March 2008 Archives by date

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Starting: Sat Mar 1 09:14:11 EST 2008
Ending: Mon Mar 31 20:02:24 EDT 2008
Messages: 118

• [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] [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] [14578] bioperl-live/trunk/scripts/seq/seqconvert.PLS: add driver/ handler support (will clean these up more for 1.7)   Christopher John Fields
• [Bioperl-guts-l] [14579] bioperl-live/trunk/Bio/TreeIO/nexus.pm: bug 2356   Christopher John Fields
• [Bioperl-guts-l] [14580] bioperl-live/trunk/t/TreeIO.t: bug 2356 ( check for correct number with multiple trees)   Christopher John Fields
• [Bioperl-guts-l] [14581] bioperl-live/trunk/Bio/TreeIO/pag.pm: add some flexibility for name length, defaulting to 10   Christopher John Fields
• [Bioperl-guts-l] [14582] bioperl-live/trunk/Bio/TreeIO/pag.pm: fix undef.   Christopher John Fields
• [Bioperl-guts-l] [Bug 2356] Bio::TreeIO::pag outputs (NEXUS parsing)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2373] Handling of multiple species or hybrid species in EMBL records   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2389] load_seqdatabase.pl crashes on varchar(n)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2389] load_seqdatabase.pl crashes on varchar(n)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2373] Handling of multiple species or hybrid species in EMBL records   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2213] crashes on downloading NCBI records   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2347] Bio::Tools::Run::Phylo::PAML::Baseml needs polishing and completion   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14583] bioperl-live/trunk/Bio/Search/HSP/GenericHSP.pm: Bug 2378   Christopher John Fields
• [Bioperl-guts-l] [Bug 2378] Getting strand of query/hit features in Bio::Search::HSP::GenericHSP   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14584] bioperl-live/trunk: revamped featurefile significantly in order for syntax to be compatible with GBrowse , and to support loading of featurefiles into GFF3 databases   Lincoln Stein
• [Bioperl-guts-l] [14585] bioperl-live/trunk/Bio/Graphics/FeatureFile.pm: added a version method to featurefile so that GBrowse can warn when the module is not up to date   Lincoln Stein
• [Bioperl-guts-l] [Bug 1825] bug in parsing gene names for swissprot entry in module Bio::SeqIO:swiss   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14586] bioperl-live/trunk/Bio/SearchIO/Writer/HTMLResultWriter.pm: partial fix for bug 2439   Christopher John Fields
• [Bioperl-guts-l] [Bug 2347] Bio::Tools::Run::Phylo::PAML::Baseml needs polishing and completion   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14587] bioperl-live/trunk/Bio/DB/SeqFeature/Store/GFF3Loader.pm: removed dangling debug statement   Lincoln Stein
• [Bioperl-guts-l] [14588] bioperl-live/trunk/Bio/DB/SeqFeature/Store/Loader.pm: added missing Loader.pm file   Lincoln Stein
• [Bioperl-guts-l] [14589] bioperl-live/trunk/Bio/SearchIO: some more for bug 2349   Christopher John Fields
• [Bioperl-guts-l] [Bug 2439] multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14590] bioperl-live/trunk/Bio/SearchIO/Writer/HTMLResultWriter.pm: bug 2449   Christopher John Fields
• [Bioperl-guts-l] [Bug 2449] HTMLWriter out of sync   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2465] New: Bio::FeatureIO::gff typo in sequence_region() function   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14591] bioperl-live/trunk/Bio/FeatureIO/gff.pm: bug 2465   Christopher John Fields
• [Bioperl-guts-l] [Bug 2465] Bio::FeatureIO::gff typo in sequence_region() function   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14592] bioperl-live/trunk/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm: bug 1707   Christopher John Fields
• [Bioperl-guts-l] [Bug 1707] Out of memory crash from Bio::DB::GFF::Adaptor::dbi::pg.pm (Postgres)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14593] bioperl-run/trunk/Bio/Tools/Run/Phylo/SLR.pm: silly type -- alignment must be sorted   Albert Vilella
• [Bioperl-guts-l] [14594] bioperl-live/trunk/Bio: fixes out-of-memory problems during gff3 file loading ( at the cost of reduced performance), and should fix the problem of bio:: graphics dying when a feature does not have the source_tag method   Lincoln Stein
• [Bioperl-guts-l] [14595] bioperl-live/trunk/Bio: fix problems parsing configuration files containing embedded "[" characters inside option values   Lincoln Stein
• [Bioperl-guts-l] [Bug 2337] BDB flatfile index should store global configuration data in BDB   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2336] bp_bioflat_index.pl and Bio::DB::Flat::BDB::fasta creates incorrect index   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2337] BDB flatfile index should store global configuration data in BDB   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2338] The first 4 bytes of flatfile index is wrong (--indextype flat)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2339] In a flat file index, the size of the final entry of a fasta file is wrong   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14596] bioperl-live/trunk/Bio/Graphics/FeatureFile.pm: config file parser should be more stable in the face of odd blank lines, funny comments, etc   Lincoln Stein
