October 2009 Archives by thread
Starting: Thu Oct 1 09:19:12 EDT 2009
Ending: Sat Oct 31 12:57:13 EDT 2009
Messages: 170
- [Bioperl-guts-l] [Bug 2920] Problem with ClustalW 1.83 profile_align function
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16227] bioperl-live/branches/anydbm-branch/Bio/DB/AnyDBMImporter.pm: convert to import method
Mark Allen Jensen
- [Bioperl-guts-l] [16228] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: several bug squishes
Mark Allen Jensen
- [Bioperl-guts-l] [Bug 2920] Problem with ClustalW 1.83 profile_align function
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2920] Problem with ClustalW 1.83 profile_align function
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2921] New: Getting model from codeml results
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16229] bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI: Added a new toplevel_types() method to enable you to recover the types of the toplevel (indexed) features only.
Lincoln Stein
- [Bioperl-guts-l] [16230] bioperl-live/branches/anydbm-branch: Index.t and transfac_pro. t now passing with the
Mark Allen Jensen
- [Bioperl-guts-l] [Bug 2922] New: [TODO] open() directive causing installation to fail
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2923] New: [TODO] open() directive causing installation to fail
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2915] Infinite loop of "_write_line_GenBank_regex" under certain conditions
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2915] Infinite loop of "_write_line_GenBank_regex" under certain conditions
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2920] Problem with ClustalW 1.83 profile_align function
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2092] Can't store proteins with species using bioperl-db
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16231] bioperl-live/branches/anydbm-branch/Bio/DB: correct internal indexing for BTREE db type
Mark Allen Jensen
- [Bioperl-guts-l] [16232] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: kludge around cruft in $value
Mark Allen Jensen
- [Bioperl-guts-l] [16233] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: remove binary kludge -- now treat all $values as SQL_BLOB
Mark Allen Jensen
- [Bioperl-guts-l] [16234] bioperl-live/branches/anydbm-branch: get unit tests passing again.. .
Mark Allen Jensen
- [Bioperl-guts-l] [16235] bioperl-live/branches/anydbm-branch/Bio: -AnyDBM_File conversions-
Mark Allen Jensen
- [Bioperl-guts-l] [16236] bioperl-run/trunk: updated my email
Mauricio Herrera Cuadra
- [Bioperl-guts-l] [Bug 2926] New: Bio:Tools::TandemRepeatsFinder cannot parse out seq_id without description present
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16237] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: rationalize db stmts
Mark Allen Jensen
- [Bioperl-guts-l] [16238] bioperl-live/branches/anydbm-branch/Bio/DB: Overhauled reference and hash cleanup (note this is on branch)
Mark Allen Jensen
- [Bioperl-guts-l] [16239] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: ' manually' reduce severity of unlink warnings
Mark Allen Jensen
- [Bioperl-guts-l] [16240] bioperl-live/branches/anydbm-branch/Bio/DB/AnyDBMImporter.pm: quell prototype "none vs ()" warnings
Mark Allen Jensen
- [Bioperl-guts-l] [16241] bioperl-live/branches/anydbm-branch/Bio/Index/Abstract.pm: bsquish
Mark Allen Jensen
- [Bioperl-guts-l] [16242] bioperl-live/branches/anydbm-branch/Bio/DB/TFBS/transfac_pro.pm: standardize tie() arguments among the many calls
Mark Allen Jensen
- [Bioperl-guts-l] [16243] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: method to initialize internal index
Mark Allen Jensen
- [Bioperl-guts-l] [16244] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: small fixes
Mark Allen Jensen
