February 2008 Archives by thread

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

Starting: Fri Feb 1 09:02:33 EST 2008
Ending: Fri Feb 29 23:51:01 EST 2008
Messages: 239

• [Bioperl-guts-l] [Bug 2438] New: no letters warning of SeqIO   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2438] no letters warning of SeqIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2439] New: multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO   bugzilla-daemon at portal.open-bio.org
  • [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] [Bug 2439] multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO   bugzilla-daemon at portal.open-bio.org
  • [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] [14461] bioperl-network/trunk/Bio/Network: Minor edits   Brian Osborne
• [Bioperl-guts-l] [14462] bioperl-network/trunk/Bio/Network/IO/psi10.pm: URL changes   Brian Osborne
• [Bioperl-guts-l] [Bug 2440] New: GenericHSP::seq_inds() reports wrong indices when parsing some reports   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2440] GenericHSP::seq_inds() reports wrong indices when parsing some reports   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2440] GenericHSP::seq_inds() reports wrong indices when parsing some reports   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2342] blastall crash & StandAloneBlast (originally described by Matthew Laird)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2342] blastall crash & StandAloneBlast (originally described by Matthew Laird)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14463] bioperl-network/trunk/t/data/human_small-01.xml: More recent file   Brian Osborne
• [Bioperl-guts-l] [14464] bioperl-network/trunk/t/IO_psi25.t: Update, all tests pass   Brian Osborne
• [Bioperl-guts-l] [14465] bioperl-network/trunk/Bio/Network/IO/psi25.pm: Add, all tests pass   Brian Osborne
• [Bioperl-guts-l] [14466] bioperl-network/trunk/t/Node.t: Fix header   Brian Osborne
• [Bioperl-guts-l] [14467] bioperl-network/trunk/t: Fix headers   Brian Osborne
• [Bioperl-guts-l] [14468] bioperl-network/trunk/t/Graph-Articulation.x: Fix headers   Brian Osborne
• [Bioperl-guts-l] [14469] bioperl-network/trunk/AUTHORS: Update   Brian Osborne
• [Bioperl-guts-l] [14470] bioperl-network/trunk/README: Both versions of PSI MI now   Brian Osborne
• [Bioperl-guts-l] [14471] bioperl-network/trunk/Bio/Network: use base pragma   Brian Osborne
• [Bioperl-guts-l] [14472] bioperl-network/trunk/t/IO_psi25.t: Add node and interaction counts   Brian Osborne
• [Bioperl-guts-l] [14473] bioperl-network/trunk/t/ProteinNet.t: Sweep   Brian Osborne
• [Bioperl-guts-l] [14474] bioperl-network/trunk/Bio/Network: Add get and set methods, add verbosity   Brian Osborne
• [Bioperl-guts-l] [14475] bioperl-network/trunk/Bio/Network/IO/psi25.pm: Add get and set methods, add verbosity   Brian Osborne
• [Bioperl-guts-l] [14476] bioperl-ext/trunk/Bio/SeqIO/staden/read.xs: Add cast to correct pointer type (get rid of warnings)   Christopher John Fields
• [Bioperl-guts-l] [14477] bioperl-network/trunk/Bio/Network/IO.pm: Typo   Brian Osborne
• [Bioperl-guts-l] [Bug 2441] New: Bio::Assembly treatment of singletons is inconsistent   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2441] Bio::Assembly treatment of singletons is inconsistent   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14478] bioperl-network/trunk/t/Graph-Articulation.x: Update, but Graph' s articulation_points() is still unreliable   Brian Osborne
• [Bioperl-guts-l] [14479] bioperl-network/trunk/t/Graph-MD5.t: Update and check   Brian Osborne
• [Bioperl-guts-l] [14480] bioperl-live/trunk/Bio/SearchIO/Writer/TextResultWriter.pm: Fixed bits/raw_score issue related to GenericHit changes to raw_score/bits   Christopher John Fields
• [Bioperl-guts-l] [Bug 2442] New: SeqFeature::Annotated constructor -feature arg breaks with another BSFA   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2442] SeqFeature::Annotated constructor -feature arg breaks with another BSFA   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2442] SeqFeature::Annotated constructor -feature arg breaks with another BSFA   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2442] SeqFeature::Annotated constructor -feature arg breaks with another BSFA   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2442] SeqFeature::Annotated constructor -feature arg breaks with another BSFA   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14481] bioperl-live/trunk: bug 2442   Christopher John Fields
