December 2009 Archives by subject

• Messages sorted by: [ thread ] [ author ] [ date ]
• More info on this list...

Starting: Tue Dec 1 22:53:14 EST 2009
Ending: Thu Dec 31 08:27:41 EST 2009
Messages: 169

• [Bioperl-guts-l] [16433] bioperl-run/trunk/lib/Bio/Tools/Run/AssemblerBase.pm: expanding dash-use options   Mark Allen Jensen
• [Bioperl-guts-l] [16434] bioperl-run/trunk/lib/Bio/Tools/Run/Phrap.pm: Fixed missing semicolon in Bio::Tools::Run::Phrap   Florent E Angly
• [Bioperl-guts-l] [16435] bioperl-live/trunk/Bio/SeqUtils.pm: reverse feat order on revcom_with_features: Thanks for the patch Roy--   Mark Allen Jensen
• [Bioperl-guts-l] [16436] bioperl-run/trunk/lib/Bio/Tools/Run/AssemblerBase.pm: _collate_subcmd_args() really belongs here...   Mark Allen Jensen
• [Bioperl-guts-l] [16437] bioperl-run/trunk/lib/Bio/Tools/Run/AssemblerBase.pm: tweak   Mark Allen Jensen
• [Bioperl-guts-l] [16438] bioperl-run/trunk/lib/Bio/Tools/Run/AssemblerBase.pm: fixed mixed dash issue   Mark Allen Jensen
• [Bioperl-guts-l] [16439] bioperl-live/trunk/Bio/SeqIO/fastq.pm: empty seqs shouldn' t be newline (fixes Dan's bug from mail list)   Christopher John Fields
• [Bioperl-guts-l] [16440] bioperl-live/trunk/ide/bioperl-mode/site-lisp: little bug fix; thanks to Christoph for the heads-up   Mark Allen Jensen
• [Bioperl-guts-l] [16441] bioperl-live/trunk/ide/bioperl-mode/dist: update to source rev 16440   Mark Allen Jensen
• [Bioperl-guts-l] [16442] bioperl-live/trunk/Bio/Tools/Protparam.pm: fixed improper use of throw() / thanks Gang Wu for heads-up   Mark Allen Jensen
• [Bioperl-guts-l] [16443] new feature: browse parent/base classes   Mark Allen Jensen
• [Bioperl-guts-l] [16444] bioperl-live/trunk/ide/bioperl-mode/dist: distro update : base class browse feature   Mark Allen Jensen
• [Bioperl-guts-l] [16445] bioperl-live/trunk/ide/bioperl-mode/site-lisp/bioperl-mode.el: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [16446] bioperl-live/trunk/ide/bioperl-mode/dist: dist update to r16445   Mark Allen Jensen
• [Bioperl-guts-l] [16447] bioperl-db/trunk/lib/Bio/DB/Query/BioQuery.pm: committing patch for bug #2958   Mark Allen Jensen
• [Bioperl-guts-l] [16448] bioperl-db/trunk/lib/Bio/DB/Query/BioQuery.pm: weird duplication removed   Mark Allen Jensen
• [Bioperl-guts-l] [16449] bioperl-live/trunk/ide/bioperl-mode: add parent/ base browsing function to source view mode (keys: B, P)   Mark Allen Jensen
• [Bioperl-guts-l] [16450] bioperl-run/trunk/lib/Bio/Tools/Run: Documentation update   Florent E Angly
• [Bioperl-guts-l] [16451] bioperl-live/trunk/Bio/Tools/Run: command extension module for WrapperBase, codifying AssemblerBase features and other goodies   Mark Allen Jensen
• [Bioperl-guts-l] [16452] bioperl-live/trunk: initial commit of SeqXML support.   Dave Messina
• [Bioperl-guts-l] [16453] bioperl-live/trunk/Bio/Root/Test.pm: more informative message when require fails   Mark Allen Jensen
• [Bioperl-guts-l] [16454] bioperl-live/trunk/t/Tools/Run: tests for WrapperBase::CommandExt   Mark Allen Jensen
• [Bioperl-guts-l] [16455] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: bugs squish   Mark Allen Jensen
• [Bioperl-guts-l] [16456] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: WB executable() override   Mark Allen Jensen
• [Bioperl-guts-l] [16457] bioperl-live/trunk: Improvements in the Bio::Assembly:: ContigSpectrum module and update of its dependencies   Florent E Angly
• [Bioperl-guts-l] [16458] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: make it actually run something   Mark Allen Jensen
• [Bioperl-guts-l] [16459] bioperl-live/trunk:   Chris Mungall
• [Bioperl-guts-l] [16460] bioperl-dev/branches/blastplus-dev-branch/: working on an integrated ncbi blast+ module set   Mark Allen Jensen