- [Bioperl-guts-l] [16245] bioperl-live/branches/anydbm-branch/Build.PL: (on branch; no fear)
Mark Allen Jensen
- [Bioperl-guts-l] [16246] bioperl-live/branches/anydbm-branch/Bio/DB/GFF/Adaptor/berkeleydb. pm: some serious kludges here--
Mark Allen Jensen
- [Bioperl-guts-l] [16247] bioperl-live/branches/anydbm-branch/Bio/DB/SeqFeature/Store/ LoadHelper.pm: LoadHelper converted to AnyDBM_File with
Mark Allen Jensen
- [Bioperl-guts-l] [16248] bioperl-live/branches/anydbm-branch/Bio/DB: small changes; inhibit some technical warnings that
Mark Allen Jensen
- [Bioperl-guts-l] [16249] bioperl-live/branches/anydbm-branch/Build.PL: Allow user to directly select BDB for Bio::DB::GFF tests
Mark Allen Jensen
- [Bioperl-guts-l] [16250] bioperl-live/branches/anydbm-branch/t/LocalDB: Tests modified to indicate DBM in use;
Mark Allen Jensen
- [Bioperl-guts-l] [16251] bioperl-live/branches/anydbm-branch: added SPLICE and user-defined collation function
Mark Allen Jensen
- [Bioperl-guts-l] [16252] bioperl-live/branches/anydbm-branch/Bio/DB/SQLite_File.pm: reorganize and add more POD
Mark Allen Jensen
- [Bioperl-guts-l] [Bug 2794] Bioperl 1.6 not available on PPM
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2928] New: GuessSeqFormat raw
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16253] bioperl-live/trunk/Bio/Tools/GuessSeqFormat.pm: fixed re: Bug #2928 (thanks Bernd)
Mark Allen Jensen
- [Bioperl-guts-l] [16254] bioperl-live/trunk/Bio/Tools/GuessSeqFormat.pm: per CJF, bug#2928
Mark Allen Jensen
- [Bioperl-guts-l] [16255] bioperl-live/branches/anydbm-branch/Bio/DB: converted to the CPAN version of
Mark Allen Jensen
- [Bioperl-guts-l] [16256] bioperl-live/branches/anydbm-branch/Bio/DB: using CPAN version now, remove these
Mark Allen Jensen
- [Bioperl-guts-l] [16257] bioperl-live/branches/anydbm-branch/t/LocalDB: remove SQLite_File tests; now in CPAN
Mark Allen Jensen
- [Bioperl-guts-l] [16258] bioperl-live/branches/anydbm-branch/Build.PL: (on branch)
Mark Allen Jensen
- [Bioperl-guts-l] [Bug 2794] Bioperl 1.6 not available on PPM
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16259] bioperl-live/trunk: Added Bio::Location:: SplitLocationI support to subtract().
Jay Hannah
- [Bioperl-guts-l] [16260] bioperl-live/trunk/t/SeqFeature/RangeI.t: Errant old copy/ paste block removed.
Jay Hannah
- [Bioperl-guts-l] [Bug 2930] New: Bio::PrimarySeqI::translate hardcoded test for '*' as terminator
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16261] bioperl-live/trunk/Bio/PrimarySeqI.pm: Adam's patch - Bug #2930
Mark Allen Jensen
- [Bioperl-guts-l] [16262] bioperl-live/trunk/t/Seq/PrimarySeq.t: Adam's patch - Bug #2930
Mark Allen Jensen
- [Bioperl-guts-l] [16263] bioperl-live/trunk/t/Seq/PrimarySeq.t: added a couple of cutoff lines (thx asjo)
Mark Allen Jensen
- [Bioperl-guts-l] [16264] bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm: Documentation updated
Marian Thieme
- [Bioperl-guts-l] [16265] bioperl-live/trunk/t/Seq/PrimarySeq.t: 3rd time = charm
Mark Allen Jensen
- [Bioperl-guts-l] [Bug 2932] New: GenBank DBLINK annotation missing
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16266] bioperl-run/trunk/t/Clustalw.t: skip only tests that fail, not all of them (these fail nastily BTW, so can't TODO ATM)
Christopher John Fields
- [Bioperl-guts-l] [16267] bioperl-run/trunk/lib/Bio/Tools/Run/Alignment/Clustalw.pm: [ RT 50363]
Christopher John Fields
- [Bioperl-guts-l] [Bug 2934] New: typo in close <fh> BinarySearch.pm
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2935] New: Bio::DB::Sam Sam.pm v 1.17 2009-09-03
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2126] t/Pise.t warning
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16268] bioperl-live/trunk/Bio/DB/Flat/BinarySearch.pm: [bug 2934]
Christopher John Fields
- [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] add mask_columns to SimpleAlign.pm
