October 2008 Archives by date

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Starting: Thu Oct 2 17:04:10 EDT 2008
Ending: Thu Oct 30 17:59:19 EDT 2008
Messages: 138

[Bioperl-guts-l] [14914] bioperl-live/trunk/Bio/AlignIO/xmfa.pm: clean up XMFA parsing, allow spaces in parsing (ende++, from IRC) Christopher John Fields
[Bioperl-guts-l] [Bug 2610] New: Fastq module next_seq() entry split problem bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2610] Fastq module next_seq() entry split problem bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14915] bioperl-live/trunk/Bio/Graphics: apply HTML escaping to imagemap title attributes rather than URL escaping Lincoln Stein
[Bioperl-guts-l] [Bug 2612] New: Warning message trying to parse xmfa file with AlignIO (all gap sequence present) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2614] New: invoking "use Bio::Tools::dpAlign; " produced error bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14916] bioperl-run/trunk: wrapper works now with PhyML 3. 0 while remaining compatible with 2.4.4 Heikki Lehvaslaiho
[Bioperl-guts-l] [Bug 2614] invoking "use Bio::Tools::dpAlign; " produced error bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2612] Warning message trying to parse xmfa file with AlignIO (all gap sequence present) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14917] bioperl-live/trunk/Bio: [bug 2612] Christopher John Fields
[Bioperl-guts-l] [14918] bioperl-live/trunk/Bio/AlignIO/xmfa.pm: [bug 2612] Christopher John Fields
[Bioperl-guts-l] [Bug 2612] Warning message trying to parse xmfa file with AlignIO (all gap sequence present) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14919] bioperl-live/trunk/t/Handler.t: TODO's work Christopher John Fields
[Bioperl-guts-l] [14920] bioperl-live/trunk/Bio/Seq/LargeSeqI.pm: add svn tag Christopher John Fields
[Bioperl-guts-l] [14921] bioperl-run/trunk/Bio/Tools/Run/Phylo/Phyml.pm: documentation and reporting fixes, method reorganisation Heikki Lehvaslaiho
[Bioperl-guts-l] [14922] bioperl-live/trunk/Bio/Graphics/FeatureFile.pm: try to distinguish between #aabbcc colors and right-hand comments Lincoln Stein
[Bioperl-guts-l] [14923] bioperl-live/trunk/Bio/Graphics/Panel.pm: added a workaround that prevents panel from crashing when trying to draw an image with no tracks in it Lincoln Stein
[Bioperl-guts-l] [14924] bioperl-live/trunk/Bio/Graphics/Panel.pm: removed stupid debugging statement Lincoln Stein
[Bioperl-guts-l] [14925] bioperl-live/trunk: fixed ps() output; spotted by Mira Han Heikki Lehvaslaiho
[Bioperl-guts-l] [14926] bioperl-live/trunk/Bio/DB/GFF/Adaptor/memory.pm: fixed broken primary_id generation in memory adaptor Lincoln Stein
[Bioperl-guts-l] [Bug 2615] New: Argument inconsistency in Bio::SearchIO bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2615] Argument inconsistency in Bio::SearchIO bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2615] Argument inconsistency in Bio::SearchIO bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2519] Bio::Assembly::IO::ace allow for non "Contig\d" naming bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2519] Bio::Assembly::IO::ace allow for non "Contig\d" naming bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2519] Bio::Assembly::IO::ace allow for non "Contig\d" naming bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14927] bioperl-live/trunk: [bug 2519] Christopher John Fields
[Bioperl-guts-l] [14928] bioperl-live/trunk/Bio/Assembly/IO/ace.pm: [bug 2519] Christopher John Fields
[Bioperl-guts-l] [14929] bioperl-live/trunk/Bio/Range.pm: typo Christopher John Fields
[Bioperl-guts-l] [Bug 2615] Argument inconsistency in Bio::SearchIO bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2581] HMMER parse error bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14930] bioperl-live/trunk/Bio/Tree/Statistics.pm: fix parsimony score of ps() to work with polytomies Heikki Lehvaslaiho
[Bioperl-guts-l] [Bug 2615] Argument inconsistency in Bio::SearchIO bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14931] bioperl-live/trunk/Bio/LocatableSeq.pm: George Hartzell
[Bioperl-guts-l] [14932] bioperl-live/trunk/t/LocatableSeq.t: George Hartzell
[Bioperl-guts-l] [14933] bioperl-live/trunk: [bug 2563] Christopher John Fields
[Bioperl-guts-l] [Bug 2563] Bio::AlignIO::arp does not parse multiple alignments bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2614] invoking "use Bio::Tools::dpAlign; " produced error bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14934] bioperl-live/trunk/Bio/AlignIO/arp.pm: add -source for ARP Christopher John Fields
[Bioperl-guts-l] [Bug 2614] invoking "use Bio::Tools::dpAlign; " produced error bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14935] bioperl-live/trunk/Bio/TreeIO/nexus.pm: Write out tags color and label as a comment understood by the FigTree program Heikki Lehvaslaiho
[Bioperl-guts-l] [14936] bioperl-live/trunk/t/LocatableSeq.t: revcom on a Bio:: LocatableSeq does not change the outcome of column_from_residue_number() no matter how counterintutive it is. Heikki Lehvaslaiho