• [Bioperl-guts-l] [16461] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run: start blastplus wrappers: to be a complete   Chris Fields
• [Bioperl-guts-l] [16461] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run: start blastplus wrappers: to be a complete   Mark Allen Jensen
• [Bioperl-guts-l] [16461]bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run:start blastplus wrappers: to be a complete   Mark A. Jensen
• [Bioperl-guts-l] [16462] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run/ StandAloneBlastPlus.pm: progress!   Mark Allen Jensen
• [Bioperl-guts-l] [16463] bioperl-live/trunk: added species support (Bio::Species, that is).   Dave Messina
• [Bioperl-guts-l] [16464] bioperl-live/trunk: added support for alternative IDs (Bio:: Annotation::DBlinks) and properties (Bio::Annotation::SimpleValues).   Dave Messina
• [Bioperl-guts-l] [16465] bioperl-live/trunk/Bio/FeatureIO/gff.pm: Fixing a bug that caused the first sequence in a ##FASTA section to be lost ; the problem was that Bio::SeqIO::fasta sets \n> as the line separator, but during processing, Bio::Fea   Scott Cain
• [Bioperl-guts-l] [16465] bioperl-live/trunk/Bio/FeatureIO/gff.pm: Fixing a bug that caused the first sequence in a ##FASTA section to be lost ; the problem was that Bio::SeqIO::fasta sets \n> as the line separator, but during processing, Bio::FeatureIO:: gff swallowed the \n before sending the filehandle to SeqIO.   Jason Stajich
• [Bioperl-guts-l] [16465] bioperl-live/trunk/Bio/FeatureIO/gff.pm: Fixing a bug that caused the first sequence in a ##FASTA section to be lost ; the problem was that Bio::SeqIO::fasta sets \n> as the line separator, but during processing, Bio::FeatureIO:: gff swallowed the \n before sending the filehandle to SeqIO.   Scott Cain
• [Bioperl-guts-l] [16466] bioperl-live/trunk: added write_seq support.   Dave Messina
• [Bioperl-guts-l] [16467] bioperl-live/trunk/Bio/SeqIO/seqxml.pm: added a little more POD.   Dave Messina
• [Bioperl-guts-l] [16468] bioperl-live/trunk/Bio/FeatureIO/gff.pm: using the _pushback method instead of seek per Jason's suggestion.   Scott Cain
• [Bioperl-guts-l] [16469] bioperl-live/trunk: Better way to handle setting the effective assembly parameter flag when doing the average of several contig spectra .   Florent E Angly
• [Bioperl-guts-l] [16470] bioperl-run/trunk: New aln_wiggle option in the Minimo wrapper   Florent E Angly
• [Bioperl-guts-l] [16471] bioperl-run/trunk/lib/Bio/Tools/Run/Cap3.pm: Typo in Cap3 wrapper   Florent E Angly
• [Bioperl-guts-l] [16472] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run: lots of fixes and addns/ can create databases and masks   Mark Allen Jensen
• [Bioperl-guts-l] [16473] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: fixes to CommandExts   Mark Allen Jensen
• [Bioperl-guts-l] [16474] bioperl-run/trunk: Transfered current state of Bowtie. pm in my bioperl-run repo.   Dan Kortschak
• [Bioperl-guts-l] [16475] bioperl-run/trunk: Mainly doc and copyright notification changes - one bug fix in Bowtie.t   Dan Kortschak
• [Bioperl-guts-l] [16476] bioperl-run/trunk/t/data: Added test suite data - permission granted by Ben Langmead.   Dan Kortschak
• [Bioperl-guts-l] [16477] bioperl-run/trunk/t/Bowtie.t: Most tests defined - need to add confirming output of a run matches expectations .   Dan Kortschak
• [Bioperl-guts-l] [16478] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie/Config.pm: Minor change to file spec definition for paired.   Dan Kortschak
• [Bioperl-guts-l] [16479] bioperl-run/trunk/t/Bowtie.t: Bug fix in inline sequence test.   Dan Kortschak
• [Bioperl-guts-l] [16480] bioperl-run/trunk/t/Bowtie.t: Minor change to Bowtie test   Dan Kortschak