• [Bioperl-guts-l] [14482] bioperl-live/trunk/Bio/Tree/Draw/Cladogram.pm: bug 2415   Christopher John Fields
• [Bioperl-guts-l] [Bug 2415] Wrong tree coloring by Tree::Draw::Cladogram   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2427] error while using Bio::Search::cross_match   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14483] bioperl-live/trunk/Bio/PrimarySeq.pm: bug 2438; 'X' no longer completely ambiguous   Christopher John Fields
• [Bioperl-guts-l] [14484] bioperl-live/trunk/Bio/DB/SeqFeature: fixed a logic error which caused undefined end coordinates when creating a feature with abs =>1, a start and an undefined end   Lincoln Stein
• [Bioperl-guts-l] [14485] bioperl-live/trunk/Bio/Graphics/FeatureFile.pm: fixed bug in featurefile processing that inappropriately grouped features with no name   Lincoln Stein
• [Bioperl-guts-l] [14486] bioperl-network/trunk/t: Add tests for MINT PSI MI 2.5, add MINT file   Brian Osborne
• [Bioperl-guts-l] [Bug 2444] New: Bio::SearchIO blast signifance contains comma   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2444] Bio::SearchIO blast signifance contains comma   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2444] Bio::SearchIO blast signifance contains comma   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2444] Bio::SearchIO blast signifance contains comma   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2444] Bio::SearchIO blast signifance contains comma   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2444] Bio::SearchIO blast signifance contains comma   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2444] Bio::SearchIO blast signifance contains comma   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2444] Bio::SearchIO blast signifance contains comma   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2445] New: Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2445] Bio::SearchIO BLAST parser gets wrong score and evalue   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14487] bioperl-network/trunk/Bio/Network/IO/psi25.pm: use base, minor edits   Brian Osborne
• [Bioperl-guts-l] [14488] bioperl-live/trunk/Bio/Search/HSP/GenericHSP.pm: bug 2444 (HSP:: significance returning wrong value)   Christopher John Fields
• [Bioperl-guts-l] [14489] bioperl-live/trunk: * small rnamotif fix   Christopher John Fields
• [Bioperl-guts-l] [14490] bioperl-live/trunk/Bio/SeqIO/genbank.pm: handles Bio:: Taxon as well as Bio::Species now ( might be worth propogating to other SeqIO modules?)   Christopher John Fields
• [Bioperl-guts-l] [14491] bioperl-live/trunk/Bio/DB/SeqHound.pm: changed URL   Christopher John Fields
• [Bioperl-guts-l] [14492] bioperl-ext/trunk/Bio/Ext/Align: Add some helper code and tests to demo evalue oddities (bug 1857); casting issue?   Christopher John Fields
• [Bioperl-guts-l] [14493] bioperl-live/trunk/Bio/DB/SeqFeature/Store.pm: Added missing documentation for memory and berkeleydb adaptors.   Lincoln Stein
• [Bioperl-guts-l] [14494] bioperl-live/trunk/Bio/Variation/IO/flat.pm: Remove dead links, don 't know what should replace them, unfortunately   Brian Osborne
• [Bioperl-guts-l] [14495] bioperl-live/trunk/Bio/SearchIO/blast.pm: bug 2445: clean up hit table regex to skip N (Bernd's suggestion); passes tests but needs more testing   Christopher John Fields
• [Bioperl-guts-l] [14496] bioperl-live/trunk/DEPENDENCIES: checking svn post commits to list   Christopher John Fields
• [Bioperl-guts-l] [14497] bioperl-live/trunk/DEPENDENCIES: test commit msgs from /usr/local/ bin   Christopher John Fields
• [Bioperl-guts-l] [14498] bioperl-live/trunk/Bio: Fix for bug 2413.   Christopher John Fields
• [Bioperl-guts-l] [Bug 2413] save_tempfiles() not working in Bio::Tools::Run::WrapperBase   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14499] bioperl-live/trunk/Bio/Tools/Run/WrapperBase.pm: remove comment ( make sure tempfile/tempdirs stored in WrapperBase are removed).   Christopher John Fields
• [Bioperl-guts-l] [Bug 2384] Segmentation Fault in Bio::Tools::dpAlign::pairwise_alignment_score   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2384] Segmentation Fault in Bio::Tools::dpAlign::pairwise_alignment_score   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2436] Inconsistencies in function HSPI::seq_inds when encountering gaps   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14500] bioperl-live/trunk: bug 2440   Christopher John Fields
