August 2008 Archives by thread
Starting: Fri Aug 1 17:34:48 EDT 2008
Ending: Sun Aug 31 21:23:59 EDT 2008
Messages: 97
- [Bioperl-guts-l] [14777] bioperl-live/trunk/Bio: did work necessary to process option callbacks in a Safe::World context
Lincoln Stein
- [Bioperl-guts-l] [14778] bioperl-ext/trunk/Bio/Ext/Align/test.pl: IUPAC DNA test case
Yee Man Chan
- [Bioperl-guts-l] [14779] bioperl-ext/trunk/Bio/Ext/Align/libs/linspc.c: IUPAC DNA support
Yee Man Chan
- [Bioperl-guts-l] [14780] bioperl-live/trunk/Bio/Tools/dpAlign.pm: edited comments related to DNA IUPAC code
Yee Man Chan
- [Bioperl-guts-l] [14781] bioperl-ext/trunk/Bio/Ext/Align/test.pl: removed DEBUG=1
Yee Man Chan
- [Bioperl-guts-l] [14782] bioperl-live/trunk/Bio/Graphics: fixes to "safe callbacks" feature
Lincoln Stein
- [Bioperl-guts-l] [Bug 2562] New: Add "-sequences" option
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2563] New: Bio::AlignIO::arp does not parse multiple alignments
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [14783] bioperl-live/trunk: Sequences weren't being parsed correctly; unfortunately this breaks multiple alignments in one ARP file, so using todo_skip() to pass over tests until bug fix is in place.
Christopher John Fields
- [Bioperl-guts-l] [14784] bioperl-live/trunk/Bio/Tools/Run/RemoteBlast.pm: Add a few new GET/ PUT parameters.
Christopher John Fields
- [Bioperl-guts-l] [14785] bioperl-run/trunk/Bio/Tools/Run/TigrAssembler.pm: Warn user when some sequences are discarded because they are too short
Florent E Angly
- [Bioperl-guts-l] [14786] bioperl-live/trunk/Bio/SearchIO/blasttable.pm: Previous changes killed RemoteBlast again; make a little more bulletproof
Christopher John Fields
- [Bioperl-guts-l] [14787] bioperl-live/trunk/t/data/2008.blasttable: For new NCBI blasttable format
Christopher John Fields
- [Bioperl-guts-l] [14788] bioperl-live/trunk/Bio/Assembly: Used weak references (Scalar::Util ::weaken) in a circular reference to fix memory leak
Florent E Angly
- [Bioperl-guts-l] [14789] bioperl-live/trunk/Bio: phyloxml: new module for clade_relation seq_relation
miraceti at dev.open-bio.org
- [Bioperl-guts-l] [14790] bioperl-live/trunk/Bio: fixed a display bug that appeared when feature start=stop=0
Lincoln Stein
- [Bioperl-guts-l] [14791] bioperl-live/trunk/Bio/Tools/Phylo/PAML.pm: adding parsing support for the Standard Errors (SE line) -- this goes into tags doing the clever mapping as in the branch mode -- only tested with Baseml executions
Albert Vilella
- [Bioperl-guts-l] [14792] bioperl-live/trunk/Bio/SeqFeature/Generic.pm: POD was a bit misleading, remove_SeqFeatures just removes features, sub- or not
Brian Osborne
- [Bioperl-guts-l] [14793] bioperl-live/trunk/Bio/Species.pm:
George Hartzell
- [Bioperl-guts-l] [14794] bioperl-live/trunk/Bio/Graphics: added feature grouping to SVG output from Bio::Graphics
Lincoln Stein
- [Bioperl-guts-l] [14795] bioperl-live/trunk/Bio/Graphics: improved the way that several glyphs are grouped when exporting panels as SVG
Lincoln Stein
- [Bioperl-guts-l] [14796] bioperl-run/trunk/Bio/Tools/Run/TigrAssembler.pm: Closed 3 filehandles that were not
Florent E Angly
- [Bioperl-guts-l] [14797] bioperl-live/trunk/Bio: phyloxml: add clade_relation to node instead of tree, write clade_relation
miraceti at dev.open-bio.org
- [Bioperl-guts-l] [14798] bioperl-live/trunk/Bio/DB/Fasta.pm: for some reason the failure to open a Bio::DB:: Fasta file was not generating an error message; this is now fixed
Lincoln Stein
- [Bioperl-guts-l] [14799] bioperl-live/trunk/Bio/Graphics/Panel.pm: Getting ready for a GBrowse release
Scott Cain
- [Bioperl-guts-l] [14800] bioperl-live/trunk: the new method Bio::Tree::Tree::subtree_length( $internal_node) is identical to total_branch_length when no Bio::Tree:: NodeI object is given as an argument
Heikki Lehvaslaiho
