May 2009 Archives by author

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Starting: Fri May 1 13:35:57 EDT 2009
Ending: Sun May 31 18:01:18 EDT 2009
Messages: 109

• [Bioperl-guts-l] [15707] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm: Added function to score a contig sprectrum   Florent E Angly
• [Bioperl-guts-l] [15661] bioperl-live/trunk: [bug 2775]   Christopher John Fields
• [Bioperl-guts-l] [15662] bioperl-live/trunk/t/Tools/Run/StandAloneBlast.t: minor formatting fix   Christopher John Fields
• [Bioperl-guts-l] [15663] bioperl-live/trunk/README: test commit   Christopher John Fields
• [Bioperl-guts-l] [15664] bioperl-live/trunk/README: revert last commit (test)   Christopher John Fields
• [Bioperl-guts-l] [15670] bioperl-live/trunk/t/SearchIO/blasttable.t: add some SeqFeature-specific tests   Christopher John Fields
• [Bioperl-guts-l] [15671] bioperl-live/trunk/Bio/SeqIO/fastq.pm: doc fix ( thanks to John Marshall from the mail list for pointing out)   Christopher John Fields
• [Bioperl-guts-l] [15672] bioperl-live/trunk/Bio/SeqIO/fastq.pm: relax warning ( patch courtesy John Marshall)   Christopher John Fields
• [Bioperl-guts-l] [15673] bioperl-live/trunk/Build.PL: To allow spaces in files for MANIFEST, now require ExtUtils::Manifest 1.52 or above   Christopher John Fields
• [Bioperl-guts-l] [15674] bioperl-live/trunk/Bio/SeqFeature/Generic.pm: remove_tag(), not remove_tags().   Christopher John Fields
• [Bioperl-guts-l] [15678] bioperl-live/trunk/t/ClusterIO/ClusterIO.t: requires XML::SAX   Christopher John Fields
• [Bioperl-guts-l] [15679] bioperl-live/trunk/Bio/Seq/LargePrimarySeq.pm: stub fix for deleting tempdirs, just in case.   Christopher John Fields
• [Bioperl-guts-l] [15680] bioperl-live/trunk/Bio/Seq/LargePrimarySeq.pm: untabify and add comment   Christopher John Fields
• [Bioperl-guts-l] [15685] bioperl-live/trunk/Bio/Root/RootI.pm: warn, not throw ( should be consisten)   Christopher John Fields
• [Bioperl-guts-l] [15686] bioperl-live/trunk/Bio/Root/RootI.pm: * switch back to throw() ( forgot this is supposed to throw)   Christopher John Fields
• [Bioperl-guts-l] [15694] bioperl-live/trunk/Bio/Search: initial crack at parsing Infernal 1. 0 output   Christopher John Fields
• [Bioperl-guts-l] [15695] bioperl-live/trunk/t: add some tests (some still failing, be forewarned)   Christopher John Fields
• [Bioperl-guts-l] [15696] bioperl-live/trunk/Bio/Search/Hit: * remove redundant code   Christopher John Fields
• [Bioperl-guts-l] [15697] bioperl-live/trunk: tests pass, but the code needs some extra tweaking   Christopher John Fields
• [Bioperl-guts-l] [15698] bioperl-live/trunk/Bio/Search: some cleanup and small bug fixes   Christopher John Fields
• [Bioperl-guts-l] [15715] bioperl-live/trunk/t/Seq/LocatableSeq.t: add tests for '*'   Christopher John Fields
• [Bioperl-guts-l] [15716] bioperl-live/trunk/Bio/AlignIO/fasta.pm: * counts as a residue; use LocatableSeq's symbols for consistency   Christopher John Fields
• [Bioperl-guts-l] [15669] bioperl-live/trunk/Bio/DB/EUtilities.pm: file and cb flipped in pod   Mark Allen Jensen
• [Bioperl-guts-l] [15675] bioperl-live/trunk/Bio/Search/SearchUtils.pm: Warn if num/ conserved or num/identical are returned as   Mark Allen Jensen
• [Bioperl-guts-l] [15681] bioperl-live/trunk/Bio/SearchIO/blasttable.pm: In characters(): set $self->{'_last_data'} to undef if $$data{Data}   Mark Allen Jensen
• [Bioperl-guts-l] [15682] bioperl-live/trunk/t/Seq/Quality.t: quieten scope mask warning   Mark Allen Jensen
• [Bioperl-guts-l] [15687] bioperl-live/trunk/t/data/contig-by-hand.wublastp: this is a contig in blast format done by hand,   Mark Allen Jensen
• [Bioperl-guts-l] [15688] bioperl-live/trunk/t/SearchIO/blast.t: mods to test B:S:SU:: tile_hsps against a   Mark Allen Jensen
• [Bioperl-guts-l] [15689] bioperl-live/trunk/Bio/Search/HSP/HSPI.pm: this patch allows B:S: HSP::HSPI::matches to   Mark Allen Jensen
• [Bioperl-guts-l] [15690] bioperl-live/trunk/t/data/contig-by-hand.wublastp: unixize ( sorry about that...)   Mark Allen Jensen
• [Bioperl-guts-l] [15691] bioperl-live/trunk/Bio/Search/SearchUtils.pm: update the secret pod   Mark Allen Jensen
• [Bioperl-guts-l] [15692] bioperl-live/trunk/t/SearchIO/blast.t: bye-bye cruft   Mark Allen Jensen
• [Bioperl-guts-l] [15693] bioperl-dev/trunk: Hit tiling object + new algorithm   Mark Allen Jensen
• [Bioperl-guts-l] [15700] bioperl-dev/trunk/Bio/Root: clear out most bplive modules   Mark Allen Jensen