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16269] bioperl-live/trunk/t/SeqFeature/RangeI.t: fix redeclared var warning
Christopher John Fields
- [Bioperl-guts-l] [16270] bioperl-live/trunk/Bio/FeatureIO/gff.pm: [bug 2843]
Christopher John Fields
- [Bioperl-guts-l] [Bug 2843] FeatureIO BED to GFF fails with no phase
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16271] bioperl-live/trunk: [bug 2845]
Christopher John Fields
- [Bioperl-guts-l] [Bug 2845] [Bio::Seq::Quality] get_clear_range return a seq with no id
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2868] Can't parse Arabidopsis TAIR9 release in TIGR XML format
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16272] bioperl-live/trunk/t/SeqIO/scf.t: [bug 2881]
Christopher John Fields
- [Bioperl-guts-l] [Bug 2881] An .scf file written from a Bio::Seq::Quality object cannot be read again
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2888] When reading blast results: spaces at end of line in multi-line query description are lost
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16273] bioperl-live/trunk/Bio/Seq/Quality.pm: [bug 2897]
Christopher John Fields
- [Bioperl-guts-l] [Bug 2897] Add a "mask_below_threshold" method to Seq::Quality (patch attached)
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2898] t/Seq/Quality.t needs more tests (patch attached)
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16274] bioperl-live/trunk/t/Seq/Quality.t: [bug 2898]
Christopher John Fields
- [Bioperl-guts-l] [Bug 2898] t/Seq/Quality.t needs more tests (patch attached)
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16275] bioperl-live/trunk/Bio/SeqIO/genbank.pm: [bug 2915]
Christopher John Fields
- [Bioperl-guts-l] [Bug 2915] Infinite loop of "_write_line_GenBank_regex" under certain conditions
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16276] bioperl-live/trunk: [bug 2926]
Christopher John Fields
- [Bioperl-guts-l] [16277] bioperl-live/trunk/Bio/SeqIO: [bug 2932]
Christopher John Fields
- [Bioperl-guts-l] [16278] bioperl-live/trunk/Bio/Root/Build.pm: [bug 2922]
Christopher John Fields
- [Bioperl-guts-l] [Bug 2900] bp_search2gff.pl's --component option is a fail
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16279] bioperl-dev/trunk: setting up place for GuessDB project
Chase Miller
- [Bioperl-guts-l] [16280] bioperl-dev/trunk/branches/:
Chase Miller
- [Bioperl-guts-l] [16281] bioperl-dev/branches/guess-db/: setting up guess-db project
Chase Miller
- [Bioperl-guts-l] [16282] bioperl-dev/branches/try/: testing testing
Mark Allen Jensen
- [Bioperl-guts-l] [16283] bioperl-dev/branches/try/: byebye try
Mark Allen Jensen
- [Bioperl-guts-l] [16284] bioperl-dev/branches/guess-db/: setting up guess-db project
Chase Miller
- [Bioperl-guts-l] [16285] bioperl-dev/branches/guess-db/: setting up guessDB project
Chase Miller
- [Bioperl-guts-l] [Bug 2900] bp_search2gff.pl's --component option is a fail
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16286] bioperl-run/trunk: [bug 2728]
Christopher John Fields
- [Bioperl-guts-l] [Bug 2728] [TODO] Update Bio::Run::Alignment::ClustalW to support ClustalW 2.0
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16287] bioperl-dev/branches/guess-db/Bio/DB/GuessDB.pm: created stubbed out GuessDB.pm module
Chase Miller
- [Bioperl-guts-l] [16288] bioperl-run/trunk/t/Clustalw.t: remove debugging; tests pass w/ Clustalw 1.82 and clustalw 2.0.12
Christopher John Fields
- [Bioperl-guts-l] [16289] bioperl-live/trunk/Bio/Search/Tiling/MapTileUtils.pm: unixize ( my apologies)
Mark Allen Jensen
- [Bioperl-guts-l] [16290] bioperl-live/trunk/Bio/DB/SwissProt.pm: [bug 2764]
Christopher John Fields
- [Bioperl-guts-l] [Bug 2764] enhance SwissProt retreival by id using IDTracker
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2876] cdd_search with perl (remote blast) ?