• [Bioperl-guts-l] [Bug 2179] bug in Bio::Restriction::IO::withrefm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14501] bioperl-live/trunk/Bio/SeqIO/abi.pm: missing getter/setter added   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] [Bug 2018] Bio::ClusterIO::dbsnp breaks with new XML output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2069] Bio::Tools:pSW stop codon bug   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2074] bioperl-ext: make test fails using io_lib v. 1.9 or higher   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2165] Bio::SeqIO does not write correct taxonomy data in SwissProt format   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2329] Enhancement to Bio::SeqIO::abi - abi_with_trace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2370] Bio::Assembly::Scaffold Source   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 2376] ID of match features in bp_search2gff.pl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2377] Target tag format in bp_search2gff.pl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2384] Segmentation Fault in Bio::Tools::dpAlign::pairwise_alignment_score   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14502] bioperl-live/trunk/Bio/SeqIO/genbank.pm: do not write a full stop at the end of the SOURCE line   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14503] bioperl-live/trunk/Bio/SeqIO/genbank.pm: removed BASE COUNT line printing code.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14504] bioperl-live/trunk: Changed the swissprot parser to work regardless of the end full stop character in DT lines .   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14505] bioperl-live/trunk/Bio/SeqIO/swiss.pm: PE (evidence) line was printed out between CC and DR lines when it needs to be between DR and KW lines   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14506] bioperl-live/trunk/Bio/SeqIO/swiss.pm: Rewrote RX line parsing and writing to allow DOI values seen and printed out   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14507] bioperl-live/trunk/DEPRECATED: not 1.5.3 (modules don' t work anymore)   Christopher John Fields
• [Bioperl-guts-l] [14508] bioperl-live/trunk/Bio/Restriction: update interface documentation   Christopher John Fields
• [Bioperl-guts-l] [Bug 2449] New: HTMLWriter out of sync   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14509] bioperl-live/trunk/Bio/SeqIO/swiss.pm: removed extra space chars and a full stop at the end of the FT HELIX and STRAND lines .   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14511] bioperl-live/trunk/Bio/SeqIO/swiss.pm: prevent line wrapping within author name (RA lines) and withing key frase (KW lines), but allow wrapping at hyphen in a title (RT lines)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14512] bioperl-live/trunk/Bio/SeqIO/swiss.pm: DOI can include   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14513] bioperl-live/trunk/t/Handler.t: TODO now works   Christopher John Fields
• [Bioperl-guts-l] [14514] bioperl-live/trunk/Bio/SeqIO/embl.pm: Reindenting the code.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14515] bioperl-live/trunk/Bio/SeqIO/swiss.pm: Reindenting the code.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14516] bioperl-live/trunk/Bio/SeqIO/swiss.pm: FTId is no longer treated a part of the description of an FT key but similarly to EMBL FT qualifiers .   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14517] bioperl-live/trunk: New module Bio::Assembly::Tools:: ContigSpectrum for dealing with contig spectra obtained from metagenome assembly   Florent E Angly
• [Bioperl-guts-l] [Bug 2451] New: Suggestions for name of module and module improvement   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2451] Suggestions for name of module and module improvement   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2451] Suggestions for name of module and module improvement   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2451] Suggestions for name of module and module improvement   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2452] New: sub _open_pipe globally modifies $SIG{CHLD}   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2452] sub _open_pipe globally modifies $SIG{CHLD}   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2453] New: Bio::AlignIO, when reading an MAF format file, a blank line between the initial comment lines and the first alignment block results in the file read but no alignment blocks recognized. this a silent thing - no errors reported, just no alignment blocks in the returned alignIO obj   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2453] Bio::AlignIO, when reading an MAF format file, a blank line between the initial comment lines and the first alignment block results in the file read but no alignment blocks recognized. this a silent thing - no errors reported, just no alignment blocks in the returned alignIO obj   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14518] bioperl-network/trunk/README: Minor edits   Brian Osborne