• [Bioperl-guts-l] [15701] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/mysql.pm: patch for bug #2835, courtesy of Dan Bolser   Mark Allen Jensen
• [Bioperl-guts-l] [15702] bioperl-dev/trunk/Bio/Search/Tiling/MapTiling.pm: filter-per-algorithm functionality (by strand, by frame)   Mark Allen Jensen
• [Bioperl-guts-l] [15703] bioperl-dev/trunk/t/SearchIO/Tiling.t: arg testing filter-per-algorithm functionality   Mark Allen Jensen
• [Bioperl-guts-l] [15704] bioperl-dev/trunk/t/SearchIO/Tiling.t: keyword subst   Mark Allen Jensen
• [Bioperl-guts-l] [15705] bioperl-dev/trunk/Bio/Search/Tiling: keyword subst   Mark Allen Jensen
• [Bioperl-guts-l] [15706] bioperl-dev/trunk/Bio/Search/Tiling/MapTiling.pm: coverage_map_as_text(): print a 'graphic'   Mark Allen Jensen
• [Bioperl-guts-l] [15708] bioperl-dev/trunk/Bio/Search/Tiling/TilingI.pm: expanded prescribed methods to include most of those   Mark Allen Jensen
• [Bioperl-guts-l] [15709] bioperl-dev/trunk/Bio/Search/Tiling: Working out coordinate system issues (dna v.   Mark Allen Jensen
• [Bioperl-guts-l] [15710] bioperl-dev/trunk/Bio/Search/Tiling/MapTiling.pm: bug-swatting   Mark Allen Jensen
• [Bioperl-guts-l] [15711] bioperl-dev/trunk/t/SearchIO: blast. t modified to use MapTiling in place of   Mark Allen Jensen
• [Bioperl-guts-l] [15712] bioperl-dev/trunk/Bio/Search/Tiling: now performs correct coordinate mapping for   Mark Allen Jensen
• [Bioperl-guts-l] [15713] bioperl-dev/trunk/t/SearchIO/blast-MapTiling.t: keyword subst   Mark Allen Jensen
• [Bioperl-guts-l] [15714] bioperl-dev/trunk/t/data/frac_problems2.blast: This version of frac_problems2.blast has   Mark Allen Jensen
• [Bioperl-guts-l] [15718] bioperl-dev/trunk/t/data/1ZZ19XR301R-Alignment.tblastn: tiling test data   Mark Allen Jensen
• [Bioperl-guts-l] [15719] bioperl-dev/trunk/t/SearchIO/Tiling.t: exhaustive (or exhausting, anyway) tests   Mark Allen Jensen
• [Bioperl-guts-l] [15720] bioperl-dev/trunk/t/SearchIO/Tiling.t: decruft   Mark Allen Jensen
• [Bioperl-guts-l] [15721] bioperl-dev/trunk/Bio/Search/Tiling/MapTileUtils.pm: Refactoring context handling   Mark Allen Jensen
• [Bioperl-guts-l] [15722] bioperl-dev/trunk/Bio/Search/Tiling/TilingI.pm: add algorithm accessor to interface   Mark Allen Jensen
• [Bioperl-guts-l] [15723] bioperl-dev/trunk/Bio/Search/Tiling/MapTiling.pm: Refactor of strand/frame context handling; correct length conversions now in _calc_coverage_map   Mark Allen Jensen
• [Bioperl-guts-l] [15724] bioperl-dev/trunk/Bio/Search/Tiling/MapTiling.pm: context for tiling iterator   Mark Allen Jensen
• [Bioperl-guts-l] [15665] bioperl-live/trunk/Bio/Tree/Node.pm: remove spurious documentation   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15666] bioperl-live/trunk: added methods sum_of_leaf_distances() and statratio()   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15699] bioperl-dev/trunk/Bio: Adding AlignIO, SeqIO, and TreeIO directories as a place to put future code for the nexml. pm modules   Chase Miller
• [Bioperl-guts-l] [15667] bioperl-run/trunk/Bio/Tools/Run/Cap3.pm: Add y   Brian Osborne
• [Bioperl-guts-l] [15668] bioperl-run/trunk/Bio/Tools/Run/Cap3.pm: Patch applied   Brian Osborne
• [Bioperl-guts-l] [15677] bioperl-live/trunk/Bio/Tools/tRNAscanSE.pm: gene and exon are the proper SO even for tRNAs.   Jason Stajich
• [Bioperl-guts-l] [15683] bioperl-live/trunk/Bio/DB/SeqFeature/Store: requires the specific Loader instance to be 'use'ed   Jason Stajich
• [Bioperl-guts-l] [15684] bioperl-live/branches/branch-1-6/Bio/DB/SeqFeature/Store: requires the specific Loader instance to be 'use'ed   Jason Stajich
• [Bioperl-guts-l] [15660] bioperl-live/trunk/Bio/DB/SeqFeature/Store.pm: fixed documentation of segment() method to indicate cases in which multiple segment errors arise   Lincoln Stein
• [Bioperl-guts-l] [15676] bioperl-live/trunk/Bio/DB/SeqFeature/Store/berkeleydb.pm: fixed bug which prevented new databases from being created by autoindexing   Lincoln Stein
• [Bioperl-guts-l] [15717] bioperl-live/trunk/Bio/DB/SeqFeature.pm: make feature_id an alias for primary_id   Lincoln Stein