[Bioperl-guts-l] [14937] bioperl-live/trunk: [bug 2441] Singlets as Bio::Assembly:: Singlet objects Florent E Angly
[Bioperl-guts-l] [Bug 2620] New: Bio::Assembly::IO::phrap is incomplete bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2441] Bio::Assembly treatment of singletons is inconsistent bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2451] Suggestions for name of module and module improvement bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2451] Suggestions for name of module and module improvement bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14938] bioperl-live/trunk: Cleanup of the Bio::Assembly::Singlet module Florent E Angly
[Bioperl-guts-l] [14939] bioperl-live/trunk/Bio/Assembly/Singlet.pm: Additional checks in the singlet code Florent E Angly
[Bioperl-guts-l] [Bug 2350] Make ID system consisten between Bio::Align::AlignI and Bio::SeqI bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2350] Make ID system consistent between Bio::Align::AlignI and Bio::SeqI bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14940] bioperl-live/trunk/Bio/Assembly/IO/ace.pm: [Bug 2519] and [Bug 2459 ] Florent E Angly
[Bioperl-guts-l] [Bug 2459] Bio::Assembly::IO::ace.pm not parsing contig names correctly bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2519] Bio::Assembly::IO::ace allow for non "Contig\d" naming bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2621] New: Bio::SeqFeature::Collection->add_feature fails to check input correctly? bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14941] bioperl-live/trunk: Fixed missing -end for the contig and singlet features in Bio::Assembly:: IO::tigr Florent E Angly
[Bioperl-guts-l] [14942] bioperl-live/trunk: [Bug 2455] Bio::Assembly::IO:: ace singlet support Florent E Angly
[Bioperl-guts-l] [Bug 2455] Bio::Assembly::IO::ace doesn't create Bio::Assembly::Singlet objects bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2455] Bio::Assembly::IO::ace doesn't create Bio::Assembly::Singlet objects bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2623] New: Bio::FeatureIO::vecscreen_simple crashes on vecscreen warnings bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2623] Bio::FeatureIO::vecscreen_simple crashes on vecscreen warnings bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14943] bioperl-live/trunk/Bio/Assembly/IO/ace.pm: Removed superfluous statement in Bio::Assembly::IO::ace Florent E Angly
[Bioperl-guts-l] [Bug 2623] Bio::FeatureIO::vecscreen_simple crashes on vecscreen warnings bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2623] Bio::FeatureIO::vecscreen_simple crashes on vecscreen warnings bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2624] New: Bio::SeqFeature::Generic scores not persisted to BioSQL via bioperl-db bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2621] Bio::SeqFeature::Collection->add_feature fails to check input correctly? bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14944] bioperl-live/trunk/Bio/Tools/BPlite.pm: fix email address Jason Stajich
[Bioperl-guts-l] [14945] bioperl-live/trunk: new module for parsing vecscreen -f 3 output, courtesy of Robert Buels Christopher John Fields
[Bioperl-guts-l] [14946] bioperl-live/trunk/t/data/vecscreen_simple.test_output: fix file properties Christopher John Fields
[Bioperl-guts-l] [14947] bioperl-live/trunk/Bio/Index/Blast.pm: fix email address Jason Stajich
[Bioperl-guts-l] [14948] bioperl-live/trunk/Bio/Tree/Node.pm: more specific warning Jason Stajich
[Bioperl-guts-l] [Bug 2621] Bio::SeqFeature::Collection->add_feature fails to check input correctly? bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14949] bioperl-live/trunk/Bio/Tree/Node.pm: Don' t include potentially undefined variables in warning message Senduran Balasubramaniam
[Bioperl-guts-l] [14950] bioperl-live/trunk/Bio/DB/Fasta.pm: Allow multi-ID indexing per sequence. Jason Stajich
[Bioperl-guts-l] [14951] bioperl-live/trunk/Bio/SearchIO/fasta.pm: FASTA - 35. 04 Parameters section parsing for Matrix Jason Stajich
[Bioperl-guts-l] [14952] bioperl-live/trunk/t/SearchIO.t: FASTA - 35. 04 Parameters section parsing for Matrix Jason Stajich
[Bioperl-guts-l] [14953] bioperl-live/trunk: support new method in API get_seq_by_id Jason Stajich
[Bioperl-guts-l] [14954] bioperl-live/trunk/Bio/Index/Blast.pm: Correct the example Brian Osborne
[Bioperl-guts-l] [14955] bioperl-live/trunk/Bio/SimpleAlign.pm: typo in docs Heikki Lehvaslaiho
[Bioperl-guts-l] [14956] bioperl-live/trunk/Bio/Index/Blast.pm: Fix for RPS-BLAST Brian Osborne
[Bioperl-guts-l] [14957] bioperl-live/trunk/t: Add tests for Index::Blast and RPSBLAST Brian Osborne
[Bioperl-guts-l] [Bug 2621] Bio::SeqFeature::Collection->add_feature fails to check input correctly? bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2594] Bio::Species memory leak bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14958] bioperl-live/trunk/t/RestrictionIO.t: bullet-proof prototype test Christopher John Fields
