January 2008 Archives by thread

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Starting: Thu Jan 3 07:24:18 EST 2008
Ending: Thu Jan 31 18:04:31 EST 2008
Messages: 67

• [Bioperl-guts-l] [Bug 2427] New: error while using Bio::Search::cross_match   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2427] error while using Bio::Search::cross_match   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2427] error while using Bio::Search::cross_match   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2428] New: GenPept Taxon SEQIO problem   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2428] GenPept Taxon SEQIO problem   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2428] GenPept Taxon SEQIO problem   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2428] GenPept Taxon SEQIO problem   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2429] New: Bio::FeatureIO gff3 fails to parse canonical GFF3 file from GFF3 spec   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2429] Bio::FeatureIO gff3 fails to parse canonical GFF3 file from GFF3 spec   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2429] Bio::FeatureIO gff3 fails to parse canonical GFF3 file from GFF3 spec   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2430] New: SeqIO wrong parse of Species and Taxonomic Class in GBK, fix proposed   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2430] SeqIO wrong parse of Species and Taxonomic Class in GBK, fix proposed   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2430] SeqIO wrong parse of Species and Taxonomic Class in GBK, fix proposed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14435] bioperl-live/trunk/README:   George Hartzell
• [Bioperl-guts-l] [Bug 2431] New: BLAST HTMLWriter makes empty lines   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2431] BLAST HTMLWriter makes empty lines   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2431] BLAST HTMLWriter makes empty lines   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2431] BLAST HTMLWriter makes empty lines   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2431] BLAST HTMLWriter makes empty lines   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2433] New: Please add quality score support to Bio::DB::GenBank   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2433] Please add quality score support to Bio::DB::GenBank   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2433] Please add quality score support to Bio::DB::GenBank   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14437] bioperl-live/trunk/README: test post-commit after fsfs transfer ( 2nd try)   Christopher John Fields
• [Bioperl-guts-l] [14438] bioperl-run/trunk/README: test   Christopher John Fields
• [Bioperl-guts-l] [Bug 2420] Bio::Index::Blast fails with blastall 2.2.16   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14439] bioperl-live/trunk/Bio/Tools/Primer3.pm: Bug 2426   Christopher John Fields
• [Bioperl-guts-l] [Bug 2426] Bio::Tools::Primer3 returns wrong result count under certain situation   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14440] bioperl-live/trunk/Bio/SeqIO/genbank.pm: fixing the missing space between the feature type name and the location when the type name is longer than 15 char .   Scott Cain
• [Bioperl-guts-l] [14441] bioperl-run/trunk: first version of Gerp wrapper, usable   Senduran Balasubramaniam
• [Bioperl-guts-l] [14442] bioperl-live/trunk: first version of Gerp parser, usable   Senduran Balasubramaniam
• [Bioperl-guts-l] [14443] bioperl-live/trunk/Bio/FeatureIO/bed.pm: improved handling of different kinds of feature object   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2356] Bio::TreeIO::pag outputs   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2356] Bio::TreeIO::pag outputs   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2356] Bio::TreeIO::pag outputs   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14444] bioperl-live/trunk/Bio/SearchIO/Writer/HTMLResultWriter.pm: bug 2431   Christopher John Fields
• [Bioperl-guts-l] [14445] bioperl-live/trunk: bug 2423   Christopher John Fields
• [Bioperl-guts-l] [Bug 2423] Bio::Tools::Glimmer - frame support for Glimmer2/3 parser   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14446] bioperl-live/trunk/Bio/Tree/Compatible.pm: fixed synopsis code to work   Senduran Balasubramaniam
• [Bioperl-guts-l] [14447] bioperl-live/trunk/Bio/Tree/Compatible.pm: more fixes for synopsis code, added warning to description   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2356] Bio::TreeIO::pag outputs (NEXUS parsing)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2424] Out of memory on SeqIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2426] Bio::Tools::Primer3 returns wrong result count under certain situation   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14448] bioperl-live/trunk/Bio/SearchIO/cross_match.pm: Tentative fix for bug 2427   Christopher John Fields
• [Bioperl-guts-l] [14449] bioperl-live/trunk/t: Starter cross_match tests and sample data.   Christopher John Fields
• [Bioperl-guts-l] [14450] bioperl-live/trunk/scripts/index/bp_fetch.PLS: bug 2433   Christopher John Fields
• [Bioperl-guts-l] [Bug 2415] Wrong tree coloring by Tree::Draw::Cladogram   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14451] bioperl-live/trunk/scripts/index/bp_fetch.PLS: remove format option for EMBL just in case...   Christopher John Fields
• [Bioperl-guts-l] [Bug 2069] Bio::Tools:pSW stop codon bug   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2069] Bio::Tools:pSW stop codon bug   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14452] bioperl-live/trunk/Build.PL: Use db settings for both BioDBGFF and BioDBSeqFeature_mysql ( needs bypass testing for Pg and other drivers)   Christopher John Fields
• [Bioperl-guts-l] [14453] bioperl-live/trunk/Bio/SeqIO/entrezgene.pm: get rid of annoying ' pseudohashes' error; tests now pass on perl 5.8.8, perl 5.10   Christopher John Fields
• [Bioperl-guts-l] [14454] bioperl-live/trunk/Bio/SeqIO/entrezgene.pm: revert last commit; problem more serious than initially appears (will require more debugging)   Christopher John Fields
• [Bioperl-guts-l] [14455] bioperl-live/trunk/Bio/Graphics/Glyph/gene.pm: fixed up the gene glyph so that it works properly with CDS-only genes   Lincoln Stein
• [Bioperl-guts-l] [14456] bioperl-live/trunk/Bio/Graphics/Glyph.pm: new feature of -strand_arrow option allows you to specify arrowheads only on first and last segment   Lincoln Stein
• [Bioperl-guts-l] [14457] bioperl-live/trunk/Bio/SeqIO/entrezgene.pm: Stefan' s fix for entrezgene which includes a fix for pseudohash warnings; works now using perl 5.10.   Christopher John Fields
• [Bioperl-guts-l] [14458] bioperl-live/trunk/t/DB.t: Returned value from EntrezGene is different   Christopher John Fields
• [Bioperl-guts-l] [Bug 2436] New: Inconsistencies in function HSPI::seq_inds when encountering gaps   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2436] Inconsistencies in function HSPI::seq_inds when encountering gaps   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2436] Inconsistencies in function HSPI::seq_inds when encountering gaps   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2436] Inconsistencies in function HSPI::seq_inds when encountering gaps   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2436] Inconsistencies in function HSPI::seq_inds when encountering gaps   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2436] Inconsistencies in function HSPI::seq_inds when encountering gaps   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2436] Inconsistencies in function HSPI::seq_inds when encountering gaps   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14459] bioperl-live/trunk/Bio/DB/EUtilities.pm: Add simple method to retrieve parameter settings   Christopher John Fields
• [Bioperl-guts-l] [Bug 2420] Bio::Index::Blast fails with blastall 2.2.16   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2305] Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14460] bioperl-live/trunk/Bio/Search/HSP/GenericHSP.pm: bug 2436; add option for 'mismatch' (no match w/o gaps)   Christopher John Fields

Last message date: Thu Jan 31 18:04:31 EST 2008
Archived on: Thu Jan 31 18:04:34 EST 2008

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