• [Bioperl-guts-l] [14519] bioperl-live/trunk/Bio/DB/WebDBSeqI.pm: bug 2452   Christopher John Fields
• [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] [Bug 2342] blastall crash & StandAloneBlast (originally described by Matthew Laird)   bugzilla-daemon at portal.open-bio.org
• [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] [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] [14520] bioperl-live/trunk/Bio/AlignIO/maf.pm: small fix for bug 2453, but see bugzilla for reasons on not closing this out   Christopher John Fields
• [Bioperl-guts-l] [14521] bioperl-live/trunk/Bio/AlignIO/maf.pm: Oops! Bug 2453 again.   Christopher John Fields
• [Bioperl-guts-l] [14522] bioperl-live/trunk/Bio/AlignIO/maf.pm: Bug 2453; needs tests   Christopher John Fields
• [Bioperl-guts-l] [14523] bioperl-live/trunk/t: tests for bug 2453   Christopher John Fields
• [Bioperl-guts-l] [Bug 2455] New: Bio::Assembly::IO::ace doesn't create Bio::Assembly::Singlet objects   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2455] Bio::Assembly::IO::ace doesn't create Bio::Assembly::Singlet objects   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2455] Bio::Assembly::IO::ace doesn't create Bio::Assembly::Singlet objects   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2455] Bio::Assembly::IO::ace doesn't create Bio::Assembly::Singlet objects   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2455] Bio::Assembly::IO::ace doesn't create Bio::Assembly::Singlet objects   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] New: reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   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 1825] bug in parsing gene names for swissprot entry in module Bio::SeqIO:swiss   bugzilla-daemon at portal.open-bio.org
• [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] [14524] bioperl-live/trunk: Now passes tests; added warnings for no returned exons when called   Christopher John Fields
• [Bioperl-guts-l] [14525] bioperl-live/trunk: fix CUTG tests   Christopher John Fields
• [Bioperl-guts-l] [14526] bioperl-live/trunk/t/SeqFeatAnnotated.t: add Graph:: Directed to requirements for tests   Christopher John Fields
• [Bioperl-guts-l] [14527] bioperl-live/trunk/Build.PL: add file test, unlink if already present   Christopher John Fields
• [Bioperl-guts-l] [14528] bioperl-live/trunk/t/PrimarySeq.t: bug 2438.   Christopher John Fields
• [Bioperl-guts-l] [14529] bioperl-live/trunk/t: Sequence gained a nucleotide   Christopher John Fields
• [Bioperl-guts-l] [14530] bioperl-live/trunk/t/protgraph.t: now deprecated   Christopher John Fields
• [Bioperl-guts-l] [14531] bioperl-live/trunk/Bio/Seq/Quality.pm: fall back to empty set   Christopher John Fields
• [Bioperl-guts-l] [14532] bioperl-live/trunk/t/swiss.t: TODO now works   Christopher John Fields
• [Bioperl-guts-l] [14533] bioperl-live/trunk/Build.PL: run tests directly in Build.PL (don' t pass code refs on to Module::Build)   Christopher John Fields
• [Bioperl-guts-l] [14534] bioperl-live/trunk/Bio/SeqIO/swiss.pm: Do not print out empty KW ( keyword) lines.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14535] bioperl-live/trunk/Bio: improved behavior of xy and density plots when spanning regions that contained undefined scores ; now just skips over these regions   Lincoln Stein
• [Bioperl-guts-l] [14536] bioperl-live/trunk/Bio/DB/SeqFeature/Store: these loaders allow gff2 and featurefile-format data to be stored into gff3 databases   Lincoln Stein
• [Bioperl-guts-l] [14537] bioperl-live/trunk/Build.PL: revert last commit (good catch Sendu)   Christopher John Fields
• [Bioperl-guts-l] [14538] bioperl-live/trunk: GN (Gene Name) line parsing rewrite.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14539] bioperl-live/trunk/Bio/SeqIO/swiss.pm: AC (accession) line now wraps if there are too many accession to fit one line   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14540] bioperl-live/trunk: GN changes   Christopher John Fields
  • [Bioperl-guts-l] [14540] bioperl-live/trunk: GN changes   Heikki Lehvaslaiho