• [Bioperl-guts-l] [16481] bioperl-run/trunk/t/Bowtie.t: Minor change to Bowtie test   Dan Kortschak
• [Bioperl-guts-l] [16482] bioperl-run/trunk/t/Bowtie.t: Reorganisation of some tests to allow for sub command param testing properly   Dan Kortschak
• [Bioperl-guts-l] [16483] bioperl-run/trunk/t/Bowtie.t: This fucking 'S' keeps coming back!   Dan Kortschak
• [Bioperl-guts-l] [16484] bioperl-run/trunk/t/Bowtie.t: Remove # from like tests.   Dan Kortschak
• [Bioperl-guts-l] [16485] bioperl-run/trunk: Various doc changes.   Dan Kortschak
• [Bioperl-guts-l] [16486] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie/Config.pm: More doc changes.   Dan Kortschak
• [Bioperl-guts-l] [16487] bioperl-run/trunk/t/Bowtie.t: Index file name var no point to the index, not an absent space.   Dan Kortschak
• [Bioperl-guts-l] [16488] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Fix close bug in _run   Dan Kortschak
• [Bioperl-guts-l] [16489] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Filespec determination in cases for single and paired bowties.   Dan Kortschak
• [Bioperl-guts-l] [16490] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Nicer version for crossbow.   Dan Kortschak
• [Bioperl-guts-l] [16491] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Drop program name off options list - not used by bowtie   Dan Kortschak
• [Bioperl-guts-l] [16492] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Dealing with residual undefs in @files.   Dan Kortschak
• [Bioperl-guts-l] [16493] bioperl-run/trunk/t/Bowtie.t: Fixed bug - calling run, rather than run_bowtie.   Dan Kortschak
• [Bioperl-guts-l] [16494] bioperl-run/trunk: run now appropriately sets named filespec params , which have been simplified in Config.pm (seq1 to seq).   Dan Kortschak
• [Bioperl-guts-l] [16495] bioperl-run/trunk/t/Bowtie.t: Clean up unused comments from Mark.   Dan Kortschak
• [Bioperl-guts-l] [16496] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Force into SAM output from bowtie.   Dan Kortschak
• [Bioperl-guts-l] [16497] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Remove redundant line left from Maq.   Dan Kortschak
• [Bioperl-guts-l] [16498] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: SAM param requirements - rest to 0 explicitly.   Dan Kortschak
• [Bioperl-guts-l] [16499] bioperl-run/trunk: Trying to sort out output file passing.   Dan Kortschak
• [Bioperl-guts-l] [16500] bioperl-run/trunk/t/Bowtie.t: Test for _run - output checked and counted.   Dan Kortschak
• [Bioperl-guts-l] [16501] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Added code to convert the SAM output of bowtie to BAM so that the B:A:I: s can cope with it.   Dan Kortschak
• [Bioperl-guts-l] [16502] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie/Config.pm: Defined version as a separate program.   Dan Kortschak
• [Bioperl-guts-l] [16503] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Fixed calls to Samtools sort.   Dan Kortschak
• [Bioperl-guts-l] [16504] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Remove default to SAM output.   Dan Kortschak
• [Bioperl-guts-l] [16505] bioperl-run/trunk/lib/Bio/Tools/Run: Version now registered, SAM format exclusive setting now presaged.   Dan Kortschak
• [Bioperl-guts-l] [16506] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Fit version call before file requirement checks.   Dan Kortschak
• [Bioperl-guts-l] [16507] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Running version program insists version switch is set.   Dan Kortschak
• [Bioperl-guts-l] [16508] bioperl-run/trunk: Removed version return function - may re-add.   Dan Kortschak
