2.2 Bio/Graphics/Glyph/generic.pm Index: Bio/Graphics/Glyph/generic.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/generic.pm,v retrieving revision 1.40.2.2 retrieving revision 1.40.2.4 diff -r1.40.2.2 -r1.40.2.4 113,115c113,115 < my $md = $self->SUPER::maxdepth; < return $md if defined $md; < return 0; --- > my $maxdepth = $self->option('maxdepth'); > return $maxdepth if defined $maxdepth; > return 1; cvs diff -r 1.6.8.1 Bio/Graphics/Glyph/box.pm Index: Bio/Graphics/Glyph/box.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/box.pm,v retrieving revision 1.6.8.1 retrieving revision 1.6.8.2 diff -r1.6.8.1 -r1.6.8.2 14a15,21 > sub maxdepth { > my $self = shift; > my $maxdepth = $self->option('maxdepth'); > return $maxdepth if defined $maxdepth; > return 0; > } > Is this intended? Are you sure this is safe to go into final release for 1.5.2? From cjfields at uiuc.edu Wed Nov 29 15:55:33 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 09:55:33 -0600 Subject: [Bioperl-l] URI, Graph, and Module::Build Message-ID: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> Sendu, For the Build.PL dependencies, do we want to use the absolute module requirements (URI::Escape, Graph::Directed, XML::SAX::Base) or the distributions they are in (URI, Graph, XML::SAX)? Or does it really make a difference? Also, you had mentioned that Bundle::Bioperl is no longer needed since you can have them installed via Build. Does that also hold true for Windows (since CPAN is, at best, very testy installing on Windows)? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Wed Nov 29 16:04:07 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 29 Nov 2006 16:04:07 +0000 Subject: [Bioperl-l] URI, Graph, and Module::Build In-Reply-To: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> References: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> Message-ID: <456DAF77.6050609@sendu.me.uk> Chris Fields wrote: > Sendu, > > For the Build.PL dependencies, do we want to use the absolute module > requirements (URI::Escape, Graph::Directed, XML::SAX::Base) or the > distributions they are in (URI, Graph, XML::SAX)? Or does it really > make a difference? It makes a difference right now only where the absolute module doesn't have a version (because in Build.PL we ask for at least version 0, which fails if version in the modules is actually undef). I'll fix that in the future, so it is best to use the absolute module for clarity. > Also, you had mentioned that Bundle::Bioperl is no longer needed since > you can have them installed via Build. Does that also hold true for > Windows (since CPAN is, at best, very testy installing on Windows)? In what way is it testy? I set up a new WinXP machine today and installed ActiveState. My Build.PL script happily offered to install Module::Build for me with CPAN and it almost worked up until CPAN needed nmake. After installing nmake I upgraded CPAN with no problems and then everything worked after that (I only tried to install one optional dep with Build.PL via CPAN, and that worked fine). So yes, I'd say it holds true for Windows. Though I haven't sorted out the ppd stuff yet. From cjfields at uiuc.edu Wed Nov 29 17:06:37 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 11:06:37 -0600 Subject: [Bioperl-l] URI, Graph, and Module::Build In-Reply-To: <456DAF77.6050609@sendu.me.uk> References: <8A1AF68B-D6ED-4F40-9657-E6195690E429@uiuc.edu> <456DAF77.6050609@sendu.me.uk> Message-ID: On Nov 29, 2006, at 10:04 AM, Sendu Bala wrote: > Chris Fields wrote: >> Sendu, >> For the Build.PL dependencies, do we want to use the absolute >> module requirements (URI::Escape, Graph::Directed, XML::SAX::Base) >> or the distributions they are in (URI, Graph, XML::SAX)? Or does >> it really make a difference? > > It makes a difference right now only where the absolute module > doesn't have a version (because in Build.PL we ask for at least > version 0, which fails if version in the modules is actually > undef). I'll fix that in the future, so it is best to use the > absolute module for clarity. That sounds fine to me. If I remember correctly, at least one example (XML::SAX::Base) used to be a separate distribution, but it should install XML::SAX now. >> Also, you had mentioned that Bundle::Bioperl is no longer needed >> since you can have them installed via Build. Does that also hold >> true for Windows (since CPAN is, at best, very testy installing on >> Windows)? > > In what way is it testy? I set up a new WinXP machine today and > installed ActiveState. My Build.PL script happily offered to > install Module::Build for me with CPAN and it almost worked up > until CPAN needed nmake. After installing nmake I upgraded CPAN > with no problems and then everything worked after that (I only > tried to install one optional dep with Build.PL via CPAN, and that > worked fine). It all depends on the modules installed. For instance, a few that include C code or required external compiled libraries had generally been much harder to install, or they were historically; I admittedly haven't tried them recently. GD, (I think) DBD::mysql, and anything using precompiled dynamic libraries were the most problematic, but PPMs and Win-compatible dynamic libraries were always available somewhere which made installing them via nmake a non-issue. One thing I noticed (and mentioned previously) is that using 'Build' also generated HTML docs on WinXP (I didn't see this on Mac OS X); I don't know if this still occurs, so I'll give it a run today. This may be a problem since the pod2html-generated formatting differs significantly from the PPM-generated docs. I'm not even sure they install in the same location as the PPM-generated pages or whether this will cause any issues. Do you also see this on your local WinXP? > So yes, I'd say it holds true for Windows. Though I haven't sorted > out the ppd stuff yet. I think recommending PPM for BioPerl installation on Windows is still the best option for now, at least until we are sure about CPAN installation and the HTML issue above. Frankly, there will just be too much demand for it just for the HTML docs alone (they are quite nice). If the prereqs are listed correctly it should install those first, but who knows with PPM4! It will also generate HTML on the fly and install it in the doc tree as expected, which I have tested. As for a new PPD/PPM, I haven't tried generating it yet via Module::Build (I thought maybe Nathan was doing this). I may give it a go today on WinXP with a fresh ActiveState install (most of my important work is now on Mac OS X, so that shouldn't interfere). My guess is the PPD will be in old PPM3 XML format. Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From chhalling at verizon.net Thu Nov 30 01:25:45 2006 From: chhalling at verizon.net (Conrad Halling) Date: Wed, 29 Nov 2006 20:25:45 -0500 Subject: [Bioperl-l] A new Bundle::BioPerl In-Reply-To: <456C1516.5050900@sendu.me.uk> References: <456BB232.4020808@verizon.net> <456C1516.5050900@sendu.me.uk> Message-ID: <456E3319.5090703@verizon.net> Sendu Bala wrote: > Conrad Halling wrote: > >> After experimenting with the existing Bundle::BioPerl version 2.1.8 >> under Perl 5.8.8 and Mac OS X 10.4.8, I found that it could not install >> all of the BioPerl dependencies unless run multiple times. >> >> I edited the the order that the dependencies were listed so I could get >> all the dependencies to install on the first try. >> > > Thank you so much for all your hard work. Its extremely valuable. That > said, I'm no longer recommending the usage of Bundle::BioPerl. Instead > what I'll do is apply your discovered order to the new Build.PL > installation system. > > You're welcome of course to contact Chris Dagdigian to make sure he > knows about your new version of Bundle::BioPerl. He can then upload it > to CPAN if he's happy with it, and people who choose to still use the > Makefile.PL installation process will surely appreciate the new version > of Bundle::BioPerl. > Good. Having Build.PL do all the work is the best solution. -- Conrad -- Conrad Halling chhalling at verizon.net From hlapp at gmx.net Thu Nov 30 04:03:08 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 29 Nov 2006 23:03:08 -0500 Subject: [Bioperl-l] release timetable Message-ID: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Sendu - what is the timetable in your mind for getting the release out? The NESCent phyloinformatics hackathon is impending and if at all possible I'd really like to see the release be out of the way when it starts so that all new code can simply go the main trunk and has no chance of interfering with the release. Do you think this won't be a problem, or should we start thinking about how to expedite the release in a sensible manner? If anyone else on the list has any concerns about that code going right into the main trunk, please let me know. We (the hackathon attendees) may have to relax the must-pass-all- tests rule, so it may take until a couple days after the end of the event until some sharp edges are smoothened out. I would rather not make any guarantees as to what we will not break, and instead focus on getting the work committed. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Thu Nov 30 04:59:50 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 29 Nov 2006 22:59:50 -0600 Subject: [Bioperl-l] release timetable In-Reply-To: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Message-ID: <8BA20ADA-5114-4DAA-A95F-CBD22C80CC26@uiuc.edu> On Nov 29, 2006, at 10:03 PM, Hilmar Lapp wrote: > Sendu - > > what is the timetable in your mind for getting the release out? The > NESCent phyloinformatics hackathon is impending and if at all > possible I'd really like to see the release be out of the way when it > starts so that all new code can simply go the main trunk and has no > chance of interfering with the release. > > Do you think this won't be a problem, or should we start thinking > about how to expedite the release in a sensible manner? > > If anyone else on the list has any concerns about that code going > right into the main trunk, please let me know. > > We (the hackathon attendees) may have to relax the must-pass-all- > tests rule, so it may take until a couple days after the end of the > event until some sharp edges are smoothened out. I would rather not > make any guarantees as to what we will not break, and instead focus > on getting the work committed. > > -hilmar I think most everyone would agree that the final rel. 1.5.2 should be out soon. I vote for a release before the hackathon, essentially for the same reasons you already outlined. This will get the 1.5.2 code out in the wild for testing, which will (hopefully) iron out any kinks with Module::Build and other residual bugs. If needed we could always have another developer release in the spring to clean up anything from the hackathon, fix bugs from this release, etc. Like you mentioned before, this is (and should be considered by all) a developer release, so not all tests need to pass. Saying that, I applaud Sendu and Nathan (and everyone else) for their hard work. I think this is the first time I can remember where all tests pass for all systems (though I only used since rel 1.0). Even if it's for a finite period of time. -chris Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From bix at sendu.me.uk Thu Nov 30 07:50:06 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 07:50:06 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> Message-ID: <456E8D2E.60908@sendu.me.uk> Hilmar Lapp wrote: > Sendu - > > what is the timetable in your mind for getting the release out? The > NESCent phyloinformatics hackathon is impending and if at all possible > I'd really like to see the release be out of the way when it starts so > that all new code can simply go the main trunk and has no chance of > interfering with the release. I'm going to do one final merge from HEAD to branch-1-5-2 and then set the final release tags later today, so a) anything done at the hackathon won't make any difference, and b) the release should go out soon. The release will go ahead when I've sorted out the Windows PPM and the Change Log (neither of which require code changes on the branch). On this schedule I won't be able to implement Conrad's pre-req installation order in Build.PL since that would require a substantial change to ModuleBuildBioperl.pm and another RC. I'll do that after release so that 1.5.3 benefits. From n.haigh at sheffield.ac.uk Thu Nov 30 08:35:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 08:35:08 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E8D2E.60908@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> Message-ID: <456E97BC.9000800@sheffield.ac.uk> Sendu Bala wrote: > Hilmar Lapp wrote: > >> Sendu - >> >> what is the timetable in your mind for getting the release out? The >> NESCent phyloinformatics hackathon is impending and if at all possible >> I'd really like to see the release be out of the way when it starts so >> that all new code can simply go the main trunk and has no chance of >> interfering with the release. >> > > I'm going to do one final merge from HEAD to branch-1-5-2 and then set > the final release tags later today, so a) anything done at the hackathon > won't make any difference, and b) the release should go out soon. > > The release will go ahead when I've sorted out the Windows PPM and the > Change Log (neither of which require code changes on the branch). > > On this schedule I won't be able to implement Conrad's pre-req > installation order in Build.PL since that would require a substantial > change to ModuleBuildBioperl.pm and another RC. I'll do that after > release so that 1.5.3 benefits. > > _______________________________________________ > I've not had the time to test out the new CPAN installation until now. I've just tried it on a clan install of ActivePerl 5.8.8.819 and it didn't install: Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/RemoteBlast.t 9 2304 13 0 0.00% ?? t/rnamotif.t 2 512 72 144 200.00% 1-72 2 tests and 197 subtests skipped. How can I get the test output from CPAN to go to a log file so I can look at the errors more closely? Nath p.s. I think nmake will need to be installed for windows but I'll doublecheck. --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-0, 29/11/2006 Tested on: 30/11/2006 08:35:09 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From bix at sendu.me.uk Thu Nov 30 08:46:44 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 08:46:44 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E97BC.9000800@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> Message-ID: <456E9A74.9020404@sendu.me.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: >> Hilmar Lapp wrote: >> >>> Sendu - >>> >>> what is the timetable in your mind for getting the release out? The >>> NESCent phyloinformatics hackathon is impending and if at all >>> possible I'd really like to see the release be out of the way when it >>> starts so that all new code can simply go the main trunk and has no >>> chance of interfering with the release. >>> >> >> I'm going to do one final merge from HEAD to branch-1-5-2 and then set >> the final release tags later today, so a) anything done at the >> hackathon won't make any difference, and b) the release should go out >> soon. >> >> The release will go ahead when I've sorted out the Windows PPM and the >> Change Log (neither of which require code changes on the branch). >> >> On this schedule I won't be able to implement Conrad's pre-req >> installation order in Build.PL since that would require a substantial >> change to ModuleBuildBioperl.pm and another RC. I'll do that after >> release so that 1.5.3 benefits. >> >> _______________________________________________ >> > > I've not had the time to test out the new CPAN installation until now. > I've just tried it 'it' being RC5? On Windows? > on a clan install of ActivePerl 5.8.8.819 and it > didn't install: > Failed Test Stat Wstat Total Fail Failed List of Failed > ------------------------------------------------------------------------------- > > t/RemoteBlast.t 9 2304 13 0 0.00% ?? > t/rnamotif.t 2 512 72 144 200.00% 1-72 > 2 tests and 197 subtests skipped. > > How can I get the test output from CPAN to go to a log file so I can > look at the errors more closely? I don't know about log files, but you can configure the cmd window to have a large history and then just copy/paste the results. You can also go into the directory that CPAN extracted the archive to and run the tests there manually. Please send me the results of those tests. From n.haigh at sheffield.ac.uk Thu Nov 30 09:28:36 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 09:28:36 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456EA444.1010705@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sendu Bala wrote: >>> Hilmar Lapp wrote: >>> >>>> Sendu - >>>> >>>> what is the timetable in your mind for getting the release out? The >>>> NESCent phyloinformatics hackathon is impending and if at all >>>> possible I'd really like to see the release be out of the way when >>>> it starts so that all new code can simply go the main trunk and has >>>> no chance of interfering with the release. >>>> >>> >>> I'm going to do one final merge from HEAD to branch-1-5-2 and then >>> set the final release tags later today, so a) anything done at the >>> hackathon won't make any difference, and b) the release should go >>> out soon. >>> >>> The release will go ahead when I've sorted out the Windows PPM and >>> the Change Log (neither of which require code changes on the branch). >>> >>> On this schedule I won't be able to implement Conrad's pre-req >>> installation order in Build.PL since that would require a >>> substantial change to ModuleBuildBioperl.pm and another RC. I'll do >>> that after release so that 1.5.3 benefits. >>> >>> _______________________________________________ >>> >> >> I've not had the time to test out the new CPAN installation until >> now. I've just tried it > > 'it' being RC5? On Windows? > > >> on a clan install of ActivePerl 5.8.8.819 and it didn't install: >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ------------------------------------------------------------------------------- >> >> t/RemoteBlast.t 9 2304 13 0 0.00% ?? >> t/rnamotif.t 2 512 72 144 200.00% 1-72 >> 2 tests and 197 subtests skipped. >> >> How can I get the test output from CPAN to go to a log file so I can >> look at the errors more closely? > > I don't know about log files, but you can configure the cmd window to > have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the archive to > and run the tests there manually. > > Please send me the results of those tests. > > While I figure this out, I've come across the following: The version of CPAN that ships with ActivePerl 5.8.8.819 is 1.7602 and the first version of CPAN to support setting the preference of Module::Build over MakeMaker with "o conf prefer_installer MB" is 1.81 according to their change log. As a result, the default installation of Bioperl on ActivePerl 5.8.8.819 will always use Makefile.PL if it's available. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-0, 29/11/2006 Tested on: 30/11/2006 09:28:37 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From n.haigh at sheffield.ac.uk Thu Nov 30 12:50:57 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 12:50:57 +0000 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456ED3B1.9060208@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> Sendu Bala wrote: >>> Hilmar Lapp wrote: >>> >>>> Sendu - >>>> >>>> what is the timetable in your mind for getting the release out? The >>>> NESCent phyloinformatics hackathon is impending and if at all >>>> possible I'd really like to see the release be out of the way when >>>> it starts so that all new code can simply go the main trunk and has >>>> no chance of interfering with the release. >>>> >>> >>> I'm going to do one final merge from HEAD to branch-1-5-2 and then >>> set the final release tags later today, so a) anything done at the >>> hackathon won't make any difference, and b) the release should go >>> out soon. >>> >>> The release will go ahead when I've sorted out the Windows PPM and >>> the Change Log (neither of which require code changes on the branch). >>> >>> On this schedule I won't be able to implement Conrad's pre-req >>> installation order in Build.PL since that would require a >>> substantial change to ModuleBuildBioperl.pm and another RC. I'll do >>> that after release so that 1.5.3 benefits. >>> >>> _______________________________________________ >>> >> >> I've not had the time to test out the new CPAN installation until >> now. I've just tried it > > 'it' being RC5? On Windows? > > >> on a clan install of ActivePerl 5.8.8.819 and it didn't install: >> Failed Test Stat Wstat Total Fail Failed List of Failed >> ------------------------------------------------------------------------------- >> >> t/RemoteBlast.t 9 2304 13 0 0.00% ?? >> t/rnamotif.t 2 512 72 144 200.00% 1-72 >> 2 tests and 197 subtests skipped. >> >> How can I get the test output from CPAN to go to a log file so I can >> look at the errors more closely? > > I don't know about log files, but you can configure the cmd window to > have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the archive to > and run the tests there manually. > > Please send me the results of those tests. > > > Hi Sendu, Installation on a clean install of ActivePerl 5.8.8.819 n WindowsXP: 1) nmake is required for CPAN installations 2) I updated CPAN to the latest version 3) Restarted CPAN and did "o conf prefer_installer MB" and "o conf commit" 4) Restarted CPAN and tried the install of bioperl 1.5.2 RC5. I still get the message saying it's using Makefile.PL and not Build.PL - not sure why! I'm going to see if updating Module::Build helps. For the time being I installed anyway..... 5) towards the end of dependency checking I get this: -- snip -- Checking if your kit is complete... Looks good Warning: prerequisite DB_File 0 not found. Writing Makefile for Bio ---- Unsatisfied dependencies detected during [S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz] ----- DB_File Shall I follow them and prepend them to the queue of modules we are processing right now? [yes] -- snip -- 6) When running the install, DB_File fails to install and that appears to be the root of the rnamotif test failing: -- snip -- t/rnamotif...................Can't locate DB_File.pm in @INC (@INC contains: t/lib C:\Perl\cpan \build\bioperl-1.5.2_005-RC\blib\lib C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\arch C:/Perl/ site/lib C:/Perl/lib .) at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SeqFeature/Coll ection.pm line 133. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SeqFe ature/Collection.pm line 133. Compilation failed in require at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Tools/RNA Motif.pm line 145. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Tools /RNAMotif.pm line 145. Compilation failed in require at t/rnamotif.t line 27. BEGIN failed--compilation aborted at t/rnamotif.t line 27. t/rnamotif...................dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-72 Failed 72/72 tests, 0.00% okay -- snip -- 7) The RemoteBlast seems to fail due to XML/SAX not being installed: --s nip t/RemoteBlast................ok 10/13Bio::SearchIO: blastxml cannot be found Exception ------------- EXCEPTION ------------- MSG: Failed to load module Bio::SearchIO::blastxml. Can't locate XML/SAX.pm in @INC (@INC conta ins: t C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib C:\Perl\cpan\build\bioperl-1.5.2_005-RC \blib\arch C:/Perl/site/lib C:/Perl/lib .) at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/ Bio\SearchIO\blastxml.pm line 112. BEGIN failed--compilation aborted at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio\Searc hIO\blastxml.pm line 112. Compilation failed in require at C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Root/Root .pm line 425. STACK Bio::Root::Root::_load_module C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Root/R oot.pm:427 STACK (eval) C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm:397 STACK Bio::SearchIO::_load_format_module C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/S earchIO.pm:396 STACK Bio::SearchIO::new C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm:176 STACK Bio::Tools::Run::RemoteBlast::retrieve_blast C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib \lib/Bio/Tools/Run/RemoteBlast.pm:603 STACK toplevel t/RemoteBlast.t:185 -------------------------------------- For more information about the SearchIO system please see the SearchIO docs. This includes ways of checking for formats at compile time, not run time Use of uninitialized value in numeric lt (<) at t/RemoteBlast.t line 187. Can't locate object method "new" via package "Bio::SearchIO::blastxml" at C:\Perl\cpan\build\bi operl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm line 177. t/RemoteBlast................dubious Test returned status 9 (wstat 2304, 0x900) after all the subtests completed successfully -- snip -- HTH, Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-1, 30/11/2006 Tested on: 30/11/2006 12:50:59 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From n.haigh at sheffield.ac.uk Thu Nov 30 12:58:08 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 12:58:08 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456E9A74.9020404@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> Message-ID: <456ED560.1020001@sheffield.ac.uk> More updates: After the failed install I updating Module::Build, and re-ran the install, I get: -- snip -- Creating new 'Build' script for 'bioperl' version '1.005002005' Warning: while trying to determine prerequisites for S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi th the help of Module::Build the following error occurred: 'Failed to re-load 'ModuleBuildBiope rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: _build\lib C:\Perl\site\lib C:\ Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. ' Falling back to META.yml for prerequisites 'YAML' not installed, cannot parse 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' -- snip -- Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-1, 30/11/2006 Tested on: 30/11/2006 12:58:09 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From djupiter at tamu.edu Thu Nov 30 06:22:57 2006 From: djupiter at tamu.edu (Daniel Jupiter) Date: Thu, 30 Nov 2006 00:22:57 -0600 Subject: [Bioperl-l] Large databases Message-ID: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> Hi all. I'm new to this list, so if my question is misdirected, or inappropriate, please let me know. The question concerns databases/hashes. I would like to have a rather large hash file. Say 10,000 keys, each with a data field containing roughly 50,000 integers. For whatever reason, the dbm implementation on Mac OSX does not seem to like things of this size. Several strange things happen. First, file size seem to increase exponentially, as I increase the data field size. Additionally, in certain situations, I am returned a rather strange error concerning an uninitialized variable, which has in fact been initialized. In great confusion, I'm just curious as to whether there is a work around for dealing with such large amounts of data, or somewhere with good documentation on using hashes. Thanks. Daniel C. Jupiter, Ph.D. Postdoctoral Research Associate Department of Systems Biology and Translational Medicine College of Medicine Texas A&M University Health Science Center 702 SW H.K. Dodgen Loop Temple, TX 76504 979.997.2106 | Fax 254.742.7145 djupitern at tamu.edu | www.tamhsc.edu ? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: -1.jpeg Type: image/jpeg Size: 19402 bytes Desc: not available URL: From cjfields at uiuc.edu Thu Nov 30 16:13:58 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 10:13:58 -0600 Subject: [Bioperl-l] release timetable In-Reply-To: <456E9A74.9020404@sendu.me.uk> Message-ID: <01b801c7149a$8a9777d0$15327e82@pyrimidine> > Nathan S. Haigh wrote: ... > > How can I get the test output from CPAN to go to a log file > so I can > > look at the errors more closely? > > I don't know about log files, but you can configure the cmd > window to have a large history and then just copy/paste the results. > > You can also go into the directory that CPAN extracted the > archive to and run the tests there manually. > > Please send me the results of those tests. Like Sendu, I usually copy from the buffer in the terminal window when running from CPAN (you can set the buffer size for Windows cmd.exe). When running tests manually, I may redirect all output to a temp file, which is a bit easier to scan through since it doesn't wrap text like a cut&paste from the terminal: # Mac OS X ./Build tests &> results.txt # WinXP Build tests > results.txt 2>&1 With Windows I find it sometimes easier to just redirect STDOUT, to avoid all of the 'Subroutine x redefined' warnings. If the CPAN tests go to STDERR you could try redirectly only that stream to a temp file. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Thu Nov 30 16:29:51 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 11:29:51 -0500 Subject: [Bioperl-l] Large databases In-Reply-To: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> References: <509C3851-98A1-4118-9566-CA3FBECCDD02@tamu.edu> Message-ID: You are aware that you are getting close (or possibly beyond, depending on the exact numbers and if there is any overhead for each integer) the 2GB signed int boundary? Did you make sure that your dbm version is 64-bit enabled and supports 64 bit for filesize? -hilmar On Nov 30, 2006, at 1:22 AM, Daniel Jupiter wrote: > Hi all. > > I'm new to this list, so if my question is misdirected, or > inappropriate, please let me know. > > The question concerns databases/hashes. I would like to have a > rather large hash file. Say 10,000 keys, each with a data field > containing roughly 50,000 integers. For whatever reason, the dbm > implementation on Mac OSX does not seem to like things of this size. > > Several strange things happen. First, file size seem to increase > exponentially, as I increase the data field size. Additionally, in > certain situations, I am returned a rather strange error concerning > an uninitialized variable, which has in fact been initialized. > > In great confusion, I'm just curious as to whether there is a work > around for dealing with such large amounts of data, or somewhere > with good documentation on using hashes. > > Thanks. > > > > Daniel C. Jupiter, Ph.D. > Postdoctoral Research Associate > Department of Systems Biology and Translational Medicine > College of Medicine > Texas A&M University Health Science Center > 702 SW H.K. Dodgen Loop > Temple, TX 76504 > > 979.997.2106 | Fax 254.742.7145 > djupitern at tamu.edu | www.tamhsc.edu > > > <-1.jpeg> > > > > > > > <-1.jpeg> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From st537 at york.ac.uk Thu Nov 30 16:52:27 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Thu, 30 Nov 2006 16:52:27 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456C2E01.5070805@sendu.me.uk> References: <456C172F.4060008@york.ac.uk> <456C2E01.5070805@sendu.me.uk> Message-ID: <456F0C4B.2000502@york.ac.uk> Hi, Thanks for helping me with the BLAST code, when I made the corections in ran fine, I'm assuming the returned object $blast_result is a kind of searchio object, although I'm not sure. I tried the code on the bioperl tutorial page for processing a searchio object returned from blast.... http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FASTA_reports_with_Search_and_SearchIO this seems to be the next stage after blasting in the bioperl tutorial but I'm sure how to process it correctly to get hit and alignment information regards, Samantha Thompson Sendu Bala wrote: >Samantha Thompson wrote: > > >>Hi, >>I am trying to learn bioperl and I'm attempting a few basic thing! I >>seem to be ok with reading in and outputting sequences and files now I >>am trying to do a simple BLAST search using a sequence (a sequence >>object in fact). The code I am attempting to run is at the bottom of the >>message... >>I am probably making a dumb mistake and don't understand the >>capabilities of the objects well enough, but the info for the >>remoteblast->submit_blast function says that it can take sequences as an >>argument, I've also tried sending the fasta file name containing my >>sequence as an argument to submit_blast, with the same result.... I >>have also tried sending $seqio_obj->next_seq........... i.e the >>following error message displayed on my terminal: >> >>Can't call method "submit_blast" on an undefined value at bioptest2.pl >>line 22, line 1. >> >> > >Always start your perl scripts with 'use strict;'. This will help you >find and fix the main problem with your script, that you made a >RemoteBlast object and stored it as $remote_blast, but then tried to use >submit_blast() on $remoteBlast which doesn't exist. > >I've rewritten your code below: > >use strict; > > >>use Bio::Seq; >>use Bio::SeqIO; >> >>use Bio::Tools::Run::RemoteBlast; >>use Bio::SearchIO; >> >>#seq bit >> >> >> ># $seq_obj = Bio::Seq->new(-format => 'fasta'); ># above line doesn't do anything, $seq_obj gets overwritten below > > >my $seqio_obj = Bio::SeqIO->new(-file => >"/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); > > >my $seq_obj = $seqio_obj->next_seq; > > >> >>#blast bit >> >> >> >my $remote_blast = Bio::Tools::Run::RemoteBlast->new(-prog => 'blastp', >-db => 'nr', -expect => '1e-15' ); > ># submit_blast takes the sequence object, not the sequence string >my $blastreturn_obj = $remote_blast->submit_blast($seq_obj); > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at uiuc.edu Thu Nov 30 17:12:32 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 11:12:32 -0600 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <456F0C4B.2000502@york.ac.uk> Message-ID: <01ba01c714a2$b9659c10$15327e82@pyrimidine> > Hi, > Thanks for helping me with the BLAST code, when I made the > corections in ran fine, I'm assuming the returned object > $blast_result is a kind of searchio object, although I'm not > sure. I tried the code on the bioperl tutorial page for > processing a searchio object returned from blast.... > http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FA > STA_reports_with_Search_and_SearchIO > this seems to be the next stage after blasting in the bioperl > tutorial but I'm sure how to process it correctly to get hit > and alignment information regards, > > Samantha Thompson It is a SearchIO object. FYI, you also have the option of saving the raw BLAST output to a file if needed (it should be described in the RemoteBlast POD). There is also a great HOWTO which goes into more detail about hits/HSPs and how to get alignments: http://www.bioperl.org/wiki/HOWTO:SearchIO chris From bix at sendu.me.uk Thu Nov 30 17:44:38 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 17:44:38 +0000 Subject: [Bioperl-l] Please help with the change log Message-ID: <456F1886.2090708@sendu.me.uk> I'm hoping someone out there is willing to help add summaries for each release to the Change Log: http://bioperl.org/wiki/Change_log Basically, just add a few bullet points about what was new or especially interesting in each release. Thank you, Sendu. From cjfields at uiuc.edu Thu Nov 30 17:50:03 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 11:50:03 -0600 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <438954.89098.qm@web50815.mail.yahoo.com> Message-ID: <000001c714a7$f6ee1300$15327e82@pyrimidine> Katie, Make sure you keep the posts on the mail list, just in case I can't respond but someone else can. > Hi all. > > I just ran the following test script: > > use strict; > use Bio::SearchIO; > my $in = new Bio::SearchIO(-format => 'blast', > -file => 'report.bls'); > while( my $result = $in->next_result ) { > while( my $hit = $result->next_hit ) { > while( my $hsp = $hit->next_hsp ) { > if( $hsp->length('total') > 100 ) { > if ( $hsp->percent_identity >= 75 ) { > print "Hit= ", $hit->name, > ",Length=", $hsp->length('total'), > ",Percent_id=", $hsp->percent_identity, "\n"; > } > } > } > } > } > > and saw the following output: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Could not open report.bls: No such file or directory > STACK: Error::throw > STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:350 > STACK: Bio::Root::IO::_initialize_io > C:/Perl/site/lib/Bio/Root/IO.pm:310 > STACK: Bio::Root::IO::new C:/Perl/site/lib/Bio/Root/IO.pm:223 > STACK: Bio::SearchIO::new C:/Perl/site/lib/Bio/SearchIO.pm:145 > STACK: Bio::SearchIO::new C:/Perl/site/lib/Bio/SearchIO.pm:177 > STACK: test.pl:3 > ----------------------------------------------------------- > > I'm using BioPerl 1.5.2 RC2 > Perl 5.8.8 (Build 819). > WinXP (SP2) > > Thanks, > > ~Katie Is there a BLAST report file named 'report.bls' in the same directory as your script? That's what the error indicates. Chris From n.haigh at sheffield.ac.uk Thu Nov 30 18:24:59 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 18:24:59 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456F2017.8000008@sendu.me.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> <456F2017.8000008@sendu.me.uk> Message-ID: <456F21FB.7090702@sheffield.ac.uk> Sendu Bala wrote: > Nathan S. Haigh wrote: >> More updates: >> >> After the failed install I updating Module::Build, and re-ran the >> install, I get: >> >> -- snip -- >> Creating new 'Build' script for 'bioperl' version '1.005002005' >> Warning: while trying to determine prerequisites for >> S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi >> th the help of Module::Build the following error occurred: 'Failed to >> re-load 'ModuleBuildBiope >> rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: >> _build\lib C:\Perl\site\lib C:\ >> Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. >> ' >> >> Falling back to META.yml for prerequisites >> 'YAML' not installed, cannot parse >> 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' >> -- snip -- > > I had that problem fleetingly and it drove me crazy because later I > couldn't reproduce it. Is it reproducible on your end? > I've seen it several time and i'm sure I could reproduce it....give me a few mins and i'll see what I can report. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 18:25:01 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From bix at sendu.me.uk Thu Nov 30 18:16:55 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 30 Nov 2006 18:16:55 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456ED560.1020001@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> Message-ID: <456F2017.8000008@sendu.me.uk> Nathan S. Haigh wrote: > More updates: > > After the failed install I updating Module::Build, and re-ran the > install, I get: > > -- snip -- > Creating new 'Build' script for 'bioperl' version '1.005002005' > Warning: while trying to determine prerequisites for > S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi > th the help of Module::Build the following error occurred: 'Failed to > re-load 'ModuleBuildBiope > rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: > _build\lib C:\Perl\site\lib C:\ > Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. > ' > > Falling back to META.yml for prerequisites > 'YAML' not installed, cannot parse > 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' > -- snip -- I had that problem fleetingly and it drove me crazy because later I couldn't reproduce it. Is it reproducible on your end? From cjfields at uiuc.edu Thu Nov 30 19:11:47 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 13:11:47 -0600 Subject: [Bioperl-l] Intermittent MySQL problems on BioPerl wiki Message-ID: <000201c714b3$6198e4e0$15327e82@pyrimidine> I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and WinXP): Database error >From BioPerl Jump to: navigation, search A database query syntax error has occurred. This may indicate a bug in the software. The last attempted database query was: (SQL query hidden) from within function "MediaWikiBagOStuff::_doquery". MySQL returned error "1205: Lock wait timeout exceeded; try restarting transaction (localhost)". This occurs intermittently when editting pages, logging in, etc. Also, pages loading to the browser seem much slower. Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Thu Nov 30 19:19:34 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 13:19:34 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl5.8.8.819 In-Reply-To: <456F2017.8000008@sendu.me.uk> Message-ID: <000301c714b4$7846e790$15327e82@pyrimidine> > Nathan S. Haigh wrote: > > More updates: > > > > After the failed install I updating Module::Build, and re-ran the > > install, I get: > > > > -- snip -- > > Creating new 'Build' script for 'bioperl' version '1.005002005' > > Warning: while trying to determine prerequisites for > > S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi th the help of > > Module::Build the following error occurred: 'Failed to re-load > > 'ModuleBuildBiope > > rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: > > _build\lib C:\Perl\site\lib C:\ > > Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. > > ' > > > > Falling back to META.yml for prerequisites 'YAML' not installed, > > cannot parse 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' > > -- snip -- > > I had that problem fleetingly and it drove me crazy because > later I couldn't reproduce it. Is it reproducible on your end? During Module::Build installation I see this: ... t\metadata........ok 8/43 skipped: YAML_support feature is not enabled t\metadata2.......ok 4/18 skipped: YAML_support feature is not enabled t\moduleinfo......ok t\notes...........ok t\parents.........ok t\pod_parser......ok t\ppm.............skipped all skipped: C_support not enabled t\runthrough......ok 7/32 skipped: YAML_support feature is not enabled t\signature.......skipped all skipped: $ENV{TEST_SIGNATURE} is not set t\tilde...........ok t\versions........ok t\xs..............skipped all skipped: C_support not enabled All tests successful, 3 tests and 27 subtests skipped. Files=21, Tests=679, 262 wallclock secs ( 0.00 cusr + 0.00 csys = 0.00 CPU) C:\WINDOWS\nmake.EXE test -- OK Running make install ... Christopher Fields Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry University of Illinois Urbana-Champaign From st537 at york.ac.uk Thu Nov 30 18:50:17 2006 From: st537 at york.ac.uk (Samantha Thompson) Date: Thu, 30 Nov 2006 18:50:17 +0000 Subject: [Bioperl-l] BLASTing with a seqio/seq object... In-Reply-To: <01ba01c714a2$b9659c10$15327e82@pyrimidine> References: <01ba01c714a2$b9659c10$15327e82@pyrimidine> Message-ID: <456F27E9.70205@york.ac.uk> Chris Fields wrote: >>Hi, >>Thanks for helping me with the BLAST code, when I made the >>corections in ran fine, I'm assuming the returned object >>$blast_result is a kind of searchio object, although I'm not >>sure. I tried the code on the bioperl tutorial page for >>processing a searchio object returned from blast.... >>http://www.bioperl.org/wiki/Bptutorial.pl#Parsing_BLAST_and_FA >>STA_reports_with_Search_and_SearchIO >>this seems to be the next stage after blasting in the bioperl >>tutorial but I'm sure how to process it correctly to get hit >>and alignment information regards, >> >>Samantha Thompson >> >> > >It is a SearchIO object. FYI, you also have the option of saving the raw >BLAST output to a file if needed (it should be described in the RemoteBlast >POD). > >There is also a great HOWTO which goes into more detail about hits/HSPs and >how to get alignments: > >http://www.bioperl.org/wiki/HOWTO:SearchIO > > >chris > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/bioper > > Hi, OK, I tried the code at the SearchIO HOWTO, I've pasted it below, you can see where I've added the SearchIO handling part I've changed $in to the $blast_report as this is returned from the submit_blast ... what happens when I run this however is that I get the following error: Can't call method "next_result" without a package or object reference at bioptest2.pl line 31, line 1. Line 31 being: while( my $result = $blast_report->next_result ) { Not sure why this is happening. Thanks for any help... Samantha Thompson use strict; use Bio::Perl; use Bio::Seq; use Bio::SeqIO; use Bio::Tools::Run::RemoteBlast; use Bio::SearchIO; #seq bit #$seq_obj = Bio::Seq->new(-format => 'fasta'); my $seqio_obj = Bio::SeqIO->new(-file => "/biol/people/mres/st537/MalEfasta.txt", -format => 'fasta'); my $seq_obj = $seqio_obj->next_seq; #blast bit my $remote_blast = Bio::Tools::Run::RemoteBlast->new ( -prog => 'blastp', -db => 'nr', -expect => '1e-15' ); my $blast_report = $remote_blast->submit_blast($seq_obj); #new part for SearchIO... while( my $result = $blast_report->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { if( $hsp->length('total') > 100 ) { if ( $hsp->percent_identity >= 75 ) { print "Hit= ", $hit->name, ",Length=", $hsp->length('total'), ",Percent_id=", $hsp->percent_identity, "\n"; } } } } } From dag at sonsorol.org Thu Nov 30 19:25:16 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 30 Nov 2006 14:25:16 -0500 Subject: [Bioperl-l] [Root-l] Intermittent MySQL problems on BioPerl wiki In-Reply-To: <000201c714b3$6198e4e0$15327e82@pyrimidine> References: <000201c714b3$6198e4e0$15327e82@pyrimidine> Message-ID: Reports like this need to go to support at helpdesk.open-bio.org so that they enter our RT helpdesk queue -- the main reason is that sometimes emails to the root-l at open-bio.org administrators mailing list can get lost in the shuffle. I am going to bounce this message into RT and will restart mysql on the portal box. This is probably something we should be doing anyway to free up memory -- the wikis in particular seem to be pretty hard on mysql and free memory. -Chris On Nov 30, 2006, at 2:11 PM, Chris Fields wrote: > I'm seeing some MySQL errors on the Bioperl wiki (using Firefox 2 and > WinXP): > > Database error >> From BioPerl > Jump to: navigation, search > A database query syntax error has occurred. This may indicate a bug > in the > software. The last attempted database query was: > > (SQL query hidden) > > from within function "MediaWikiBagOStuff::_doquery". MySQL returned > error > "1205: Lock wait timeout exceeded; try restarting transaction > (localhost)". > > > This occurs intermittently when editting pages, logging in, etc. > Also, > pages loading to the browser seem much slower. > > Christopher Fields > Postdoctoral Researcher - Switzer Lab > Dept. of Biochemistry > University of Illinois Urbana-Champaign > > > _______________________________________________ > Root-l mailing list > Root-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/root-l From n.haigh at sheffield.ac.uk Thu Nov 30 20:07:24 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 20:07:24 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXP ActivePerl 5.8.8.819 In-Reply-To: <456F21FB.7090702@sheffield.ac.uk> References: <9A1C8CF0-238E-4AF6-A113-5EE62C976890@gmx.net> <456E8D2E.60908@sendu.me.uk> <456E97BC.9000800@sheffield.ac.uk> <456E9A74.9020404@sendu.me.uk> <456ED560.1020001@sheffield.ac.uk> <456F2017.8000008@sendu.me.uk> <456F21FB.7090702@sheffield.ac.uk> Message-ID: <456F39FC.9070805@sheffield.ac.uk> Nathan S. Haigh wrote: > Sendu Bala wrote: > >> Nathan S. Haigh wrote: >> >>> More updates: >>> >>> After the failed install I updating Module::Build, and re-ran the >>> install, I get: >>> >>> -- snip -- >>> Creating new 'Build' script for 'bioperl' version '1.005002005' >>> Warning: while trying to determine prerequisites for >>> S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz wi >>> th the help of Module::Build the following error occurred: 'Failed to >>> re-load 'ModuleBuildBiope >>> rl': Can't locate ModuleBuildBioperl.pm in @INC (@INC contains: >>> _build\lib C:\Perl\site\lib C:\ >>> Perl\lib C:\Documents and Settings\test) at (eval 105) line 1. >>> ' >>> >>> Falling back to META.yml for prerequisites >>> 'YAML' not installed, cannot parse >>> 'C:\Perl\cpan\build\bioperl-1.5.2_005-RC\META.yml' >>> -- snip -- >>> >> I had that problem fleetingly and it drove me crazy because later I >> couldn't reproduce it. Is it reproducible on your end? >> >> > > I've seen it several time and i'm sure I could reproduce it....give me a > few mins and i'll see what I can report. > > Nath > > > --- > avast! Antivirus: Outbound message clean. > Virus Database (VPS): 0652-2, 30/11/2006 > Tested on: 30/11/2006 18:25:01 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > --- > avast! Antivirus: Inbound message clean. > Virus Database (VPS): 0652-2, 30/11/2006 > Tested on: 30/11/2006 18:50:39 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > > Reproduce: 1) clean install of ActivePerl 5.8.8.819 on WinXP 2) Install nmake in path 3) run "cpan CPAN" to install the latest version of CPAN module 4) ran cpan, accepted default for new CPAN configuration, ran "o conf prefer_installer MB" and "o conf commit" then "q" 5) run "cpan Module::Build" to install the latest version of Module::Build 6) run "cpan" and then "install S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" 7) Choose not to install optional modules 8) Error shows here Installing all optional modules doesn't produce the error. However, It produces the problem i've told you about missing "scripts" dir (actually, it's not just the scripts dir - it's all but the base dir it was unpacked into). Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 20:07:25 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From cjfields at uiuc.edu Thu Nov 30 20:48:26 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 14:48:26 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install on WinXPActivePerl 5.8.8.819 In-Reply-To: <456F39FC.9070805@sheffield.ac.uk> Message-ID: <000801c714c0$e26eff70$15327e82@pyrimidine> > Nathan S. Haigh wrote: > Reproduce: > 1) clean install of ActivePerl 5.8.8.819 on WinXP > 2) Install nmake in path > 3) run "cpan CPAN" to install the latest version of CPAN module > 4) ran cpan, accepted default for new CPAN configuration, ran > "o conf prefer_installer MB" and "o conf commit" then "q" > 5) run "cpan Module::Build" to install the latest version of > Module::Build > 6) run "cpan" and then "install > S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" > 7) Choose not to install optional modules > 8) Error shows here > > Installing all optional modules doesn't produce the error. > However, It produces the problem i've told you about missing > "scripts" dir (actually, it's not just the scripts dir - it's > all but the base dir it was unpacked into). > > Nath Confirmed, using same setup as Nathan. chris From cjfields at uiuc.edu Thu Nov 30 21:27:17 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 15:27:17 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <000801c714c0$e26eff70$15327e82@pyrimidine> Message-ID: <002401c714c6$53f65080$15327e82@pyrimidine> > > Nathan S. Haigh wrote: > > Reproduce: > > 1) clean install of ActivePerl 5.8.8.819 on WinXP > > 2) Install nmake in path > > 3) run "cpan CPAN" to install the latest version of CPAN module > > 4) ran cpan, accepted default for new CPAN configuration, > ran "o conf > > prefer_installer MB" and "o conf commit" then "q" > > 5) run "cpan Module::Build" to install the latest version of > > Module::Build > > 6) run "cpan" and then "install > > S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" > > 7) Choose not to install optional modules > > 8) Error shows here > > > > Installing all optional modules doesn't produce the error. > > However, It produces the problem i've told you about > missing "scripts" > > dir (actually, it's not just the scripts dir - it's all but > the base > > dir it was unpacked into). > > > > Nath > > Confirmed, using same setup as Nathan. > > chris Okay, revise that. I get the message you mentioned, but installation only fails after tests are run. The single failed test (rnamotif.t) is due to DB_File not being installed, which Sendu has corrected in CVS and (I think) the 1.5.2 branch. However, I can't get DB_File to install via CPAN (I have VC++ Express Edition installed). I think XML::SAX and a few others fail as well. Chris From n.haigh at sheffield.ac.uk Thu Nov 30 21:41:30 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Thu, 30 Nov 2006 21:41:30 +0000 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <002401c714c6$53f65080$15327e82@pyrimidine> References: <002401c714c6$53f65080$15327e82@pyrimidine> Message-ID: <456F500A.7010707@sheffield.ac.uk> Chris Fields wrote: >>> Nathan S. Haigh wrote: >>> Reproduce: >>> 1) clean install of ActivePerl 5.8.8.819 on WinXP >>> 2) Install nmake in path >>> 3) run "cpan CPAN" to install the latest version of CPAN module >>> 4) ran cpan, accepted default for new CPAN configuration, >>> >> ran "o conf >> >>> prefer_installer MB" and "o conf commit" then "q" >>> 5) run "cpan Module::Build" to install the latest version of >>> Module::Build >>> 6) run "cpan" and then "install >>> S/SE/SENDU/bioperl-1.5.2_005-RC*b*.tar.gz" >>> 7) Choose not to install optional modules >>> 8) Error shows here >>> >>> Installing all optional modules doesn't produce the error. >>> However, It produces the problem i've told you about >>> >> missing "scripts" >> >>> dir (actually, it's not just the scripts dir - it's all but >>> >> the base >> >>> dir it was unpacked into). >>> >>> Nath >>> >> Confirmed, using same setup as Nathan. >> >> chris >> > > Okay, revise that. I get the message you mentioned, but installation only > fails after tests are run. The single failed test (rnamotif.t) is due to > DB_File not being installed, which Sendu has corrected in CVS and (I think) > the 1.5.2 branch. However, I can't get DB_File to install via CPAN (I have > VC++ Express Edition installed). I think XML::SAX and a few others fail as > well. > > Chris > > > Yes that's correct, I get the message but things then seem to proceed normally (not that I know what normal is!). I had to install DB_File via PPM and install XML::SAX explicitly in CPAN. That then seems to have cleared things up and the tests pass and bioperl core is installed. However, there are other optional dependencies that didn't install successfully - I suppose I should investigate those tomorrow. Nath --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0652-2, 30/11/2006 Tested on: 30/11/2006 21:41:31 avast! - copyright (c) 1988-2006 ALWIL Software. http://www.avast.com From gwu at molbio.mgh.harvard.edu Thu Nov 30 22:08:08 2006 From: gwu at molbio.mgh.harvard.edu (gang wu) Date: Thu, 30 Nov 2006 17:08:08 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> Message-ID: <456F5648.6070207@molbio.mgh.harvard.edu> Thanks Hilmar. Do you mean the NVL() clause will make load_seqdatabase.pl not work when update? I have problem with updating. Seems load_seqdatabase.pl only tries to insert instead of update. I used one of the test genbank file coming whith bioperl-db. Please take a look at the attached output. Thanks. Gang ========================================= >perl load_seqdatabase.pl -lookup -host elegans -driver Oracle -dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank -namespace test /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/AP000868.gb Loading /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/AP000868.gb ... -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("This sequence was reannotated via the Ensembl system. Please visit the Ensembl web site, http://www.ensembl.org/ for more information. ","1") FKs (389109) ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) violated (DBD ERROR: OCIStmtExecute) --------------------------------------------------- -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("The /gene indicates a unique id for a gene, /cds a unique id for a translation and a /exon a unique id for an exon. These ids are maintained wherever possible between versions. For more information on how to interpret the feature table, please visit http://www.ensembl.org/Docs/embl.html. ","2") FKs (389109) ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) violated (DBD ERROR: OCIStmtExecute) --------------------------------------------------- ... ... ========================================================== Hilmar Lapp wrote: > These are the protein translations stored in the feature table as > tags of features, right? > > You can change the type of the column (although there may be some > issues when you update the column because the NVL() clause won't work > if I recall that correctly), but doing so will deprive you of any > 'normal' searches against that column. (You can still use functions > from the DBMS_LOB package, but they will be much slower and are > completely non-standard.) > > It is up to you whether that is too big of a price to pay for having > some redundant protein translations (translating the feature's DNA > sequence should give you the same) in the database. I always trimmed > those feature tags off (using a custom SeqProcessor). An alternative > is to convert these feature tags into actual bioentries (i.e., > Bio::Seq objects; again, a custom SeqProcessor will allow you to do > that). > > -hilmar > > On Nov 28, 2006, at 4:13 PM, gang wu wrote: > > >> Hi everyone, >> >> I'm using load_seqdatabase.pl to upload some Genbank genome >> sequences to >> my Oracle BioSQL database. I saw some errors(See attached warning >> message) related to seqfeature_qualifier_value >> (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data >> type of maximum 4000 bytes. Did anybody mention this issue before? >> Should I just modify the column to a type being able store more data >> such as LONG or CLOB? >> >> Thanks. >> >> Gang >> >> >> Log information: >> ============================================ >> >> load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser >> biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank >> /genomeseq/arabidopsis//NC_003070.gbk >> >> >> Loading /genomeseq/arabidopsis//NC_003070.gbk ... >> >> >> -------------------- WARNING --------------------- >> MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement >> execution: ORA-01461: can bind a LONG value only for insert into a >> LONG >> column (DBD ERROR: error possibly near <*> indicator at char 12 in >> 'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, >> rank) VALUES (:p1, :p2, :p3, :p4)') >> name: INSERT ASSOC [2] >> Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue >> values: FK[Bio::SeqFeature::Generic]:14898, >> FK[Bio::Annotation::SimpleValue]:800, >> value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFV >> GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADR >> GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEI >> LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFP >> WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERA >> SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRY >> IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEA >> EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDI >> NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDW >> RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFAL >> DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDN >> QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRY >> MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYT >> FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGL >> VQATYQASA! >> >> PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKV >> HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAY >> TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFV >> SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSE >> KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLG >> NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEV >> TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQL >> EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTL >> SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVT >> ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRL >> MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAV >> PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEY >> TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVD >> ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLR >> VKLDFNFM! >> >> YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQS >> QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSN >> TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCL >> SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWD >> ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSE >> IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASV >> TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGL >> HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSS >> KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDF >> QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGL >> HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVA >> RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCL >> LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRN >> GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVE >> NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPL >> WLSVGADAS! >> >> VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVY >> LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITND >> SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQES >> AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTS >> DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSV >> FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESW >> QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIV >> RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMS >> VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRV >> YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAM >> SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDI >> LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAK >> SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLR >> PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMG >> QRKFIPAK! >> >> DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQ >> AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", >> rank:"1" >> -------------------------------------------------- >> >> >> ============================================= >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > From cjfields at uiuc.edu Thu Nov 30 22:16:02 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 30 Nov 2006 16:16:02 -0600 Subject: [Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819 In-Reply-To: <456F500A.7010707@sheffield.ac.uk> References: <002401c714c6$53f65080$15327e82@pyrimidine> <456F500A.7010707@sheffield.ac.uk> Message-ID: <202B1F50-E905-46DE-9EB5-5F206AC04523@uiuc.edu> On Nov 30, 2006, at 3:41 PM, Nathan S. Haigh wrote: > ... >> >> Okay, revise that. I get the message you mentioned, but >> installation only >> fails after tests are run. The single failed test (rnamotif.t) is >> due to >> DB_File not being installed, which Sendu has corrected in CVS and >> (I think) >> the 1.5.2 branch. However, I can't get DB_File to install via >> CPAN (I have >> VC++ Express Edition installed). I think XML::SAX and a few >> others fail as >> well. >> >> Chris >> >> >> > > Yes that's correct, I get the message but things then seem to > proceed normally (not that I know what normal is!). > I had to install DB_File via PPM and install XML::SAX explicitly in > CPAN. That then seems to have cleared things up and the tests pass > and bioperl core is installed. However, there are other optional > dependencies that didn't install successfully - I suppose I should > investigate those tomorrow. > > Nath The DB_File failure is due to compilation problems. BTW, I can get XML::SAX to install, so that shouldn't be an issue. I know that setting up the PPM is a pain, but I have to say it is much faster, and all required PPMs are available. Which makes me curious: why bother with trying out a CPAN installation process at this point, especially when you have to use PPM to install some of the prereqs properly anyway? Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From pelikan at cs.pitt.edu Thu Nov 30 22:19:29 2006 From: pelikan at cs.pitt.edu (pelikan at cs.pitt.edu) Date: Thu, 30 Nov 2006 17:19:29 -0500 (EST) Subject: [Bioperl-l] Error with supplied lineages importing uniprot data Message-ID: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> Hello all, I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows, without Cygwin. The "make test"s have all completed without error. This is my first time dealing with bioperl, so bear with me. I've successfully loaded the most recent taxonomy information using the biosql-schema scripts. After this, I attempted to load the most recent release of the uniprot flat file dataset with the following command: load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat I am subsequently greeted by many of the following errors: Could not store Q7N3Q6: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: The supplied lineage does not start near 'Photorhabdus luminescens subsp. laumondii' STACK: Error::throw STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio\Root\Root.pm:359 STACK: Bio::Species::classification C:/Perl/site/lib/Bio\Species.pm:166 STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:55 STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row C:/Perl/site/lib/Bio\DB\BioSQL\SpeciesAdaptor.pm:281 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key C:/Perl/site/lib/Bio/DB/BioSQL/BasePersisten STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenc STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: STACK: Bio::DB::Persistent::PersistentObject::create C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:244 STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:2 STACK: Bio::DB::Persistent::PersistentObject::store C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:271 STACK: C:\DATA\MYSQL\cvs\src\bioperl\bioperl-db-1.5.2_005-RC\scripts\biosql\load_seqdatabase.pl:620 ----------------------------------------------------------- Can someone shed some light on why this may be taking place? -Richard From hlapp at gmx.net Thu Nov 30 23:28:40 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 18:28:40 -0500 Subject: [Bioperl-l] One more load_seqdatabase.pl question In-Reply-To: <456F5648.6070207@molbio.mgh.harvard.edu> References: <4a9ad8800611270907x64a4a4c0jad92bff6641e300@mail.gmail.com> <53C6D534-6E36-4061-B955-E74537839265@gmx.net> <456CA667.6010609@molbio.mgh.harvard.edu> <456F5648.6070207@molbio.mgh.harvard.edu> Message-ID: <70B28FBB-0250-4EB8-8775-CD0537369A3D@gmx.net> Right. You need to tell it to lookup sequences first if you know that you are loading sequences which may be in the database already (see the POD of load_seqdatabase.pl, switch --lookup; there are several other command line options that control what will happen if a sequence entry is already present in the database.). The messages in you report are warnings, not errors. It looks like some of the comments are duplicated for a sequence, it doesn't look like reason for concern. Is not so good if you get errors thrown. -hilmar On Nov 30, 2006, at 5:08 PM, gang wu wrote: > Thanks Hilmar. Do you mean the NVL() clause will make > load_seqdatabase.pl not work when update? > > I have problem with updating. Seems load_seqdatabase.pl only tries > to insert instead of update. I used one of the test genbank file > coming whith bioperl-db. Please take a look at the attached output. > > Thanks. > > Gang > > ========================================= > >perl load_seqdatabase.pl -lookup -host elegans -driver Oracle - > dbname sparc -dbuser biosqldb-sgowner -dbpass PASS -format genbank - > namespace test /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/ > biosql/data/AP000868.gb > Loading /root/.cpan/build/bioperl-db-1.5.2-RC3/scripts/biosql/data/ > AP000868.gb ... > > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, > values were ("This sequence was reannotated via the Ensembl system. > Please visit the Ensembl web site, http://www.ensembl.org/ for more > information. ","1") FKs (389109) > ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) > violated (DBD ERROR: OCIStmtExecute) > --------------------------------------------------- > > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, > values were ("The /gene indicates a unique id for a gene, /cds a > unique id for a translation and a /exon a unique id for an exon. > These ids are maintained wherever possible between versions. For > more information on how to interpret the feature table, please > visit http://www.ensembl.org/Docs/embl.html. ","2") FKs (389109) > ORA-00001: unique constraint (BIOSQLDB_SGOWNER.XAK1COMMENT) > violated (DBD ERROR: OCIStmtExecute) > --------------------------------------------------- > ... > ... > ========================================================== > Hilmar Lapp wrote: >> These are the protein translations stored in the feature table as >> tags of features, right? You