    • [Bioperl-guts-l] [14540] bioperl-live/trunk: GN changes   Chris Fields
• [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] [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] [14541] bioperl-live/trunk/Bio/SeqIO/swiss.pm: documentation for the GN line parsing and management   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14542] bioperl-live/trunk/Bio/SeqIO/swiss.pm: minor edits to docs   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14543] bioperl-live/trunk/Bio/SeqIO/embl.pm: better roundtip when preventing line wrapping between author surname and initials   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14544] bioperl-live/trunk/Bio/SeqIO/embl.pm: RC (reference comment) line was printed in wrong place.   Heikki Lehvaslaiho
• [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] [14545] bioperl-run/trunk/Bio/Tools/Run/Phylo/Phast/PhastCons.pm: throw some spaces in there to prevent Pdoc URL slurping   Jason Stajich
• [Bioperl-guts-l] [14546] bioperl-live/trunk/Bio/Assembly/IO/ace.pm: Russell's fixes   Christopher John Fields
• [Bioperl-guts-l] [Bug 2458] New: enhancement of Bio::SeqIO::kegg - parse POSITION field   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2458] enhancement of Bio::SeqIO::kegg - parse POSITION field   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2458] enhancement of Bio::SeqIO::kegg - parse POSITION field   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2458] enhancement of Bio::SeqIO::kegg - parse POSITION field   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2458] enhancement of Bio::SeqIO::kegg - parse POSITION field   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14547] bioperl-live/trunk: bug 2458   Christopher John Fields
• [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] [14548] bioperl-live/trunk/ModuleBuildBioperl.pm: No longers stores code refs via Data::Dumper, avoiding possible warnings   Senduran Balasubramaniam
• [Bioperl-guts-l] [14549] bioperl-live/trunk/Build.PL: No longer makes db test if user chose not to run them   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2459] New: Bio::Assembly::IO::ace.pm not parsing contig names correctly   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2459] Bio::Assembly::IO::ace.pm not parsing contig names correctly   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2460] New: die with $CHILD_ERROR insead of $OS_ERROR in Bio::Tools::Run modules using IPC::Run   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2460] die with $CHILD_ERROR insead of $OS_ERROR in Bio::Tools::Run modules using IPC::Run   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2460] die with $CHILD_ERROR insead of $OS_ERROR in Bio::Tools::Run modules using IPC::Run   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2460] die with $CHILD_ERROR insead of $OS_ERROR in Bio::Tools::Run modules using IPC::Run   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2460] die with $CHILD_ERROR insead of $OS_ERROR in Bio::Tools::Run modules using IPC::Run   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14550] bioperl-run/trunk/Bio/Tools/Run: bug 2460   Christopher John Fields
• [Bioperl-guts-l] [14551] bioperl-live/trunk/Bio/Annotation: add error message for callbacks if no code reference   Christopher John Fields
• [Bioperl-guts-l] [14552] bioperl-live/trunk/Bio/Annotation/StructuredTag.pm: StructuredTag - AnnotationI which uses Data:: Stag for structured tag representation.   Christopher John Fields
• [Bioperl-guts-l] [14553] bioperl-live/trunk/Bio/Annotation/StructuredValue.pm: Remove Data:: Stag cruft (use a reimplementation instead)   Christopher John Fields
• [Bioperl-guts-l] [14554] bioperl-live/trunk/t/Annotation.t: Add some tests, more to follow upon implementation...   Christopher John Fields
• [Bioperl-guts-l] [Bug 2461] New: had two non-consecutive nodes with the same name. Can't cope!   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2461] had two non-consecutive nodes with the same name. Can't cope!   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2461] had two non-consecutive nodes with the same name. Can't cope!   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2461] had two non-consecutive nodes with the same name. Can't cope!   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14555] bioperl-live/trunk/Bio/Annotation/StructuredTag.pm: changes and additions (can't fairly implement StructureValue's methods, so we'll go another route)...   Christopher John Fields