- [Bioperl-guts-l] [14801] bioperl-live/trunk/Bio/DB/SeqFeature: made -gff an alias for -dsn in Bio::DB::Seqfeature::Store:: memory adaptor new() call, since people are having trouble adapting to shift between Bio::DB:: GFF and Bio::Db::SeqFeature::Store
Lincoln Stein
- [Bioperl-guts-l] [14802] bioperl-live/trunk/Bio: get_nested_Annotations
miraceti at dev.open-bio.org
- [Bioperl-guts-l] [Bug 2567] New: AlignIO::stockholm concatenates sequences
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [14803] bioperl-live/trunk/Bio/DB/SeqFeature/Store/memory.pm: fix for windows: glob() isn't working for paths with spaces in them
Scott Cain
- [Bioperl-guts-l] [14804] bioperl-live/trunk/Bio: added nowarnonempty arg to Bio::PrimarySeq
miraceti at dev.open-bio.org
- [Bioperl-guts-l] [14805] bioperl-live/trunk: phyloxml: bug fixes and tests
miraceti at dev.open-bio.org
- [Bioperl-guts-l] [14806] bioperl-live/trunk: phyloxml more tests
miraceti at dev.open-bio.org
- [Bioperl-guts-l] [14807] bioperl-live/trunk/Bio/DB/SeqFeature.pm: fully implement Bio:: LocationI
Jason Stajich
- [Bioperl-guts-l] [14808] bioperl-live/trunk/Bio/Tree/TreeFunctionsI.pm: deprecate findnode_by_id
Heikki Lehvaslaiho
- [Bioperl-guts-l] [14809] bioperl-live/trunk/Bio/Tree: phyloxml use filehandle instead of file name
miraceti at dev.open-bio.org
- [Bioperl-guts-l] [14810] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: phyloxml documentation
miraceti at dev.open-bio.org
- [Bioperl-guts-l] [14811] bioperl-live/trunk/Bio: fixed bugs in the ideogram glyphs that caused them to draw the label and description incorrectly
Lincoln Stein
- [Bioperl-guts-l] [14812] bioperl-live/trunk/Bio/Graphics/Glyph: fixed bugs in the ideogram glyphs that caused them to draw the label and description incorrectly
Lincoln Stein
- [Bioperl-guts-l] [14813] bioperl-live/trunk: added regression tests for the safe() flag
Lincoln Stein
- [Bioperl-guts-l] [14814] bioperl-live/trunk/Bio/Graphics/Panel.pm: fixed rotation of imagemaps, which was not correct
Lincoln Stein
- [Bioperl-guts-l] [Bug 2569] New: parsing PROJECT field in genbank files
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [14815] bioperl-live/trunk/Bio/SeqIO/genbank.pm: add PROJECT support ( bug 2569)
Christopher John Fields
- [Bioperl-guts-l] [14816] bioperl-live/trunk: * write PROJECT support
Christopher John Fields
- [Bioperl-guts-l] [14817] bioperl-live/trunk/Bio: added a get_feature_by_id() method to Bio:: DB::SeqFeature::Store as an alias for the non-intuitive fetch() method that does the same thing
Lincoln Stein
- [Bioperl-guts-l] [14818] bioperl-network/trunk/ModuleBuildBioperl.pm: Hash ref, not array ref
Brian Osborne
- [Bioperl-guts-l] [14819] bioperl-network/trunk/ModuleBuildBioperl.pm: Remove all script installation functionality, all tests pass
Brian Osborne
- [Bioperl-guts-l] [14820] bioperl-live/trunk/Bio/DB/SeqFeature/Store.pm: added get_feature_by_primary_id() method
Lincoln Stein
- [Bioperl-guts-l] [14821] bioperl-live/trunk/ModuleBuildBioperl.pm: don't complain if there' s no scripts directory
Senduran Balasubramaniam
- [Bioperl-guts-l] [14822] bioperl-network/trunk/ModuleBuildBioperl.pm: reinstated latest version from bioperl-live: doesn' t complain about no scripts directory
Senduran Balasubramaniam
- [Bioperl-guts-l] [14823] bioperl-live/trunk/Bio/Graphics/Glyph/ideogram.pm: added a background color fallback option
Lincoln Stein
- [Bioperl-guts-l] [14824] bioperl-run/trunk/Bio/Tools/Run/Alignment/Clustalw.pm: * add_sequences option (adds sequences to an alignment) - bug 2562
Christopher John Fields
- [Bioperl-guts-l] [14825] bioperl-live/trunk: added an option to bp_seqfeature_load to ignore ##sequence-region directives in the gff3 file
Lincoln Stein
- [Bioperl-guts-l] [14826] bioperl-live/trunk/Bio: Add some print_* methods for einfo, esummary, etc.