• [Bioperl-guts-l] [16509] bioperl-run/trunk/t/Bowtie.t: Nicer line count code for output test .   Dan Kortschak
• [Bioperl-guts-l] [16510] bioperl-run/trunk/t/Bowtie.t: Test numbers now correct.   Dan Kortschak
• [Bioperl-guts-l] [16511] bioperl-run/trunk/lib/Bio/Tools/Run: Parameter following - prevent incompatible switches/params, ensure requirements.   Dan Kortschak
• [Bioperl-guts-l] [16512] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Tried to build on AssmeblyBase method - no good.   Dan Kortschak
• [Bioperl-guts-l] [16513] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Documentation largely up-to-date.   Dan Kortschak
• [Bioperl-guts-l] [16514] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Try sort out inline sequence passing.   Dan Kortschak
• [Bioperl-guts-l] [16515] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Inline sequences now handled appropriately.   Dan Kortschak
• [Bioperl-guts-l] [16516] bioperl-live/trunk: file-level metadata parsing of the opening < seqXML> tag now done when the seqIO object is created (in _initialize), rather than waiting till we get to next_seq.   Dave Messina
• [Bioperl-guts-l] [16517] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run/ StandAloneBlastPlus.pm: masking works pretty well; start db make and mask integration   Mark Allen Jensen
• [Bioperl-guts-l] [16518] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run/ StandAloneBlastPlus.pm: ok, looks like its actually masking on request   Mark Allen Jensen
• [Bioperl-guts-l] [16519] bioperl-run/trunk/t/Bowtie.t: Tests for exclusive paramter setting   Dan Kortschak
• [Bioperl-guts-l] [16520] bioperl-run/trunk: Crossbow file format handling implemented - unsafely.   Dan Kortschak
• [Bioperl-guts-l] [16521] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run/ StandAloneBlastPlus.pm: building out pod   Mark Allen Jensen
• [Bioperl-guts-l] [16522] bioperl-live/trunk/Bio/Tools/GuessSeqFormat.pm: Add format guesser for crossbow format.   Dan Kortschak
• [Bioperl-guts-l] [16523] bioperl-run/trunk: Add format guesser for crossbow format.   Dan Kortschak
• [Bioperl-guts-l] [16524] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run/ StandAloneBlastPlus.pm: tempfile cleanup machinery   Mark Allen Jensen
• [Bioperl-guts-l] [16525] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [16526] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: keyword subst   Mark Allen Jensen
• [Bioperl-guts-l] [16527] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run: building out POD, other tweaks   Mark Allen Jensen
• [Bioperl-guts-l] [16528] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run/ StandAloneBlastPlus.pm: more POD! I love POD...   Mark Allen Jensen
• [Bioperl-guts-l] [16529] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run/ StandAloneBlastPlus.pm: very close now   Mark Allen Jensen
• [Bioperl-guts-l] [16530] bioperl-dev/branches/blastplus-dev-branch/t: StandAloneBlastPlus tests/data   Mark Allen Jensen
• [Bioperl-guts-l] [16531] bioperl-dev/branches/blastplus-dev-branch/t: clean up tests, more data   Mark Allen Jensen
• [Bioperl-guts-l] [16532] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run: BlastMethods runs blast   Mark Allen Jensen
• [Bioperl-guts-l] [16533] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run: bl2seq added, other tweaks   Mark Allen Jensen
• [Bioperl-guts-l] [16534] bioperl-dev/branches/blastplus-dev-branch/t/SABlastPlus.t: blast method tests   Mark Allen Jensen
• [Bioperl-guts-l] [16535] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run/ StandAloneBlastPlus/BlastMethods.pm: POD for BlastMethods   Mark Allen Jensen
• [Bioperl-guts-l] [16536] bioperl-dev/branches/blastplus-dev-branch/lib/Bio/Tools/Run/ StandAloneBlastPlus.pm: POD tweaks   Mark Allen Jensen
