From David.Messina at sbc.su.se Tue Jun 1 15:45:43 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 1 Jun 2010 21:45:43 +0200 Subject: [Bioperl-guts-l] bugzilla reminder emails now available Message-ID: <12EB61F6-1D32-4718-9B2D-8051161B29E4@sbc.su.se> Hi devs, I've turned on Bugzilla's "whining" feature, which allows you to send yourself bug-related reminder emails. It works by executing searches on a schedule and is quite flexible, so you set up things like: "every Sunday at 2 am send me a list of open bugs in the bioperl-run queue that are assigned to me". You can configure your own here: http://bugzilla.open-bio.org/editwhines.cgi Instructions here: http://www.bugzilla.org/docs/2.20/html/whining.html Let me know if you run into any issues. Dave From bugzilla-daemon at portal.open-bio.org Tue Jun 1 19:14:32 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 1 Jun 2010 19:14:32 -0400 Subject: [Bioperl-guts-l] [Bug 3089] New: HSPTableWriter cannot process Bio::Search::Hit::GenericHit objects Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=3089 Summary: HSPTableWriter cannot process Bio::Search::Hit::GenericHit objects Product: BioPerl Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Bio::Search/Bio::SearchIO AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: robfsouza at gmail.com I'm trying to convert BLAST XML output to a BLAST table which should be identical to a BLAST output generated using "-m 8". In the script below, if $type is "BLAST", the script works if $writer is TextResultWriter but when I try to generate BLAST compatible (i.e. like "-m 8") tables using $writer = "HSPTableWriter" it fails with the message Using default column map. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Trouble in ResultTableWriter::_set_row_data_func() eval: Can't locate object method "iteration" via package "Bio::Search::Hit::GenericHit" at (eval 58) line 1, line 3020. STACK: Error::throw STACK: Bio::Root::Root::throw /panfs/pan1/proteinworld/tools/perl/lib/site_perl/5.8.8/Bio/Root/Root.pm:368 STACK: try{} block /panfs/pan1/proteinworld/tools/perl/lib/site_perl/5.8.8/Bio/SearchIO/Writer/ResultTableWriter.pm:339 STACK: Bio::SearchIO::Writer::HSPTableWriter::to_string /panfs/pan1/proteinworld/tools/perl/lib/site_perl/5.8.8/Bio/SearchIO/Writer/HSPTableWriter.pm:263 STACK: Bio::SearchIO::write_result /panfs/pan1/proteinworld/tools/perl/lib/site_perl/5.8.8/Bio/SearchIO.pm:344 STACK: /home/desouza/projects/mytools/bin/blastxml2blast:22 ----------------------------------------------------------- Is there a way to fix this? Or should I use another approach to get "-m 8" compatible tables? Thanks, Robson #!/usr/bin/env perl #==================== use strict; use warnings; use Bio::SearchIO; use Getopt::Long; my $writer = "TextResultWriter"; my $type = "PSIBLAST"; GetOptions("w=s"=>\$writer, "t=s" => \$type); # Load writer use Module::Load; my $writer = "Bio::SearchIO::Writer::".$writer; load $writer; $writer = $writer->new(); # Open and convert input my $out = Bio::SearchIO->new(-writer => $writer); foreach my $file (@ARGV) { my $in = Bio::SearchIO->new(-format => "blastxml", -file => "<$file"); $in->blasttype($type); while( my $r = $in->next_result) { $out->write_result($r); } } exit 0; -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 2 22:29:39 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 2 Jun 2010 22:29:39 -0400 Subject: [Bioperl-guts-l] [Bug 3090] New: Unable to case insensitivelyt parse 'Effective length of query', 'Effective length of database', 'Effective search space', and 'Effective search space used' from BLAST reports Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=3090 Summary: Unable to case insensitivelyt parse 'Effective length of query', 'Effective length of database', 'Effective search space', and 'Effective search space used' from BLAST reports Product: BioPerl Version: 1.6 branch Platform: All OS/Version: All Status: NEW Severity: enhancement Priority: P2 Component: Bio::Search/Bio::SearchIO AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: razi.khaja at gmail.com Unable to case insensitively parse 'Effective length of query', 'Effective length of database', 'Effective search space', and 'Effective search space used' from several BLAST reports. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 2 22:30:04 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 2 Jun 2010 22:30:04 -0400 Subject: [Bioperl-guts-l] [Bug 3090] Unable to case insensitively parse 'Effective length of query', 'Effective length of database', 'Effective search space', and 'Effective search space used' from BLAST reports In-Reply-To: Message-ID: <201006030230.o532U4fj029499@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3090 razi.khaja at gmail.com changed: What |Removed |Added ---------------------------------------------------------------------------- Summary|Unable to case |Unable to case insensitively |insensitivelyt parse |parse 'Effective length of |'Effective length of query',|query', 'Effective length of |'Effective length of |database', 'Effective search |database', 'Effective search|space', and 'Effective |space', and 'Effective |search space used' from |search space used' from |BLAST reports |BLAST reports | -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 2 22:46:37 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 2 Jun 2010 22:46:37 -0400 Subject: [Bioperl-guts-l] [Bug 3090] Unable to case insensitively parse 'Effective length of query', 'Effective length of database', 'Effective search space', and 'Effective search space used' from BLAST reports In-Reply-To: Message-ID: <201006030246.o532kbrO029704@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3090 razi.khaja at gmail.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|bioperl-guts-l at bioperl.org |razi.khaja at gmail.com Status|NEW |ASSIGNED ------- Comment #1 from razi.khaja at gmail.com 2010-06-02 22:46 EST ------- Created an attachment (id=1512) --> (http://bugzilla.open-bio.org/attachment.cgi?id=1512&action=view) patch for Bio/SearchIO/blast.pm, and t/SearchIO/blast.t to enhance and test case insentively parse 'Effective *' BLAST report statistics Patch/Enhancement to case insensitively parse 'Effective length of query', 'Effectivelength of database', 'Effective search space', and 'Effective search space used' from several BLAST reports. Modified method next_result in Bio/SearchIO/blast.pm to case insensitively match and parse these BLAST statistics by including /i regular expression modifier in 'if' conditions. Added 78 tests to t/SearchIO/blast.t to test for these BLAST statistics in several historical and new BLAST reports. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 2 22:55:58 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 2 Jun 2010 22:55:58 -0400 Subject: [Bioperl-guts-l] [Bug 3090] Unable to case insensitively parse 'Effective length of query', 'Effective length of database', 'Effective search space', and 'Effective search space used' from BLAST reports In-Reply-To: Message-ID: <201006030255.o532twZS029821@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3090 razi.khaja at gmail.com changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|razi.khaja at gmail.com |bioperl-guts-l at bioperl.org Status|ASSIGNED |NEW -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Thu Jun 3 17:39:45 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 3 Jun 2010 14:39:45 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-hmmer3] 52c3bf: Fix parsing of the hit description Message-ID: <20100603213945.9437C422D5@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-hmmer3 Commit: 52c3bf8f258aea09f23b1ea9b0e71c7609073f0e http://github.com/bioperl/bioperl-hmmer3/commit/52c3bf8f258aea09f23b1ea9b0e71c7609073f0e Author: Kai Blin Date: 2010-06-03 (Thu, 03 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm M t/SearchIO/hmmer3.t Log Message: ----------- Fix parsing of the hit description The description field is allowed to contain spaces, don't stop parsing the description on the first space From noreply at github.com Thu Jun 3 17:46:45 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 3 Jun 2010 14:46:45 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-hmmer3] e581e9: Fix indentation of previous patch Message-ID: <20100603214645.784AE4208F@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-hmmer3 Commit: e581e94fafefbd02d4dffe096b3249374d97609c http://github.com/bioperl/bioperl-hmmer3/commit/e581e94fafefbd02d4dffe096b3249374d97609c Author: Kai Blin Date: 2010-06-03 (Thu, 03 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm Log Message: ----------- Fix indentation of previous patch Commit: 7e6f1e39165c8630d13342200c7e39b6cabc6c78 http://github.com/bioperl/bioperl-hmmer3/commit/7e6f1e39165c8630d13342200c7e39b6cabc6c78 Author: Kai Blin Date: 2010-06-03 (Thu, 03 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm Log Message: ----------- Fix hit description parsing for hits below the inclusion threshold From bugzilla-daemon at portal.open-bio.org Thu Jun 3 21:15:34 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 3 Jun 2010 21:15:34 -0400 Subject: [Bioperl-guts-l] [Bug 3091] New: blastplus cant recognize psiblast report Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=3091 Summary: blastplus cant recognize psiblast report Product: BioPerl Version: 1.6 branch Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: bioperl-run AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: dimitark at bii.a-star.edu.sg The module BlastMethods for StandAloneBlastPlus doesnt recognize the psiblast(and most probably rps and rpst) result and therefore doesnt parse it. The problem was in the 'run' method where the match doesnt match properly: ------ m/^[t]?blast[npx]/ && do { #original line ------- Suggested solution is the line below which works fine: ------ m/^(t|psi|rps|rpst)?blast[npx]?/ && do { ------ -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Fri Jun 4 11:29:37 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 4 Jun 2010 08:29:37 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 0b38f9: speling mstake Message-ID: <20100604152937.A417942280@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 0b38f94aa63aa1d78f2464c9f0d678aaa4c10f27 http://github.com/bioperl/bioperl-live/commit/0b38f94aa63aa1d78f2464c9f0d678aaa4c10f27 Author: Chris Fields Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M Bio/Seq.pm Log Message: ----------- speling mstake Commit: 4ac37bb8c28cc2fd2d19b201c98e1cee98bb5233 http://github.com/bioperl/bioperl-live/commit/4ac37bb8c28cc2fd2d19b201c98e1cee98bb5233 Author: Chris Fields Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M Bio/AlignIO/phylip.pm M Bio/Assembly/IO/ace.pm M t/Assembly/Assembly.t Log Message: ----------- Merge branch 'master' of github.com:bioperl/bioperl-live From noreply at github.com Fri Jun 4 18:31:20 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 4 Jun 2010 15:31:20 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 701a51: documentation typo; thanks to Peng Yu Message-ID: <20100604223120.EC1BB422F5@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 701a5190d5ddef3674f1d1fe8abe6ba891bfbc86 http://github.com/bioperl/bioperl-live/commit/701a5190d5ddef3674f1d1fe8abe6ba891bfbc86 Author: DaveMessina Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M Bio/DB/EUtilities.pm Log Message: ----------- documentation typo; thanks to Peng Yu From noreply at github.com Fri Jun 4 19:05:07 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 4 Jun 2010 16:05:07 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 4e28fa: documentation typo; thanks to Peng Yu Message-ID: <20100604230507.76511422FE@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 4e28face5c408949f711b1358fdff79fa1dbad58 http://github.com/bioperl/bioperl-live/commit/4e28face5c408949f711b1358fdff79fa1dbad58 Author: DaveMessina Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M Bio/Tools/EUtilities/Info/FieldInfo.pm Log Message: ----------- documentation typo; thanks to Peng Yu From noreply at github.com Fri Jun 4 19:21:06 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 4 Jun 2010 16:21:06 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b70aa6: yup, another documentation typo; again thanks to P... Message-ID: <20100604232106.53C19422E7@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: b70aa6da2b40ebf0ef641e411a77a693cdb5a8f2 http://github.com/bioperl/bioperl-live/commit/b70aa6da2b40ebf0ef641e411a77a693cdb5a8f2 Author: DaveMessina Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M Bio/Tools/EUtilities/Info/LinkInfo.pm Log Message: ----------- yup, another documentation typo; again thanks to Peng Yu From noreply at github.com Fri Jun 4 20:32:08 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 4 Jun 2010 17:32:08 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 09151b: bug 3091 - patch courtesy of Dimitar Kenanov Message-ID: <20100605003208.242A4422A5@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: 09151b6a82ffbe4d8875f5fc474456d7f3459fa6 http://github.com/bioperl/bioperl-run/commit/09151b6a82ffbe4d8875f5fc474456d7f3459fa6 Author: DaveMessina Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Log Message: ----------- bug 3091 - patch courtesy of Dimitar Kenanov From bugzilla-daemon at portal.open-bio.org Fri Jun 4 20:33:19 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 4 Jun 2010 20:33:19 -0400 Subject: [Bioperl-guts-l] [Bug 3091] blastplus cant recognize psiblast report In-Reply-To: Message-ID: <201006050033.o550XJhl002618@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3091 online at davemessina.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from online at davemessina.com 2010-06-04 20:33 EST ------- committed in 09151b6. Thanks for the patch! -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Fri Jun 4 20:35:25 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 4 Jun 2010 17:35:25 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 4ce636: added comment with the bases used in the codon tab... Message-ID: <20100605003525.B6490422FF@smtp1.rs.github.com> Branch: refs/heads/topic/longest_orf Home: http://github.com/bioperl/bioperl-live Commit: 4ce6366234fbb243ca38f604ea954880e9219a26 http://github.com/bioperl/bioperl-live/commit/4ce6366234fbb243ca38f604ea954880e9219a26 Author: Robert Buels Date: 2010-05-21 (Fri, 21 May 2010) Changed paths: M Bio/Tools/CodonTable.pm Log Message: ----------- added comment with the bases used in the codon table columns, makes it much easier to understand their layout Commit: 06fe978223c38a80f9fb60fb9c5996e02998fa1e http://github.com/bioperl/bioperl-live/commit/06fe978223c38a80f9fb60fb9c5996e02998fa1e Author: Robert Buels Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M Bio/PrimarySeqI.pm Log Message: ----------- more sane (maintainable) format for translate() option documentation Commit: 3db3025440c20096b19918de02f22e3d20981a09 http://github.com/bioperl/bioperl-live/commit/3db3025440c20096b19918de02f22e3d20981a09 Author: Robert Buels Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M Bio/PrimarySeqI.pm Log Message: ----------- another translate() docpatch for better rendering on search.cpan.org Commit: 6fe8afbb7ce16f515ffddc16f62d0e53fcffd0ef http://github.com/bioperl/bioperl-live/commit/6fe8afbb7ce16f515ffddc16f62d0e53fcffd0ef Author: Robert Buels Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M Bio/PrimarySeqI.pm Log Message: ----------- tweaked translate() args format, removed -longest_orf arg, instead making the -orf arg do double duty, with "longest" triggering the longest_orf behavior, and other true values finding the first ORF (for backcompat) From noreply at github.com Fri Jun 4 20:39:28 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 4 Jun 2010 17:39:28 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] d1937b: updating MANIFEST to correspond to change in 6444b... Message-ID: <20100605003928.8FCA2422BB@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: d1937b25556980995c770eef15c6bd758cbf58d3 http://github.com/bioperl/bioperl-live/commit/d1937b25556980995c770eef15c6bd758cbf58d3 Author: DaveMessina Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M MANIFEST Log Message: ----------- updating MANIFEST to correspond to change in 6444b22 From noreply at github.com Fri Jun 4 21:20:27 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 4 Jun 2010 18:20:27 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 50e62b: added test requirement/skip for GD so no longer er... Message-ID: <20100605012027.6BCAA42301@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 50e62b43c783ce38aa8a95d11b4bf756b629834e http://github.com/bioperl/bioperl-live/commit/50e62b43c783ce38aa8a95d11b4bf756b629834e Author: DaveMessina Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M t/Align/Graphics.t Log Message: ----------- added test requirement/skip for GD so no longer errors out; now using Bio::Root::Test. From noreply at github.com Fri Jun 4 21:36:52 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 4 Jun 2010 18:36:52 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6ea85d: updating test count for tests added in 48d9789 Message-ID: <20100605013652.39E4B422E9@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 6ea85d2c1023b168e0b9c1a8c1a8b40fddb27fe2 http://github.com/bioperl/bioperl-live/commit/6ea85d2c1023b168e0b9c1a8c1a8b40fddb27fe2 Author: DaveMessina Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M t/Assembly/Assembly.t Log Message: ----------- updating test count for tests added in 48d9789 From noreply at github.com Fri Jun 4 21:46:44 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 4 Jun 2010 18:46:44 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b4fb80: patch for Bug 3090, courtesy of Razi Khaja. New te... Message-ID: <20100605014644.4FE47422F5@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: b4fb809970686f8a974e38e9b8440ca341483066 http://github.com/bioperl/bioperl-live/commit/b4fb809970686f8a974e38e9b8440ca341483066 Author: DaveMessina Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M Bio/SearchIO/blast.pm M t/SearchIO/blast.t Log Message: ----------- patch for Bug 3090, courtesy of Razi Khaja. New tests, even. Woo hoo! Thanks, Razi. From bugzilla-daemon at portal.open-bio.org Fri Jun 4 21:47:29 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 4 Jun 2010 21:47:29 -0400 Subject: [Bioperl-guts-l] [Bug 3090] Unable to case insensitively parse 'Effective length of query', 'Effective length of database', 'Effective search space', and 'Effective search space used' from BLAST reports In-Reply-To: Message-ID: <201006050147.o551lT1G003921@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3090 online at davemessina.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #2 from online at davemessina.com 2010-06-04 21:47 EST ------- Committed to bioperl-live as of revision b4fb809. Thanks for the patch! -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From razi.khaja at gmail.com Fri Jun 4 22:10:32 2010 From: razi.khaja at gmail.com (Razi Khaja) Date: Fri, 4 Jun 2010 22:10:32 -0400 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b4fb80: patch for Bug 3090, courtesy of Razi Khaja. New te... In-Reply-To: <20100605014644.4FE47422F5@smtp1.rs.github.com> References: <20100605014644.4FE47422F5@smtp1.rs.github.com> Message-ID: Your welcome! Thanks for the enthusiasm about the tests! Now I just have to figure out how to use github and send pull or push requests. I will try and figure that out for my next set of patch(es). Razi On Fri, Jun 4, 2010 at 9:46 PM, wrote: > Branch: refs/heads/master > Home: http://github.com/bioperl/bioperl-live > > Commit: b4fb809970686f8a974e38e9b8440ca341483066 > > http://github.com/bioperl/bioperl-live/commit/b4fb809970686f8a974e38e9b8440ca341483066 > Author: DaveMessina > Date: 2010-06-04 (Fri, 04 Jun 2010) > > Changed paths: > M Bio/SearchIO/blast.pm > M t/SearchIO/blast.t > > Log Message: > ----------- > patch for Bug 3090, courtesy of Razi Khaja. New tests, even. Woo hoo! > Thanks, Razi. > > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l > From rmb32 at cornell.edu Fri Jun 4 22:49:32 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 04 Jun 2010 19:49:32 -0700 Subject: [Bioperl-guts-l] rfc: topic/longest_orf Message-ID: <4C09BB3C.1060405@cornell.edu> Could I get a code review on topic/longest_orf? I think it's ready to merge. The objective of this branch was to give Bio::PrimarySeq::translate() the capability to find the longest ORF in a given sequence, not just the first ORF. I did this by expanding the range of values its -orf argument can take, so that -orf => 1 still does the same thing it always did, but -orf => 'longest' finds the longest ORF, (and of course -orf 0 or no -orf does not do any ORF stuff). Branch compare link, probably the easiest way to review: http://github.com/bioperl/bioperl-live/compare/master...topic;longest_orf Rob From David.Messina at sbc.su.se Sat Jun 5 06:38:04 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sat, 5 Jun 2010 12:38:04 +0200 Subject: [Bioperl-guts-l] rfc: topic/longest_orf In-Reply-To: <4C09BB3C.1060405@cornell.edu> References: <4C09BB3C.1060405@cornell.edu> Message-ID: <5571E098-02D6-463D-B5C7-B77C58108D87@sbc.su.se> Hey Rob, I'm taking a look. I'll make comments inline on github and probably copy them here for posterity. Dave On Jun 5, 2010, at 4:49 AM, Robert Buels wrote: > Could I get a code review on topic/longest_orf? I think it's ready to merge. > > The objective of this branch was to give Bio::PrimarySeq::translate() the capability to find the longest ORF in a given sequence, not just the first ORF. I did this by expanding the range of values its -orf argument can take, so that -orf => 1 still does the same thing it always did, but -orf => 'longest' finds the longest ORF, (and of course -orf 0 or no -orf does not do any ORF stuff). > > Branch compare link, probably the easiest way to review: > http://github.com/bioperl/bioperl-live/compare/master...topic;longest_orf > > Rob > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l From cjfields at illinois.edu Sat Jun 5 08:48:21 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 5 Jun 2010 07:48:21 -0500 Subject: [Bioperl-guts-l] rfc: topic/longest_orf In-Reply-To: <4C09BB3C.1060405@cornell.edu> References: <4C09BB3C.1060405@cornell.edu> Message-ID: <8F792551-3AB2-410D-9CC3-5A28ADA70CF4@illinois.edu> On Jun 4, 2010, at 9:49 PM, Robert Buels wrote: > Could I get a code review on topic/longest_orf? I think it's ready to merge. > > The objective of this branch was to give Bio::PrimarySeq::translate() the capability to find the longest ORF in a given sequence, not just the first ORF. I did this by expanding the range of values its -orf argument can take, so that -orf => 1 still does the same thing it always did, but -orf => 'longest' finds the longest ORF, (and of course -orf 0 or no -orf does not do any ORF stuff). > > Branch compare link, probably the easiest way to review: > http://github.com/bioperl/bioperl-live/compare/master...topic;longest_orf > > Rob Ah, how I wish one could add code review comments at the diff (e.g. select the version to add comments to). Maybe down the line... Anyway, here are mine: PrimarySeqI: the name of the method _find_orf was changed to _find_orfs_nucleotide. Personally I don't have a problem with it (anyone calling a private method and having it break on them probably deserves it a little). Just not sure how others feel. CodonTable: \o/ for getting rid of redundant code! I say merge it. chris From noreply at github.com Sat Jun 5 09:30:09 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 06:30:09 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b6f2b3: get_replaced_terms<- (courtesy Peng Yu) Message-ID: <20100605133009.B89FE42306@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: b6f2b3c1a9ebab00133610db30b2a60ee24a78e2 http://github.com/bioperl/bioperl-live/commit/b6f2b3c1a9ebab00133610db30b2a60ee24a78e2 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M Bio/Tools/EUtilities.pm Log Message: ----------- get_replaced_terms<- (courtesy Peng Yu) Commit: b5f9183fe30437b99a952cf50b5fc66c23c5ea32 http://github.com/bioperl/bioperl-live/commit/b5f9183fe30437b99a952cf50b5fc66c23c5ea32 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M .gitignore Log Message: ----------- add MYMETA.yml, any *.bak files From David.Messina at sbc.su.se Sat Jun 5 09:43:46 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sat, 5 Jun 2010 15:43:46 +0200 Subject: [Bioperl-guts-l] rfc: topic/longest_orf In-Reply-To: <8F792551-3AB2-410D-9CC3-5A28ADA70CF4@illinois.edu> References: <4C09BB3C.1060405@cornell.edu> <8F792551-3AB2-410D-9CC3-5A28ADA70CF4@illinois.edu> Message-ID: Rob, My main comments are about some of the documentation and so don't affect the code. I agree; go ahead and merge. I'll follow up with you on the doc suggestions later. Dave On Jun 5, 2010, at 14:48, Chris Fields wrote: > On Jun 4, 2010, at 9:49 PM, Robert Buels wrote: > >> Could I get a code review on topic/longest_orf? I think it's ready >> to merge. >> >> The objective of this branch was to give Bio::PrimarySeq::translate >> () the capability to find the longest ORF in a given sequence, not >> just the first ORF. I did this by expanding the range of values >> its -orf argument can take, so that -orf => 1 still does the same >> thing it always did, but -orf => 'longest' finds the longest ORF, >> (and of course -orf 0 or no -orf does not do any ORF stuff). >> >> Branch compare link, probably the easiest way to review: >> http://github.com/bioperl/bioperl-live/compare/master...topic;longest_orf >> >> Rob > > Ah, how I wish one could add code review comments at the diff (e.g. > select the version to add comments to). Maybe down the line... > > Anyway, here are mine: > > PrimarySeqI: the name of the method _find_orf was changed to > _find_orfs_nucleotide. Personally I don't have a problem with it > (anyone calling a private method and having it break on them > probably deserves it a little). Just not sure how others feel. > > CodonTable: \o/ for getting rid of redundant code! > > > > I say merge it. > > chris > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l From bugzilla-daemon at portal.open-bio.org Sat Jun 5 15:05:59 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sat, 5 Jun 2010 15:05:59 -0400 Subject: [Bioperl-guts-l] [Bug 3092] New: Unable to parse 'Number of HSP's better than without gapping', 'Number of HSP's gapped', 'Number of HSP's successfully gapped' and 'Length adjustment' from BLAST reports Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=3092 Summary: Unable to parse 'Number of HSP's better than without gapping', 'Number of HSP's gapped', 'Number of HSP's successfully gapped' and 'Length adjustment' from BLAST reports Product: BioPerl Version: main-trunk Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Bio::Search/Bio::SearchIO AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: razi.khaja at gmail.com Unable to parse 'Number of HSP's better than without gapping', 'Number of HSP's gapped', 'Number of HSP's successfully gapped' and 'Length adjustment' from BLAST reports -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sat Jun 5 15:11:01 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sat, 5 Jun 2010 15:11:01 -0400 Subject: [Bioperl-guts-l] [Bug 3092] Unable to parse 'Number of HSP's better than without gapping', 'Number of HSP's gapped', 'Number of HSP's successfully gapped' and 'Length adjustment' from BLAST reports In-Reply-To: Message-ID: <201006051911.o55JB14D026694@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3092 ------- Comment #1 from razi.khaja at gmail.com 2010-06-05 15:11 EST ------- Created an attachment (id=1513) --> (http://bugzilla.open-bio.org/attachment.cgi?id=1513&action=view) patch for Bio/SearchIO/blast.pm, and t/SearchIO/blast.t to enhance and test parsing indicated BLAST statistics Patch/Enhancement to parse 'Number of HSP's better than without gapping', 'Number of HSP's gapped', 'Number of HSP's successfully gapped' and 'Length adjustment' from BLAST reports. Modified method next_result inBio/SearchIO/blast.pm to parse these BLAST statistics. Added 12 tests to t/SearchIO/blast.t to test parsing of these BLAST statistics. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sat Jun 5 15:13:03 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sat, 5 Jun 2010 15:13:03 -0400 Subject: [Bioperl-guts-l] [Bug 3092] Unable to parse 'Number of HSP's better than without gapping', 'Number of HSP's gapped', 'Number of HSP's successfully gapped' and 'Length adjustment' from BLAST reports In-Reply-To: Message-ID: <201006051913.o55JD3a4026754@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3092 razi.khaja at gmail.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Sat Jun 5 16:52:57 2010 From: noreply at github.com (GitHub) Date: Sat, 5 Jun 2010 13:52:57 -0700 Subject: [Bioperl-guts-l] [GitHub] DaveMessina commented on a commit [bioperl/bioperl-live df0fb23] Message-ID: <4c0ab92915cd6_1db93ffcda6e0afc17d@fe2.rs.github.com.tmail> It would be great if you added a POD block to document _codon_is From: DaveMessina View this commit online: http://github.com/bioperl/bioperl-live/commit/df0fb23ec87e2e079d2378249509ef6e772142ed From noreply at github.com Sat Jun 5 16:59:27 2010 From: noreply at github.com (GitHub) Date: Sat, 5 Jun 2010 13:59:27 -0700 Subject: [Bioperl-guts-l] [GitHub] DaveMessina commented on a commit [bioperl/bioperl-live 06fe978] Message-ID: <4c0abaaf24e56_59903fc163f992f0186@fe2.rs.github.com.tmail> For these many args to truncate, it's a bit unclear which are boolean, which expect an integer or which expect a string. And if they do take a value, what possible values can that be. Would you consider elaborating on the docs here and specifying: - the type of the argument (boolean, string, etc) - the possible values the argument takes (or an example if there are too many to list) From: DaveMessina View this commit online: http://github.com/bioperl/bioperl-live/commit/06fe978223c38a80f9fb60fb9c5996e02998fa1e From noreply at github.com Sat Jun 5 21:59:37 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 18:59:37 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] a95133: add default .shipit file Message-ID: <20100606015937.43EAE42177@smtp1.rs.github.com> Branch: refs/heads/topic/refactor Home: http://github.com/bioperl/Bio-FeatureIO Commit: a951334c6b6378dcb995e4009bef3d50a4dae132 http://github.com/bioperl/Bio-FeatureIO/commit/a951334c6b6378dcb995e4009bef3d50a4dae132 Author: Chris Fields Date: 2010-05-17 (Mon, 17 May 2010) Changed paths: A .shipit Log Message: ----------- add default .shipit file Commit: a5c1a15db106e430b3addf5e0a7e7d85b9b1e047 http://github.com/bioperl/Bio-FeatureIO/commit/a5c1a15db106e430b3addf5e0a7e7d85b9b1e047 Author: Chris Fields Date: 2010-05-17 (Mon, 17 May 2010) Changed paths: M t/data/knownGene.gff3 A t/data/knownGene2.gff3 Log Message: ----------- add test files from branch back to master Commit: 3d09f734d474b1e9c4994d116e4a370862e7e1d9 http://github.com/bioperl/Bio-FeatureIO/commit/3d09f734d474b1e9c4994d116e4a370862e7e1d9 Author: Chris Fields Date: 2010-05-17 (Mon, 17 May 2010) Changed paths: A .gitignore M t/FeatureIO.t A t/FeatureIO.x A t/gff.t A t/ptt.t A t/vecscreen.t Log Message: ----------- pull split tests over from refactor branch Commit: b432d295fcce1e5333e4b061a5889822d9de26ae http://github.com/bioperl/Bio-FeatureIO/commit/b432d295fcce1e5333e4b061a5889822d9de26ae Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Log Message: ----------- Merge branch 'master' of github.com:bioperl/Bio-FeatureIO into topic/refactor From noreply at github.com Sat Jun 5 22:15:47 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 19:15:47 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6e2bc2: small doc fixes Message-ID: <20100606021547.8B248422A5@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 6e2bc2392160b5c4aa1ab222143984f2decbc521 http://github.com/bioperl/bioperl-live/commit/6e2bc2392160b5c4aa1ab222143984f2decbc521 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M Bio/Tools/EUtilities.pm M Bio/Tools/EUtilities/Query.pm Log Message: ----------- small doc fixes From noreply at github.com Sat Jun 5 22:18:50 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 19:18:50 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 8ac5f4: fixed wrong interpretation of locations in bed fil... Message-ID: <20100606021850.465A2422A5@smtp1.rs.github.com> Branch: refs/heads/local/vinanna/master Home: http://github.com/bioperl/bioperl-live Commit: 8ac5f4d1a02e67be30338f70429efde3e20b23a0 http://github.com/bioperl/bioperl-live/commit/8ac5f4d1a02e67be30338f70429efde3e20b23a0 Author: pkensche Date: 2010-05-14 (Fri, 14 May 2010) Changed paths: M Bio/FeatureIO/bed.pm M t/SeqFeature/FeatureIO.t A t/data/1.bed Log Message: ----------- fixed wrong interpretation of locations in bed files; added a test file plus tests for this From noreply at github.com Sat Jun 5 22:18:52 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 19:18:52 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6e2bc2: small doc fixes Message-ID: <20100606021852.2CCAF422A5@smtp1.rs.github.com> Branch: refs/heads/topic/rm_seqfeat_annotated Home: http://github.com/bioperl/bioperl-live Commit: 6e2bc2392160b5c4aa1ab222143984f2decbc521 http://github.com/bioperl/bioperl-live/commit/6e2bc2392160b5c4aa1ab222143984f2decbc521 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M Bio/Tools/EUtilities.pm M Bio/Tools/EUtilities/Query.pm Log Message: ----------- small doc fixes From noreply at github.com Sat Jun 5 22:34:18 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 19:34:18 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6e2bc2: small doc fixes Message-ID: <20100606023418.3C903422AB@smtp1.rs.github.com> Branch: refs/heads/topic/switch_sf_annotated Home: http://github.com/bioperl/bioperl-live Commit: 6e2bc2392160b5c4aa1ab222143984f2decbc521 http://github.com/bioperl/bioperl-live/commit/6e2bc2392160b5c4aa1ab222143984f2decbc521 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M Bio/Tools/EUtilities.pm M Bio/Tools/EUtilities/Query.pm Log Message: ----------- small doc fixes From noreply at github.com Sat Jun 5 22:44:04 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 19:44:04 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 23590e: initial changeover to simple SF::Generic Message-ID: <20100606024404.355B5422CF@smtp1.rs.github.com> Branch: refs/heads/topic/switch_sf_annotated Home: http://github.com/bioperl/bioperl-live Commit: 23590eeec7b8f01703a149a302151e48af0dda7f http://github.com/bioperl/bioperl-live/commit/23590eeec7b8f01703a149a302151e48af0dda7f Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M Bio/Tools/Match.pm M Bio/Tools/Phylo/Gerp.pm M Bio/Tools/Phylo/Gumby.pm Log Message: ----------- initial changeover to simple SF::Generic From noreply at github.com Sat Jun 5 22:54:38 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 19:54:38 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 2b1489: alias source_tag() to source() Message-ID: <20100606025438.C07D34219F@smtp1.rs.github.com> Branch: refs/heads/topic/switch_sf_annotated Home: http://github.com/bioperl/bioperl-live Commit: 2b1489da0d5aad839588e5e1cde2bd330fb5233c http://github.com/bioperl/bioperl-live/commit/2b1489da0d5aad839588e5e1cde2bd330fb5233c Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M Bio/SeqFeature/Generic.pm Log Message: ----------- alias source_tag() to source() Commit: 89f34ce5634b99b99fe0a59d4a5c9c75f7d23749 http://github.com/bioperl/bioperl-live/commit/89f34ce5634b99b99fe0a59d4a5c9c75f7d23749 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M t/Tools/Match.t Log Message: ----------- get tests for Match.t working; should check interface (which SF::Annotated broke) and converge usage of source/source_tag for the time being to be consistent From noreply at github.com Sat Jun 5 23:04:07 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 20:04:07 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 4207d8: Gerp.t now passes Message-ID: <20100606030407.E568142096@smtp1.rs.github.com> Branch: refs/heads/topic/switch_sf_annotated Home: http://github.com/bioperl/bioperl-live Commit: 4207d8bfe8644fe66b0f5ff620a1f30b48d27de2 http://github.com/bioperl/bioperl-live/commit/4207d8bfe8644fe66b0f5ff620a1f30b48d27de2 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M t/Tools/Match.t M t/Tools/Phylo/Gerp.t Log Message: ----------- Gerp.t now passes Commit: 2a2155692ea2927d91256b95cbc4cddce9d23062 http://github.com/bioperl/bioperl-live/commit/2a2155692ea2927d91256b95cbc4cddce9d23062 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M Bio/Tools/Match.pm M Bio/Tools/Phylo/Gerp.pm M Bio/Tools/Phylo/Gumby.pm Log Message: ----------- add message about the changeover From noreply at github.com Sat Jun 5 23:09:26 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 20:09:26 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 08154e: remove Bio::SF::Annotated and tests Message-ID: <20100606030926.39C7C42173@smtp1.rs.github.com> Branch: refs/heads/topic/switch_sf_annotated Home: http://github.com/bioperl/bioperl-live Commit: 08154e451dc589e23fd8c998f1d9817cc7010c04 http://github.com/bioperl/bioperl-live/commit/08154e451dc589e23fd8c998f1d9817cc7010c04 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: R Bio/SeqFeature/Annotated.pm R t/SeqFeature/SeqFeatAnnotated.t Log Message: ----------- remove Bio::SF::Annotated and tests From noreply at github.com Sat Jun 5 23:10:56 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 20:10:56 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] df7205: add SF::Annotated and tests Message-ID: <20100606031056.15C6342171@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: df720565b65b8a0f9e9e20fa725898c1d344414c http://github.com/bioperl/Bio-FeatureIO/commit/df720565b65b8a0f9e9e20fa725898c1d344414c Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: A lib/Bio/SeqFeature/Annotated.pm A t/SeqFeature/Annotated.t Log Message: ----------- add SF::Annotated and tests From noreply at github.com Sat Jun 5 23:12:08 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 20:12:08 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 15f917: add bed fixes from live Message-ID: <20100606031209.0980342171@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 15f917042ce67d2ed2d8e4ccb34d018a15edf9c6 http://github.com/bioperl/Bio-FeatureIO/commit/15f917042ce67d2ed2d8e4ccb34d018a15edf9c6 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M lib/Bio/FeatureIO/bed.pm Log Message: ----------- add bed fixes from live Commit: aeea2fea4439815105c0f85a043134a8f94b33f5 http://github.com/bioperl/Bio-FeatureIO/commit/aeea2fea4439815105c0f85a043134a8f94b33f5 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M t/FeatureIO.t Log Message: ----------- add modules for comp check From noreply at github.com Sat Jun 5 23:13:44 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 20:13:44 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 4b4ea7: add test bed file Message-ID: <20100606031344.9015E42171@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 4b4ea70a54243fef90a444b9e1dbe1e0bc3ff2cd http://github.com/bioperl/Bio-FeatureIO/commit/4b4ea70a54243fef90a444b9e1dbe1e0bc3ff2cd Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: A t/data/1.bed Log Message: ----------- add test bed file From noreply at github.com Sat Jun 5 23:21:42 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 20:21:42 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] fe2ae0: tweaks to get network tests running, recursive tes... Message-ID: <20100606032142.1E92B4229B@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: fe2ae0e7317024ab73933d549a0421b7048e95e1 http://github.com/bioperl/Bio-FeatureIO/commit/fe2ae0e7317024ab73933d549a0421b7048e95e1 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M Build.PL Log Message: ----------- tweaks to get network tests running, recursive tests, etc. Commit: fb402f465ddc9537c654f00a0302f32b685366bf http://github.com/bioperl/Bio-FeatureIO/commit/fb402f465ddc9537c654f00a0302f32b685366bf Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: A t/bed.t Log Message: ----------- add bed.t From noreply at github.com Sat Jun 5 23:24:17 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 20:24:17 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 379e2f: repo changed Message-ID: <20100606032417.30E964229E@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 379e2f23555e218d486143aa3e81339848a6f1c7 http://github.com/bioperl/Bio-FeatureIO/commit/379e2f23555e218d486143aa3e81339848a6f1c7 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M Build.PL Log Message: ----------- repo changed From noreply at github.com Sat Jun 5 23:25:37 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 20:25:37 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 720e8e: rm empty class and dir for the time being (cleanup... Message-ID: <20100606032537.41AA7422A2@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 720e8ec1279d74dba4e4f7c4d375f6c91283520a http://github.com/bioperl/Bio-FeatureIO/commit/720e8ec1279d74dba4e4f7c4d375f6c91283520a Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: R lib/Bio/Factory/FeatureFactory.pm Log Message: ----------- rm empty class and dir for the time being (cleanup) From noreply at github.com Sat Jun 5 23:34:39 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 20:34:39 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 96b9aa: remove two interface tests for SF::Annotated to Bi... Message-ID: <20100606033439.5CF89422A5@smtp1.rs.github.com> Branch: refs/heads/topic/switch_sf_annotated Home: http://github.com/bioperl/bioperl-live Commit: 96b9aa4fc66a04b4cc35afabb4837ef2f8d4ee1d http://github.com/bioperl/bioperl-live/commit/96b9aa4fc66a04b4cc35afabb4837ef2f8d4ee1d Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M t/Annotation/Annotation.t Log Message: ----------- remove two interface tests for SF::Annotated to Bio-FeatureIO From noreply at github.com Sat Jun 5 23:35:32 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 20:35:32 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 1a3503: add interface tests for SF::Annotated Message-ID: <20100606033532.782F2422A5@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 1a3503de445fc7b93adf04b1095e6c589c599f5c http://github.com/bioperl/Bio-FeatureIO/commit/1a3503de445fc7b93adf04b1095e6c589c599f5c Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M t/FeatureIO.t M t/SeqFeature/Annotated.t Log Message: ----------- add interface tests for SF::Annotated From noreply at github.com Sat Jun 5 23:36:48 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 20:36:48 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] f593ac: update MANIFEST Message-ID: <20100606033648.BCE19422A5@smtp1.rs.github.com> Branch: refs/heads/topic/switch_sf_annotated Home: http://github.com/bioperl/bioperl-live Commit: f593ac605ac2df3c474730f2f11a5d409c71fe41 http://github.com/bioperl/bioperl-live/commit/f593ac605ac2df3c474730f2f11a5d409c71fe41 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M MANIFEST Log Message: ----------- update MANIFEST From noreply at github.com Sun Jun 6 00:06:12 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 21:06:12 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 2ccc1a: merge two files over from the branch Message-ID: <20100606040612.7AC6B422CF@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 2ccc1a335fd2647461be4350f97b6aeb05735ba3 http://github.com/bioperl/Bio-FeatureIO/commit/2ccc1a335fd2647461be4350f97b6aeb05735ba3 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: A lib/Bio/Event/SimpleEventGeneratorI.pm A lib/Bio/FeatureIO/Handler/GenericFeatureHandler.pm Log Message: ----------- merge two files over from the branch Commit: ce1ce6c65f7f09477a0c59fbec2c95b4c50d35a2 http://github.com/bioperl/Bio-FeatureIO/commit/ce1ce6c65f7f09477a0c59fbec2c95b4c50d35a2 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: R lib/Bio/Event/SimpleEventGeneratorI.pm R lib/Bio/FeatureIO/Handler/GenericFeatureHandler.pm Log Message: ----------- Revert "merge two files over from the branch" This reverts commit 2ccc1a335fd2647461be4350f97b6aeb05735ba3. Commit: b9ec9ce85c29d7181ed6b5b021e56c65fcf313f5 http://github.com/bioperl/Bio-FeatureIO/commit/b9ec9ce85c29d7181ed6b5b021e56c65fcf313f5 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: A MANIFEST Log Message: ----------- update manifest From noreply at github.com Sun Jun 6 01:07:44 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 22:07:44 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] fe0ee5: init refactoring of FeatureIO, just a simple strea... Message-ID: <20100606050744.9FA31422AE@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: fe0ee5320345504a721819b572fc57f9c3730c00 http://github.com/bioperl/Bio-FeatureIO/commit/fe0ee5320345504a721819b572fc57f9c3730c00 Author: cjfields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M lib/Bio/FeatureIO.pm M lib/Bio/FeatureIO/gff.pm M t/gff.t Log Message: ----------- init refactoring of FeatureIO, just a simple stream of Generics at the moment Commit: a6c05c68a3b704686be092835e60f7973d6528d5 http://github.com/bioperl/Bio-FeatureIO/commit/a6c05c68a3b704686be092835e60f7973d6528d5 Author: cjfields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: A lib/Bio/FeatureIO/Handler/GenericFeatureHandler.pm A lib/Bio/FeatureIO/Handler/GenericHandler.pm Log Message: ----------- add handler svn path=/Bio-FeatureIO/trunk/; revision=16850 Commit: 577e8dc6b90c93502937662fc84a23770a636520 http://github.com/bioperl/Bio-FeatureIO/commit/577e8dc6b90c93502937662fc84a23770a636520 Author: cjfields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: R lib/Bio/FeatureIO/Handler/GenericHandler.pm Log Message: ----------- remove redundant handler svn path=/Bio-FeatureIO/trunk/; revision=16851 Commit: 49f3ee94a7f89bed3b91d087b4d4ca1b439b463b http://github.com/bioperl/Bio-FeatureIO/commit/49f3ee94a7f89bed3b91d087b4d4ca1b439b463b Author: rbuels Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M lib/Bio/FeatureIO/bed.pm M lib/Bio/FeatureIO/interpro.pm Log Message: ----------- removed unnecessary use of Bio::OntologyIO from interpro and bed FeatureIO drivers svn path=/Bio-FeatureIO/trunk/; revision=16921 From noreply at github.com Sun Jun 6 01:09:46 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 22:09:46 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 5758a7: get sequence parsing working Message-ID: <20100606050946.9E714422AE@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 5758a7150ab2f578260ada0ea7aa2c429120bd5b http://github.com/bioperl/Bio-FeatureIO/commit/5758a7150ab2f578260ada0ea7aa2c429120bd5b Author: cjfields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M lib/Bio/FeatureIO.pm M lib/Bio/FeatureIO/Handler/GenericFeatureHandler.pm M lib/Bio/FeatureIO/gff.pm Log Message: ----------- get sequence parsing working From noreply at github.com Sun Jun 6 01:11:51 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 22:11:51 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 0b77e5: get sequence parsing working Message-ID: <20100606051151.36D92422AE@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 0b77e59d91c790011524ef0e2d24c99d2149e524 http://github.com/bioperl/Bio-FeatureIO/commit/0b77e59d91c790011524ef0e2d24c99d2149e524 Author: cjfields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M lib/Bio/FeatureIO/gff.pm Log Message: ----------- get sequence parsing working svn path=/Bio-FeatureIO/trunk/; revision=16936 Commit: 77cab7cf66e01be3113f94736bcb4ef4d36180d1 http://github.com/bioperl/Bio-FeatureIO/commit/77cab7cf66e01be3113f94736bcb4ef4d36180d1 Author: cjfields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M lib/Bio/FeatureIO/Handler/GenericFeatureHandler.pm M lib/Bio/FeatureIO/gff.pm Log Message: ----------- use interface, not implementation svn path=/Bio-FeatureIO/trunk/; revision=16937 Commit: e259d358b63d9c024c2872cc5dc29a84f95db9e6 http://github.com/bioperl/Bio-FeatureIO/commit/e259d358b63d9c024c2872cc5dc29a84f95db9e6 Author: cjfields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M lib/Bio/FeatureIO/Handler/GenericFeatureHandler.pm M lib/Bio/FeatureIO/gff.pm M t/gff.t Log Message: ----------- simple feature groups implemented, but this should delegate to a database iterator svn path=/Bio-FeatureIO/trunk/; revision=16938 From noreply at github.com Sun Jun 6 01:13:42 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 22:13:42 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] fec78f: how about actually testing the features themselves... Message-ID: <20100606051342.B5284422AE@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: fec78f23f784ac12c2db4bfb85731242339b840e http://github.com/bioperl/Bio-FeatureIO/commit/fec78f23f784ac12c2db4bfb85731242339b840e Author: cjfields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M lib/Bio/FeatureIO/Handler/GenericFeatureHandler.pm M lib/Bio/FeatureIO/gff.pm M t/gff.t Log Message: ----------- how about actually testing the features themselves, instead of just relying on whether it exists or not svn path=/Bio-FeatureIO/trunk/; revision=16939 From noreply at github.com Sun Jun 6 01:14:45 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 22:14:45 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 66ca49: get iterative feature groups working along with se... Message-ID: <20100606051445.A7746422D2@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 66ca4929616018122357209f2ac84314f7800d56 http://github.com/bioperl/Bio-FeatureIO/commit/66ca4929616018122357209f2ac84314f7800d56 Author: cjfields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M