can change the type of the column >> (although there may be some issues when you update the column >> because the NVL() clause won't work if I recall that correctly), >> but doing so will deprive you of any 'normal' searches against >> that column. (You can still use functions >from the DBMS_LOB >> package, but they will be much slower and are completely non- >> standard.) It is up to you whether that is too big of a price to >> pay for having some redundant protein translations (translating >> the feature's DNA sequence should give you the same) in the >> database. I always trimmed those feature tags off (using a custom >> SeqProcessor). An alternative is to convert these feature tags >> into actual bioentries (i.e., Bio::Seq objects; again, a custom >> SeqProcessor will allow you to do that). -hilmar On Nov 28, 2006, >> at 4:13 PM, gang wu wrote: >>> Hi everyone, I'm using load_seqdatabase.pl to upload some Genbank >>> genome sequences to my Oracle BioSQL database. I saw some errors >>> (See attached warning message) related to >>> seqfeature_qualifier_value (SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE >>> column), which has Varchar2 data type of maximum 4000 bytes. Did >>> anybody mention this issue before? Should I just modify the >>> column to a type being able store more data such as LONG or CLOB? >>> Thanks. Gang Log information: >>> ============================================ load_seqdatabase.pl - >>> host elegans -driver Oracle -dbname sparc -dbuser biosqldb- >>> sgowner -dbpass PASS -format genbank -namespace genbank / >>> genomeseq/arabidopsis//NC_003070.gbk Loading /genomeseq/ >>> arabidopsis//NC_003070.gbk ... -------------------- WARNING >>> --------------------- MSG: SimpleValueAdaptor::add_assoc: >>> unexpected failure of statement execution: ORA-01461: can bind a >>> LONG value only for insert into a LONG column (DBD ERROR: error >>> possibly near <*> indicator at char 12 in 'INSERT INTO >>> <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, rank) >>> VALUES (:p1, :p2, :p3, :p4)') name: INSERT ASSOC [2] >>> Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue values: FK >>> [Bio::SeqFeature::Generic]:14898, FK >>> [Bio::Annotation::SimpleValue]:800, >>> value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSG >>> FV >>> GTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASA >>> DR >>> GTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSS >>> EI >>> LASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNS >>> FP >>> WEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFE >>> RA >>> SVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYT >>> RY >>> IQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRT >>> EA >>> EDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIV >>> DI >>> NQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENI >>> DW >>> RLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRF >>> AL >>> DIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGS >>> DN >>> QGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPT >>> RY >>> MRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYL >>> YT >>> FESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLR >>> GL VQATYQASA! >>> PLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGG >>> KV >>> HLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDED >>> AY >>> TDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSD >>> FV >>> SVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSD >>> SE >>> KETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGT >>> LG >>> NFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQ >>> EV >>> TAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLG >>> QL >>> EVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVP >>> TL >>> SVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRT >>> VT >>> ILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEM >>> RL >>> MLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRIL >>> AV >>> PDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGID >>> EY >>> TYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDG >>> VD >>> ISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKL >>> LR VKLDFNFM! >>> YASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNL >>> QS >>> QVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAV >>> SN >>> TYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVY >>> CL >>> SIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSG >>> WD >>> ILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADD >>> SE >>> IAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEA >>> SV >>> TRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLD >>> GL >>> HGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQ >>> SS >>> KPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDED >>> DF >>> QTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAK >>> GL >>> HIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKG >>> VA >>> RLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNG >>> CL >>> LISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSM >>> RN >>> GRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPK >>> VE >>> NSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSK >>> PL WLSVGADAS! >>> VLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRP >>> VY >>> LTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWIT >>> ND >>> SYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQ >>> ES >>> AGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNM >>> TS >>> DRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPF >>> SV >>> FSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSE >>> SW >>> QFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKN >>> IV >>> RISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILY >>> MS >>> VQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDL >>> RV >>> YPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSM >>> AM >>> SPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGV >>> DI >>> LGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEG >>> AK >>> SSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSL >>> LR >>> PYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNI >>> MG QRKFIPAK! >>> DACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAI >>> DQ AINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", >>> rank:"1" -------------------------------------------------- >>> ============================================= >>> _______________________________________________ Bioperl-l mailing >>> list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/ >>> mailman/listinfo/bioperl-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Nov 30 23:31:41 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 30 Nov 2006 18:31:41 -0500 Subject: [Bioperl-l] Error with supplied lineages importing uniprot data In-Reply-To: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> References: <1348.130.49.222.58.1164925169.squirrel@webmail.cs.pitt.edu> Message-ID: <24C694D6-1124-48A9-8C7C-FA58AB598F01@gmx.net> Maybe Sendu can shed light on what might be happening here? On Nov 30, 2006, at 5:19 PM, pelikan at cs.pitt.edu wrote: > Hello all, > > I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows, > without Cygwin. The "make test"s have all completed without error. > This > is my first time dealing with bioperl, so bear with me. > > I've successfully loaded the most recent taxonomy information > using the > biosql-schema scripts. After this, I attempted to load the most recent > release of the uniprot flat file dataset with the following command: > > load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass > ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat > > I am subsequently greeted by many of the following errors: > > Could not store Q7N3Q6: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: The supplied lineage does not start near 'Photorhabdus > luminescens > subsp. laumondii' > STACK: Error::throw > STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio\Root\Root.pm:359 > STACK: Bio::Species::classification C:/Perl/site/lib/Bio\Species.pm: > 166 > STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:55 > STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row > C:/Perl/site/lib/Bio\DB\BioSQL\SpeciesAdaptor.pm:281 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersisten > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenc > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: > STACK: Bio::DB::Persistent::PersistentObject::create > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:244 > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: > STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:2 > STACK: Bio::DB::Persistent::PersistentObject::store > C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:271 > STACK: > C:\DATA\MYSQL\cvs\src\bioperl\bioperl-db-1.5.2_005-RC\scripts\biosql > \load_seqdatabase.pl:620 > ----------------------------------------------------------- > > Can someone shed some light on why this may be taking place? > > -Richard > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From The_Polymorph at rocketmail.com Thu Nov 30 23:58:22 2006 From: The_Polymorph at rocketmail.com (Caitlin) Date: Thu, 30 Nov 2006 15:58:22 -0800 (PST) Subject: [Bioperl-l] Upgrading my BioPerl RC via ppm? In-Reply-To: <000001c714a7$f6ee1300$15327e82@pyrimidine> Message-ID: <519167.29410.qm@web50804.mail.yahoo.com> Hi all. I'm currently using BioPerl 1.5.2 RC2 but I've seen multiple references to 1.5.2 RC5. Can anyone tell me how to upgrade to the latest version? The ppm GUI (ActivePerl Build 819) doesn't include any BioPerl packages among those deemed upgradable. Thanks, ~Katie "Be who you are and say what you feel because those who mind don't matter and those who matter don't mind." - Dr. Seuss, "Oh the Places You'll Go" ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com