• [Bioperl-guts-l] [16537] bioperl-run/trunk/lib/Bio/Tools/Run: merge BlastPlus goodies up to bioperl-live trunk   Mark A. Jensen
• [Bioperl-guts-l] [16537] bioperl-run/trunk/lib/Bio/Tools/Run: merge BlastPlus goodies up to bioperl-live trunk   Mark Allen Jensen
• [Bioperl-guts-l] [16538] bioperl-run/trunk/t: merge BlastPlus tests and data to bioperl-run trunk   Mark Allen Jensen
• [Bioperl-guts-l] [16539] bioperl-dev/tags/blastplus-port-to-run-121909/: tag the branch merged up to bioperl-run   Mark Allen Jensen
• [Bioperl-guts-l] [16540] bioperl-live/trunk/Bio/SearchIO/blast.pm: Robson' s patch for buggy blastpgp output   Christopher John Fields
• [Bioperl-guts-l] [16541] bioperl-live/trunk/Bio/LocatableSeq.pm: NSE now allows strand information, see thread: http://lists.open-bio.org/ pipermail/bioperl-l/2009-December/031772.html   Christopher John Fields
• [Bioperl-guts-l] [16542] bioperl-live/trunk/Bio/LocatableSeq.pm: Actually commit that last change   Christopher John Fields
• [Bioperl-guts-l] [16543] bioperl-live/trunk/Bio/AlignIO/maf.pm: maf didn' t conform to bp standard of -1, 0, 1 (used +/-)   Christopher John Fields
• [Bioperl-guts-l] [16544] bioperl-live/trunk/t/AlignIO/maf.t: maf tests now conform to expected output   Christopher John Fields
• [Bioperl-guts-l] [16545] bioperl-live/trunk/t/AlignIO: tests now allow strandedness; add strand check for those seqs that are now changed   Christopher John Fields
• [Bioperl-guts-l] [16546] bioperl-live/trunk/Bio/DB/SwissProt.pm: missing comma   Christopher John Fields
• [Bioperl-guts-l] [16547] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [16548] bioperl-live/trunk/t/Tools/Run: test fixes   Mark Allen Jensen
• [Bioperl-guts-l] [16549] bioperl-run/trunk/t/SABlastPlus.t: test fixes   Mark Allen Jensen
• [Bioperl-guts-l] [16550] bioperl-live/trunk/Bio/Tools/GuessSeqFormat.pm: Added guesser for bowtie alignment output format and fixed unreasonable tightness on first field of crossbow guesser - also placed entries in alphabetical order .   Dan Kortschak
• [Bioperl-guts-l] [16551] bioperl-live/trunk: moved writing of closing </seqXML> tag from DESTROY to close().   Dave Messina
• [Bioperl-guts-l] [16552] bioperl-run/trunk/t/SABlastPlus.t: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [16553] bioperl-run/trunk/t/SABlastPlus.t: DOH!   Mark Allen Jensen
• [Bioperl-guts-l] [16554] bioperl-run/trunk/t/SABlastPlus.t: better checking   Mark Allen Jensen
• [Bioperl-guts-l] [16555] bioperl-live/trunk/t/SeqTools/GuessSeqFormat.t: fix test count   Christopher John Fields
• [Bioperl-guts-l] [16555]bioperl-live/trunk/t/SeqTools/GuessSeqFormat.t: fix test count   Mark A. Jensen
• [Bioperl-guts-l] [16556] bioperl-live/trunk/t/SeqTools/SeqUtils.t: pull seqfeatures by name, check primary tags against original sfs prior to revcom, then check that the location is actually revcom correctly   Christopher John Fields
• [Bioperl-guts-l] [16557] bioperl-run/trunk/lib/Bio/Tools/Run: consistent directories   Mark Allen Jensen
• [Bioperl-guts-l] [16558] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: add optional state to stdout filespec/thanks Dan   Mark Allen Jensen
• [Bioperl-guts-l] [16559] bioperl-live/trunk/Bio/Structure/IO/pdb.pm: added PMID and DOI parsing/thanx Sung for heads-up   Mark Allen Jensen
• [Bioperl-guts-l] [16560] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Add version return function.   Dan Kortschak
• [Bioperl-guts-l] [16561] bioperl-run/trunk/lib/Bio/Tools/Run: Code added to allow whole suite of bowtie programs to be run from a bowtie object .   Dan Kortschak
• [Bioperl-guts-l] [16562] bioperl-run/trunk/t/EMBOSS.t: bump tests/thx to TimP   Mark Allen Jensen
