July 2008 Archives by date

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Starting: Tue Jul 1 12:05:47 EDT 2008
Ending: Thu Jul 31 21:54:29 EDT 2008
Messages: 54

• [Bioperl-guts-l] [Bug 2534] New: uniprot_trembl parsing   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14748] bioperl-live/trunk/Bio/Tree: phyloxml to_string <name>, < branch_length>   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14749] bioperl-live/trunk: nested annotation collection instead of structuredValue   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14750] bioperl-live/trunk: element_default instead of element_name _branch _confidence   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14751] bioperl-live/trunk: phyloxml write_tree   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14752] bioperl-live/trunk/Bio/DB/SeqFeature.pm: Minor edits   Brian Osborne
• [Bioperl-guts-l] [Bug 2537] New: num_conserved reports incorrect value during FASTA34 parsing   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2537] num_conserved reports incorrect value during FASTA34 parsing   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2539] New: SeqIO::pir parser fails for codes other than P1   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14753] bioperl-live/trunk/Bio/SeqIO/pir.pm: bug 2539   Christopher John Fields
• [Bioperl-guts-l] [Bug 2539] SeqIO::pir parser fails for codes other than P1   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2504] Bug in Bio::SearchIO module   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14754] bioperl-live/trunk/Bio/Tree/TreeI.pm: Can't inherit from oneself   Christopher John Fields
• [Bioperl-guts-l] [Bug 2504] Bug in Bio::SearchIO module   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14755] bioperl-live/trunk/Bio/Graphics/FeatureFile.pm: accept $seq_id or $seqid in link substitution rules   Lincoln Stein
• [Bioperl-guts-l] [Bug 2534] uniprot_trembl parsing   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2504] Bug in Bio::SearchIO module   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2534] uniprot_trembl parsing   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14756] bioperl-live/trunk/Bio/SeqIO: bug 2534   Christopher John Fields
• [Bioperl-guts-l] [Bug 2534] uniprot_trembl parsing   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14757] bioperl-live/trunk: phyloxml: taxonomy, distribution, annotation, events, date, etc   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14758] bioperl-live/trunk/Bio/DB/SeqFeature/Store: workaround a bug that emerges when the memory adapter automatically assigns a primary id of 0   Lincoln Stein
• [Bioperl-guts-l] [14759] bioperl-live/trunk/t/RemoteBlast.t: bulletproof test; remote tabular BLAST is failing for some reason...   Christopher John Fields
• [Bioperl-guts-l] [14760] bioperl-live/trunk/Bio: fixed bug in the memory adapter which prevented features with a primary ID of "0" from being loaded   Lincoln Stein
• [Bioperl-guts-l] [Bug 2546] New: RemoteBlast blasttable parsing is broken.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2546] RemoteBlast blasttable parsing is broken.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14761] bioperl-live/trunk: phyloxml: create Bio::Seq for <sequence>   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [Bug 2549] New: species not parsed correctly in Bio::SeqIO::kegg module   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14762] bioperl-live/trunk/Bio: glyphs will now display the first alias as the label if the display_name() is not defined   Lincoln Stein
• [Bioperl-guts-l] [14763] bioperl-live/trunk: add multiple record support ( courtesy of Jorge Duarte, per mail list)   Christopher John Fields
• [Bioperl-guts-l] [14764] bioperl-live/trunk/Bio: fixed error in which spaces are not properly escaped in GFF3 files   Lincoln Stein
• [Bioperl-guts-l] [14765] bioperl-live/trunk/Bio/Graphics/FeatureBase.pm: pretty formatting of gff3 attributes   Lincoln Stein
• [Bioperl-guts-l] [14766] bioperl-live/trunk/Bio: modified fix so that it doesn' t break compatibility with those who use '+' to describe the strand of the target   Lincoln Stein
• [Bioperl-guts-l] [Bug 2555] New: Bio::Biblio::IO parse error (medlinexml.pm)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2534] uniprot_trembl parsing   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14767] bioperl-live/trunk: bug 2549; fixed small bug in Bio:: Taxon which doesn't catch -common_name   Christopher John Fields
• [Bioperl-guts-l] [Bug 2549] species not parsed correctly in Bio::SeqIO::kegg module   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14768] bioperl-live/trunk/Bio/Biblio/IO/medlinexml.pm: bug 2555   Christopher John Fields
• [Bioperl-guts-l] [Bug 2555] Bio::Biblio::IO parse error (medlinexml.pm)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14769] bioperl-live/trunk: phyloxml seq_relation clade_relation   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [Bug 2556] New: Bio::Tools::Primer3->next_primer fails when plain sequence is supplied to Bio::Tools::Primer3::Run   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2556] Bio::Tools::Primer3->next_primer fails when plain sequence is supplied to Bio::Tools::Primer3::Run   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14770] bioperl-live/trunk: Bug 2546   Christopher John Fields
• [Bioperl-guts-l] [Bug 2546] RemoteBlast blasttable parsing is broken.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14771] bioperl-live/trunk/Bio/Tools/Primer3.pm: bug 2556:   Christopher John Fields
• [Bioperl-guts-l] [Bug 2556] Bio::Tools::Primer3->next_primer fails when plain sequence is supplied to Bio::Tools::Primer3::Run   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2522] Bio::Ontology::Ontology->get_all_terms() returns an empty list after reading an obo file.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14772] bioperl-live/trunk/Bio/Tools/Primer3.pm: revert Roy's patch (my bad )   Christopher John Fields
• [Bioperl-guts-l] [14773] bioperl-run/trunk/Bio/Tools/Run/Primer3.pm: patching the correct Primer3.pm (not Bio::Tools::Primer3.pm)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2559] New: Out of memory (malloc error)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2559] Out of memory (malloc error)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14774] bioperl-live/trunk/t/RootIO.t: tests should use is/ isnt when possible, not ok()   Christopher John Fields
• [Bioperl-guts-l] [14775] bioperl-live/trunk/Bio/Graphics/Glyph/xyplot.pm: fixed zero-width rectangles which were breaking GD:: SVG representations of xyplot data   Lincoln Stein
• [Bioperl-guts-l] [14776] bioperl-db/trunk: Fixed inconsistencies in the PODs of the loading scripts.   Hilmar Lapp

Last message date: Thu Jul 31 21:54:29 EDT 2008
Archived on: Thu Jul 31 21:54:39 EDT 2008

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