lib/Bio/FeatureIO/Handler/GenericFeatureHandler.pm M lib/Bio/FeatureIO/gff.pm Log Message: ----------- get iterative feature groups working along with sequence stream svn path=/Bio-FeatureIO/trunk/; revision=16940 From noreply at github.com Sun Jun 6 01:20:08 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 22:20:08 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 6b1cf2: update manifest Message-ID: <20100606052008.96AAE422CF@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 6b1cf20083b14fdcf86e69d7b425c4d13c446d3d http://github.com/bioperl/Bio-FeatureIO/commit/6b1cf20083b14fdcf86e69d7b425c4d13c446d3d Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M MANIFEST Log Message: ----------- update manifest Commit: 8e084c271edea26affa762e8e8f6a5ce6e04fad7 http://github.com/bioperl/Bio-FeatureIO/commit/8e084c271edea26affa762e8e8f6a5ce6e04fad7 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M MANIFEST Log Message: ----------- no, really update manifest Commit: 344ae6fec26aecd293b8b17abcfc2473c5743238 http://github.com/bioperl/Bio-FeatureIO/commit/344ae6fec26aecd293b8b17abcfc2473c5743238 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M .gitignore A MANIFEST.SKIP Log Message: ----------- add MANIFEST.SKIP, .gitignore From noreply at github.com Sun Jun 6 01:31:15 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 22:31:15 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] dd9e93: fix gff tests (missing paren) Message-ID: <20100606053115.B97B4422CF@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: dd9e932319d86e72637f3220d663b2e712528c31 http://github.com/bioperl/Bio-FeatureIO/commit/dd9e932319d86e72637f3220d663b2e712528c31 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M t/gff.t Log Message: ----------- fix gff tests (missing paren) Commit: fdd5fc986f983825ec184e8182f6276b861097af http://github.com/bioperl/Bio-FeatureIO/commit/fdd5fc986f983825ec184e8182f6276b861097af Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M lib/Bio/FeatureIO.pm Log Message: ----------- remove old interface, which should be defined in core at some point (maybe after talking at BOSC) From noreply at github.com Sun Jun 6 01:36:26 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 22:36:26 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 4295cc: all tests now pass, but require core Bio::Root::Te... Message-ID: <20100606053627.095AB42290@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 4295cccf68ce7844f7425d4a3443e4cab8b4251e http://github.com/bioperl/Bio-FeatureIO/commit/4295cccf68ce7844f7425d4a3443e4cab8b4251e Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M t/FeatureIO.t M t/SeqFeature/Annotated.t Log Message: ----------- all tests now pass, but require core Bio::Root::Test tweaks for done_testing compat From noreply at github.com Sun Jun 6 01:38:05 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 22:38:05 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 04fa25: allow condition where no tests are passed in (for ... Message-ID: <20100606053805.41A8C42290@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 04fa25a71d0feab90536370b952e08e1dd703388 http://github.com/bioperl/bioperl-live/commit/04fa25a71d0feab90536370b952e08e1dd703388 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M Bio/Root/Test.pm Log Message: ----------- allow condition where no tests are passed in (for done_testing() compat) From razi.khaja at gmail.com Sun Jun 6 10:15:31 2010 From: razi.khaja at gmail.com (Razi Khaja) Date: Sun, 6 Jun 2010 10:15:31 -0400 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b4fb80: patch for Bug 3090, courtesy of Razi Khaja. New te... In-Reply-To: <7AE7A1CD-21DF-401D-A10E-6EC7DB3C17E5@sbc.su.se> References: <20100605014644.4FE47422F5@smtp1.rs.github.com> <7AE7A1CD-21DF-401D-A10E-6EC7DB3C17E5@sbc.su.se> Message-ID: Hi Dave, I did read the Using_Git page, and tried following the instructions, but I think that the Using_Git page is written for core developers and collaborators. I think that the HOWTO:SubmitPatch page needs to be updated to reflect the use of github without developer accounts. http://www.bioperl.org/wiki/HOWTO:SubmitPatch For my next patch, I'll try experimenting with github again. Razi On Sun, Jun 6, 2010 at 8:07 AM, Dave Messina wrote: > Hi Razi, > > > On Jun 5, 2010, at 4:10 AM, Razi Khaja wrote: > > > Your welcome! Thanks for the enthusiasm about the tests! > > Absolutely! Your work is much appreciated. (Please do more! :) > > > > Now I just have to > > figure out how to use github and send pull or push requests. I will try > and > > figure that out for my next set of patch(es). > > If you haven't already, take a look at our Using Git page: > > http://www.bioperl.org/wiki/Using_Git > > > But no hurry. I saw you submitted another patch via Bugzilla, which is just > fine. > > > Dave > > From noreply at github.com Sun Jun 6 14:01:17 2010 From: noreply at github.com (noreply at github.com) Date: Sun, 6 Jun 2010 11:01:17 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] a82f88: Merge branch 'master' into topic/update-1-6 Message-ID: <20100606180118.09010422AB@smtp1.rs.github.com> Branch: refs/heads/topic/update-1-6 Home: http://github.com/bioperl/bioperl-live Commit: a82f8875d2ef955845fa52f4a6c31369287d50c8 http://github.com/bioperl/bioperl-live/commit/a82f8875d2ef955845fa52f4a6c31369287d50c8 Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: A .gitignore A .shipit M Bio/Align/DNAStatistics.pm A Bio/Align/Graphics.pm M Bio/AlignIO.pm M Bio/AlignIO/arp.pm M Bio/AlignIO/clustalw.pm M Bio/AlignIO/emboss.pm M Bio/AlignIO/fasta.pm M Bio/AlignIO/largemultifasta.pm M Bio/AlignIO/maf.pm M Bio/AlignIO/mase.pm M Bio/AlignIO/mega.pm M Bio/AlignIO/meme.pm M Bio/AlignIO/metafasta.pm M Bio/AlignIO/msf.pm A Bio/AlignIO/nexml.pm M Bio/AlignIO/nexus.pm M Bio/AlignIO/pfam.pm M Bio/AlignIO/phylip.pm M Bio/AlignIO/po.pm M Bio/AlignIO/proda.pm M Bio/AlignIO/prodom.pm M Bio/AlignIO/psi.pm M Bio/AlignIO/selex.pm M Bio/AlignIO/stockholm.pm M Bio/AlignIO/xmfa.pm M Bio/Annotation/Relation.pm M Bio/Assembly/Contig.pm M Bio/Assembly/IO.pm M Bio/Assembly/IO/ace.pm A Bio/Assembly/IO/bowtie.pm A Bio/Assembly/IO/maq.pm M Bio/Assembly/IO/phrap.pm A Bio/Assembly/IO/sam.pm M Bio/Assembly/IO/tigr.pm M Bio/Assembly/Scaffold.pm M Bio/Assembly/Singlet.pm M Bio/Assembly/Tools/ContigSpectrum.pm M Bio/DB/CUTG.pm M Bio/DB/DBFetch.pm M Bio/DB/EUtilities.pm M Bio/DB/Fasta.pm M Bio/DB/Flat/BinarySearch.pm M Bio/DB/GFF.pm M Bio/DB/GFF/Adaptor/dbi.pm M Bio/DB/GFF/Adaptor/dbi/oracle.pm M Bio/DB/SeqFeature/Segment.pm M Bio/DB/SeqFeature/Store.pm M Bio/DB/SeqFeature/Store/DBI/Pg.pm M Bio/DB/SeqFeature/Store/DBI/SQLite.pm M Bio/DB/SeqFeature/Store/DBI/mysql.pm M Bio/DB/SeqFeature/Store/FeatureFileLoader.pm M Bio/DB/SeqFeature/Store/GFF3Loader.pm M Bio/DB/SeqFeature/Store/Loader.pm M Bio/DB/SeqFeature/Store/berkeleydb3.pm M Bio/DB/SeqFeature/Store/memory.pm M Bio/DB/SwissProt.pm M Bio/DB/TFBS/transfac_pro.pm M Bio/DB/Taxonomy/entrez.pm M Bio/DB/Taxonomy/flatfile.pm A Bio/Draw/Pictogram.pm M Bio/FeatureHolderI.pm M Bio/FeatureIO.pm M Bio/FeatureIO/bed.pm M Bio/FeatureIO/gff.pm M Bio/Index/Abstract.pm M Bio/Index/Blast.pm M Bio/Index/BlastTable.pm M Bio/LocatableSeq.pm M Bio/Location/Split.pm A Bio/Microarray/Tools/MitoChipV2Parser.pm A Bio/Microarray/Tools/ReseqChip.pm A Bio/Nexml/Factory.pm A Bio/NexmlIO.pm M Bio/Ontology/OBOEngine.pm M Bio/OntologyIO/obo.pm M Bio/Perl.pm M Bio/PrimarySeq.pm M Bio/PrimarySeqI.pm M Bio/PullParserI.pm M Bio/Range.pm M Bio/RangeI.pm M Bio/Restriction/Analysis.pm M Bio/Restriction/IO/base.pm M Bio/Restriction/IO/withrefm.pm M Bio/Root/Build.pm M Bio/Root/HTTPget.pm M Bio/Root/IO.pm M Bio/Root/Root.pm M Bio/Root/Test.pm M Bio/Root/Version.pm M Bio/Search/HSP/BlastHSP.pm M Bio/Search/HSP/GenericHSP.pm M Bio/Search/Hit/BlastPullHit.pm M Bio/Search/Hit/ModelHit.pm M Bio/Search/Result/BlastPullResult.pm M Bio/Search/Result/GenericResult.pm M Bio/Search/Result/ResultI.pm M Bio/Search/SearchUtils.pm M Bio/Search/Tiling/MapTileUtils.pm M Bio/Search/Tiling/MapTiling.pm M Bio/SearchIO/Writer/ResultTableWriter.pm M Bio/SearchIO/blast.pm M Bio/SearchIO/blasttable.pm M Bio/SearchIO/exonerate.pm M Bio/SearchIO/fasta.pm M Bio/SearchIO/gmap_f9.pm M Bio/SearchIO/megablast.pm M Bio/SearchIO/psl.pm M Bio/SearchIO/sim4.pm M Bio/SearchIO/wise.pm M Bio/Seq.pm M Bio/Seq/Meta/Array.pm M Bio/Seq/Quality.pm M Bio/Seq/RichSeq.pm M Bio/Seq/RichSeqI.pm M Bio/Seq/SeqFastaSpeedFactory.pm M Bio/SeqFeature/Lite.pm M Bio/SeqFeature/Tools/IDHandler.pm M Bio/SeqFeature/Tools/TypeMapper.pm M Bio/SeqFeature/Tools/Unflattener.pm M Bio/SeqIO.pm M Bio/SeqIO/Handler/GenericRichSeqHandler.pm M Bio/SeqIO/abi.pm M Bio/SeqIO/embl.pm M Bio/SeqIO/fastq.pm A Bio/SeqIO/gbxml.pm M Bio/SeqIO/genbank.pm A Bio/SeqIO/nexml.pm M Bio/SeqIO/scf.pm A Bio/SeqIO/seqxml.pm M Bio/SeqUtils.pm M Bio/SimpleAlign.pm M Bio/Species.pm M Bio/Structure/IO/pdb.pm M Bio/Structure/SecStr/DSSP/Res.pm M Bio/Tools/EUtilities.pm M Bio/Tools/EUtilities/EUtilDataI.pm M Bio/Tools/EUtilities/EUtilParameters.pm M Bio/Tools/EUtilities/HistoryI.pm M Bio/Tools/EUtilities/Info/FieldInfo.pm M Bio/Tools/EUtilities/Info/LinkInfo.pm M Bio/Tools/EUtilities/Link.pm M Bio/Tools/EUtilities/Link/LinkSet.pm M Bio/Tools/EUtilities/Link/UrlLink.pm M Bio/Tools/EUtilities/Query.pm M Bio/Tools/EUtilities/Summary.pm M Bio/Tools/Fgenesh.pm M Bio/Tools/GFF.pm M Bio/Tools/GuessSeqFormat.pm M Bio/Tools/Phylo/PAML.pm M Bio/Tools/Protparam.pm M Bio/Tools/Run/RemoteBlast.pm M Bio/Tools/Run/StandAloneNCBIBlast.pm M Bio/Tools/Run/WrapperBase.pm A Bio/Tools/Run/WrapperBase/CommandExts.pm M Bio/Tools/TandemRepeatsFinder.pm M Bio/Tree/TreeFunctionsI.pm A Bio/TreeIO/nexml.pm M Bio/TreeIO/phyloxml.pm M Build.PL M Changes M DEPENDENCIES M INSTALL.WIN A MANIFEST A MANIFEST.SKIP M README M examples/longorf.pl A ide/bioperl-mode/dist/Changes M ide/bioperl-mode/dist/bioperl-mode-xemacs.tar M ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5 M ide/bioperl-mode/dist/bioperl-mode.tar M ide/bioperl-mode/dist/bioperl-mode.tar.md5 M ide/bioperl-mode/site-lisp/bioperl-init.el M ide/bioperl-mode/site-lisp/bioperl-mode.el M ide/bioperl-mode/site-lisp/bioperl-skel.el M scripts/Bio-DB-EUtilities/einfo.PLS M scripts/Bio-DB-GFF/genbank2gff3.PLS M scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS M t/Align/AlignStats.t A t/Align/Graphics.t M t/Align/SimpleAlign.t M t/AlignIO/maf.t A t/AlignIO/nexml.t M t/AlignIO/stockholm.t M t/AlignIO/xmfa.t M t/Assembly/Assembly.t M t/Assembly/ContigSpectrum.t A t/Draw/Pictogram.t R t/LocalDB/BlastIndex.t M t/LocalDB/DBFasta.t R t/LocalDB/Index.t A t/LocalDB/Index/Blast.t A t/LocalDB/Index/BlastTable.t A t/LocalDB/Index/Index.t M t/LocalDB/SeqFeature.t M t/Map/Map.t A t/Microarray/Tools/ReseqChip.t M t/RemoteDB/EUtilities.t M t/RemoteDB/Query/GenBank.t M t/RemoteDB/SwissProt.t M t/RemoteDB/Taxonomy.t M t/Restriction/Analysis-refac.t A t/Root/HTTPget.t M t/Root/RootIO.t M t/SearchIO/Tiling.t M t/SearchIO/blast.t M t/SearchIO/fasta.t M t/SearchIO/gmap_f9.t M t/SearchIO/infernal.t M t/SearchIO/rnamotif.t M t/Seq/PrimarySeq.t M t/Seq/Quality.t M t/Seq/Seq.t M t/SeqFeature/FeatureIO.t M t/SeqFeature/RangeI.t M t/SeqFeature/Unflattener.t M t/SeqIO/embl.t A t/SeqIO/gbxml.t M t/SeqIO/genbank.t A t/SeqIO/nexml.t M t/SeqIO/scf.t A t/SeqIO/seqxml.t M t/SeqTools/GuessSeqFormat.t M t/SeqTools/SeqUtils.t M t/Tools/EUtilities/EUtilParameters.t M t/Tools/Phylo/PAML.t A t/Tools/Run/Dummy.pm A t/Tools/Run/Dummy/Config.pm M t/Tools/Run/RemoteBlast.t M t/Tools/Run/RemoteBlast_rpsblast.t A t/Tools/Run/WBCommandExts.t M t/Tools/Run/WrapperBase.t M t/Tools/TandemRepeatsFinder.t M t/Tree/TreeIO.t A t/Tree/TreeIO/nexml.t M t/Tree/TreeIO/phyloxml.t A t/data/01_basic.xml A t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml A t/data/02_dogfish_no_taxrefs.xml A t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml A t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml A t/data/02_mackerel_dict_cdao_lsid_taxrefs.xml A t/data/02_mackerel_no_taxrefs.xml A t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml A t/data/02_mackerel_rdfa_tdwg_lsid_taxrefs.xml A t/data/03_bootstraps.xml A t/data/03_bootstraps_in_tag.xml A t/data/04_labeled_ancestors.xml A t/data/05_ancestral_states.xml A t/data/1.bed A t/data/27-contig_Newbler.ace A t/data/EG352462.gbxml A t/data/Fang_2003.xml A t/data/ReseqChip_ParamsNcall.csv A t/data/U71225.gb.unix A t/data/U71225.gb.win M t/data/assembly_with_singlets.ace A t/data/blast_plus.blastp A t/data/bug2869.tree A t/data/bug2901.fa A t/data/bug2937.fasta A t/data/bug2942.blastx A t/data/bug2982.embl A t/data/bug2982.gb A t/data/bug3021.gmap A t/data/bug3086.embl A t/data/characters+trees.nexml.xml A t/data/characters.nexml.old.xml A t/data/characters.nexml.xml A t/data/codeml43.mlc A t/data/codeml43_nssites.mlc A t/data/codeml_nan.mlc R t/data/contigspectrumtest.asm A t/data/contigspectrumtest.tigr A t/data/multi.blast.m8 A t/data/multi.blast.m9 M t/data/phyloxml_examples.xml A t/data/reference_ace.ace A t/data/ribosome-slippage.gb A t/data/roa1.gbxml R t/data/sample_dataset.tasm A t/data/sample_dataset.tigr A t/data/seqxml.xml A t/data/tandem_repeats_finder_no_desc.dat M t/data/taxdump/names.dmp A t/data/test.bam A t/data/test.bowtie A t/data/test.cns.fastq A t/data/test.fastq A t/data/test.maq A t/data/test.ref.fas M t/data/test_clear_range.fastq A t/data/test_singlets.cns.fastq A t/data/test_singlets.maq A t/data/testaln.fastq A t/data/trees.nexml.old.xml A t/data/trees.nexml.xml A t/nexml.t Log Message: ----------- Merge branch 'master' into topic/update-1-6 Conflicts: Bio/Align/DNAStatistics.pm Bio/AlignIO/msf.pm Bio/Assembly/Contig.pm Bio/Assembly/IO/phrap.pm Bio/Assembly/IO/tigr.pm Bio/Assembly/Tools/ContigSpectrum.pm Bio/DB/SeqFeature/Store/DBI/Pg.pm Bio/DB/SeqFeature/Store/DBI/SQLite.pm Bio/DB/SeqFeature/Store/DBI/mysql.pm Bio/DB/SeqFeature/Store/FeatureFileLoader.pm Bio/DB/SeqFeature/Store/GFF3Loader.pm Bio/DB/SeqFeature/Store/Loader.pm Bio/DB/SeqFeature/Store/berkeleydb3.pm Bio/DB/SeqFeature/Store/memory.pm Bio/DB/SwissProt.pm Bio/Microarray/Tools/MitoChipV2Parser.pm Bio/Microarray/Tools/ReseqChip.pm Bio/PrimarySeq.pm Bio/Restriction/IO/withrefm.pm Bio/Root/Build.pm Bio/Root/IO.pm Bio/Root/Test.pm Bio/Root/Version.pm Bio/Search/Tiling/MapTileUtils.pm Bio/Search/Tiling/MapTiling.pm Bio/SearchIO/gmap_f9.pm Bio/SearchIO/psl.pm Bio/Seq/Quality.pm Bio/SeqFeature/Lite.pm Bio/SeqFeature/Tools/TypeMapper.pm Bio/SeqIO.pm Bio/SeqIO/embl.pm Bio/SeqIO/fastq.pm Bio/SeqIO/genbank.pm Bio/SeqIO/scf.pm Bio/Tools/Phylo/PAML.pm Bio/Tools/Run/RemoteBlast.pm Build.PL Changes DEPENDENCIES README ide/bioperl-mode/dist/bioperl-mode-xemacs.tar ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5 ide/bioperl-mode/dist/bioperl-mode.tar ide/bioperl-mode/dist/bioperl-mode.tar.md5 ide/bioperl-mode/site-lisp/bioperl-init.el ide/bioperl-mode/site-lisp/bioperl-mode.el ide/bioperl-mode/site-lisp/bioperl-skel.el scripts/Bio-DB-EUtilities/einfo.PLS scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS t/Align/SimpleAlign.t t/Assembly/Assembly.t t/Assembly/ContigSpectrum.t t/LocalDB/DBFasta.t t/LocalDB/SeqFeature.t t/Map/Map.t t/Microarray/Tools/ReseqChip.t t/RemoteDB/Query/GenBank.t t/RemoteDB/SwissProt.t t/Restriction/Analysis-refac.t t/SearchIO/Tiling.t t/SearchIO/blast.t t/SearchIO/fasta.t t/SearchIO/gmap_f9.t t/SearchIO/infernal.t t/Seq/PrimarySeq.t t/Seq/Quality.t t/Seq/Seq.t t/SeqIO/embl.t t/SeqIO/genbank.t t/SeqIO/scf.t t/SeqTools/SeqUtils.t t/Tools/Run/RemoteBlast_rpsblast.t t/Tree/TreeIO.t t/Tree/TreeIO/phyloxml.t t/data/test_clear_range.fastq Signed-off-by: Chris Fields From noreply at github.com Sun Jun 6 14:16:14 2010 From: noreply at github.com (noreply at github.com) Date: Sun, 6 Jun 2010 11:16:14 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 01d967: added more intensive tests for longest-orf-finding... Message-ID: <20100606181614.5F2CB4202C@smtp1.rs.github.com> Branch: refs/heads/topic/longest_orf Home: http://github.com/bioperl/bioperl-live Commit: 01d967281382b6528f9250db80387f108f42d77e http://github.com/bioperl/bioperl-live/commit/01d967281382b6528f9250db80387f108f42d77e Author: Robert Buels Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M t/Seq/PrimarySeq.t Log Message: ----------- added more intensive tests for longest-orf-finding translate() From noreply at github.com Sun Jun 6 14:32:25 2010 From: noreply at github.com (noreply at github.com) Date: Sun, 6 Jun 2010 11:32:25 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 04fa25: allow condition where no tests are passed in (for ... Message-ID: <20100606183225.8AA9B422A7@smtp1.rs.github.com> Branch: refs/heads/topic/update-1-6 Home: http://github.com/bioperl/bioperl-live Commit: 04fa25a71d0feab90536370b952e08e1dd703388 http://github.com/bioperl/bioperl-live/commit/04fa25a71d0feab90536370b952e08e1dd703388 Author: Chris Fields Date: 2010-06-05 (Sat, 05 Jun 2010) Changed paths: M Bio/Root/Test.pm Log Message: ----------- allow condition where no tests are passed in (for done_testing() compat) From noreply at github.com Sun Jun 6 15:47:56 2010 From: noreply at github.com (noreply at github.com) Date: Sun, 6 Jun 2010 12:47:56 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] c1b897: Merge Brian's branch Message-ID: <20100606194756.EF1644216F@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: c1b897bcd59dc6dcedb8fff52cd107595647584a http://github.com/bioperl/bioperl-live/commit/c1b897bcd59dc6dcedb8fff52cd107595647584a Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: R examples/root/lib/Bio/PrimarySeq.pm R examples/root/lib/Bio/PrimarySeqI.pm R examples/root/lib/Bio/Seq.pm R examples/root/lib/Bio/SeqI.pm Log Message: ----------- Merge Brian's branch Merge branch 'my_root_branch' From noreply at github.com Sun Jun 6 17:20:18 2010 From: noreply at github.com (noreply at github.com) Date: Sun, 6 Jun 2010 14:20:18 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 04f47a: [bug 3092] parse additional stats from text BLAST ... Message-ID: <20100606212018.996DE42290@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 04f47af9992da7d4176423aeedf6edcae01ffc6d http://github.com/bioperl/bioperl-live/commit/04f47af9992da7d4176423aeedf6edcae01ffc6d Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: M Bio/SearchIO/blast.pm M t/SearchIO/blast.t Log Message: ----------- [bug 3092] parse additional stats from text BLAST reports, patch courtesy Razi Khaja From bugzilla-daemon at portal.open-bio.org Sun Jun 6 17:21:08 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 6 Jun 2010 17:21:08 -0400 Subject: [Bioperl-guts-l] [Bug 3092] Unable to parse 'Number of HSP's better than without gapping', 'Number of HSP's gapped', 'Number of HSP's successfully gapped' and 'Length adjustment' from BLAST reports In-Reply-To: Message-ID: <201006062121.o56LL88w014061@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3092 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |FIXED ------- Comment #2 from cjfields at bioperl.org 2010-06-06 17:21 EST ------- Patch committed to github. Thanks! -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Sun Jun 6 18:40:24 2010 From: noreply at github.com (noreply at github.com) Date: Sun, 6 Jun 2010 15:40:24 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 69f542: expected answer off by two (frameshift Message-ID: <20100606224024.4CDB842039@smtp1.rs.github.com> Branch: refs/heads/topic/bug3084 Home: http://github.com/bioperl/bioperl-live Commit: 69f542c744aa2279bbc67489af7245006edb3c61 http://github.com/bioperl/bioperl-live/commit/69f542c744aa2279bbc67489af7245006edb3c61 Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: M t/SearchIO/fasta.t Log Message: ----------- expected answer off by two (frameshift From bugzilla-daemon at portal.open-bio.org Sun Jun 6 18:51:44 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 6 Jun 2010 18:51:44 -0400 Subject: [Bioperl-guts-l] [Bug 3084] HSPI, frac_identical gives wrong results In-Reply-To: Message-ID: <201006062251.o56MpiXI015664@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3084 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |INVALID ------- Comment #3 from cjfields at bioperl.org 2010-06-06 18:51 EST ------- (In reply to comment #0) > Consider the following HSP: > ------------- > Score = 48.9 bits (115), Expect = 8e-04, Method: Compositional matrix adjust. > Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 14/77 (18%) > Frame = +1 > > Query 371 PSGMLLA-----SCSDDMTLKIWSMKQEVCIHDLQAHNKEIYTIKWSPTGPATSNPNSNI > 425 > P LLA S S D T+++W ++Q VC H L H + +Y++ +SP G > Sbjct 6955270 PGLQLLAFSHPPSASFDSTVRLWDVEQGVCTHTLMKHQEPVYSVAFSPDGK--------- > 6955422 > > Query 426 MLASASFDSTVRLWDIE 442 > LAS SFD V +W+ + > Sbjct 6955423 YLASGSFDKYVHIWNTQ 6955473 > --------------- > > The method 'frac_identical' is not functioning right. > ------------- > Title : frac_identical > Usage : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); > Function: Returns the fraction of identitical positions for this HSP > Returns : Float in range 0.0 -> 1.0 > Args : 'query' = num identical / length of query seq (without gaps) > 'hit' = num identical / length of hit seq (without gaps) > 'total' = num identical / length of alignment (with gaps) > default = 'total' > --------------- > According to the method description, for the HSP above, 'frac_identical' should > return '0.42' with 'hit'. But it doesnt. Now with 'hit' gives '0.13'. With > 'total' gives as expected '0.35'. Hit frac_identical should be 27/((6955473-6955270+1)/3), or 27/68, or 0.397. As for the first HSP in the attached report, the hit frac_identical should be 111/291, or 0.381443. That's exactly what I get using the following, even before I cleaned up GenericHSP (third value in output is the hit). Make sure you are running a current version from git/github, just in case. pyrimidine1:3084 cjfields$ cat test.pl #!/usr/bin/perl -w use Modern::Perl; use Bio::SearchIO; my $in = Bio::SearchIO->new(-file => shift, -format => 'blast'); my $ct = 0; RESULT: while (my $res = $in->next_result) { while (my $hit = $res->next_hit) { while (my $hsp = $hit->next_hsp) { last RESULT if $ct++ == 1; say join("\t", map {$hsp->frac_identical($_)} qw(query total hit)); } } } pyrimidine1:3084 cjfields$ perl test.pl attachment.cgi.txt 0.375 0.373737373737374 0.381443298969072 -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Sun Jun 6 19:26:35 2010 From: noreply at github.com (noreply at github.com) Date: Sun, 6 Jun 2010 16:26:35 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] a6abc2: move seq offset calc into a separate method Message-ID: <20100606232635.1F0B24229C@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: a6abc2474480e1e2fabcd72fe883963576395276 http://github.com/bioperl/bioperl-live/commit/a6abc2474480e1e2fabcd72fe883963576395276 Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: M Bio/Search/HSP/GenericHSP.pm Log Message: ----------- move seq offset calc into a separate method Commit: f600f06cdb475667e5c45387c9ab26cfa761133c http://github.com/bioperl/bioperl-live/commit/f600f06cdb475667e5c45387c9ab26cfa761133c Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: M Bio/Search/HSP/GenericHSP.pm Log Message: ----------- more cleanup of methods Commit: 69f542c744aa2279bbc67489af7245006edb3c61 http://github.com/bioperl/bioperl-live/commit/69f542c744aa2279bbc67489af7245006edb3c61 Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: M t/SearchIO/fasta.t Log Message: ----------- expected answer off by two (frameshift From bugzilla-daemon at portal.open-bio.org Sun Jun 6 21:33:18 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 6 Jun 2010 21:33:18 -0400 Subject: [Bioperl-guts-l] [Bug 3093] New: perldoc Bio::Location::Simple to_FTstring() => to_FTstring Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=3093 Summary: perldoc Bio::Location::Simple to_FTstring() => to_FTstring Product: BioPerl Version: unspecified Platform: PC OS/Version: Windows Status: NEW Severity: normal Priority: P2 Component: Core Components AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: pengyu.ut at gmail.com In perldoc Bio::Location::Simple, "$location->to_FTstring()" should be corrected as "$location->to_FTstring" to_FTstring Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sun Jun 6 21:36:25 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 6 Jun 2010 21:36:25 -0400 Subject: [Bioperl-guts-l] [Bug 3094] New: Bio::Location::Simple valid_location missing Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=3094 Summary: Bio::Location::Simple valid_location missing Product: BioPerl Version: unspecified Platform: PC OS/Version: Windows Status: NEW Severity: normal Priority: P2 Component: Documentation AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: pengyu.ut at gmail.com perldoc Bio::Location::Simple has valid_location. But it is not available in the source code. Should it be removed from perldoc? -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Sun Jun 6 23:19:48 2010 From: noreply at github.com (noreply at github.com) Date: Sun, 6 Jun 2010 20:19:48 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 4b3399: add is_remote docs from Bio::LocationI to Atomic a... Message-ID: <20100607031948.DA78D4205A@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 4b3399d32226e52db2765fd8937592c33debb0a2 http://github.com/bioperl/bioperl-live/commit/4b3399d32226e52db2765fd8937592c33debb0a2 Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: M Bio/Location/Atomic.pm M Bio/Location/Simple.pm Log Message: ----------- add is_remote docs from Bio::LocationI to Atomic and Simple From noreply at github.com Sun Jun 6 23:20:56 2010 From: noreply at github.com (noreply at github.com) Date: Sun, 6 Jun 2010 20:20:56 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] bcb335: small tweak to add for Args in docs Message-ID: <20100607032056.9140D42098@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: bcb335eb2b86e964ab7ce41d513c999ef85a0c8c http://github.com/bioperl/bioperl-live/commit/bcb335eb2b86e964ab7ce41d513c999ef85a0c8c Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: M Bio/Location/Simple.pm M Bio/LocationI.pm Log Message: ----------- small tweak to add for Args in docs From bugzilla-daemon at portal.open-bio.org Sun Jun 6 23:23:55 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 6 Jun 2010 23:23:55 -0400 Subject: [Bioperl-guts-l] [Bug 3093] perldoc Bio::Location::Simple to_FTstring() => to_FTstring In-Reply-To: Message-ID: <201006070323.o573Nt7P020906@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3093 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |INVALID ------- Comment #1 from cjfields at bioperl.org 2010-06-06 23:23 EST ------- The method call is valid either way. It's the same as: my $start = $location->start; -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sun Jun 6 23:25:47 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 6 Jun 2010 23:25:47 -0400 Subject: [Bioperl-guts-l] [Bug 3094] Bio::Location::Simple valid_location missing In-Reply-To: Message-ID: <201006070325.o573PlJS020984@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3094 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |INVALID ------- Comment #1 from cjfields at bioperl.org 2010-06-06 23:25 EST ------- No, it has the method, it is defined in the parent class, Bio::Location::Atomic. But we include the documentation to indicate it can do the method. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Sun Jun 6 23:44:32 2010 From: noreply at github.com (noreply at github.com) Date: Sun, 6 Jun 2010 20:44:32 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] de6316: [bug 3089] iteration and found_again added to Gene... Message-ID: <20100607034432.082594216F@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: de6316c652a9c919dc0e8e9c20ed57750ec93a8d http://github.com/bioperl/bioperl-live/commit/de6316c652a9c919dc0e8e9c20ed57750ec93a8d Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: M Bio/Search/Hit/GenericHit.pm Log Message: ----------- [bug 3089] iteration and found_again added to GenericHit for consistency (not applicable to anything but PSI-BLAST Commit: 4561de10d6db72294ddd474b3494c24025bbcf93 http://github.com/bioperl/bioperl-live/commit/4561de10d6db72294ddd474b3494c24025bbcf93 Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: M Bio/Search/Hit/GenericHit.pm Log Message: ----------- Merge branch 'topic/bug3089' From bugzilla-daemon at portal.open-bio.org Sun Jun 6 23:47:21 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 6 Jun 2010 23:47:21 -0400 Subject: [Bioperl-guts-l] [Bug 3089] HSPTableWriter cannot process Bio::Search::Hit::GenericHit objects In-Reply-To: Message-ID: <201006070347.o573lLaB021356@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3089 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from cjfields at bioperl.org 2010-06-06 23:47 EST ------- The method was missing from the main Hit class. I gave added them in on github, now seems to work fine. Thanks for the bug report! -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Mon Jun 7 00:05:48 2010 From: noreply at github.com (noreply at github.com) Date: Sun, 6 Jun 2010 21:05:48 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 368a23: [bug 3028] some rearrangement for FigTree output Message-ID: <20100607040548.834374219F@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 368a23bc908f0db64388747fd56b3e29ba111099 http://github.com/bioperl/bioperl-live/commit/368a23bc908f0db64388747fd56b3e29ba111099 Author: Chris Fields Date: 2010-06-06 (Sun, 06 Jun 2010) Changed paths: M Bio/TreeIO/nexus.pm Log Message: ----------- [bug 3028] some rearrangement for FigTree output From bugzilla-daemon at portal.open-bio.org Mon Jun 7 00:11:22 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 7 Jun 2010 00:11:22 -0400 Subject: [Bioperl-guts-l] [Bug 3028] Bio::TreeIO::nexus Fails to correctly output FigTree Formatting tags In-Reply-To: Message-ID: <201006070411.o574BMA1021915@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3028 ------- Comment #5 from cjfields at bioperl.org 2010-06-07 00:11 EST ------- Committed to master branch, works fine and passes current tests, but we would like additional test data if possible. Do you have an example tree for this? Or should we use one of the examples that come with FigTree? -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 7 00:20:47 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 7 Jun 2010 00:20:47 -0400 Subject: [Bioperl-guts-l] [Bug 3027] Bio::SearchIO crashes with PSI-BLAST "no hits found" after the first round In-Reply-To: Message-ID: <201006070420.o574Klr6022183@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3027 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |WORKSFORME ------- Comment #2 from cjfields at bioperl.org 2010-06-07 00:20 EST ------- This seems to be working with the latest code on bioperl-live github master. Will close out, but feel free to reopen if you see the same problem with the latest code. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 7 01:01:35 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 7 Jun 2010 01:01:35 -0400 Subject: [Bioperl-guts-l] [Bug 2347] Bio::Tools::Run::Phylo::PAML::Baseml needs polishing and completion In-Reply-To: Message-ID: <201006070501.o5751ZFn023141@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2347 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #6 from cjfields at bioperl.org 2010-06-07 01:01 EST ------- Sendu, I think Dave has fixed this with more recent PAML updates, but we can't test it w.o some example code. I'm closing this out for the time being; if you have something to test with that fails feel free to reopen. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 7 01:06:20 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 7 Jun 2010 01:06:20 -0400 Subject: [Bioperl-guts-l] [Bug 2463] bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface In-Reply-To: Message-ID: <201006070506.o5756JeX023324@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2463 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |WONTFIX ------- Comment #8 from cjfields at bioperl.org 2010-06-07 01:06 EST ------- No response in over a year. Closing this out. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Jun 7 01:17:21 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 7 Jun 2010 01:17:21 -0400 Subject: [Bioperl-guts-l] [Bug 3095] New: seq_version() in Bio::PrimarySeq not found Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=3095 Summary: seq_version() in Bio::PrimarySeq not found Product: BioPerl Version: unspecified Platform: PC OS/Version: Windows Status: NEW Severity: normal Priority: P2 Component: Core Components AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: pengyu.ut at gmail.com According to perldoc Bio::Seq, seq_version should be available in Bio::PrimarySeq. Bear in mind that some of these methods come from PrimarySeq objects, which are simpler than Seq objects, stripped of features (see Bio::PrimarySeq for more information). ... $seqobj->seq_version() # when there, the version But I only found version instead of seq_version in perldoc Bio::PrimarySeq. Is it a bug? -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Mon Jun 7 15:05:22 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 7 Jun 2010 12:05:22 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 1ef6c2: added comment (not pod) block for internal _codon_... Message-ID: <20100607190522.11522422C6@smtp1.rs.github.com> Branch: refs/heads/topic/longest_orf Home: http://github.com/bioperl/bioperl-live Commit: 1ef6c247ebd217960f0840a57d25363b7e334aaa http://github.com/bioperl/bioperl-live/commit/1ef6c247ebd217960f0840a57d25363b7e334aaa Author: Robert Buels Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M Bio/Tools/CodonTable.pm Log Message: ----------- added comment (not pod) block for internal _codon_is in CodonTable.pm Commit: 9e96c957552d0b54a56fc7ca88a09e0584f876b8 http://github.com/bioperl/bioperl-live/commit/9e96c957552d0b54a56fc7ca88a09e0584f876b8 Author: Robert Buels Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M Bio/PrimarySeqI.pm Log Message: ----------- clarified some translate() POD Commit: 6e421634700e6d36904444940f42c1671130717a http://github.com/bioperl/bioperl-live/commit/6e421634700e6d36904444940f42c1671130717a Author: Robert Buels Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M Bio/PrimarySeqI.pm Log Message: ----------- PrimarySeqI.pm whitespace cleanup From noreply at github.com Mon Jun 7 15:13:23 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 7 Jun 2010 12:13:23 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 1ef6c2: added comment (not pod) block for internal _codon_... Message-ID: <20100607191323.A5F85422C5@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 1ef6c247ebd217960f0840a57d25363b7e334aaa http://github.com/bioperl/bioperl-live/commit/1ef6c247ebd217960f0840a57d25363b7e334aaa Author: Robert Buels Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M Bio/Tools/CodonTable.pm Log Message: ----------- added comment (not pod) block for internal _codon_is in CodonTable.pm Commit: 9e96c957552d0b54a56fc7ca88a09e0584f876b8 http://github.com/bioperl/bioperl-live/commit/9e96c957552d0b54a56fc7ca88a09e0584f876b8 Author: Robert Buels Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M Bio/PrimarySeqI.pm Log Message: ----------- clarified some translate() POD Commit: 6e421634700e6d36904444940f42c1671130717a http://github.com/bioperl/bioperl-live/commit/6e421634700e6d36904444940f42c1671130717a Author: Robert Buels Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M Bio/PrimarySeqI.pm Log Message: ----------- PrimarySeqI.pm whitespace cleanup Commit: fa43e16ca64d59aca3e57e776599e28f0b3eb0e3 http://github.com/bioperl/bioperl-live/commit/fa43e16ca64d59aca3e57e776599e28f0b3eb0e3 Author: Robert Buels Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M Bio/PrimarySeqI.pm M Bio/Tools/CodonTable.pm M t/Seq/PrimarySeq.t Log Message: ----------- Merge branch 'topic/longest_orf' into moster Conflicts: t/Seq/PrimarySeq.t From bugzilla-daemon at portal.open-bio.org Mon Jun 7 16:18:54 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 7 Jun 2010 16:18:54 -0400 Subject: [Bioperl-guts-l] [Bug 3095] seq_version() in Bio::PrimarySeq not found In-Reply-To: Message-ID: <201006072018.o57KIsDY019338@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3095 ------- Comment #1 from jason at bioperl.org 2010-06-07 16:18 EST ------- I think you just want to use 'version' seq_version is in Bio::Seq::RichSeqI which refers to extra fields in GenBank/EMBL/Swissprot data I am not sure why the Bio::Seq documentation mentions seq_version -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Mon Jun 7 22:05:37 2010 From: noreply at github.com (GitHub) Date: Mon, 7 Jun 2010 19:05:37 -0700 Subject: [Bioperl-guts-l] [GitHub] rkhaja sent you a pull request from rkhaja/bioperl-live Message-ID: <4c0da571e98c0_555d3fcaa6cda87445f@fe2.rs.github.com.tmail> rkhaja wants you to pull from rkhaja/bioperl-live at master Body: * new blast input file * 106 new test cases for blast.t, 5 tests fail parsing "Features in/flanking ..." * fix for Bio/SearchIO/blast.pm that gets the 5 new tests working View repository: http://github.com/rkhaja/bioperl-live/tree/master From noreply at github.com Mon Jun 7 22:40:22 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 7 Jun 2010 19:40:22 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6c3004: Added new blast output file ZABJ4EA7014.CH878695.1... Message-ID: <20100608024022.6E105422B8@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 6c300466dc4e735310c15426bae5deddc576db7b http://github.com/bioperl/bioperl-live/commit/6c300466dc4e735310c15426bae5deddc576db7b Author: Razi Khaja Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: A t/data/ZABJ4EA7014.CH878695.1.blast.txt Log Message: ----------- Added new blast output file ZABJ4EA7014.CH878695.1.blast.txt to test SearchIO blast parsing of 'Features in/flanking this part of a subject sequence' Commit: 66199821376d2b18ec0166d6b95436fff0d7f679 http://github.com/bioperl/bioperl-live/commit/66199821376d2b18ec0166d6b95436fff0d7f679 Author: Razi Khaja Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M t/SearchIO/blast.t Log Message: ----------- Modified t/SearchIO/blast.t to include 106 new tests that test parsing of details from new blast output file ZABJ4EA7014.CH878695.1.blast.txt. In particular, test parsing of 5 "Features in/flanking this part of subject sequence:". Demonstrated that existing code in Bio/SearchIO/blast.pm fails 5 tests in parsing "Features in/flanking this part of subject sequence:". Commit: 09f33f9cb4a3d5be730ebfa232af04d19686be7b http://github.com/bioperl/bioperl-live/commit/09f33f9cb4a3d5be730ebfa232af04d19686be7b Author: Razi Khaja Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M Bio/SearchIO/blast.pm Log Message: ----------- Modified Bio/SearchIO/blast.pm to fix 5 failed test in parsing "Features in/flanking this part of subject sequence:" for ZABJ4EA7014.CH878695.1.blast.txt Did not break old tests for parsing "Features in/flanking this part of subject sequence:" for old input file t/data/new_blastn.txt Commit: fccda775ce9a39186e921f96fb4ab362e8d49e5e http://github.com/bioperl/bioperl-live/commit/fccda775ce9a39186e921f96fb4ab362e8d49e5e Author: Razi Khaja Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M t/data/ZABJ4EA7014.CH878695.1.blast.txt Log Message: ----------- Reduced size of test data file ZABJ4EA7014.CH878695.1.blast.txt from 6MB to less than 1MB From jay at jays.net Mon Jun 7 22:46:14 2010 From: jay at jays.net (Jay Hannah) Date: Mon, 7 Jun 2010 21:46:14 -0500 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6c3004: Added new blast output file ZABJ4EA7014.CH878695.1... In-Reply-To: <20100608024022.6E105422B8@smtp1.rs.github.com> References: <20100608024022.6E105422B8@smtp1.rs.github.com> Message-ID: <877EC755-1DAE-489B-839E-8951B5B58373@jays.net> On Jun 7, 2010, at 9:40 PM, noreply at github.com wrote: > Commit: fccda775ce9a39186e921f96fb4ab362e8d49e5e > Reduced size of test data file ZABJ4EA7014.CH878695.1.blast.txt from 6MB to less than 1MB Don't know if anyone's worried about that 6MB being in git history forever and ever. Or if there's anything that can be done about it. Jay Hannah http://biodoc.ist.unomaha.edu/wiki/User:Jhannah From jay at jays.net Mon Jun 7 22:25:38 2010 From: jay at jays.net (Jay Hannah) Date: Mon, 7 Jun 2010 21:25:38 -0500 Subject: [Bioperl-guts-l] [GitHub] rkhaja sent you a pull request from rkhaja/bioperl-live In-Reply-To: <4c0da571e98c0_555d3fcaa6cda87445f@fe2.rs.github.com.tmail> References: <4c0da571e98c0_555d3fcaa6cda87445f@fe2.rs.github.com.tmail> Message-ID: <96F00772-1F74-4492-AD33-0F10361E2CF4@jays.net> On Jun 7, 2010, at 9:05 PM, GitHub wrote: > rkhaja wants you to pull from rkhaja/bioperl-live at master > > Body: * new blast input file > * 106 new test cases for blast.t, 5 tests fail parsing "Features in/flanking ..." > * fix for Bio/SearchIO/blast.pm that gets the 5 new tests working > > View repository: http://github.com/rkhaja/bioperl-live/tree/master Currently being discussed in IRC. Would be nice if the 6MB t/data/ZABJ4EA7014.CH878695.1.blast.txt file didn't enter into our repo history. Jay Hannah http://biodoc.ist.unomaha.edu/wiki/User:Jhannah From cjfields at illinois.edu Mon Jun 7 23:09:46 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 7 Jun 2010 22:09:46 -0500 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6c3004: Added new blast output file ZABJ4EA7014.CH878695.1... In-Reply-To: <877EC755-1DAE-489B-839E-8951B5B58373@jays.net> References: <20100608024022.6E105422B8@smtp1.rs.github.com> <877EC755-1DAE-489B-839E-8951B5B58373@jays.net> Message-ID: <6D9D54BB-4C74-44EA-9AA8-2C8C27E51E5B@illinois.edu> On Jun 7, 2010, at 9:46 PM, Jay Hannah wrote: > On Jun 7, 2010, at 9:40 PM, noreply at github.com wrote: >> Commit: fccda775ce9a39186e921f96fb4ab362e8d49e5e >> Reduced size of test data file ZABJ4EA7014.CH878695.1.blast.txt from 6MB to less than 1MB > > Don't know if anyone's worried about that 6MB being in git history forever and ever. Or if there's anything that can be done about it. > > Jay Hannah > http://biodoc.ist.unomaha.edu/wiki/User:Jhannah Meh, not too worried personally. chris From razi.khaja at gmail.com Mon Jun 7 23:56:53 2010 From: razi.khaja at gmail.com (Razi Khaja) Date: Mon, 7 Jun 2010 23:56:53 -0400 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b4fb80: patch for Bug 3090, courtesy of Razi Khaja. New te... In-Reply-To: References: <20100605014644.4FE47422F5@smtp1.rs.github.com> <7AE7A1CD-21DF-401D-A10E-6EC7DB3C17E5@sbc.su.se>

Message-ID: > > For my next patch, I'll try experimenting with github again. > > > Great. And if you want some help with it, don't hesitate to go to our IRC > room. There's usually folks in there who can help. > > http://www.bioperl.org/wiki/IRC > I went on IRC today and Jay Hannah helped me get my newest patch accepted and applied via a pull request. From noreply at github.com Tue Jun 8 06:49:21 2010 From: noreply at github.com (noreply at github.com) Date: Tue, 8 Jun 2010 03:49:21 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b7b20e: Reworked Bio::SeqIO::phd->next_seq so that it is m... Message-ID: <20100608104921.493F1422B7@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: b7b20e428b613e06adb7bfc970db8c0abac06698 http://github.com/bioperl/bioperl-live/commit/b7b20e428b613e06adb7bfc970db8c0abac06698 Author: Florent Angly Date: 2010-06-08 (Tue, 08 Jun 2010) Changed paths: M Bio/SeqIO/phd.pm M t/SeqIO/phd.t A t/data/multiseq_tags.phd Log Message: ----------- Reworked Bio::SeqIO::phd->next_seq so that it is more robust, especially when parsing phd files that have WR tags Commit: 0e70e88a76d638d9f0406643c37691bb20d60ceb http://github.com/bioperl/bioperl-live/commit/0e70e88a76d638d9f0406643c37691bb20d60ceb Author: Florent Angly Date: 2010-06-08 (Tue, 08 Jun 2010) Changed paths: M Bio/SearchIO/blast.pm M t/SearchIO/blast.t A t/data/ZABJ4EA7014.CH878695.1.blast.txt Log Message: ----------- Merge branch 'master' of github.com:bioperl/bioperl-live From jay at jays.net Tue Jun 8 06:34:15 2010 From: jay at jays.net (Jay Hannah) Date: Tue, 8 Jun 2010 05:34:15 -0500 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6c3004: Added new blast output file ZABJ4EA7014.CH878695.1... In-Reply-To: <6D9D54BB-4C74-44EA-9AA8-2C8C27E51E5B@illinois.edu> References: <20100608024022.6E105422B8@smtp1.rs.github.com> <877EC755-1DAE-489B-839E-8951B5B58373@jays.net> <6D9D54BB-4C74-44EA-9AA8-2C8C27E51E5B@illinois.edu> Message-ID: On Jun 7, 2010, at 10:09 PM, Chris Fields wrote: On Jun 7, 2010, at 9:46 PM, Jay Hannah wrote: >> On Jun 7, 2010, at 9:40 PM, noreply at github.com wrote: >>> Commit: fccda775ce9a39186e921f96fb4ab362e8d49e5e >>> Reduced size of test data file ZABJ4EA7014.CH878695.1.blast.txt from 6MB to less than 1MB >> >> Don't know if anyone's worried about that 6MB being in git history forever and ever. Or if there's anything that can be done about it. > > Meh, not too worried personally. Roger that. Presumably if someone committed a 6TB file then went "oops!" and deleted it again, some git wizard would have to do something clever to the repo in order to avoid every git fetch / clone from that point forward taking *forever*... Wouldn't they? That's one hypothetical in which git's "every repo has all history for all time" strategy scares me. Jay Hannah http://biodoc.ist.unomaha.edu/wiki/User:Jhannah From cjfields at illinois.edu Tue Jun 8 09:48:35 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 8 Jun 2010 08:48:35 -0500 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6c3004: Added new blast output file ZABJ4EA7014.CH878695.1... In-Reply-To: References: <20100608024022.6E105422B8@smtp1.rs.github.com> <877EC755-1DAE-489B-839E-8951B5B58373@jays.net> <6D9D54BB-4C74-44EA-9AA8-2C8C27E51E5B@illinois.edu> Message-ID: <8C2A7D9C-EF9D-43E2-9AEC-ACDA626698AE@illinois.edu> On Jun 8, 2010, at 5:34 AM, Jay Hannah wrote: > On Jun 7, 2010, at 10:09 PM, Chris Fields wrote: > On Jun 7, 2010, at 9:46 PM, Jay Hannah wrote: >>> On Jun 7, 2010, at 9:40 PM, noreply at github.com wrote: >>>> Commit: fccda775ce9a39186e921f96fb4ab362e8d49e5e >>>> Reduced size of test data file ZABJ4EA7014.CH878695.1.blast.txt from 6MB to less than 1MB >>> >>> Don't know if anyone's worried about that 6MB being in git history forever and ever. Or if there's anything that can be done about it. >> >> Meh, not too worried personally. > > Roger that. Presumably if someone committed a 6TB file then went "oops!" and deleted it again, some git wizard would have to do something clever to the repo in order to avoid every git fetch / clone from that point forward taking *forever*... Wouldn't they? Yes, we would have to delete that somehow. And then we would shellac said committer. > That's one hypothetical in which git's "every repo has all history for all time" strategy scares me. > > Jay Hannah > http://biodoc.ist.unomaha.edu/wiki/User:Jhannah I believe there are ways around this (I know this has been encountered before). The process is history-revising, so would have to be done carefully (on a branch, then merged), but it is possible. chris From bugzilla-daemon at portal.open-bio.org Tue Jun 8 17:20:17 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 8 Jun 2010 17:20:17 -0400 Subject: [Bioperl-guts-l] [Bug 2463] bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface In-Reply-To: Message-ID: <201006082120.o58LKHSQ026922@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2463 ------- Comment #9 from mmokrejs at ribosome.natur.cuni.cz 2010-06-08 17:20 EST ------- I use from EMBOSS "revseq -reverse -complement" on FASTA files for my needs. I haven't touched perl for a few years. ;-) Thanks anyway for the other improvements you did in the past. I would have closed as "CODE_FIX" but it is your choice. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Wed Jun 9 04:52:49 2010 From: noreply at github.com (GitHub) Date: Wed, 9 Jun 2010 01:52:49 -0700 Subject: [Bioperl-guts-l] [GitHub] viklund sent you a pull request from viklund/bioperl-live Message-ID: <4c0f5661467ee_75033fa9def4f87c122@fe1.rs.github.com.tmail> viklund wants you to pull from viklund/bioperl-live at 263cad6 Body: A small bugfix for ProteinStatistics.pm. View repository: http://github.com/viklund/bioperl-live/tree/263cad662cdd8ea82993ac9f7b7eb1a4706ed716 From noreply at github.com Wed Jun 9 05:12:44 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 9 Jun 2010 02:12:44 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] cea70e: Fixed bug with ambiguity comparisons in Bio/Align/... Message-ID: <20100609091244.B9492421AD@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: cea70ed4b4b5cb8d4fe217f9602681e2acca7ec5 http://github.com/bioperl/bioperl-live/commit/cea70ed4b4b5cb8d4fe217f9602681e2acca7ec5 Author: Johan Viklund Date: 2010-06-09 (Wed, 09 Jun 2010) Changed paths: M Bio/Align/ProteinStatistics.pm Log Message: ----------- Fixed bug with ambiguity comparisons in Bio/Align/ProteinStatistics::_check_ambiguity_protein From noreply at github.com Wed Jun 9 08:06:46 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 9 Jun 2010 05:06:46 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 3ba5f6: Bio::Assembly::Tools::ContigSpectrum: Message-ID: <20100609120646.F2FFC422B8@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 3ba5f6cf2af9fa7c27272c638207e77b7dd4c415 http://github.com/bioperl/bioperl-live/commit/3ba5f6cf2af9fa7c27272c638207e77b7dd4c415 Author: Florent Angly Date: 2010-06-09 (Wed, 09 Jun 2010) Changed paths: M Bio/Assembly/Tools/ContigSpectrum.pm M t/Assembly/ContigSpectrum.t Log Message: ----------- Bio::Assembly::Tools::ContigSpectrum: * Fixed bug where large cross-contigs were not processed properly * Dissolve() and cross() methods are now capable of exposing their underlying contigs Commit: 72b289436911bea30c86d9a66049a2586b1d57d7 http://github.com/bioperl/bioperl-live/commit/72b289436911bea30c86d9a66049a2586b1d57d7 Author: Florent Angly Date: 2010-06-09 (Wed, 09 Jun 2010) Changed paths: M Bio/Align/ProteinStatistics.pm Log Message: ----------- Merge branch 'master' of github.com:bioperl/bioperl-live From bugzilla-daemon at portal.open-bio.org Wed Jun 9 11:23:24 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 9 Jun 2010 11:23:24 -0400 Subject: [Bioperl-guts-l] [Bug 3097] New: -task blastn option is not available in Bio::Tools::Run::StandAloneBlastPlus Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=3097 Summary: -task blastn option is not available in Bio::Tools::Run::StandAloneBlastPlus Product: BioPerl Version: unspecified Platform: PC OS/Version: Mac OS Status: NEW Severity: normal Priority: P2 Component: bioperl-run AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: pengyu.ut at gmail.com Anyway, I restate my original problem below. bioperl's bl2seq by default is equivalent to the following command. blastn -query first.fa -subject second.fa I want to add the option '-task blastn'. blastn -task blastn -query first.fa -subject second.fa But I don't find such option in bioperl's bl2seq. BTW, the bioperl code I used is listed below, where $seq1 and $seq2 are constructed from Bio::SeqIO->new. my $factory = Bio::Tools::Run::StandAloneBlastPlus->new(); my $result=$factory->bl2seq( -method=>'blastn', -query=> $seq1, -subject=> $seq2 ); $factory->cleanup; -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Wed Jun 9 12:44:21 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 9 Jun 2010 09:44:21 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] e9ce51: fix parsing of FASTA results; patch courtesy of Aa... Message-ID: <20100609164421.95082422B6@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: e9ce514236c240e718c6b6a117395f09e96de66a http://github.com/bioperl/bioperl-live/commit/e9ce514236c240e718c6b6a117395f09e96de66a Author: DaveMessina Date: 2010-06-09 (Wed, 09 Jun 2010) Changed paths: M Bio/SearchIO/fasta.pm Log Message: ----------- fix parsing of FASTA results; patch courtesy of Aaron Mackey From noreply at github.com Thu Jun 10 13:21:45 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 10 Jun 2010 10:21:45 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6e1103: Ben's changes to fix bug with file, along with com... Message-ID: <20100610172145.52870422A5@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 6e1103463bf1582ca836eb3229a14807d563e209 http://github.com/bioperl/bioperl-live/commit/6e1103463bf1582ca836eb3229a14807d563e209 Author: Chris Fields Date: 2010-06-10 (Thu, 10 Jun 2010) Changed paths: M Bio/Tools/Run/WrapperBase/CommandExts.pm Log Message: ----------- Ben's changes to fix bug with file, along with comment and link on possible concerns From noreply at github.com Thu Jun 10 16:13:10 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 10 Jun 2010 13:13:10 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 33075e: Merge branch 'master' of git@github.com:bioperl/bi... Message-ID: <20100610201310.EE405422A5@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 33075ebe436a4097e44e3f3b541f9ea7adbbbf53 http://github.com/bioperl/bioperl-live/commit/33075ebe436a4097e44e3f3b541f9ea7adbbbf53 Author: Lincoln Stein Date: 2010-06-10 (Thu, 10 Jun 2010) Changed paths: M .gitignore M Bio/Align/Graphics.pm M Bio/Align/ProteinStatistics.pm M Bio/AlignIO/phylip.pm M Bio/Assembly/IO/ace.pm M Bio/Assembly/Tools/ContigSpectrum.pm M Bio/DB/EUtilities.pm M Bio/DB/Taxonomy/flatfile.pm M Bio/Location/Atomic.pm M Bio/Location/Simple.pm M Bio/LocationI.pm M Bio/PrimarySeqI.pm M Bio/Root/Test.pm M Bio/Search/HSP/GenericHSP.pm M Bio/Search/Hit/GenericHit.pm M Bio/SearchIO/blast.pm M Bio/SearchIO/fasta.pm M Bio/Seq.pm M Bio/SeqIO/embl.pm M Bio/SeqIO/phd.pm M Bio/Tools/CodonTable.pm M Bio/Tools/EUtilities.pm M Bio/Tools/EUtilities/Info/FieldInfo.pm M Bio/Tools/EUtilities/Info/LinkInfo.pm M Bio/Tools/EUtilities/Query.pm M Bio/Tools/Run/WrapperBase/CommandExts.pm M Bio/TreeIO/nexus.pm M Build.PL A MANIFEST A MANIFEST.SKIP M examples/longorf.pl R examples/root/lib/Bio/PrimarySeq.pm R examples/root/lib/Bio/PrimarySeqI.pm R examples/root/lib/Bio/Seq.pm R examples/root/lib/Bio/SeqI.pm A t/Align/Graphics.t R t/AlignGraphics.t M t/Assembly/Assembly.t M t/Assembly/ContigSpectrum.t M t/SearchIO/blast.t M t/SearchIO/fasta.t M t/Seq/PrimarySeq.t M t/SeqIO/embl.t M t/SeqIO/phd.t A t/data/ZABJ4EA7014.CH878695.1.blast.txt A t/data/bug3086.embl A t/data/multiseq_tags.phd Log Message: ----------- Merge branch 'master' of git at github.com:bioperl/bioperl-live Commit: d737515abe154501da31ffe118fdb7d51f96a727 http://github.com/bioperl/bioperl-live/commit/d737515abe154501da31ffe118fdb7d51f96a727 Author: Lincoln Stein Date: 2010-06-10 (Thu, 10 Jun 2010) Changed paths: M scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS Log Message: ----------- seqfeature store database loader turns on summary statistics on new database creation From bugzilla-daemon at portal.open-bio.org Fri Jun 11 12:06:29 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 11 Jun 2010 12:06:29 -0400 Subject: [Bioperl-guts-l] [Bug 3099] New: New SeqIO module to read ms output files from Hudson's ms Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=3099 Summary: New SeqIO module to read ms output files from Hudson's ms Product: BioPerl Version: unspecified Platform: Macintosh OS/Version: Mac OS Status: NEW Keywords: Bioperl Severity: enhancement Priority: P2 Component: Bio::SeqIO AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: wkretzsch at gmail.com Bio::SeqIO::msout.pm is designed to be used with Bio::SeqIO to read output from Hudson's ms. This is my first submission to bioperl, so I'm sure I still have a lot to learn. One possible issue I see with the code is that I read from $self->{_filehandle} instead of from $self->_readline(). If this is a problem, I can fix it. Thank you for reviewing. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Jun 11 12:19:01 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 11 Jun 2010 12:19:01 -0400 Subject: [Bioperl-guts-l] [Bug 3099] New SeqIO module to read ms output files from Hudson's ms In-Reply-To: Message-ID: <201006111619.o5BGJ1ka001330@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3099 ------- Comment #1 from wkretzsch at gmail.com 2010-06-11 12:19 EST ------- I'm having some issues uploading the files, but I will do so as soon as support gets back to me. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Jun 11 12:27:10 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 11 Jun 2010 12:27:10 -0400 Subject: [Bioperl-guts-l] [Bug 3099] New SeqIO module to read ms output files from Hudson's ms In-Reply-To: Message-ID: <201006111627.o5BGRAd6001587@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3099 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Comment #2 from cjfields at bioperl.org 2010-06-11 12:27 EST ------- Warren, if you send them to me as attachments that would work as well. In order to include it into the code base we will need some test data and a basic set of regression tests: http://www.bioperl.org/wiki/HOWTO:Writing_BioPerl_Tests -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Fri Jun 11 14:12:50 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 11 Jun 2010 11:12:50 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 0fe10c: [bug 3099] initial msout Seq parser, courtesy Warr... Message-ID: <20100611181250.6158E42304@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 0fe10c54b76a1938133cdafe2c21afc433af3e90 http://github.com/bioperl/bioperl-live/commit/0fe10c54b76a1938133cdafe2c21afc433af3e90 Author: Chris Fields Date: 2010-06-11 (Fri, 11 Jun 2010) Changed paths: A Bio/SeqIO/msout.pm A t/SeqIO/msout.t A t/data/msout_infile1 A t/data/msout_infile1.gz A t/data/msout_infile2 A t/data/msout_infile2.gz Log Message: ----------- [bug 3099] initial msout Seq parser, courtesy Warren Kretzschmar From bugzilla-daemon at portal.open-bio.org Fri Jun 11 14:14:42 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 11 Jun 2010 14:14:42 -0400 Subject: [Bioperl-guts-l] [Bug 3099] New SeqIO module to read ms output files from Hudson's ms In-Reply-To: Message-ID: <201006111814.o5BIEgSa004577@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3099 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |FIXED ------- Comment #3 from cjfields at bioperl.org 2010-06-11 14:14 EST ------- Warren, made a few small changes (wrapped text, removed Switch dependency due to it's deprecation), but it's now in core. We will likely be doing some code rearrangement fairly soon in order to make core more modular, but we post something on the list about this. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Sat Jun 12 06:53:50 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 12 Jun 2010 03:53:50 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 68ffe4: Removed temporary debugging code Message-ID: <20100612105350.34859422AE@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 68ffe485d4886bbe841c8bfcd89e7e34085507a8 http://github.com/bioperl/bioperl-live/commit/68ffe485d4886bbe841c8bfcd89e7e34085507a8 Author: Florent Angly Date: 2010-06-12 (Sat, 12 Jun 2010) Changed paths: M Bio/Assembly/IO/ace.pm Log Message: ----------- Removed temporary debugging code Commit: 3fc2a56c7c1bac87783dfb77c7f41c61c74a95dc http://github.com/bioperl/bioperl-live/commit/3fc2a56c7c1bac87783dfb77c7f41c61c74a95dc Author: Florent Angly Date: 2010-06-12 (Sat, 12 Jun 2010) Changed paths: M Bio/DB/SeqFeature/Store/DBI/SQLite.pm M Bio/SearchIO/fasta.pm A Bio/SeqIO/msout.pm M Bio/Tools/Run/WrapperBase/CommandExts.pm M scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS A t/SeqIO/msout.t A t/data/msout_infile1 A t/data/msout_infile1.gz A t/data/msout_infile2 A t/data/msout_infile2.gz Log Message: ----------- Merge branch 'master' of github.com:bioperl/bioperl-live Commit: 7c4d7897653645b4c20495b1c9088f0524494d71 http://github.com/bioperl/bioperl-live/commit/7c4d7897653645b4c20495b1c9088f0524494d71 Author: Florent Angly Date: 2010-06-12 (Sat, 12 Jun 2010) Changed paths: M Bio/Assembly/Tools/ContigSpectrum.pm M t/Assembly/ContigSpectrum.t Log Message: ----------- More robust creation of cross-contigs From noreply at github.com Mon Jun 14 16:22:30 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 14 Jun 2010 13:22:30 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] c5cba4: Added Bio::Root::Root clone() (which uses Storable... Message-ID: <20100614202230.CFC3142038@smtp1.rs.github.com> Branch: refs/heads/topic/jhannah-seqfeature-clone Home: http://github.com/bioperl/bioperl-live Commit: c5cba4c9c6b70afc3e0443e4389b8caac7455a51 http://github.com/bioperl/bioperl-live/commit/c5cba4c9c6b70afc3e0443e4389b8caac7455a51 Author: Jay Hannah Date: 2010-06-14 (Mon, 14 Jun 2010) Changed paths: M Bio/Root/Root.pm A t/SeqFeature/Clone.t Log Message: ----------- Added Bio::Root::Root clone() (which uses Storable dclone()) so I can clone Bio::SeqFeature::Generic objects. Or anything else, for that matter(?). t/SeqFeature/Clone.t seems happy so far. From noreply at github.com Mon Jun 14 16:31:00 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 14 Jun 2010 13:31:00 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 8105a0: Bio/SeqIO/msout.pm 1.1.3 Message-ID: <20100614203100.70BC242039@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 8105a05014a4acbda4df6092f277ad9f6154bca9 http://github.com/bioperl/bioperl-live/commit/8105a05014a4acbda4df6092f277ad9f6154bca9 Author: Warren Kretzschmar Date: 2010-06-14 (Mon, 14 Jun 2010) Changed paths: M Bio/SeqIO/msout.pm Log Message: ----------- Bio/SeqIO/msout.pm 1.1.3 Made some changes to the POD file From noreply at github.com Mon Jun 14 16:35:37 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 14 Jun 2010 13:35:37 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 8105a0: Bio/SeqIO/msout.pm 1.1.3 Message-ID: <20100614203536.F2A6F4203C@smtp1.rs.github.com> Branch: refs/heads/topic/cjfields-foobar Home: http://github.com/bioperl/bioperl-live Commit: 8105a05014a4acbda4df6092f277ad9f6154bca9 http://github.com/bioperl/bioperl-live/commit/8105a05014a4acbda4df6092f277ad9f6154bca9 Author: Warren Kretzschmar Date: 2010-06-14 (Mon, 14 Jun 2010) Changed paths: M Bio/SeqIO/msout.pm Log Message: ----------- Bio/SeqIO/msout.pm 1.1.3 Made some changes to the POD file From noreply at github.com Mon Jun 14 17:02:19 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 14 Jun 2010 14:02:19 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] f7ad7a: added 'xref' identifier recognition for obo files.... Message-ID: <20100614210219.3F1A44204A@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: f7ad7aa93c6b37e5ec010c325a3fa389a5c83045 http://github.com/bioperl/bioperl-live/commit/f7ad7aa93c6b37e5ec010c325a3fa389a5c83045 Author: Naama Menda Date: 2010-06-14 (Mon, 14 Jun 2010) Changed paths: M Bio/OntologyIO/obo.pm Log Message: ----------- added 'xref' identifier recognition for obo files. xref fields are stored as secondary_ids Signed-off-by: Chris Fields From noreply at github.com Tue Jun 15 15:42:46 2010 From: noreply at github.com (noreply at github.com) Date: Tue, 15 Jun 2010 12:42:46 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] ea368a: Added Bio::Root::Root clone() (which uses Storable... Message-ID: <20100615194246.24CDB422B0@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: ea368afd86ae571ca8bda213cdd073d2c4ad8ec3 http://github.com/bioperl/bioperl-live/commit/ea368afd86ae571ca8bda213cdd073d2c4ad8ec3 Author: Jay Hannah Date: 2010-06-15 (Tue, 15 Jun 2010) Changed paths: M Bio/Root/Root.pm A t/SeqFeature/Clone.t Log Message: ----------- Added Bio::Root::Root clone() (which uses Storable dclone()) so I can clone Bio::SeqFeature::Generic objects. Or anything else, for that matter(?). t/SeqFeature/Clone.t seems happy so far. From noreply at github.com Wed Jun 16 07:45:32 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 16 Jun 2010 04:45:32 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-hmmer3] 36f027: Fix detecting the hit table header line Message-ID: <20100616114532.B9B7D422C9@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-hmmer3 Commit: 36f027548a6d4a184c59aa98ee9bda3a72de23ad http://github.com/bioperl/bioperl-hmmer3/commit/36f027548a6d4a184c59aa98ee9bda3a72de23ad Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm Log Message: ----------- Fix detecting the hit table header line Commit: b798b5722db99c0803005d3158b900cf7b7f8f72 http://github.com/bioperl/bioperl-hmmer3/commit/b798b5722db99c0803005d3158b900cf7b7f8f72 Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm Log Message: ----------- Bio::SearchIO::hmmer3: Fix up some whitespace From bugzilla-daemon at portal.open-bio.org Wed Jun 16 12:37:04 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 16 Jun 2010 12:37:04 -0400 Subject: [Bioperl-guts-l] [Bug 2899] problem with t/LocalDB/SeqFeature.t when host ne localhost In-Reply-To: Message-ID: <201006161637.o5GGb4Ur013790@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2899 ------- Comment #2 from Daniel.Lang at biologie.uni-freiburg.de 2010-06-16 12:37 EST ------- Created an attachment (id=1514) --> (http://bugzilla.open-bio.org/attachment.cgi?id=1514&action=view) Bug in field mysql field definition The mysql error is due to a "bug" in the SQL definitions of BioPerl-1.6.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm. The field lengths of the tag fields in several tables is set to 256 instead of the maximal 255. See http://dev.mysql.com/doc/refman/5.0/en/char.html -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 16 12:51:22 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 16 Jun 2010 12:51:22 -0400 Subject: [Bioperl-guts-l] [Bug 2899] problem with t/LocalDB/SeqFeature.t when host ne localhost In-Reply-To: Message-ID: <201006161651.o5GGpM2m014072@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2899 Daniel.Lang at biologie.uni-freiburg.de changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |Daniel.Lang at biologie.uni- | |freiburg.de ------- Comment #3 from Daniel.Lang at biologie.uni-freiburg.de 2010-06-16 12:51 EST ------- The bug should only affect systems with http://bugzilla.open-bio.org/show_bug.cgi?id=3101 Summary: New SeqIO parser to read output created by Teshima and Innan's mbs Product: BioPerl Version: unspecified Platform: Macintosh OS/Version: MacOS X Status: NEW Severity: enhancement Priority: P2 Component: Bio::SeqIO AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: wkretzsch at gmail.com I am submitting a perl module (Bio/SeqIO/mbsout.pm) and test file (t/SeqIO/mbsout.t) for a parser to read output created by Teshima and Innan's mbs. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 16 14:23:16 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 16 Jun 2010 14:23:16 -0400 Subject: [Bioperl-guts-l] [Bug 3101] New SeqIO parser to read output created by Teshima and Innan's mbs In-Reply-To: Message-ID: <201006161823.o5GINGUr020213@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3101 ------- Comment #1 from wkretzsch at gmail.com 2010-06-16 14:23 EST ------- Created an attachment (id=1515) --> (http://bugzilla.open-bio.org/attachment.cgi?id=1515&action=view) perl module -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed Jun 16 14:23:51 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 16 Jun 2010 14:23:51 -0400 Subject: [Bioperl-guts-l] [Bug 3101] New SeqIO parser to read output created by Teshima and Innan's mbs In-Reply-To: Message-ID: <201006161823.o5GINpNp020259@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3101 ------- Comment #2 from wkretzsch at gmail.com 2010-06-16 14:23 EST ------- Created an attachment (id=1516) --> (http://bugzilla.open-bio.org/attachment.cgi?id=1516&action=view) test file -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Thu Jun 17 02:53:32 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 16 Jun 2010 23:53:32 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-hmmer3] cf471c: Bio::SearchIO::hmmer3: rename (hit|hsp)info arrays... Message-ID: <20100617065332.94998422D1@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-hmmer3 Commit: cf471cdd412eb6fa5313335c2e4b8a64fc7e7d09 http://github.com/bioperl/bioperl-hmmer3/commit/cf471cdd412eb6fa5313335c2e4b8a64fc7e7d09 Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm Log Message: ----------- Bio::SearchIO::hmmer3: rename (hit|hsp)info arrays to (hit|hsp)_list to make code more readable There's also hashmaps called hitinfo and hspinfo, making the code more complicated than necessary Commit: f51086663ba1c17ed586312ded4930288d7d8d45 http://github.com/bioperl/bioperl-hmmer3/commit/f51086663ba1c17ed586312ded4930288d7d8d45 Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm M t/SearchIO/hmmer3.t A t/data/hmmsearch3.out Log Message: ----------- Bio::SearchIO::hmmer3: Create hit and hsp entries after parsing. This is needed so result files without alignments parse correctly. This code is probably broken for results with more than one Hsp per Hit. I need a result file to test that. From noreply at github.com Thu Jun 17 04:23:05 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 17 Jun 2010 01:23:05 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-hmmer3] 059feb: Bio::SearchIO::hmmer3: Fix parsing hmmscan results... Message-ID: <20100617082305.931CE422E1@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-hmmer3 Commit: 059feb798d254387c3724e823ede0060299fdaeb http://github.com/bioperl/bioperl-hmmer3/commit/059feb798d254387c3724e823ede0060299fdaeb Author: Kai Blin Date: 2010-06-17 (Thu, 17 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm M t/SearchIO/hmmer3.t A t/data/hmmscan_multi_domain.out Log Message: ----------- Bio::SearchIO::hmmer3: Fix parsing hmmscan results with multiple domains The fix to support hmmer results without alignments broke the parser for results with multiple alignments per hit. Rework the code to support this. From bugzilla-daemon at portal.open-bio.org Thu Jun 17 12:26:57 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 17 Jun 2010 12:26:57 -0400 Subject: [Bioperl-guts-l] [Bug 3102] New: Error converting sff into fastaq Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=3102 Summary: Error converting sff into fastaq Product: BioPerl Version: unspecified Platform: PC OS/Version: Windows Status: NEW Severity: normal Priority: P2 Component: Bio::SeqIO AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: gcasaburi at tiscali.it Hello, after reading an sff file comnig from 454, appera this message, the same message appear whenever i try to convert the sff file into a fastaq file. Everyone know how i can resolve this problem? Thank you very much "Traceback (most recent call last): File "", line 1, in for record in SeqIO.parse("C:\Users\Giorgio Casaburi\Desktop\sff\GIK1EHM01.sff", "sff-trim"): File "C:\Python26\lib\site-packages\Bio\SeqIO\SffIO.py", line 665, in SffIterator trim) File "C:\Python26\lib\site-packages\Bio\SeqIO\SffIO.py", line 518, in _sff_read_seq_record % padding) ValueError: Post quality 6 byte padding region contained data" -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Sat Jun 5 22:18:50 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 5 Jun 2010 19:18:50 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 4ac37b: Merge branch 'master' of github.com:bioperl/bioper... Message-ID: <20100606021850.DF5BD422A7@smtp1.rs.github.com> Branch: refs/heads/topic/any_primaryseq Home: http://github.com/bioperl/bioperl-live Commit: 4ac37bb8c28cc2fd2d19b201c98e1cee98bb5233 http://github.com/bioperl/bioperl-live/commit/4ac37bb8c28cc2fd2d19b201c98e1cee98bb5233 Author: Chris Fields Date: 2010-06-04 (Fri, 04 Jun 2010) Changed paths: M Bio/AlignIO/phylip.pm M Bio/Assembly/IO/ace.pm M t/Assembly/Assembly.t Log Message: ----------- Merge branch 'master' of github.com:bioperl/bioperl-live From David.Messina at sbc.su.se Sun Jun 6 08:07:34 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 6 Jun 2010 14:07:34 +0200 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b4fb80: patch for Bug 3090, courtesy of Razi Khaja. New te... In-Reply-To: References: <20100605014644.4FE47422F5@smtp1.rs.github.com> Message-ID: <7AE7A1CD-21DF-401D-A10E-6EC7DB3C17E5@sbc.su.se> Hi Razi, On Jun 5, 2010, at 4:10 AM, Razi Khaja wrote: > Your welcome! Thanks for the enthusiasm about the tests! Absolutely! Your work is much appreciated. (Please do more! :) > Now I just have to > figure out how to use github and send pull or push requests. I will try and > figure that out for my next set of patch(es). If you haven't already, take a look at our Using Git page: http://www.bioperl.org/wiki/Using_Git But no hurry. I saw you submitted another patch via Bugzilla, which is just fine. Dave From David.Messina at sbc.su.se Sun Jun 6 10:23:54 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 6 Jun 2010 16:23:54 +0200 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b4fb80: patch for Bug 3090, courtesy of Razi Khaja. New te... In-Reply-To: References: <20100605014644.4FE47422F5@smtp1.rs.github.com> <7AE7A1CD-21DF-401D-A10E-6EC7DB3C17E5@sbc.su.se> Message-ID: On Jun 6, 2010, at 4:15 PM, Razi Khaja wrote: > Hi Dave, > > I did read the Using_Git page, and tried following the instructions, but I think that the Using_Git page is written for core developers and collaborators. Partially, yes, but it's also for others contributing code, (like you!). See in particular: 6.3 Submitting a Pull Request http://github.com/guides/pull-requests and you can fork the repository from Github. http://www.bioperl.org/wiki/Using_Git#Instructions_for_downloading_any_BioPerl_repository_via_Github_.28read-only.29 > I think that the HOWTO:SubmitPatch page needs to be updated to reflect the use of github without developer accounts. > http://www.bioperl.org/wiki/HOWTO:SubmitPatch Yep, it does. Thanks for pointing that out. > For my next patch, I'll try experimenting with github again. Great. And if you want some help with it, don't hesitate to go to our IRC room. There's usually folks in there who can help. http://www.bioperl.org/wiki/IRC From noreply at github.com Mon Jun 7 15:19:10 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 7 Jun 2010 12:19:10 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 75ab71: Merge branch 'master' of github.com:bioperl/bioper... Message-ID: <20100607191910.B680F422CC@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 75ab7133a265564a96d388c3ecb1550387a9d241 http://github.com/bioperl/bioperl-live/commit/75ab7133a265564a96d388c3ecb1550387a9d241 Author: Robert Buels Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M .gitignore M Bio/Location/Atomic.pm M Bio/Location/Simple.pm M Bio/LocationI.pm M Bio/PrimarySeqI.pm M Bio/Root/Test.pm M Bio/Search/HSP/GenericHSP.pm M Bio/Search/Hit/GenericHit.pm M Bio/SearchIO/blast.pm M Bio/Tools/CodonTable.pm M Bio/Tools/EUtilities.pm M Bio/Tools/EUtilities/Query.pm M Bio/TreeIO/nexus.pm R examples/root/lib/Bio/PrimarySeq.pm R examples/root/lib/Bio/PrimarySeqI.pm R examples/root/lib/Bio/Seq.pm R examples/root/lib/Bio/SeqI.pm M t/SearchIO/blast.t M t/SearchIO/fasta.t M t/Seq/PrimarySeq.t Log Message: ----------- Merge branch 'master' of github.com:bioperl/bioperl-live From noreply at github.com Mon Jun 7 22:09:27 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 7 Jun 2010 19:09:27 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 6789d5: Merge branch 'master' of github.com:bioperl/bioper... Message-ID: <20100608020927.E7D6E422A2@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 6789d5fd9826125b56d7e5d5567af8e2dc53c14c http://github.com/bioperl/bioperl-live/commit/6789d5fd9826125b56d7e5d5567af8e2dc53c14c Author: Florent Angly Date: 2010-06-07 (Mon, 07 Jun 2010) Changed paths: M Bio/Location/Atomic.pm M Bio/Location/Simple.pm M Bio/LocationI.pm M Bio/PrimarySeqI.pm M Bio/Search/HSP/GenericHSP.pm M Bio/Search/Hit/GenericHit.pm M Bio/SearchIO/blast.pm M Bio/Tools/CodonTable.pm M Bio/TreeIO/nexus.pm R examples/root/lib/Bio/PrimarySeq.pm R examples/root/lib/Bio/PrimarySeqI.pm R examples/root/lib/Bio/Seq.pm R examples/root/lib/Bio/SeqI.pm M t/Assembly/Assembly.t M t/SearchIO/blast.t M t/SearchIO/fasta.t M t/Seq/PrimarySeq.t Log Message: ----------- Merge branch 'master' of github.com:bioperl/bioperl-live From David.Messina at sbc.su.se Tue Jun 8 06:30:36 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 8 Jun 2010 12:30:36 +0200 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b4fb80: patch for Bug 3090, courtesy of Razi Khaja. New te... In-Reply-To: References: <20100605014644.4FE47422F5@smtp1.rs.github.com> <7AE7A1CD-21DF-401D-A10E-6EC7DB3C17E5@sbc.su.se>