• [Bioperl-guts-l] [14556] bioperl-live/trunk/Bio/Annotation: Change name to TagTree   Christopher John Fields
• [Bioperl-guts-l] [14557] bioperl-live/trunk/Bio/Graphics: worked around different behavior in Text::ParseWords:: shellwords under perl 5.8 and 5. 10 -- should be relatively stable over various versions   Lincoln Stein
• [Bioperl-guts-l] [Bug 2462] New: No tests for Bio::Tools::Fgenesh   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2462] No tests for Bio::Tools::Fgenesh   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2462] No tests for Bio::Tools::Fgenesh   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2462] No tests for Bio::Tools::Fgenesh   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14558] bioperl-live/trunk/t: bug 2462   Christopher John Fields
• [Bioperl-guts-l] [14559] bioperl-live/trunk: More tests   Christopher John Fields
• [Bioperl-guts-l] [14560] bioperl-live/trunk/t/Annotation.t: check tagtree in collection   Christopher John Fields
• [Bioperl-guts-l] [14561] bioperl-live/trunk/Bio/Seq/SequenceTrace.pm: removed unused dependency to Dumpvalue module   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14562] bioperl-live/trunk/Bio: bug 1825: updating swiss.pm/ tests to try out TagTree (passes all tests).   Christopher John Fields
• [Bioperl-guts-l] [14563] bioperl-live/trunk/t/swiss.t: bug 1825   Christopher John Fields
• [Bioperl-guts-l] [14564] bioperl-live/trunk/Bio/Annotation/Collection.pm: minor word wrapping for error message   Christopher John Fields
• [Bioperl-guts-l] [14565] bioperl-live/trunk/Build.PL: add Data::Stag to require ( may change to recommend based on other core dev input)   Christopher John Fields
• [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] [14566] bioperl-live/trunk: * Implement StructureValue-like get_all_values( ) (flattened value array)   Christopher John Fields
• [Bioperl-guts-l] [14567] bioperl-live/trunk: fix Handler tests   Christopher John Fields
• [Bioperl-guts-l] [Bug 2463] New: bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2463] bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2463] bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14568] bioperl-live/trunk/Bio/DB/Taxonomy/list.pm: fixed bug6421: reimplemented main code to cope with non-unique names in a lineage.   Senduran Balasubramaniam
• [Bioperl-guts-l] [14569] bioperl-live/trunk/t/Taxonomy.t: tests for bug6421   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 1572] no docs and possible typo in Bio::Location::Simple/Atomic::trunc   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14570] bioperl-live/trunk/Bio/ClusterIO/dbsnp.pm: Note about XML format ( related to bug 2018)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2018] Bio::ClusterIO::dbsnp breaks with new XML output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14571] bioperl-live/trunk: bug 2128   Christopher John Fields
• [Bioperl-guts-l] [Bug 2128] Bio::Restriction::EnzymeCollection cutters()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14572] bioperl-live/trunk: bug 2179   Christopher John Fields
• [Bioperl-guts-l] [Bug 2179] bug in Bio::Restriction::IO::withrefm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2424] Out of memory on SeqIO   bugzilla-daemon at portal.open-bio.org
• [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] [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] [14573] bioperl-live/trunk/Bio/Restriction/IO/prototype.pm: parser for neo/ prototype format from REBASE   Christopher John Fields
• [Bioperl-guts-l] [14574] bioperl-live/trunk/Bio/Restriction: Add in support for grabbing most current data via ftp; add prototype/ neoschizomer support   Christopher John Fields
• [Bioperl-guts-l] [14575] bioperl-live/trunk: clean up inheritance tree; add remote database test   Christopher John Fields
• [Bioperl-guts-l] [14576] bioperl-live/trunk/Bio/Restriction/IO/base.pm: added prototype-checking method (bug 2179)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2179] bug in Bio::Restriction::IO::withrefm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2191] Bio::Tree::Node is missing delete_edge function   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2332] Software for analysis of redundant fragments of affys human mitochip v2   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14577] bioperl-live/trunk/Bio/Restriction/IO/base.pm: add some docs   Christopher John Fields

Last message date: Fri Feb 29 23:51:01 EST 2008
Archived on: Fri Feb 29 23:51:09 EST 2008

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