• [Bioperl-guts-l] [16563] bioperl-run/trunk/lib/Bio/Tools/Run: Removed commands 'map' and ' convert'.   Dan Kortschak
• [Bioperl-guts-l] [16564] bioperl-run/trunk/lib/Bio/Tools/Run/AssemblerBase.pm: check defined to avoid irritating warnings   Mark Allen Jensen
• [Bioperl-guts-l] [16565] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: dan' s patches   Mark Allen Jensen
• [Bioperl-guts-l] [16566] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: Fix patch logic error and improve efficiency/ style of switch expansion in arrayref expansion loop.   Dan Kortschak
• [Bioperl-guts-l] [16567] bioperl-dev/branches/blastplus-dev-branch/: remove branch ( final state tagged in bioperl-dev/tags)   Mark Allen Jensen
• [Bioperl-guts-l] [16568] bioperl-dev/branches/eutils-soap/: branch for entrez soap interface dev   Mark Allen Jensen
• [Bioperl-guts-l] [16569] bioperl-dev/branches/eutils-soap-run/: run branch for entrez soap access dev   Mark Allen Jensen
• [Bioperl-guts-l] [Bioperl-l] PAML parser failed for PAML 4.3b and 4.1   Dave Messina
• [Bioperl-guts-l] [Bug 2958] association table alias is not honored   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2959] Bio::SeqUtils->revcom_with_features should reverse order of features   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2959] Bio::SeqUtils->revcom_with_features should reverse order of features   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2959] Bio::SeqUtils->revcom_with_features should reverse order of features   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2959] New: Bio::SeqUtils->revcom_with_features should reverse order of features   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2960] New: HOWTO:EUtilities_Cookbook   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2970] Doesn't like: LVLNNNNNNNNNNLVNNNNNNNNNNNNNNNNNNNNNNNNVTTKPNK   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2970] Doesn't like: LVLNNNNNNNNNNLVNNNNNNNNNNNNNNNNNNNNNNNNVTTKPNK   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2970] New: Doesn't like: LVLNNNNNNNNNNLVNNNNNNNNNNNNNNNNNNNNNNNNVTTKPNK   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2972] Bio::SeqFeature::Generic->seq() wrong for split locations   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2972] New: Bio::SeqFeature::Generic->seq() wrong for split locations   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2973] Failed EMBOSSS test   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2973] New: Failed EMBOSSS test   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2974] New: PAML parser failed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2974] PAML parser failed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2974] PAML parser failed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2975] New: Network access despite network tests skipped.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2976] New: hss memory allocation 1-off error in HMM.xs::HMM_viterbi   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2977] New: TreeIO problems   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2977] TreeIO problems   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2977] TreeIO problems   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2977] TreeIO problems   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2977] TreeIO problems   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] A Bioperl Problem   wluo01 at students.poly.edu
• [Bioperl-guts-l] A Bioperl Problem   Dave Messina

Last message date: Thu Dec 31 08:27:41 EST 2009
Archived on: Thu Dec 31 08:27:44 EST 2009

• Messages sorted by: [ thread ] [ author ] [ date ]
• More info on this list...