Message-ID: Great! Thanks so much for contributing to BioPerl, Razi! Dave On Jun 8, 2010, at 5:56 AM, Razi Khaja wrote: >> For my next patch, I'll try experimenting with github again. > > Great. And if you want some help with it, don't hesitate to go to our IRC room. There's usually folks in there who can help. > > http://www.bioperl.org/wiki/IRC > > > I went on IRC today and Jay Hannah helped me get my newest patch accepted and applied via a pull request. From noreply at github.com Wed Jun 9 17:35:19 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 9 Jun 2010 14:35:19 -0700 Subject: [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 890c9d: Merge branch 'master' of git@github.com:bioperl/Bi... Message-ID: <20100609213519.30539422EE@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/Bio-FeatureIO Commit: 890c9de1d8755d541497a2e2355f1e3b445e9b99 http://github.com/bioperl/Bio-FeatureIO/commit/890c9de1d8755d541497a2e2355f1e3b445e9b99 Author: Chris Fields Date: 2010-06-09 (Wed, 09 Jun 2010) Changed paths: M .gitignore M Build.PL M MANIFEST M MANIFEST.SKIP R lib/Bio/Factory/FeatureFactory.pm M lib/Bio/FeatureIO.pm A lib/Bio/FeatureIO/Handler/GenericFeatureHandler.pm M lib/Bio/FeatureIO/bed.pm M lib/Bio/FeatureIO/gff.pm M lib/Bio/FeatureIO/interpro.pm A lib/Bio/SeqFeature/Annotated.pm M t/FeatureIO.t A t/SeqFeature/Annotated.t A t/bed.t A t/data/1.bed M t/gff.t Log Message: ----------- Merge branch 'master' of git at github.com:bioperl/Bio-FeatureIO Conflicts (fixed): MANIFEST MANIFEST.SKIP From noreply at github.com Sat Jun 12 17:46:39 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 12 Jun 2010 14:46:39 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] c65976: Works great in Bio::DB::SeqFeature::Store::DBI::SQ... Message-ID: <20100612214639.2D12542096@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: c6597683cc1ea662c5839b593db877c4ca45fc12 http://github.com/bioperl/bioperl-live/commit/c6597683cc1ea662c5839b593db877c4ca45fc12 Author: Jay Hannah Date: 2010-06-12 (Sat, 12 Jun 2010) Changed paths: M Bio/DB/SeqFeature/Store.pm Log Message: ----------- Works great in Bio::DB::SeqFeature::Store::DBI::SQLite too. From bugzilla-daemon at portal.open-bio.org Thu Jun 17 13:34:50 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 17 Jun 2010 13:34:50 -0400 Subject: [Bioperl-guts-l] [Bug 3102] Error converting sff into fastaq In-Reply-To: Message-ID: <201006171734.o5HHYoAp029657@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3102 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Component|Bio::SeqIO |Main Distribution Product|BioPerl |Biopython Target Milestone|1.6.3 point release |--- Version|unspecified |1.54b ------- Comment #1 from cjfields at bioperl.org 2010-06-17 13:34 EST ------- I'm making a wild guess that this is Biopython and not BioPerl. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Thu Jun 17 17:27:40 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 17 Jun 2010 14:27:40 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 64ab09: test message Message-ID: <20100617212740.4BE0B422EF@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 64ab09ecd40abb8cd06e9b80aafcda323d1dc47e http://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e Author: Thomas Sharpton Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: A Bio/Search/HSP/hmmer3HSP.pm A Bio/Search/Hit/hmmer3Hit.pm A Bio/Search/Result/hmmer3Result.pm A Bio/SearchIO/hmmer3.pm A Bio/SearchIO/hmmer3.pm~ A Bio/Tools/Run/hmmer3.pm Log Message: ----------- test message Commit: 57b49b6a9a441adbc8b10006ed60e475701eec47 http://github.com/bioperl/bioperl-live/commit/57b49b6a9a441adbc8b10006ed60e475701eec47 Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/Search/Result/hmmer3Result.pm A t/SearchIO/hmmer3.t A t/data/hmmscan.out Log Message: ----------- SearchIO::hmmer3 Start basic unit test for hmmscan output Commit: 9a428569323b9fde89bc04bab7c9a5c58df3909e http://github.com/bioperl/bioperl-live/commit/9a428569323b9fde89bc04bab7c9a5c58df3909e Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm M t/SearchIO/hmmer3.t Log Message: ----------- SearchIO::hmmer3 Save the full sequence score, add more tests Commit: c58b6f67e56bc5b107ff57e4f514b4d529750e35 http://github.com/bioperl/bioperl-live/commit/c58b6f67e56bc5b107ff57e4f514b4d529750e35 Author: Thomas Sharpton Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: R Bio/SearchIO/hmmer3.pm~ Log Message: ----------- cleaning up repo by removing hmmer.pm (v2) and tmp files Commit: ef031b0ffe7e8458bfd0fe2ab3fe9c3b831fb9ef http://github.com/bioperl/bioperl-live/commit/ef031b0ffe7e8458bfd0fe2ab3fe9c3b831fb9ef Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm M t/SearchIO/hmmer3.t Log Message: ----------- Fix parsing of the hit description The description field is allowed to contain spaces, don't stop parsing the description on the first space Commit: c8f14c609298ef6b977588009975d8cb62746fbe http://github.com/bioperl/bioperl-live/commit/c8f14c609298ef6b977588009975d8cb62746fbe Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm Log Message: ----------- Fix indentation of previous patch Commit: b87b9b69a89f524667da2a4882f44ae1f9ba9592 http://github.com/bioperl/bioperl-live/commit/b87b9b69a89f524667da2a4882f44ae1f9ba9592 Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm Log Message: ----------- Fix hit description parsing for hits below the inclusion threshold Commit: 92cb350c140d4b1767b32dbe0dd12b6fa51466f2 http://github.com/bioperl/bioperl-live/commit/92cb350c140d4b1767b32dbe0dd12b6fa51466f2 Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm Log Message: ----------- Fix detecting the hit table header line Commit: 92effa6652b23401d3e69177cd7076c4f5d57e68 http://github.com/bioperl/bioperl-live/commit/92effa6652b23401d3e69177cd7076c4f5d57e68 Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm Log Message: ----------- Bio::SearchIO::hmmer3: Fix up some whitespace Commit: 3ad1d999c366e28f0bf4e7a719f67d1d3759597c http://github.com/bioperl/bioperl-live/commit/3ad1d999c366e28f0bf4e7a719f67d1d3759597c Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm Log Message: ----------- Bio::SearchIO::hmmer3: rename (hit|hsp)info arrays to (hit|hsp)_list to make code more readable There's also hashmaps called hitinfo and hspinfo, making the code more complicated than necessary Commit: 773ff1428491d0c5ac8f13fb14a6a74d2bc93e7d http://github.com/bioperl/bioperl-live/commit/773ff1428491d0c5ac8f13fb14a6a74d2bc93e7d Author: Kai Blin Date: 2010-06-16 (Wed, 16 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm M t/SearchIO/hmmer3.t A t/data/hmmsearch3.out Log Message: ----------- Bio::SearchIO::hmmer3: Create hit and hsp entries after parsing. This is needed so result files without alignments parse correctly. This code is probably broken for results with more than one Hsp per Hit. I need a result file to test that. Commit: 7402205cf2ec65750c4b72993da52b4a06685819 http://github.com/bioperl/bioperl-live/commit/7402205cf2ec65750c4b72993da52b4a06685819 Author: Kai Blin Date: 2010-06-17 (Thu, 17 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm M t/SearchIO/hmmer3.t A t/data/hmmscan_multi_domain.out Log Message: ----------- Bio::SearchIO::hmmer3: Fix parsing hmmscan results with multiple domains The fix to support hmmer results without alignments broke the parser for results with multiple alignments per hit. Rework the code to support this. From cjfields at illinois.edu Thu Jun 17 17:58:24 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 17 Jun 2010 16:58:24 -0500 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 64ab09: test message In-Reply-To: <20100617212740.4BE0B422EF@smtp1.rs.github.com> References: <20100617212740.4BE0B422EF@smtp1.rs.github.com> Message-ID: <939323BA-B512-49CC-A760-57506B296D0A@illinois.edu> Guessing that whole bit where we would have liked to do this on a branch went missing? ;> chris On Jun 17, 2010, at 4:27 PM, noreply at github.com wrote: > Branch: refs/heads/master > Home: http://github.com/bioperl/bioperl-live > > Commit: 64ab09ecd40abb8cd06e9b80aafcda323d1dc47e > http://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e > Author: Thomas Sharpton > Date: 2010-06-16 (Wed, 16 Jun 2010) > > Changed paths: > A Bio/Search/HSP/hmmer3HSP.pm > A Bio/Search/Hit/hmmer3Hit.pm > A Bio/Search/Result/hmmer3Result.pm > A Bio/SearchIO/hmmer3.pm > A Bio/SearchIO/hmmer3.pm~ > A Bio/Tools/Run/hmmer3.pm > > Log Message: > ----------- > test message > > > Commit: 57b49b6a9a441adbc8b10006ed60e475701eec47 > http://github.com/bioperl/bioperl-live/commit/57b49b6a9a441adbc8b10006ed60e475701eec47 > Author: Kai Blin > Date: 2010-06-16 (Wed, 16 Jun 2010) > > Changed paths: > M Bio/Search/Result/hmmer3Result.pm > A t/SearchIO/hmmer3.t > A t/data/hmmscan.out > > Log Message: > ----------- > SearchIO::hmmer3 Start basic unit test for hmmscan output > > > Commit: 9a428569323b9fde89bc04bab7c9a5c58df3909e > http://github.com/bioperl/bioperl-live/commit/9a428569323b9fde89bc04bab7c9a5c58df3909e > Author: Kai Blin > Date: 2010-06-16 (Wed, 16 Jun 2010) > > Changed paths: > M Bio/SearchIO/hmmer3.pm > M t/SearchIO/hmmer3.t > > Log Message: > ----------- > SearchIO::hmmer3 Save the full sequence score, add more tests > > > Commit: c58b6f67e56bc5b107ff57e4f514b4d529750e35 > http://github.com/bioperl/bioperl-live/commit/c58b6f67e56bc5b107ff57e4f514b4d529750e35 > Author: Thomas Sharpton > Date: 2010-06-16 (Wed, 16 Jun 2010) > > Changed paths: > R Bio/SearchIO/hmmer3.pm~ > > Log Message: > ----------- > cleaning up repo by removing hmmer.pm (v2) and tmp files > > > Commit: ef031b0ffe7e8458bfd0fe2ab3fe9c3b831fb9ef > http://github.com/bioperl/bioperl-live/commit/ef031b0ffe7e8458bfd0fe2ab3fe9c3b831fb9ef > Author: Kai Blin > Date: 2010-06-16 (Wed, 16 Jun 2010) > > Changed paths: > M Bio/SearchIO/hmmer3.pm > M t/SearchIO/hmmer3.t > > Log Message: > ----------- > Fix parsing of the hit description > > The description field is allowed to contain spaces, don't stop parsing > the description on the first space > > > Commit: c8f14c609298ef6b977588009975d8cb62746fbe > http://github.com/bioperl/bioperl-live/commit/c8f14c609298ef6b977588009975d8cb62746fbe > Author: Kai Blin > Date: 2010-06-16 (Wed, 16 Jun 2010) > > Changed paths: > M Bio/SearchIO/hmmer3.pm > > Log Message: > ----------- > Fix indentation of previous patch > > > Commit: b87b9b69a89f524667da2a4882f44ae1f9ba9592 > http://github.com/bioperl/bioperl-live/commit/b87b9b69a89f524667da2a4882f44ae1f9ba9592 > Author: Kai Blin > Date: 2010-06-16 (Wed, 16 Jun 2010) > > Changed paths: > M Bio/SearchIO/hmmer3.pm > > Log Message: > ----------- > Fix hit description parsing for hits below the inclusion threshold > > > Commit: 92cb350c140d4b1767b32dbe0dd12b6fa51466f2 > http://github.com/bioperl/bioperl-live/commit/92cb350c140d4b1767b32dbe0dd12b6fa51466f2 > Author: Kai Blin > Date: 2010-06-16 (Wed, 16 Jun 2010) > > Changed paths: > M Bio/SearchIO/hmmer3.pm > > Log Message: > ----------- > Fix detecting the hit table header line > > > Commit: 92effa6652b23401d3e69177cd7076c4f5d57e68 > http://github.com/bioperl/bioperl-live/commit/92effa6652b23401d3e69177cd7076c4f5d57e68 > Author: Kai Blin > Date: 2010-06-16 (Wed, 16 Jun 2010) > > Changed paths: > M Bio/SearchIO/hmmer3.pm > > Log Message: > ----------- > Bio::SearchIO::hmmer3: Fix up some whitespace > > > Commit: 3ad1d999c366e28f0bf4e7a719f67d1d3759597c > http://github.com/bioperl/bioperl-live/commit/3ad1d999c366e28f0bf4e7a719f67d1d3759597c > Author: Kai Blin > Date: 2010-06-16 (Wed, 16 Jun 2010) > > Changed paths: > M Bio/SearchIO/hmmer3.pm > > Log Message: > ----------- > Bio::SearchIO::hmmer3: rename (hit|hsp)info arrays to (hit|hsp)_list to make code more readable > > There's also hashmaps called hitinfo and hspinfo, making the code more complicated than necessary > > > Commit: 773ff1428491d0c5ac8f13fb14a6a74d2bc93e7d > http://github.com/bioperl/bioperl-live/commit/773ff1428491d0c5ac8f13fb14a6a74d2bc93e7d > Author: Kai Blin > Date: 2010-06-16 (Wed, 16 Jun 2010) > > Changed paths: > M Bio/SearchIO/hmmer3.pm > M t/SearchIO/hmmer3.t > A t/data/hmmsearch3.out > > Log Message: > ----------- > Bio::SearchIO::hmmer3: Create hit and hsp entries after parsing. > > This is needed so result files without alignments parse correctly. > > This code is probably broken for results with more than one Hsp per Hit. I need a result file to test that. > > > Commit: 7402205cf2ec65750c4b72993da52b4a06685819 > http://github.com/bioperl/bioperl-live/commit/7402205cf2ec65750c4b72993da52b4a06685819 > Author: Kai Blin > Date: 2010-06-17 (Thu, 17 Jun 2010) > > Changed paths: > M Bio/SearchIO/hmmer3.pm > M t/SearchIO/hmmer3.t > A t/data/hmmscan_multi_domain.out > > Log Message: > ----------- > Bio::SearchIO::hmmer3: Fix parsing hmmscan results with multiple domains > > The fix to support hmmer results without alignments broke the parser for > results with multiple alignments per hit. Rework the code to support > this. > > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l From bugzilla-daemon at portal.open-bio.org Fri Jun 18 01:25:23 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 18 Jun 2010 01:25:23 -0400 Subject: [Bioperl-guts-l] [Bug 2483] request for implementation of write_assembly In-Reply-To: Message-ID: <201006180525.o5I5PNc6008200@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2483 florent.angly at gmail.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #3 from florent.angly at gmail.com 2010-06-18 01:25 EST ------- There is now support for writing ACE files in Bio::Assembly::IO. Closing this bug. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Fri Jun 18 01:55:13 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 17 Jun 2010 22:55:13 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 85bdf8: Updated 'Changes' file regarding assembly improvem... Message-ID: <20100618055513.E1A89422B3@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 85bdf82fd72c1ce478d837366054e121014eae88 http://github.com/bioperl/bioperl-live/commit/85bdf82fd72c1ce478d837366054e121014eae88 Author: Florent Angly Date: 2010-06-17 (Thu, 17 Jun 2010) Changed paths: M Changes Log Message: ----------- Updated 'Changes' file regarding assembly improvements since bioperl-live v1.6.1 From noreply at github.com Fri Jun 18 02:21:39 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 17 Jun 2010 23:21:39 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] d7fea4: Updated 'Changes' files for new assembly-related a... Message-ID: <20100618062139.8512A422DF@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: d7fea4848c3f74778219337b63938e8bfbbbefdb http://github.com/bioperl/bioperl-run/commit/d7fea4848c3f74778219337b63938e8bfbbbefdb Author: Florent Angly Date: 2010-06-17 (Thu, 17 Jun 2010) Changed paths: M Changes Log Message: ----------- Updated 'Changes' files for new assembly-related additions since v1.6.1 From noreply at github.com Fri Jun 18 03:04:10 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 18 Jun 2010 00:04:10 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] b91617: Support for assembly variants in Bio::Tools::Run::... Message-ID: <20100618070410.B1B55422A9@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: b916172f82f3626f9ccaba646da1e6d3443d3854 http://github.com/bioperl/bioperl-run/commit/b916172f82f3626f9ccaba646da1e6d3443d3854 Author: Florent Angly Date: 2010-06-18 (Fri, 18 Jun 2010) Changed paths: M lib/Bio/Tools/Run/AssemblerBase.pm M lib/Bio/Tools/Run/Newbler.pm M t/Newbler.t Log Message: ----------- Support for assembly variants in Bio::Tools::Run::AssemblerBase Bio::Tools::Run::Newbler fixed to output ACE-454 variant From kai.blin at biotech.uni-tuebingen.de Fri Jun 18 02:51:39 2010 From: kai.blin at biotech.uni-tuebingen.de (Kai Blin) Date: Fri, 18 Jun 2010 08:51:39 +0200 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 64ab09: test message In-Reply-To: <939323BA-B512-49CC-A760-57506B296D0A@illinois.edu> References: <20100617212740.4BE0B422EF@smtp1.rs.github.com> <939323BA-B512-49CC-A760-57506B296D0A@illinois.edu> Message-ID: <1276843899.31442.186.camel@mikropc7.biotech.uni-tuebingen.de> On Thu, 2010-06-17 at 16:58 -0500, Chris Fields wrote: > Guessing that whole bit where we would have liked to do this on a branch went missing? ;> > Ah, so that's what you meant. A slight miscommunication there, sorry. I understood your previous emails as "make sure you have this as a branch on your bioperl-live tree", which I had, and the "push when ready" as "feel free to push when you're ready". I'm happy to revert the patches and put them on a real branch first, so we can merge it into master when you guys think they're ready. Sorry for the fuss, Kai -- Dipl.-Inform. Kai Blin kai.blin at biotech.uni-tuebingen.de Interfakult?res Institut f?r Mikrobiologie und Infektionsmedizin Abteilung Mikrobiologie/Biotechnologie Eberhard-Karls-Universit?t T?bingen Auf der Morgenstelle 28 Phone : ++49 7071 29-78841 D-72076 T?bingen Fax : ++49 7071 29-5979 Deutschland Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben From bugzilla-daemon at portal.open-bio.org Fri Jun 18 03:50:29 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 18 Jun 2010 03:50:29 -0400 Subject: [Bioperl-guts-l] [Bug 2758] assemblyIO - can't read phredPhrap ace file with tagged repeats In-Reply-To: Message-ID: <201006180750.o5I7oTLj011470@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2758 florent.angly at gmail.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #4 from florent.angly at gmail.com 2010-06-18 03:50 EST ------- Thanks for the bug report Janet. I committed a fix in the git repository. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Jun 18 04:03:24 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 18 Jun 2010 04:03:24 -0400 Subject: [Bioperl-guts-l] [Bug 3102] Error converting sff into fastaq In-Reply-To: Message-ID: <201006180803.o5I83On1012251@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3102 ------- Comment #2 from gcasaburi at tiscali.it 2010-06-18 04:03 EST ------- (In reply to comment #1) > I'm making a wild guess that this is Biopython and not BioPerl. Yes, it's Biopython, Can you halp me, please? or can you give me a link where to find the answer for my problem? Thank you very much. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Jun 18 09:18:59 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 18 Jun 2010 09:18:59 -0400 Subject: [Bioperl-guts-l] [Bug 3102] Error converting sff into fastaq In-Reply-To: Message-ID: <201006181318.o5IDIxqN022972@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3102 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|bioperl-guts-l at bioperl.org |biopython-dev at biopython.org ------- Comment #3 from cjfields at bioperl.org 2010-06-18 09:18 EST ------- (In reply to comment #2) > (In reply to comment #1) > > I'm making a wild guess that this is Biopython and not BioPerl. > > Yes, it's Biopython, Can you halp me, please? or can you give me a link where > to find the answer for my problem? Thank you very much. Reassigning to the Biopython devs. This should go to their list now, hopefully you'll get a response. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. You are the assignee for the bug, or are watching the assignee. From cjfields at illinois.edu Fri Jun 18 09:16:25 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 18 Jun 2010 08:16:25 -0500 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 64ab09: test message In-Reply-To: <1276843899.31442.186.camel@mikropc7.biotech.uni-tuebingen.de> References: <20100617212740.4BE0B422EF@smtp1.rs.github.com> <939323BA-B512-49CC-A760-57506B296D0A@illinois.edu> <1276843899.31442.186.camel@mikropc7.biotech.uni-tuebingen.de> Message-ID: <60CB394A-C25E-4AE4-8A4D-7A3631274036@illinois.edu> On Jun 18, 2010, at 1:51 AM, Kai Blin wrote: > On Thu, 2010-06-17 at 16:58 -0500, Chris Fields wrote: >> Guessing that whole bit where we would have liked to do this on a branch went missing? ;> >> > > Ah, so that's what you meant. A slight miscommunication there, sorry. I > understood your previous emails as "make sure you have this as a branch > on your bioperl-live tree", which I had, and the "push when ready" as > "feel free to push when you're ready". > > I'm happy to revert the patches and put them on a real branch first, so > we can merge it into master when you guys think they're ready. > > Sorry for the fuss, > Kai No worries (hence the smiley). We've had much worse happen on main trunk. I'm just trying to prod development on branches a lot more. chris From noreply at github.com Mon Jun 21 17:17:22 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 21 Jun 2010 14:17:22 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 132a6e: in-memory adaptor now produces a warning if the fa... Message-ID: <20100621211722.D2D3542170@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 132a6e0ad79f3e90fec42db5b173e1134bbade8a http://github.com/bioperl/bioperl-live/commit/132a6e0ad79f3e90fec42db5b173e1134bbade8a Author: Lincoln Stein Date: 2010-06-21 (Mon, 21 Jun 2010) Changed paths: M Bio/DB/Fasta.pm M Bio/DB/SeqFeature/Store/memory.pm Log Message: ----------- in-memory adaptor now produces a warning if the fasta file didnt index Commit: e9b935597e5d2e4723edb49ddfd1f7c60b71f3e5 http://github.com/bioperl/bioperl-live/commit/e9b935597e5d2e4723edb49ddfd1f7c60b71f3e5 Author: Lincoln Stein Date: 2010-06-21 (Mon, 21 Jun 2010) Changed paths: M Bio/Assembly/Contig.pm M Bio/Assembly/IO/ace.pm M Bio/Assembly/Tools/ContigSpectrum.pm M Bio/DB/SeqFeature/Store.pm M Bio/OntologyIO/obo.pm M Bio/Root/Root.pm A Bio/Search/HSP/hmmer3HSP.pm A Bio/Search/Hit/hmmer3Hit.pm A Bio/Search/Result/hmmer3Result.pm A Bio/SearchIO/hmmer3.pm A Bio/SeqIO/msout.pm A Bio/Tools/Run/hmmer3.pm M Changes M t/Assembly/ContigSpectrum.t A t/SearchIO/hmmer3.t A t/SeqFeature/Clone.t A t/SeqIO/msout.t A t/data/hmmscan.out A t/data/hmmscan_multi_domain.out A t/data/hmmsearch3.out A t/data/msout_infile1 A t/data/msout_infile1.gz A t/data/msout_infile2 A t/data/msout_infile2.gz Log Message: ----------- Merge branch 'master' of git at github.com:bioperl/bioperl-live From noreply at github.com Tue Jun 22 10:19:33 2010 From: noreply at github.com (noreply at github.com) Date: Tue, 22 Jun 2010 07:19:33 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] bc3b50: Typo correction Message-ID: <20100622141933.9CE2A422A9@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: bc3b5043cdc347f3d4c4e31f18cb7d0ea61c19a8 http://github.com/bioperl/bioperl-live/commit/bc3b5043cdc347f3d4c4e31f18cb7d0ea61c19a8 Author: Jay Hannah Date: 2010-06-22 (Tue, 22 Jun 2010) Changed paths: M scripts/utilities/download_query_genbank.PLS Log Message: ----------- Typo correction Thanks to Paul Cantalupo in IRC! From noreply at github.com Tue Jun 22 12:01:15 2010 From: noreply at github.com (noreply at github.com) Date: Tue, 22 Jun 2010 09:01:15 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 8bb3ad: Fixed typos in Bio::Assembly::Contig Message-ID: <20100622160115.B1A24422E1@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 