• [Bioperl-guts-l] [14597] bioperl-live/trunk/Bio: quenched many warnings and small bugs that crop up when processing slightly invalid config files   Lincoln Stein
• [Bioperl-guts-l] [14598] bioperl-live/trunk/Bio: fixed an issue that prevented DAS features from rendering correctly on Bio ::Graphics::Panels (label missing)   Lincoln Stein
• [Bioperl-guts-l] [14599] bioperl-db/trunk/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: Throw if no primary key defined ( cases where the persistent object is not created and one attempts to remove in same run ).   Christopher John Fields
• [Bioperl-guts-l] [14600] bioperl-live/trunk/Bio/SeqIO/entrezgene.pm: Add example   Brian Osborne
• [Bioperl-guts-l] [14601] bioperl-db/trunk/Bio/DB/BioSQL/SeqAdaptor.pm: bug 2226   Christopher John Fields
• [Bioperl-guts-l] [Bug 2226] wrong retrieval order from seqfeature table   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14602] bioperl-db/trunk/Bio/DB/BioSQL/BaseDriver.pm: get rid of undefined string warnings in verbose output   Christopher John Fields
• [Bioperl-guts-l] [Bug 2280] crash on the attempt to store same sequence in a diff. namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2281] unable to copy a sequence from one namespace to another one   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14603] bioperl-live/trunk/Bio/DB/SeqFeature/Store/GFF3Loader.pm: fixed loading problem that arose when a feature had two parents but feature repeated twice on different lines   Lincoln Stein
• [Bioperl-guts-l] [Bug 2413] save_tempfiles() not working in Bio::Tools::Run::WrapperBase   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] svn issue?   Sheldon McKay
• [Bioperl-guts-l] svn issue?   Chris Fields
• [Bioperl-guts-l] [Bug 2466] New: NCBIHelper redirecting RefSeq sequence download to EBI server   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] svn issue?   Dave Messina
• [Bioperl-guts-l] [Bug 2413] save_tempfiles() not working in Bio::Tools::Run::WrapperBase   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14604] bioperl-live/trunk: adding an option for `perl Build. PL` to accept the default of asked questions.   Scott Cain
• [Bioperl-guts-l] [Bug 2337] BDB flatfile index should store global configuration data in BDB   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2281] unable to copy a sequence from one namespace to another one   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2281] unable to copy a sequence from one namespace to another one   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2280] crash on the attempt to store same sequence in a diff. namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2280] crash on the attempt to store same sequence in a diff. namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14605] bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm: Minor Changes   Marian Thieme
• [Bioperl-guts-l] [14606] bioperl-live/trunk/Bio/DB/SeqFeature/Store/GFF3Loader.pm: bitten by "!=" ne "ne"   Lincoln Stein
• [Bioperl-guts-l] [14607] bioperl-live/trunk/Bio: killed horrible bug that was preventing segmented features from loading correctly   Lincoln Stein
• [Bioperl-guts-l] [14608] bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm: Removed obsolete Function _get_refseq_max_ins_offset()   Marian Thieme
• [Bioperl-guts-l] [14609] bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm: Updated Documentation   Marian Thieme
• [Bioperl-guts-l] [14610] bioperl-live/trunk/scripts/seq/seqretsplit.PLS: split sequence database into individual sequence files   Jason Stajich
• [Bioperl-guts-l] [14611] bioperl-live/trunk/Bio/Tools/Phylo/Gerp.pm: slightly improved docs   Senduran Balasubramaniam
• [Bioperl-guts-l] [14612] bioperl-live/trunk/Bio/Assembly/IO/tigr.pm: use base, not ISA   Senduran Balasubramaniam
• [Bioperl-guts-l] [14613] bioperl-live/trunk/Bio/SearchIO/cross_match.pm: use base, not ISA   Senduran Balasubramaniam
• [Bioperl-guts-l] [14614] bioperl-live/trunk/Bio/Search/Result/CrossMatchResult.pm: use base, not ISA   Senduran Balasubramaniam
• [Bioperl-guts-l] [14615] bioperl-live/trunk/Bio/Graphics/FeatureFile.pm: under some circumstances, the link_pattern() routine might think the reference sequence for a feature is empty and fail to replace $ref correctly   Lincoln Stein
• [Bioperl-guts-l] [14616] bioperl-live/trunk/Bio/Annotation: No need to use Bio::AnnotationI   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14617] bioperl-live/trunk/Bio: use base, not ISA   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14618] bioperl-live/trunk/maintenance/module_usage.pl: new script to look at BioPerl module usage   Senduran Balasubramaniam
• [Bioperl-guts-l] [14619] bioperl-live/trunk/Bio/DB/GFF/Adaptor/berkeleydb.pm: quiet some warnings on initialization   Jason Stajich