Christopher John Fields
- [Bioperl-guts-l] [14827] bioperl-live/trunk/Bio/DB: set the mysql autoreconnect flag
Lincoln Stein
- [Bioperl-guts-l] [14828] bioperl-live/trunk/Bio/DB/GFF/Typename.pm: quashed an uninit variable warning
Lincoln Stein
- [Bioperl-guts-l] [14829] bioperl-live/trunk/Bio/Align/DNAStatistics.pm: _build_nt_matrix() now uses $self-> warn rather than straight print to report on ambiguous residues ( suggested by Dominic Rose on the bioperl mailing list)
Heikki Lehvaslaiho
- [Bioperl-guts-l] [14830] bioperl-live/trunk/Bio/Search/HSP/GenericHSP.pm: complete sentence
Christopher John Fields
- [Bioperl-guts-l] [14831] bioperl-live/trunk/Bio/LocatableSeq.pm: Update documentation
Christopher John Fields
- [Bioperl-guts-l] [Bug 2572] New: get_dblinks in load_seqdatabase.pl is deprecated
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2573] New: Ontology tests failing
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [14832] bioperl-live/trunk/Bio/Ontology: [bug 2573]
Christopher John Fields
- [Bioperl-guts-l] [14833] bioperl-live/trunk/Bio/Ontology/OBOEngine.pm: grep not needed ( check for ontology is in Ontology::get_predicate_terms)
Christopher John Fields
- [Bioperl-guts-l] [14834] bioperl-live/trunk/Bio/Coordinate/GeneMapper.pm: Fix a typo in pod doc
George Hartzell
- [Bioperl-guts-l] [Bug 2575] New: Easy request - a frac_identical_total column in HSPTableWriter.pm?
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2576] New: SearchIO is ignoring an excellent match
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [14835] bioperl-live/trunk/Bio/SearchIO/blast.pm: [bug 2576]
Christopher John Fields
- [Bioperl-guts-l] [14836] bioperl-live/trunk/Bio/Assembly/Contig.pm: Fixed bug for set_consensus_sequence->end: end needs to take into account sequence gaps
Florent E Angly
- [Bioperl-guts-l] [14837] bioperl-live/trunk/Bio/Assembly/Contig.pm: Fixed bug for add_seq: $seq->end now based on ungapped length
Florent E Angly
- [Bioperl-guts-l] [Bug 2577] New: Bio::Assembly and Bio::Assembly::IO can exceed the set open file ulimit
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [14838] bioperl-live/trunk/Bio/Assembly/IO/tigr.pm: Fixed bug: all LocatableSeq->end specified based on gapped length ( instead of ungapped) now not specified
Florent E Angly
- [Bioperl-guts-l] [14839] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm: Fixed bug: not using gapped length to calculate LocatableSeq-> end in _overlap_alignment.
Florent E Angly
- [Bioperl-guts-l] [14840] bioperl-live/trunk/Bio: Allow other Bio::SeqFeature::CollectionI
Christopher John Fields
Last message date:
Sun Aug 31 21:23:59 EDT 2008
Archived on: Sun Aug 31 21:24:03 EDT 2008
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