[Bioperl-guts-l] [14959] bioperl-live/trunk/Bio/Location/Simple.pm: [bug 2621] Christopher John Fields
[Bioperl-guts-l] [Bug 2621] Bio::SeqFeature::Collection->add_feature fails to check input correctly? bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14960] bioperl-live/trunk/Bio/SeqFeature/Generic.pm: [bug 2624] Christopher John Fields
[Bioperl-guts-l] [14961] bioperl-db/trunk/t/05seqfeature.t: [bug 2624] Christopher John Fields
[Bioperl-guts-l] [Bug 2624] Bio::SeqFeature::Generic scores not persisted to BioSQL via bioperl-db bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14962] bioperl-live/trunk: [bug 2621] Christopher John Fields
[Bioperl-guts-l] [14963] bioperl-live/trunk/Bio: [bug 2621] Christopher John Fields
[Bioperl-guts-l] [Bug 2621] Bio::SeqFeature::Collection->add_feature fails to check input correctly? bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14964] bioperl-live/trunk/Bio/Location: add docs for LocationI method valid_Location Christopher John Fields
[Bioperl-guts-l] [14965] bioperl-live/trunk/Bio/SeqIO/game/featHandler.pm: use valid_Location to check Location state Christopher John Fields
[Bioperl-guts-l] [14966] bioperl-live/trunk/Bio/Coordinate/GeneMapper.pm: end = start if only start is passed Christopher John Fields
[Bioperl-guts-l] [14967] bioperl-live/trunk/t/Handler.t: Fix unlink() warning Christopher John Fields
[Bioperl-guts-l] [Bug 2621] Bio::SeqFeature::Collection->add_feature fails to check input correctly? bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2615] Argument inconsistency in Bio::SearchIO bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14968] bioperl-live/trunk/Bio/Tools/Hmmpfam.pm: clarifying example code. Dave Messina
[Bioperl-guts-l] [Bug 2630] New: Bio::LocatableSeq range validation does not work with translated sequence coordinates bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14969] bioperl-run/trunk/Bio/Tools/Run/Hmmer.pm: Fixed example code. Dave Messina
[Bioperl-guts-l] [14970] bioperl-run/trunk/Bio/Tools/Run/Hmmer.pm: Clarifying default input sequence format. Dave Messina
[Bioperl-guts-l] [Bug 2632] New: hmmpfam parsers are broken (both hmmer and hmmer_pull) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2633] New: Incorrect identity calculation in Bio::SearchIO::fasta bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2633] Incorrect identity calculation in Bio::SearchIO::fasta bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14971] bioperl-live/trunk: [bug 2630] Christopher John Fields
[Bioperl-guts-l] [Bug 2630] Bio::LocatableSeq range validation does not work with translated sequence coordinates bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14972] bioperl-live/trunk/t/data/BOSS_DROME.FASTP_v35_04: jasonfail. Jason Stajich
[Bioperl-guts-l] [14973] bioperl-live/trunk/Bio/Search: [bug 2633] Christopher John Fields
[Bioperl-guts-l] [Bug 2633] Incorrect identity calculation in Bio::SearchIO::fasta bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2633] Incorrect identity calculation in Bio::SearchIO::fasta bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2635] New: New Bio::SimpleAlign method for concatenating alignments bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2635] New Bio::SimpleAlign method for concatenating alignments bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2635] New Bio::SimpleAlign method for concatenating alignments bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2635] New Bio::SimpleAlign method for concatenating alignments bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2635] New Bio::SimpleAlign method for concatenating alignments bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2636] New: New version of PAML changes output bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2636] New version of PAML changes output bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14974] bioperl-live/trunk/Bio/Search/HSP/GenericHSP.pm: fix seq_inds(); wasn't calling identical residues for FASTA parsing Christopher John Fields
[Bioperl-guts-l] [Bug 2636] New version of PAML changes output bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2635] New Bio::SimpleAlign method for concatenating alignments bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2635] New Bio::SimpleAlign method for concatenating alignments bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2636] New version of PAML changes output bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2633] Incorrect identity calculation in Bio::SearchIO::fasta bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2637] New: new modules for HIV sequence queries bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull) bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [14975] bioperl-live/trunk/Bio/SearchIO/hmmer.pm: [bug 2632] Christopher John Fields
[Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull) bugzilla-daemon at portal.open-bio.org

Last message date: Thu Oct 30 17:59:19 EDT 2008
Archived on: Thu Oct 30 17:59:21 EDT 2008

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