March 2009 Archives by author

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Starting: Sun Mar 1 14:25:20 EST 2009
Ending: Mon Mar 30 13:49:51 EDT 2009
Messages: 100

[Bioperl-guts-l] [15586] bioperl-live/trunk: [bug 2766] Christopher John Fields
[Bioperl-guts-l] [15587] bioperl-live/trunk: * NCBI allows 3 requests per second now Christopher John Fields
[Bioperl-guts-l] [15588] bioperl-live/trunk/Bio/Index/Hmmer.pm: speling Christopher John Fields
[Bioperl-guts-l] [15596] bioperl-live/trunk/Bio/SeqIO/genbank.pm: [bug 2784] Christopher John Fields
[Bioperl-guts-l] [15597] bioperl-live/trunk/Bio/SeqIO/scf.pm: use statement missing Christopher John Fields
[Bioperl-guts-l] [15598] bioperl-live/trunk: * tweak last commit (wasn't passing other tests ) - now allows either UniProt or SwissProt Christopher John Fields
[Bioperl-guts-l] [15599] bioperl-live/trunk/Bio/SeqIO/Handler/GenericRichSeqHandler.pm: update handler to sync with genbank Christopher John Fields
[Bioperl-guts-l] [15600] bioperl-live/trunk/Bio/SeqIO/chadoxml.pm: [bug 2785] Christopher John Fields
[Bioperl-guts-l] [15601] bioperl-db/trunk/Bio/DB/BioSQL/Oracle/BiosequenceAdaptorDriver.pm: [bug 2757] Christopher John Fields
[Bioperl-guts-l] [15604] bioperl-live/trunk/Bio/AlignIO/stockholm.pm: [bug 2796] Christopher John Fields
[Bioperl-guts-l] [15605] bioperl-live/trunk/Bio/AlignIO/stockholm.pm: [bug 2796] Christopher John Fields
[Bioperl-guts-l] [15606] bioperl-live/trunk/Bio/AlignIO/Handler/GenericAlignHandler.pm: [ bug 2796] Christopher John Fields
[Bioperl-guts-l] [15609] bioperl-live/trunk/Bio/AlignIO/stockholm.pm: [Bug 2796] Christopher John Fields
[Bioperl-guts-l] [15610] bioperl-live/trunk/Bio/AlignIO/stockholm.pm: add some docs for how to add custom annotation ( as well as warnings about possible future changes) Christopher John Fields
[Bioperl-guts-l] [15611] bioperl-live/trunk/Bio/AlignIO/stockholm.pm: make prettier for perldoc Christopher John Fields
[Bioperl-guts-l] [15612] bioperl-run/trunk: [bug 2798] Christopher John Fields
[Bioperl-guts-l] [15613] bioperl-live/trunk/Bio/SeqFeatureI.pm: remove comments ( left over from rollback, not pertinent anymore) Christopher John Fields
[Bioperl-guts-l] [15614] bioperl-live/trunk/Bio/AlignIO/stockholm.pm: remove debugging line Christopher John Fields
[Bioperl-guts-l] [15615] bioperl-live/trunk: [bug 2456] Christopher John Fields
[Bioperl-guts-l] [15585] bioperl-live/trunk/Build.PL: adding recommendation for XML::Simple (reqd by Bio::Tools::EUtilities, Mark Allen Jensen
[Bioperl-guts-l] [15590] bioperl-live/trunk/Bio/DB/HIV/lanl-schema.xml: fixed misplaced sfield closing tags Mark Allen Jensen
[Bioperl-guts-l] [15591] bioperl-live/trunk/Bio/DB/HIV/HIVQueryHelper.pm: put_value now puts an undef if VALUE is undef (before, created Mark Allen Jensen
[Bioperl-guts-l] [15592] bioperl-live/trunk/Bio/DB/Query/HIVQuery.pm: added some external pod (for get_keys() method) Mark Allen Jensen
[Bioperl-guts-l] [15593] bioperl-live/trunk/Bio/DB/HIV/HIVQueryHelper.pm: mod to loadHIVSchema: now returns the desc attributes associated Mark Allen Jensen
[Bioperl-guts-l] [15594] bioperl-live/trunk/Bio/DB/Query/HIVQuery.pm: get_accessions now properly delivers GenBank accession number Mark Allen Jensen
[Bioperl-guts-l] [15607] bioperl-live/trunk/Bio/SimpleAlign.pm: patch for bug#2793, based on a solution of Jay Hannah/thanks Mark Allen Jensen
[Bioperl-guts-l] [15608] bioperl-live/trunk/t/Align/SimpleAlign.t: Tests for bug#2793 patch from Jay Hannah/thanks Mark Allen Jensen
[Bioperl-guts-l] [15616] bioperl-dev/trunk: I christen thee "bioperl-dev". Mark Allen Jensen
[Bioperl-guts-l] [15617] bioperl-dev/trunk/README: dagnab it-- Mark Allen Jensen
[Bioperl-guts-l] [15618] bioperl-dev/trunk/Bio: exptl routines for Bio::DB::HIV, supporting schema-valid Mark Allen Jensen
[Bioperl-guts-l] [15595] bioperl-live/trunk/Bio/SearchIO.pm: updating SearchIO POD to reflect WU-BLAST tabular format support that' s present in blasttable.pm Dave Messina
[Bioperl-guts-l] [15584] bioperl-live/trunk/INSTALL: Remove mention of GD Brian Osborne
[Bioperl-guts-l] [15589] bioperl-live/trunk/scripts/utilities/revtrans-motif.PLS: Add Bruno' s script Brian Osborne
[Bioperl-guts-l] [15619] bioperl-dev/trunk: added slim seqfeatures array-based instead of hash-based, get about 30-40% speedup if I remember correctly Jason Stajich
[Bioperl-guts-l] [15583] bioperl-live/trunk/Bio/DB: berkeleydb database now autoindexes wig files and locks correctly Lincoln Stein
[Bioperl-guts-l] [15602] bioperl-live/trunk/Bio/DB/SeqFeature: killed fencepost error when fetching features by seqid without start or end defined Lincoln Stein
[Bioperl-guts-l] [15603] bioperl-live/trunk/Bio/DB/SeqFeature/Store/memory.pm: better fix Lincoln Stein
[Bioperl-guts-l] [15620] bioperl-live/trunk/Bio: relaxed constraint on gff3 start/ end coordinates Lincoln Stein
[Bioperl-guts-l] [Bug 2775] New: is_circular not maintained through ->trunc bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2775] is_circular not maintained through ->trunc bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2775] is_circular not maintained through ->revcom bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2766] SeqUtils not copying SeqFeature tags bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2775] is_circular not maintained through ->revcom bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2764] enhance SwissProt retreival by id using IDTracker bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2766] SeqUtils not copying SeqFeature tags bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2773] Bio::Tree::Node gets destroyed even though it is still live bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2782] New: Bio::Tools::Run::Phylo::Phylip::SeqBoot WON'T RUN bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2782] Bio::Tools::Run::Phylo::Phylip::SeqBoot WON'T RUN bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2784] New: DBSOURCE DB.t test failure bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2784] DBSOURCE DB.t test failure bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2785] New: genbank to chadoxml bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2786] New: StandAlone Blast problem bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2789] New: Script submission: reverse translate Profam motifs bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2789] Script submission: reverse translate Profam motifs bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2789] Script submission: reverse translate Profam motifs bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2785] genbank to chadoxml bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2785] genbank to chadoxml bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2792] New: Bio::Root::Build may cause an infinite loop during some installations bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2784] DBSOURCE DB.t test failure bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2785] genbank to chadoxml bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2786] StandAlone Blast problem bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2785] genbank to chadoxml bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2746] [TODO] Update TCoffee wrapper for later versions bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2747] [TODO] Build.PL requirement for Bio::Root::Build needs to be eval'd bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2757] DBI $sth->execute() with no error check in Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2793] New: Bio::SimpleAlign::add_seq() : zero-origin sequence order bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2793] Bio::SimpleAlign::add_seq() : zero-origin sequence order bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2794] New: Bioperl 1.6 not available on PPM bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2793] Bio::SimpleAlign::add_seq() : zero-origin sequence order bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2793] Bio::SimpleAlign::add_seq() : zero-origin sequence order bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2796] New: AlignIO::stockholm sequence parsing bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2796] AlignIO::stockholm sequence parsing bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2796] AlignIO::stockholm sequence parsing bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2796] AlignIO::stockholm sequence parsing bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2793] Bio::SimpleAlign::add_seq() : zero-origin sequence order bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2794] Bioperl 1.6 not available on PPM bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2782] Bio::Tools::Run::Phylo::Phylip::SeqBoot WON'T RUN bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2758] assemblyIO - can't read phredPhrap ace file with tagged repeats bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2758] assemblyIO - can't read phredPhrap ace file with tagged repeats bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2793] Bio::SimpleAlign::add_seq() : zero-origin sequence order bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2796] AlignIO::stockholm sequence parsing bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2793] Bio::SimpleAlign::add_seq() : zero-origin sequence order bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2793] Bio::SimpleAlign::add_seq() : zero-origin sequence order bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2796] AlignIO::stockholm sequence parsing 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 2798] New: Bio::Tools::Run::Alignment::Clustalw.pm can't open .dnd file when calling the `run' method bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2798] Bio::Tools::Run::Alignment::Clustalw.pm can't open .dnd file when calling the `run' method bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2798] Bio::Tools::Run::Alignment::Clustalw.pm can't open .dnd file when calling the `run' method bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2798] Bio::Tools::Run::Alignment::Clustalw.pm can't open .dnd file when calling the `run' method bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2798] Bio::Tools::Run::Alignment::Clustalw.pm can't open .dnd file when calling the `run' method bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2798] Bio::Tools::Run::Alignment::Clustalw.pm can't open .dnd file when calling the `run' method bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2691] Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2702] [TODO] scripts recopied upon each call to './Build test' bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2796] AlignIO::stockholm sequence parsing bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2775] is_circular not maintained through ->revcom bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2673] original fields not inherited by seq objects in alignment slices bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2800] New: Bio::Matrix::IO::phylip warn "The number of entries N is not the same 0" when parsing multiple data sets bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2800] Bio::Matrix::IO::phylip warn "The number of entries N is not the same 0" when parsing multiple data sets bugzilla-daemon at portal.open-bio.org
[Bioperl-guts-l] [Bug 2801] New: SimpleAlig remove_columns bugzilla-daemon at portal.open-bio.org

Last message date: Mon Mar 30 13:49:51 EDT 2009
Archived on: Mon Mar 30 13:50:22 EDT 2009

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