• [Bioperl-guts-l] [14620] bioperl-live/trunk/Bio/Tree: tag/ value pairing associating with Trees   Jason Stajich
• [Bioperl-guts-l] [14621] bioperl-live/trunk/maintenance/module_usage.pl: added -i option to choose format; improved docs; now clusters modules in the same subdir; now colours edges according to inheritance or usage   Senduran Balasubramaniam
• [Bioperl-guts-l] [14622] bioperl-live/trunk/Bio/FeatureIO/gff.pm: futher changes now that B: :SF::Annotated to behave more like Generic   Senduran Balasubramaniam
• [Bioperl-guts-l] [14623] bioperl-live/trunk/Bio/FeatureIO/gff.pm: final (?!) changes now that B::SF::Annotated behaves more like Generic   Senduran Balasubramaniam
• [Bioperl-guts-l] [14624] bioperl-run/trunk: new wrapper for MCS   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2472] New: postgreSQL v8.3 automatic casts limited may necessitate explicit cast   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2473] New: error in finding query length from FASTA34 output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2473] error in finding query length from FASTA34 output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2473] error in finding query length from FASTA34 output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2473] error in finding query length from FASTA34 output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2474] New: postgres 8.3 - load_seqdatabase.pl / swissprot   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2474] postgres 8.3 - load_seqdatabase.pl / swissprot   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2473] error in finding query length from FASTA34 output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14625] bioperl-live/trunk: bug 2473 (with tests)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2473] error in finding query length from FASTA34 output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2466] NCBIHelper redirecting RefSeq sequence download to EBI server   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] New: "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2478] New: Bio::SeqIO::fastq subqual reassignment of qualities results in replacement of end characters with '!'   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2478] Bio::SeqIO::fastq subqual reassignment of qualities results in replacement of end characters with '!'   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2478] Bio::SeqIO::fastq subqual reassignment of qualities results in replacement of end characters with '!'   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2478] Bio::SeqIO::fastq subqual reassignment of qualities results in replacement of end characters with '!'   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14626] bioperl-live/trunk/Bio/Search/HSP/GenericHSP.pm: Marc' s bug from mail list; repeat the seq position for gaps > 1.   Christopher John Fields
• [Bioperl-guts-l] [14627] bioperl-live/trunk/Bio/Search/SearchUtils.pm: Collapse repeated sequence indices into one position   Christopher John Fields
• [Bioperl-guts-l] [14628] bioperl-live/trunk/t/SearchIO.t: using seq_inds() with 'gaps' now repeats sequence indices based on the number of inserted gaps; repeated indices now collapsed into one   Christopher John Fields
• [Bioperl-guts-l] [14629] bioperl-live/trunk/Bio/Search/SearchUtils.pm: remove extraneous comment   Christopher John Fields
• [Bioperl-guts-l] [Bug 2329] Enhancement to Bio::SeqIO::abi - abi_with_trace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14630] bioperl-live/trunk/Bio/Search: * Allow gap symbol to be set   Christopher John Fields
• [Bioperl-guts-l] [14631] bioperl-run/trunk/Bio/Tools/Run/Phylo/PAML/Codeml.pm: paml 4b now accepts more codon frequency models   Albert Vilella
• [Bioperl-guts-l] [14632] bioperl-live/trunk: * revert symbol passing ( forgot query and hit have different gap symbols)   Christopher John Fields
• [Bioperl-guts-l] [14633] bioperl-live/trunk/t/hmmer.t: add some seq_inds() tests ( appears fine)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2479] New: bp_pg_bulk_load_gff.pl postgres GFF bulk loader broken   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2479] bp_pg_bulk_load_gff.pl postgres GFF bulk loader broken   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14634] bioperl-run/trunk/Bio/Tools/Run/Phylo/Gumby.pm: added POD warnings for coordinate issues; added automatic correction for result feature coordinates   Senduran Balasubramaniam
• [Bioperl-guts-l] [14635] bioperl-live/trunk/Bio/Tools/Phylo/Gumby.pm: added POD warning about coordinate issue   Senduran Balasubramaniam
• [Bioperl-guts-l] [14636] bioperl-run/trunk/Bio/Tools/Run/Phylo/Phast/PhastCons.pm: correction now that B::SF::Annotated behaves more like Generic   Senduran Balasubramaniam
• [Bioperl-guts-l] [14637] bioperl-live/trunk/Bio/SeqIO/embl.pm: Make regex matches safer   Christopher John Fields

Last message date: Mon Mar 31 20:02:24 EDT 2008
Archived on: Mon Mar 31 20:02:35 EDT 2008

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