• [Bioperl-guts-l] [Bug 2823] New: Bio::SeqIO::embl->next_seq corrupted with "Segmentation fault" when parsing million-line entries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2823] Bio::SeqIO::embl->next_seq corrupted with "Segmentation fault" when parsing million-line entries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2823] Bio::SeqIO::embl->next_seq corrupted with "Segmentation fault" when parsing million-line entries   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 2773] Bio::Tree::Node gets destroyed even though it is still live   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2823] Bio::SeqIO::embl->next_seq corrupted with "Segmentation fault" when parsing million-line entries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2823] Bio::SeqIO::embl->next_seq corrupted with "Segmentation fault" when parsing million-line entries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2823] Bio::SeqIO::embl->next_seq corrupted with "Segmentation fault" when parsing million-line entries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2823] Bio::SeqIO::embl->next_seq corrupted with "Segmentation fault" when parsing million-line entries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2823] Bio::SeqIO::embl->next_seq corrupted with "Segmentation fault" when parsing million-line entries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2713] [TODO] Update core Infernal parsing to v1.0, add related tests to bioperl-run   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2828] New: Unrecognized line error, when parsing hmmsearch output, in module Bio::SearchIO::hmmer   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2828] Unrecognized line error, when parsing hmmsearch output, in module Bio::SearchIO::hmmer   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2828] Unrecognized line error, when parsing hmmsearch output, in module Bio::SearchIO::hmmer   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2830] New: Bio::Search::Tiling development/use case data   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2830] Bio::Search::Tiling development/use case data   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2830] Bio::Search::Tiling development/use case data   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2831] New: Build.PL appears to break automated testing with CPANPLUS   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2832] New: Add support for CPANPLUS to Bio::Root::Build   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2831] Build.PL appears to break automated testing with CPANPLUS   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2832] Add support for CPANPLUS to Bio::Root::Build   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2834] New: Bio::Root::Build breaks Module::Build API   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2399] BlastHSP::n gives empty values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2835] New: "Bio::DB::SeqFeature::Store->new( ... -namespace => 'x' )->attributes" borked   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2835] "Bio::DB::SeqFeature::Store->new( ... -namespace => 'x' )->attributes" borked   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2836] New: The bp_seqfeature_load.pl script dosn't support the '-namespace' option to new Bio::DB::SeqFeature::Store   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2836] The bp_seqfeature_load.pl script dosn't support the '-namespace' option to new Bio::DB::SeqFeature::Store   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2836] The bp_seqfeature_load.pl script dosn't support the '-namespace' option to new Bio::DB::SeqFeature::Store   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2842] New: add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2843] New: FeatureIO BED to GFF fails with no phase   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2843] FeatureIO BED to GFF fails with no phase   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2843] FeatureIO BED to GFF fails with no phase   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2844] New: Patch to add "revtrans" method to Bio::Tools::SeqPattern   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2844] Patch to add "revtrans" method to Bio::Tools::SeqPattern   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2844] Patch to add "revtrans" method to Bio::Tools::SeqPattern   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2844] Patch to add "revtrans" method to Bio::Tools::SeqPattern   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2844] Patch to add "revtrans" method to Bio::Tools::SeqPattern   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2844] Patch to add "revtrans" method to Bio::Tools::SeqPattern   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2844] Patch to add "revtrans" method to Bio::Tools::SeqPattern   bugzilla-daemon at portal.open-bio.org

Last message date: Sun May 31 18:01:18 EDT 2009
Archived on: Sun May 31 18:01:22 EDT 2009

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