8bb3ad2244482a5beb25c4a3957dcdb4bfed95a4 http://github.com/bioperl/bioperl-live/commit/8bb3ad2244482a5beb25c4a3957dcdb4bfed95a4 Author: Florent Angly Date: 2010-06-22 (Tue, 22 Jun 2010) Changed paths: M Bio/Assembly/Contig.pm Log Message: ----------- Fixed typos in Bio::Assembly::Contig Commit: 38210d2d0712a4e325905d402e807293e87b6e15 http://github.com/bioperl/bioperl-live/commit/38210d2d0712a4e325905d402e807293e87b6e15 Author: Florent Angly Date: 2010-06-22 (Tue, 22 Jun 2010) Changed paths: M Bio/Assembly/IO/ace.pm Log Message: ----------- Removed temporary debugging code Commit: 474ebc059be3903f10f1c13a092dfe83c876b04b http://github.com/bioperl/bioperl-live/commit/474ebc059be3903f10f1c13a092dfe83c876b04b Author: Florent Angly Date: 2010-06-22 (Tue, 22 Jun 2010) Changed paths: M Bio/Assembly/Tools/ContigSpectrum.pm M t/Assembly/ContigSpectrum.t Log Message: ----------- More robust creation of cross-contigs Commit: 3ffea8f0291fbf666f380ad4d621a86324c5eba8 http://github.com/bioperl/bioperl-live/commit/3ffea8f0291fbf666f380ad4d621a86324c5eba8 Author: Jay Hannah Date: 2010-06-22 (Tue, 22 Jun 2010) Changed paths: M Bio/DB/SeqFeature/Store.pm Log Message: ----------- Works great in Bio::DB::SeqFeature::Store::DBI::SQLite too. Commit: ddb78a5e2ed16396fda88d26b107ea9dcc191da8 http://github.com/bioperl/bioperl-live/commit/ddb78a5e2ed16396fda88d26b107ea9dcc191da8 Author: Warren Kretzschmar Date: 2010-06-22 (Tue, 22 Jun 2010) Changed paths: M Bio/SeqIO/msout.pm Log Message: ----------- Bio/SeqIO/msout.pm 1.1.3 Made some changes to the POD file Commit: b310c08f455321f7eb8e288a3c748595d466cc20 http://github.com/bioperl/bioperl-live/commit/b310c08f455321f7eb8e288a3c748595d466cc20 Author: Warren Kretzschmar Date: 2010-06-22 (Tue, 22 Jun 2010) Changed paths: M Bio/SeqIO/msout.pm M t/SeqIO/msout.t Log Message: ----------- Bio/SeqIO/msout.pm 1.1.4 Removed calls to $self->close() simplified some logic before the return in get_next_hap() Made the return value of get_next_pop, get_next_run, and get_next_seq to be undef if these methods were asked to return haps past the input stream. t/msout.t 1.1.4 Added tests to examine what happens when haps are read from an empty stream Commit: 9b88c49b4ff3ad1855614c78ef71de09615c7f8a http://github.com/bioperl/bioperl-live/commit/9b88c49b4ff3ad1855614c78ef71de09615c7f8a Author: Warren Kretzschmar Date: 2010-06-22 (Tue, 22 Jun 2010) Changed paths: M Bio/SeqIO/msout.pm M t/SeqIO/msout.t Log Message: ----------- Bio/SeqIO/msout.pm 1.1.5 added match operators where they were missing changed our $VERSION to our $API_VERSION t/SeqIO/msout.t 1.1.5 changed our $VERSION to our $API_VERSION got rid of gzipped test files all other test files are now saved to t/data/msout/ changed 'throw' calls to 'die' calls as msout.t does not inherit these functions Commit: 41c94948b3316649946f4bc6357934092f8e41a4 http://github.com/bioperl/bioperl-live/commit/41c94948b3316649946f4bc6357934092f8e41a4 Author: Chris Fields Date: 2010-06-22 (Tue, 22 Jun 2010) Changed paths: M Bio/DB/Fasta.pm M Bio/DB/SeqFeature/Store/memory.pm M Bio/OntologyIO/obo.pm M Bio/Root/Root.pm A Bio/Search/HSP/hmmer3HSP.pm A Bio/Search/Hit/hmmer3Hit.pm A Bio/Search/Result/hmmer3Result.pm A Bio/SearchIO/hmmer3.pm A Bio/Tools/Run/hmmer3.pm M Changes M scripts/utilities/download_query_genbank.PLS A t/SearchIO/hmmer3.t A t/SeqFeature/Clone.t A t/data/hmmscan.out A t/data/hmmscan_multi_domain.out A t/data/hmmsearch3.out Log Message: ----------- fix conflict From noreply at github.com Thu Jun 24 16:09:27 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 24 Jun 2010 13:09:27 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 83cf97: make this a real-world example Message-ID: <20100624200926.672B1422A9@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 83cf9726c05227222cd1d85847375f0e151b3e41 http://github.com/bioperl/bioperl-live/commit/83cf9726c05227222cd1d85847375f0e151b3e41 Author: Chris Fields Date: 2010-06-24 (Thu, 24 Jun 2010) Changed paths: M Bio/Location/Atomic.pm M Bio/Location/Simple.pm M Bio/LocationI.pm Log Message: ----------- make this a real-world example From noreply at github.com Thu Jun 24 18:07:52 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 24 Jun 2010 15:07:52 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 71d9aa: added _seq_id method to many SeqFeature::Store dat... Message-ID: <20100624220750.AF3424219B@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 71d9aa5f6a899a7d3a5889507d0505c760fb894c http://github.com/bioperl/bioperl-live/commit/71d9aa5f6a899a7d3a5889507d0505c760fb894c Author: Lincoln Stein Date: 2010-06-24 (Thu, 24 Jun 2010) Changed paths: M Bio/DB/SeqFeature/Store/GFF3Loader.pm M Bio/DB/SeqFeature/Store/berkeleydb3.pm M Bio/DB/SeqFeature/Store/memory.pm Log Message: ----------- added _seq_id method to many SeqFeature::Store databases From noreply at github.com Thu Jun 24 18:21:13 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 24 Jun 2010 15:21:13 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 788a93: silence warnings with a default of 0 Message-ID: <20100624222111.C3D4E422F0@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 788a93b5edb1ae1f4326b4da696b9620f8fd215c http://github.com/bioperl/bioperl-live/commit/788a93b5edb1ae1f4326b4da696b9620f8fd215c Author: Chris Fields Date: 2010-06-24 (Thu, 24 Jun 2010) Changed paths: M Bio/SearchIO/hmmer3.pm Log Message: ----------- silence warnings with a default of 0 From noreply at github.com Thu Jun 24 18:35:20 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 24 Jun 2010 15:35:20 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 7a3652: move clone() method from TreeFunctionsI to Tree, a... Message-ID: <20100624223518.CA6D0422EB@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 7a365298405466a82e4bd2a0b0fe1a2235f420bc http://github.com/bioperl/bioperl-live/commit/7a365298405466a82e4bd2a0b0fe1a2235f420bc Author: Chris Fields Date: 2010-06-24 (Thu, 24 Jun 2010) Changed paths: M Bio/Tree/Tree.pm M Bio/Tree/TreeFunctionsI.pm Log Message: ----------- move clone() method from TreeFunctionsI to Tree, as it isn't inherited properly with the new Root::clone method. Now it just overrides Root::clone() From noreply at github.com Fri Jun 25 01:36:14 2010 From: noreply at github.com (noreply at github.com) Date: Thu, 24 Jun 2010 22:36:14 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] bff079: overhaul Root::clone to use either Clone, Storable... Message-ID: <20100625053612.1039A422B6@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: bff07931777eb9f09594966414afc501e6fae623 http://github.com/bioperl/bioperl-live/commit/bff07931777eb9f09594966414afc501e6fae623 Author: Chris Fields Date: 2010-06-24 (Thu, 24 Jun 2010) Changed paths: M Bio/Root/Root.pm M t/Root/RootI.t Log Message: ----------- overhaul Root::clone to use either Clone, Storable, or pure perl, and add tests From kai.blin at biotech.uni-tuebingen.de Fri Jun 25 06:46:42 2010 From: kai.blin at biotech.uni-tuebingen.de (Kai Blin) Date: Fri, 25 Jun 2010 12:46:42 +0200 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 788a93: silence warnings with a default of 0 In-Reply-To: <20100624222111.C3D4E422F0@smtp1.rs.github.com> References: <20100624222111.C3D4E422F0@smtp1.rs.github.com> Message-ID: <1277462802.31442.438.camel@mikropc7.biotech.uni-tuebingen.de> On Thu, 2010-06-24 at 15:21 -0700, noreply at github.com wrote: > Log Message: > ----------- > silence warnings with a default of 0 Good catch, thanks. Kai -- Dipl.-Inform. Kai Blin kai.blin at biotech.uni-tuebingen.de Interfakult?res Institut f?r Mikrobiologie und Infektionsmedizin Abteilung Mikrobiologie/Biotechnologie Eberhard-Karls-Universit?t T?bingen Auf der Morgenstelle 28 Phone : ++49 7071 29-78841 D-72076 T?bingen Fax : ++49 7071 29-5979 Deutschland Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben From bugzilla-daemon at portal.open-bio.org Fri Jun 25 12:08:13 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 25 Jun 2010 12:08:13 -0400 Subject: [Bioperl-guts-l] [Bug 2744] Bio::LocatableSeq end. In-Reply-To: Message-ID: <201006251608.o5PG8DXD025916@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2744 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #4 from cjfields at bioperl.org 2010-06-25 12:08 EST ------- Readdressing this below: (In reply to comment #2) > Sure. > It seems bioperl-live is not yet updated? > The end was only overwritten with the calculated one if verbosity was > 0; this > is still the case on bioperl-live, but not on CPAN. This is now working on main trunk with verbosity set either way. > In addition, for refactoring, would it be an idea to only calculate e.g. length > and end if they have not been calculated and when the seq is changed? Also, > where possible, replace the =~s/..//g with =~tr///? I realize this is often > difficult as tr does not interpolate. Dealing with state changes is one of the major problems with LocatableSeq at the moment. This is outside of the scope of this bug report, though, but you are more than welcome to file this as a separate bug report. Also, use of tr/// is not possible as explained before (we have to deal with changes in various symbols so need interpolation). > Somehow CPAN > (http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/Bio/LocatableSeq.pm#end) > shows the "Note" > Note : although this is a get/set, it checks passed values against the > calculated end point ( derived from the sequence and based on > > But doc.bioperl does not (see > http://doc.bioperl.org/bioperl-live/Bio/LocatableSeq.html#POD2) This is now showing up. Closing this report out, as the original problem appears to be addressed. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Jun 25 12:46:42 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 25 Jun 2010 12:46:42 -0400 Subject: [Bioperl-guts-l] [Bug 2691] Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency In-Reply-To: Message-ID: <201006251646.o5PGkg7i032367@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2691 ------- Comment #8 from cjfields at bioperl.org 2010-06-25 12:46 EST ------- (In reply to comment #7) > I haven't heard anything from miriam about status of this module (including bug > fixes and reduction of dependencies). If nothing pops up in the next month > I'll move the code out of bioperl-live into bioperl-dev. I have sent out a post to the mail list about moving this code to it's own distribution or into bioperl-microarray. If there aren't complaints, I'll move it into a separate distribution. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Jun 25 13:13:14 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 25 Jun 2010 13:13:14 -0400 Subject: [Bioperl-guts-l] [Bug 2673] original fields not inherited by seq objects in alignment slices In-Reply-To: Message-ID: <201006251713.o5PHDE6J008824@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2673 ------- Comment #9 from cjfields at bioperl.org 2010-06-25 13:13 EST ------- (In reply to comment #8) > For those interested in perl6, this is actually quite easy using .clone > > my $newseq = $oldseq.clone( seq => $newstr, start => $newstart, end => newend); > > The above clones the old seq object but replaces the attributes indicated. The > named arguments are built into the language, so no need for _rearrange. We now have the beginnings of a default clone() method in Bio::Root::Root that accepts parameter arguments for setting. It defaults to the most optimized cloning method (Clone::clone(), then Storable::dclone(), then a pure perl kludge fallback). Probably needs a bit more work before a release, though (needs some decent testing). Parameters passed are checked with can() and called on the object, so anything passed should be capable of resetting attributes in the clone. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Fri Jun 25 13:19:55 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 10:19:55 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 1389c8: update MANIFEST Message-ID: <20100625171952.12BF3422A4@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 1389c8b31532fbfc20038e763f2855605d8b4661 http://github.com/bioperl/bioperl-live/commit/1389c8b31532fbfc20038e763f2855605d8b4661 Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: M MANIFEST Log Message: ----------- update MANIFEST From noreply at github.com Fri Jun 25 14:12:16 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 11:12:16 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 06e6bf: move sub creation to BEGIN, and document the _dclo... Message-ID: <20100625181213.8B0644203A@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 06e6bf29cf5c27ce2041df0cf1712a10aed1fd2a http://github.com/bioperl/bioperl-live/commit/06e6bf29cf5c27ce2041df0cf1712a10aed1fd2a Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: M Bio/Root/Root.pm Log Message: ----------- move sub creation to BEGIN, and document the _dclone method a bit more to differentiate it from clone; use Scalar::Util From noreply at github.com Fri Jun 25 14:18:23 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 11:18:23 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 7723bb: uncomment remove_dir() to cleanup files Message-ID: <20100625181820.35419422E3@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 7723bb2b27b1dd6b8c3ce05e2d13e69d5995dba5 http://github.com/bioperl/bioperl-live/commit/7723bb2b27b1dd6b8c3ce05e2d13e69d5995dba5 Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: M t/SeqIO/msout.t Log Message: ----------- uncomment remove_dir() to cleanup files From noreply at github.com Fri Jun 25 14:18:53 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 11:18:53 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] f8123b: update MANIFEST Message-ID: <20100625181850.404A6422E3@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: f8123b46e51d4933cae863b68b2f165e3723b87b http://github.com/bioperl/bioperl-live/commit/f8123b46e51d4933cae863b68b2f165e3723b87b Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: M MANIFEST Log Message: ----------- update MANIFEST From noreply at github.com Fri Jun 25 15:10:47 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 12:10:47 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-microarray] 4c17d8: remove Makefile Message-ID: <20100625191044.6CA7E422BB@smtp1.rs.github.com> Branch: refs/heads/topic/expression_migration Home: http://github.com/bioperl/bioperl-microarray Commit: 4c17d899d4169bcc7876e3dcbc3f0689ab14adad http://github.com/bioperl/bioperl-microarray/commit/4c17d899d4169bcc7876e3dcbc3f0689ab14adad Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: R Makefile Log Message: ----------- remove Makefile From noreply at github.com Fri Jun 25 15:17:17 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 12:17:17 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 4cf778: remove dependencies Message-ID: <20100625191714.32442422CE@smtp1.rs.github.com> Branch: refs/heads/topic/cleanup_microarray Home: http://github.com/bioperl/bioperl-live Commit: 4cf778f9c36d183f79a1e8ead072d9e69b5de17f http://github.com/bioperl/bioperl-live/commit/4cf778f9c36d183f79a1e8ead072d9e69b5de17f Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: M Build.PL Log Message: ----------- remove dependencies From noreply at github.com Fri Jun 25 15:18:52 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 12:18:52 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 5cfc08: update MANIFEST Message-ID: <20100625191849.8C727422CE@smtp1.rs.github.com> Branch: refs/heads/topic/cleanup_microarray Home: http://github.com/bioperl/bioperl-live Commit: 5cfc08a5635c1e803d0c91867071455b8e0918f0 http://github.com/bioperl/bioperl-live/commit/5cfc08a5635c1e803d0c91867071455b8e0918f0 Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: M MANIFEST Log Message: ----------- update MANIFEST From noreply at github.com Fri Jun 25 15:33:55 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 12:33:55 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 04e36c: add documentation on code move Message-ID: <20100625193352.9369B422E6@smtp1.rs.github.com> Branch: refs/heads/topic/cleanup_microarray Home: http://github.com/bioperl/bioperl-live Commit: 04e36cc0ee54771d7ad9acf816815787de7745d9 http://github.com/bioperl/bioperl-live/commit/04e36cc0ee54771d7ad9acf816815787de7745d9 Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: M Changes M DEPRECATED Log Message: ----------- add documentation on code move From bugzilla-daemon at portal.open-bio.org Fri Jun 25 16:33:47 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 25 Jun 2010 16:33:47 -0400 Subject: [Bioperl-guts-l] [Bug 3095] seq_version() in Bio::PrimarySeq not found In-Reply-To: Message-ID: <201006252033.o5PKXlAo002448@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3095 ------- Comment #2 from cjfields at bioperl.org 2010-06-25 16:33 EST ------- Posted about this to the list, hopefully will get some responses. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Sat Jun 26 00:24:06 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 21:24:06 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 24af44: protein molecule type not switched, correct bad te... Message-ID: <20100626042403.16845422B3@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 24af44758dd7b9b9ae0b1dbe7069d1b759a18be2 http://github.com/bioperl/bioperl-live/commit/24af44758dd7b9b9ae0b1dbe7069d1b759a18be2 Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: M Bio/SeqIO/genbank.pm M t/SeqIO/genbank.t Log Message: ----------- protein molecule type not switched, correct bad test data; molecule shouldn't be linear From bugzilla-daemon at portal.open-bio.org Sat Jun 26 00:54:36 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sat, 26 Jun 2010 00:54:36 -0400 Subject: [Bioperl-guts-l] [Bug 3053] incorrect formatting of LOCUS line in genbank output In-Reply-To: Message-ID: <201006260454.o5Q4sa8v025698@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3053 cjfields at bioperl.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #7 from cjfields at bioperl.org 2010-06-26 00:54 EST ------- I have added a validation check upon reading in the sequence which caught a minor error with protein sequences, but the output generated appears to be correct if using bioperl-live ('DNA' for molecule() is uppercase). Is it possible FlyBase is using an old version of bioperl? Anyway, the problem appears very likely to be on their end. Closing this out; feel free to reopen if the bug can be demonstrated to be on our end. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Sat Jun 26 01:17:33 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 22:17:33 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 634b5d: fix error where, with protein seqs the division an... Message-ID: <20100626051729.6A0E4422F0@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 634b5df44030a8281c2eb5fdc3ddd0c951d7b4d9 http://github.com/bioperl/bioperl-live/commit/634b5df44030a8281c2eb5fdc3ddd0c951d7b4d9 Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: M Bio/SeqIO/genbank.pm M t/SeqIO/genbank.t Log Message: ----------- fix error where, with protein seqs the division and dates were merged together From noreply at github.com Sat Jun 26 01:23:30 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 22:23:30 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] a68909: update bad test check Message-ID: <20100626052327.1B58F42175@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: a689099a175751da1633a23a52533eb6f20a55e8 http://github.com/bioperl/bioperl-live/commit/a689099a175751da1633a23a52533eb6f20a55e8 Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: M t/SeqFeature/Clone.t M t/SeqIO/Handler.t Log Message: ----------- update bad test check From noreply at github.com Sat Jun 26 01:34:07 2010 From: noreply at github.com (noreply at github.com) Date: Fri, 25 Jun 2010 22:34:07 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] edcb76: fix lower-case issue with moltype Message-ID: <20100626053403.AD62E422AE@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: edcb761bd922f6840e2eaffeb391308039774b0b http://github.com/bioperl/bioperl-live/commit/edcb761bd922f6840e2eaffeb391308039774b0b Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: M Bio/SeqIO/genbank.pm Log Message: ----------- fix lower-case issue with moltype From bugzilla-daemon at portal.open-bio.org Sat Jun 26 21:24:27 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sat, 26 Jun 2010 21:24:27 -0400 Subject: [Bioperl-guts-l] [Bug 3017] use threads to get genbank file error In-Reply-To: Message-ID: <201006270124.o5R1ORme029172@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3017 ------- Comment #2 from cjfields at bioperl.org 2010-06-26 21:24 EST ------- Confirmed (using perl 5.12.1), will take a look. The fail is due to a scalar ref to undef being assigned. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sat Jun 26 22:52:54 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sat, 26 Jun 2010 22:52:54 -0400 Subject: [Bioperl-guts-l] [Bug 3017] use threads to get genbank file error In-Reply-To: Message-ID: <201006270252.o5R2qsUx022664@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3017 ------- Comment #3 from cjfields at bioperl.org 2010-06-26 22:52 EST ------- This appears related to the use of weaken() in Bio::Species, so is blocking on that (and is one significant reason we need to rethink how that is implemented). I'm thinking the best option is to make Bio::Species a proxy class that has-a Bio::Taxon and the resulting tree (not is-a, which is the current problem). Vould solve a lot of bugs... -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Sat Jun 26 23:38:29 2010 From: noreply at github.com (noreply at github.com) Date: Sat, 26 Jun 2010 20:38:29 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b7bf0d: catch refs that sneak through, such as during thre... Message-ID: <20100627033824.5FFED421AE@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: b7bf0dae07f237d37db17489fd2380bf2fac082d http://github.com/bioperl/bioperl-live/commit/b7bf0dae07f237d37db17489fd2380bf2fac082d Author: Chris Fields Date: 2010-06-26 (Sat, 26 Jun 2010) Changed paths: M Bio/Taxon.pm Log Message: ----------- catch refs that sneak through, such as during thread issues (bug 3017) From noreply at github.com Mon Jun 28 14:22:07 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 28 Jun 2010 11:22:07 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 1687dc: Bio::Species delegates to Bio::Taxon and Bio::Tree... Message-ID: <20100628182207.353794204B@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: 1687dcef058351a6f8020a76690c9018132852f4 http://github.com/bioperl/bioperl-live/commit/1687dcef058351a6f8020a76690c9018132852f4 Author: Chris Fields Date: 2010-06-28 (Mon, 28 Jun 2010) Changed paths: M Bio/Species.pm Log Message: ----------- Bio::Species delegates to Bio::Taxon and Bio::Tree::Tree; this removes the need for weaken() as Bio::Species just acts as a proxy class. Needs further testing to ensure no mem leaks persist From noreply at github.com Mon Jun 28 14:52:58 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 28 Jun 2010 11:52:58 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 5cba9a: remove code refs for index tests, a few doc change... Message-ID: <20100628185258.F2FDA42281@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: 5cba9a67eb377a8a63fe6750b11da5ec810b82f2 http://github.com/bioperl/bioperl-live/commit/5cba9a67eb377a8a63fe6750b11da5ec810b82f2 Author: Chris Fields Date: 2010-06-28 (Mon, 28 Jun 2010) Changed paths: M Bio/Species.pm Log Message: ----------- remove code refs for index tests, a few doc changes and comments From noreply at github.com Mon Jun 28 15:07:37 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 28 Jun 2010 12:07:37 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 9ca1de: bit premature to check for this (API indicates thi... Message-ID: <20100628190737.4E4B542170@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: 9ca1de97fd2966c4b62fa7c56132c5430169bcba http://github.com/bioperl/bioperl-live/commit/9ca1de97fd2966c4b62fa7c56132c5430169bcba Author: Chris Fields Date: 2010-06-28 (Mon, 28 Jun 2010) Changed paths: M t/SeqIO/Handler.t M t/SeqIO/swiss.t Log Message: ----------- bit premature to check for this (API indicates this should be the more general Bio::Species until we deprecate it) From noreply at github.com Mon Jun 28 17:38:03 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 28 Jun 2010 14:38:03 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 04253f: add test for mem leak (may have to be modified) Message-ID: <20100628213803.D0EB242199@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: 04253fec3705ad9abb5958a89649af50361bed97 http://github.com/bioperl/bioperl-live/commit/04253fec3705ad9abb5958a89649af50361bed97 Author: Chris Fields Date: 2010-06-28 (Mon, 28 Jun 2010) Changed paths: M t/Species.t Log Message: ----------- add test for mem leak (may have to be modified) From noreply at github.com Mon Jun 28 17:41:50 2010 From: noreply at github.com (noreply at github.com) Date: Mon, 28 Jun 2010 14:41:50 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 457ad8: clean up cleaning up (e.g. DESTROY properly) Message-ID: <20100628214150.79D3E42096@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: 457ad8972cdae98d4c36c6e39ad3aaa4c4082188 http://github.com/bioperl/bioperl-live/commit/457ad8972cdae98d4c36c6e39ad3aaa4c4082188 Author: Chris Fields Date: 2010-06-28 (Mon, 28 Jun 2010) Changed paths: M Bio/Species.pm M Bio/Taxon.pm M Bio/Tree/Node.pm M Bio/Tree/Tree.pm Log Message: ----------- clean up cleaning up (e.g. DESTROY properly) From bugzilla-daemon at portal.open-bio.org Mon Jun 28 17:54:50 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 28 Jun 2010 17:54:50 -0400 Subject: [Bioperl-guts-l] [Bug 3017] use threads to get genbank file error In-Reply-To: Message-ID: <201006282154.o5SLsoth019003@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3017 ------- Comment #4 from cjfields at bioperl.org 2010-06-28 17:54 EST ------- This is fixed in a branch of bioperl-live that will be merged into the master branch once more tests are complete. http://github.com/bioperl/bioperl-live/tree/topic/species_proxy Perform a regular checkout of the repository, and then checkout the topic/species_proxy branch. I'll close this bug out when the code has been tested and merged to trunk. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Tue Jun 29 15:51:35 2010 From: noreply at github.com (noreply at github.com) Date: Tue, 29 Jun 2010 12:51:35 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] b1f8cf: revert species to the prior version (all tests now... Message-ID: <20100629195135.000DA422CE@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: b1f8cfe61f1626e382011a598220f16e791fc109 http://github.com/bioperl/bioperl-live/commit/b1f8cfe61f1626e382011a598220f16e791fc109 Author: Chris Fields Date: 2010-06-29 (Tue, 29 Jun 2010) Changed paths: M Bio/Species.pm M t/Species.t Log Message: ----------- revert species to the prior version (all tests now pass) From noreply at github.com Tue Jun 29 15:54:13 2010 From: noreply at github.com (noreply at github.com) Date: Tue, 29 Jun 2010 12:54:13 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] f1cea6: add ss-RNA to allowed moltypes Message-ID: <20100629195413.C784E422DE@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: f1cea60f9db81b9c06ddba872058ef03f8e581c5 http://github.com/bioperl/bioperl-live/commit/f1cea60f9db81b9c06ddba872058ef03f8e581c5 Author: Chris Fields Date: 2010-06-29 (Tue, 29 Jun 2010) Changed paths: M Bio/SeqIO/genbank.pm Log Message: ----------- add ss-RNA to allowed moltypes From noreply at github.com Tue Jun 29 15:58:31 2010 From: noreply at github.com (noreply at github.com) Date: Tue, 29 Jun 2010 12:58:31 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] fbc8f9: remote database change (ensembl ID not present in ... Message-ID: <20100629195831.7C008422CE@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: fbc8f9a9f6ae6f7f981450ed061b40437872704b http://github.com/bioperl/bioperl-live/commit/fbc8f9a9f6ae6f7f981450ed061b40437872704b Author: Chris Fields Date: 2010-06-29 (Tue, 29 Jun 2010) Changed paths: M t/RemoteDB/SwissProt.t Log Message: ----------- remote database change (ensembl ID not present in mapper any more) From noreply at github.com Tue Jun 29 17:03:49 2010 From: noreply at github.com (noreply at github.com) Date: Tue, 29 Jun 2010 14:03:49 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] f1cea6: add ss-RNA to allowed moltypes Message-ID: <20100629210349.7669D422E1@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: f1cea60f9db81b9c06ddba872058ef03f8e581c5 http://github.com/bioperl/bioperl-live/commit/f1cea60f9db81b9c06ddba872058ef03f8e581c5 Author: Chris Fields Date: 2010-06-29 (Tue, 29 Jun 2010) Changed paths: M Bio/SeqIO/genbank.pm Log Message: ----------- add ss-RNA to allowed moltypes Commit: fbc8f9a9f6ae6f7f981450ed061b40437872704b http://github.com/bioperl/bioperl-live/commit/fbc8f9a9f6ae6f7f981450ed061b40437872704b Author: Chris Fields Date: 2010-06-29 (Tue, 29 Jun 2010) Changed paths: M t/RemoteDB/SwissProt.t Log Message: ----------- remote database change (ensembl ID not present in mapper any more) Commit: d14fe40ea17fb8d3e558db65a655700f26594ea8 http://github.com/bioperl/bioperl-live/commit/d14fe40ea17fb8d3e558db65a655700f26594ea8 Author: Chris Fields Date: 2010-06-29 (Tue, 29 Jun 2010) Changed paths: M Bio/SeqIO/genbank.pm M t/RemoteDB/SwissProt.t Log Message: ----------- Merge branch 'master' into topic/species_proxy From noreply at github.com Tue Jun 29 17:25:09 2010 From: noreply at github.com (noreply at github.com) Date: Tue, 29 Jun 2010 14:25:09 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] e96a87: added routines to fetch all seqids Message-ID: <20100629212509.66297422DD@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: e96a873eade592e2c290f43660a2f1020b5f0ba3 http://github.com/bioperl/bioperl-live/commit/e96a873eade592e2c290f43660a2f1020b5f0ba3 Author: Lincoln Stein Date: 2010-06-29 (Tue, 29 Jun 2010) Changed paths: M Bio/DB/SeqFeature/Store/FeatureFileLoader.pm M Bio/DB/SeqFeature/Store/GFF3Loader.pm M Bio/DB/SeqFeature/Store/Loader.pm M Bio/DB/SeqFeature/Store/berkeleydb.pm Log Message: ----------- added routines to fetch all seqids Commit: c0b0e506b3bb8c77d42001313be86f45b3fcbb26 http://github.com/bioperl/bioperl-live/commit/c0b0e506b3bb8c77d42001313be86f45b3fcbb26 Author: Lincoln Stein Date: 2010-06-29 (Tue, 29 Jun 2010) Changed paths: M Bio/Root/Root.pm M Bio/SearchIO/hmmer3.pm M Bio/SeqIO/genbank.pm M Bio/Taxon.pm M Bio/Tree/Tree.pm M Bio/Tree/TreeFunctionsI.pm M MANIFEST M t/RemoteDB/SwissProt.t M t/Root/RootI.t M t/SeqFeature/Clone.t M t/SeqIO/Handler.t M t/SeqIO/genbank.t M t/SeqIO/msout.t Log Message: ----------- Merge branch 'master' of git at github.com:bioperl/bioperl-live From noreply at github.com Wed Jun 30 10:04:21 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 07:04:21 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 11c21f: move check for Leaktrace into BEGIN, then skip if ... Message-ID: <20100630140421.90C3942031@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: 11c21fac32e9e85b2ed8bd53ee45f59d404fbc57 http://github.com/bioperl/bioperl-live/commit/11c21fac32e9e85b2ed8bd53ee45f59d404fbc57 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/Species.t Log Message: ----------- move check for Leaktrace into BEGIN, then skip if needed From noreply at github.com Wed Jun 30 10:08:45 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 07:08:45 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 091750: require, not use (I always screw that up) Message-ID: <20100630140845.14423422EF@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: 0917504176833f904870a66a514d482070b6e866 http://github.com/bioperl/bioperl-live/commit/0917504176833f904870a66a514d482070b6e866 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/Species.t Log Message: ----------- require, not use (I always screw that up) From noreply at github.com Wed Jun 30 12:21:25 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 09:21:25 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 4ea296: switch to Test::Weaken, optionally run Message-ID: <20100630162125.670D0422F0@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: 4ea2968fd0304de88d463edcd2f7810b68cb21f0 http://github.com/bioperl/bioperl-live/commit/4ea2968fd0304de88d463edcd2f7810b68cb21f0 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/Species.t Log Message: ----------- switch to Test::Weaken, optionally run From noreply at github.com Wed Jun 30 12:24:54 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 09:24:54 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] f4fc35: fix skip test number Message-ID: <20100630162454.C04B042031@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: f4fc350ac7d042036026cbddc85b4b119f5d0c70 http://github.com/bioperl/bioperl-live/commit/f4fc350ac7d042036026cbddc85b4b119f5d0c70 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/Species.t Log Message: ----------- fix skip test number From noreply at github.com Wed Jun 30 14:04:06 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 11:04:06 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-db] e56b75: add minimal .gitignore file Message-ID: <20100630180406.9E7D34204B@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-db Commit: e56b7579a079e11c5bb2185bb8c6734d468f5aee http://github.com/bioperl/bioperl-db/commit/e56b7579a079e11c5bb2185bb8c6734d468f5aee Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: A .gitignore Log Message: ----------- add minimal .gitignore file From noreply at github.com Wed Jun 30 14:07:06 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 11:07:06 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-db] a98d2d: ignore conf file Message-ID: <20100630180706.57F94422FB@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-db Commit: a98d2d5eb2094471ea7cf814070ac522c8f3c113 http://github.com/bioperl/bioperl-db/commit/a98d2d5eb2094471ea7cf814070ac522c8f3c113 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M .gitignore Log Message: ----------- ignore conf file Commit: 4774e1fec6962b071920c540d4ca8e24482b9d6b http://github.com/bioperl/bioperl-db/commit/4774e1fec6962b071920c540d4ca8e24482b9d6b Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M lib/Bio/DB/Query/QueryConstraint.pm Log Message: ----------- squash perl 5.12 warning From noreply at github.com Wed Jun 30 14:08:23 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 11:08:23 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] abf0d5: make sure only defined values are passed on Message-ID: <20100630180823.B8804422F5@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: abf0d5f9f74f14535183a022e84319ffdf6e043c http://github.com/bioperl/bioperl-live/commit/abf0d5f9f74f14535183a022e84319ffdf6e043c Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M Bio/Tree/Node.pm Log Message: ----------- make sure only defined values are passed on From noreply at github.com Wed Jun 30 14:25:39 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 11:25:39 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 0b508d: remove microarray-specific code into either bioper... Message-ID: <20100630182539.765B442170@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 0b508d28764b8bcdedb5143c8334e7bb16d32df8 http://github.com/bioperl/bioperl-live/commit/0b508d28764b8bcdedb5143c8334e7bb16d32df8 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: R Bio/Expression/Contact.pm R Bio/Expression/DataSet.pm R Bio/Expression/FeatureGroup.pm R Bio/Expression/FeatureGroup/FeatureGroupMas50.pm R Bio/Expression/FeatureI.pm R Bio/Expression/FeatureSet/FeatureSetMas50.pm R Bio/Expression/Platform.pm R Bio/Expression/ProbeI.pm R Bio/Expression/Sample.pm R Bio/Microarray/Tools/MitoChipV2Parser.pm R Bio/Microarray/Tools/ReseqChip.pm R t/Microarray/Tools/ReseqChip.t R t/data/ReseqChip_ExampleData.fasta R t/data/ReseqChip_ParamsNcall.csv R t/data/ReseqChip_RefSeq.fasta R t/data/ReseqChip_mtDNA_design_annotation_file_FINAL.xls Log Message: ----------- remove microarray-specific code into either bioperl-microarray(deprecated) or Bio-Microarray (ReSeq code) Commit: 3cd6abb20358c09bffd3466cd6b695c51ee85633 http://github.com/bioperl/bioperl-live/commit/3cd6abb20358c09bffd3466cd6b695c51ee85633 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M Build.PL Log Message: ----------- remove dependencies Commit: f9978d616e52d5ef7f7201893c5ea2c58858dcb6 http://github.com/bioperl/bioperl-live/commit/f9978d616e52d5ef7f7201893c5ea2c58858dcb6 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M MANIFEST Log Message: ----------- update MANIFEST Commit: 1a43589ae46f62cff3d70047745fd217b4a62d5f http://github.com/bioperl/bioperl-live/commit/1a43589ae46f62cff3d70047745fd217b4a62d5f Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M Changes M DEPRECATED Log Message: ----------- add documentation on code move Signed-off-by: Chris Fields From noreply at github.com Wed Jun 30 14:35:50 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 11:35:50 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-microarray] ee0fc1: move Bio::Expression completely into bioperl-micro... Message-ID: <20100630183550.E3236422F6@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-microarray Commit: ee0fc180b7be18b01cb8d6c94653a82803ec9fa9 http://github.com/bioperl/bioperl-microarray/commit/ee0fc180b7be18b01cb8d6c94653a82803ec9fa9 Author: Chris Fields Date: 2010-06-25 (Fri, 25 Jun 2010) Changed paths: A .gitignore A Bio/Expression/Contact.pm A Bio/Expression/DataSet.pm A Bio/Expression/FeatureGroup.pm A Bio/Expression/FeatureGroup/FeatureGroupMas50.pm A Bio/Expression/FeatureI.pm A Bio/Expression/FeatureSet/FeatureSetMas50.pm A Bio/Expression/Platform.pm A Bio/Expression/ProbeI.pm A Bio/Expression/Sample.pm A Makefile Log Message: ----------- move Bio::Expression completely into bioperl-microarray Commit: e93dfa742cef6b5cd1e7588a252bdd5ccc808842 http://github.com/bioperl/bioperl-microarray/commit/e93dfa742cef6b5cd1e7588a252bdd5ccc808842 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: R Makefile Log Message: ----------- remove Makefile From bugzilla-daemon at portal.open-bio.org Wed Jun 30 15:38:33 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 30 Jun 2010 15:38:33 -0400 Subject: [Bioperl-guts-l] [Bug 3104] New: Bio::Species::classification() unhappy with single node "hierarchies" Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=3104 Summary: Bio::Species::classification() unhappy with single node "hierarchies" Product: BioPerl Version: unspecified Platform: PC URL: http://permalink.gmane.org/gmane.comp.lang.perl.bio.gene ral/22641 OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Unclassified AssignedTo: bioperl-guts-l at bioperl.org ReportedBy: charles.tilford at bms.com Up front, I may be misusing the module. I've been using it as a generic taxonomy node to hold arbitrary taxa, not just formal species. If that's inappropriate - eg I should use Bio::DB::Taxonomy - then this really isn't a bug (although it might still benefit from early argument sanity-checking). The problem arises when I try to provide single node classification trees. The issue cropped up with this "species" from a sequence DB we use: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=12908 I populate the object ala: use Bio::Species; my $specobj = Bio::Species->new(); $specobj->classification("unclassified sequences"); Using ( $Id: Species.pm 16700 2010-01-15 19:50:11Z dave_messina $) this throws: Use of uninitialized value $vals[1] in quotemeta at Bio/Species.pm line 179 ... and the relevant code is: sub classification { my ($self, @vals) = @_; if (@vals) { if (ref($vals[0]) eq 'ARRAY') { @vals = @{$vals[0]}; } # make sure the lineage contains us as first or second element # (lineage may have subspecies, species, genus ...) my $name = $self->node_name; my ($genus, $species) = (quotemeta($vals[1]), quotemeta($vals[0])); That is, it's expecting at least (species, genus) in the passed array. This block a little lower down: unless ($self->rank) { # and that we are rank species $self->rank('species'); } ... /implies/ that the module can be used for taxa ranks other than species. However, doing so would not prevent the module being aggravated over a null $vals[1]. Even if I'm abusing the extent to which the module was meant to be used, it might still be nice to check for a minimum of two arguments being passed before streaming the array through quotemeta. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Wed Jun 30 16:09:40 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 13:09:40 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 038a04: [bug 3014] passed values should be defined, defaul... Message-ID: <20100630200940.DAF47422F6@smtp1.rs.github.com> Branch: refs/heads/topic/species_proxy Home: http://github.com/bioperl/bioperl-live Commit: 038a040e46f8b3a15d34c6ad10b241c5caf2c4ca http://github.com/bioperl/bioperl-live/commit/038a040e46f8b3a15d34c6ad10b241c5caf2c4ca Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M Bio/Species.pm Log Message: ----------- [bug 3014] passed values should be defined, default to empty string From bugzilla-daemon at portal.open-bio.org Wed Jun 30 16:11:21 2010 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Wed, 30 Jun 2010 16:11:21 -0400 Subject: [Bioperl-guts-l] [Bug 3104] Bio::Species::classification() unhappy with single node "hierarchies" In-Reply-To: Message-ID: <201006302011.o5UKBLOf008903@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=3104 ------- Comment #1 from cjfields at bioperl.org 2010-06-30 16:11 EST ------- Charles, I fixed this on a Bio::Species-related branch which will be merged back into main trunk soon (pending comments). Will leave this open for the time being until the merge occurs. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From noreply at github.com Wed Jun 30 16:30:18 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 13:30:18 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-live] 7d4949: squash warning Message-ID: <20100630203018.F0711422ED@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-live Commit: 7d49494c6988b81e09a918310441af4a14358a4c http://github.com/bioperl/bioperl-live/commit/7d49494c6988b81e09a918310441af4a14358a4c Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/SeqFeature/Clone.t Log Message: ----------- squash warning From noreply at github.com Wed Jun 30 17:06:27 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 14:06:27 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 8283ed: Merge branch 'master' of github.com:bioperl/bioper... Message-ID: <20100630210627.846B5422B3@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: 8283ed1b5ee96754e53f91b290af848ca24445fe http://github.com/bioperl/bioperl-run/commit/8283ed1b5ee96754e53f91b290af848ca24445fe Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M Changes M lib/Bio/Tools/Run/AssemblerBase.pm M lib/Bio/Tools/Run/Newbler.pm M lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm M t/Newbler.t Log Message: ----------- Merge branch 'master' of github.com:bioperl/bioperl-run Commit: f1d3d58f938e546fee77e7afb27e366cccf2f3f7 http://github.com/bioperl/bioperl-run/commit/f1d3d58f938e546fee77e7afb27e366cccf2f3f7 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/Cap3.t Log Message: ----------- skip test count off, fixed Commit: b5bc8c150e57b64d36f9dbe4b588ae425b438a64 http://github.com/bioperl/bioperl-run/commit/b5bc8c150e57b64d36f9dbe4b588ae425b438a64 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/Newbler.t M t/Phrap.t M t/TigrAssembler.t Log Message: ----------- correct skipped number of tests From noreply at github.com Wed Jun 30 17:20:35 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 14:20:35 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 85e3f0: add email Message-ID: <20100630212035.A43B0422D6@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: 85e3f093e8318204db881deea67d7c7ae436e23f http://github.com/bioperl/bioperl-run/commit/85e3f093e8318204db881deea67d7c7ae436e23f Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/BEDTools.t M t/Bowtie.t M t/SoapEU-function.t M t/data/cysprot1a.msf M t/data/cysprot1b.msf Log Message: ----------- add email From noreply at github.com Wed Jun 30 17:29:05 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 14:29:05 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 17270d: add ulimit -n check, as these tests fail from too ... Message-ID: <20100630212905.6F1F1422FA@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: 17270ddcc565b4691fd0e34bbd52abd29005072a http://github.com/bioperl/bioperl-run/commit/17270ddcc565b4691fd0e34bbd52abd29005072a Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/Bowtie.t Log Message: ----------- add ulimit -n check, as these tests fail from too many open filehandles (bug 2577) From noreply at github.com Wed Jun 30 17:31:29 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 14:31:29 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 949e2a: add minimal gitignore Message-ID: <20100630213129.AAC4B422FB@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: 949e2add95aa2f0aa93b7e079b7266ef12e2c80e http://github.com/bioperl/bioperl-run/commit/949e2add95aa2f0aa93b7e079b7266ef12e2c80e Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: A .gitignore Log Message: ----------- add minimal gitignore From noreply at github.com Wed Jun 30 17:48:48 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 14:48:48 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 148ece: fix odd verbosity-dependent bug with EMBOSS tests Message-ID: <20100630214848.D10E3422E1@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: 148ece7ab5f2dd08079974d33306f9ac0615aa1f http://github.com/bioperl/bioperl-run/commit/148ece7ab5f2dd08079974d33306f9ac0615aa1f Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/EMBOSS.t Log Message: ----------- fix odd verbosity-dependent bug with EMBOSS tests From noreply at github.com Wed Jun 30 18:46:08 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 15:46:08 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 50e6ed: align left Message-ID: <20100630224608.87A0142305@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: 50e6edaed4b2ebd9efd1306c9d44ee5ea2c8dd99 http://github.com/bioperl/bioperl-run/commit/50e6edaed4b2ebd9efd1306c9d44ee5ea2c8dd99 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/EMBOSS.t Log Message: ----------- align left Commit: 959d4e28555bbf19256d5135eb9af3b49d27c162 http://github.com/bioperl/bioperl-run/commit/959d4e28555bbf19256d5135eb9af3b49d27c162 Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M lib/Bio/Tools/Run/Primer3.pm Log Message: ----------- add version() (backport from primer3redux) From noreply at github.com Wed Jun 30 18:46:48 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 15:46:48 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] b46abd: skip if version greater than 1.2 (old primer3 code... Message-ID: <20100630224648.5DC6D422EF@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: b46abd72eb25afde99f7a21081ecfe9c9d82f02e http://github.com/bioperl/bioperl-run/commit/b46abd72eb25afde99f7a21081ecfe9c9d82f02e Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/Primer3.t Log Message: ----------- skip if version greater than 1.2 (old primer3 code) From noreply at github.com Wed Jun 30 18:58:58 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 15:58:58 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 6d7b6d: is(), not ok() Message-ID: <20100630225858.95401422EF@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: 6d7b6dc70ab59d28b678204fe097a327249675de http://github.com/bioperl/bioperl-run/commit/6d7b6dc70ab59d28b678204fe097a327249675de Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/Blat.t Log Message: ----------- is(), not ok() From noreply at github.com Wed Jun 30 19:06:07 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 16:06:07 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 5d97c4: more robust call to ulimit Message-ID: <20100630230607.EA2914204F@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: 5d97c44ff2c2e31c80a3f39ac50f2d136fe1c1ad http://github.com/bioperl/bioperl-run/commit/5d97c44ff2c2e31c80a3f39ac50f2d136fe1c1ad Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/Bowtie.t Log Message: ----------- more robust call to ulimit From noreply at github.com Wed Jun 30 19:09:12 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 16:09:12 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 9b9181: some tweaks to get rid of warnings Message-ID: <20100630230912.48E3B4204F@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: 9b9181caa15ce69c66715630167c734016f8654e http://github.com/bioperl/bioperl-run/commit/9b9181caa15ce69c66715630167c734016f8654e Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M lib/Bio/Tools/Run/Cap3.pm M lib/Bio/Tools/Run/Maq.pm Log Message: ----------- some tweaks to get rid of warnings From noreply at github.com Wed Jun 30 19:18:04 2010 From: noreply at github.com (noreply at github.com) Date: Wed, 30 Jun 2010 16:18:04 -0700 Subject: [Bioperl-guts-l] [bioperl/bioperl-run] 75cddb: no_sequences -> num_sequences Message-ID: <20100630231804.CECE7422ED@smtp1.rs.github.com> Branch: refs/heads/master Home: http://github.com/bioperl/bioperl-run Commit: 75cddb27655302ea7538c90a30d909c8d6a54c9a http://github.com/bioperl/bioperl-run/commit/75cddb27655302ea7538c90a30d909c8d6a54c9a Author: Chris Fields Date: 2010-06-30 (Wed, 30 Jun 2010) Changed paths: M t/Amap.t M t/Kalign.t M t/MAFFT.t M t/Muscle.t M t/Probalign.t M t/Probcons.t M t/TCoffee.t Log Message: ----------- no_sequences -> num_sequences