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2886] support for HPRD PSI-MI 2.5 XML, was: Bioperl-network parsing error
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16291] bioperl-live/trunk/Bio/Root/IO.pm: [bug 843]
Christopher John Fields
- [Bioperl-guts-l] [Bug 2936] New: "to_FTstring" goes wrong when Strand is missing in a Bio::Location::Split object
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 843] _readline() in SeqIO.pm
bugzilla-daemon at portal.open-bio.org
- [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] [Bug 2888] When reading blast results: spaces at end of line in multi-line query description are lost
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2937] New: Strand in fasta35 output does not seem to be parsed
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16292] bioperl-live/trunk/Bio/Tree/TreeFunctionsI.pm: fix broken pod
Mark Allen Jensen
- [Bioperl-guts-l] [16293] bioperl-live/trunk/t/LocalDB: organizing Bio::Index tests
Christopher John Fields
- [Bioperl-guts-l] [16294] bioperl-live/trunk/t/LocalDB: move Index.t (seq-based) to Bio:: Index-specific test directory.
Christopher John Fields
- [Bioperl-guts-l] [16295] bioperl-live/trunk/t/data: test files for tabular blast indexing
Christopher John Fields
- [Bioperl-guts-l] [16296] bioperl-live/trunk/t/LocalDB/Index/BlastTable.t: add BlastTable tests (simple, no -m 8 yet)
Christopher John Fields
- [Bioperl-guts-l] [16297] bioperl-live/trunk/t/LocalDB/Index/BlastTable.t: remove verbose flag
Christopher John Fields
- [Bioperl-guts-l] [16298] bioperl-live/trunk/Bio/Index/BlastTable.pm: intermediate commit, fixes a few small bugs
Christopher John Fields
- [Bioperl-guts-l] [16299] bioperl-live/trunk: add support for -m 8 format, along with some tests
Christopher John Fields
- [Bioperl-guts-l] [16300] bioperl-live/trunk/t/LocalDB/Index/BlastTable.t: bah.
Christopher John Fields
- [Bioperl-guts-l] [16301] bioperl-live/trunk/Bio/Index/BlastTable.pm: now works with -m 8 (no , really)
Christopher John Fields
- [Bioperl-guts-l] [16302] bioperl-live/trunk/Bio/Index/BlastTable.pm: small POD update
Christopher John Fields
- [Bioperl-guts-l] [Bug 2939] New: Miss handling of PDB residue insertion codes
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16303] bioperl-live/trunk/Bio/Structure/SecStr/DSSP/Res.pm: Bug#2939; thanks for the patch, John
Mark Allen Jensen
- [Bioperl-guts-l] [16304] bioperl-run/trunk/Changes: update Changes
Christopher John Fields
- [Bioperl-guts-l] [Bug 2940] New: PPM issues on Windows (assuming Activeperl)
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2942] New: MapTiling returning incorrect lengths
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [16305] bioperl-live/trunk/Bio/Search/Tiling/MapTiling.pm: Bug#2942 ( thanks Fred)
Mark Allen Jensen
Last message date:
Sat Oct 31 12:57:13 EDT 2009
Archived on: Sat Oct 31 12:57:17 EDT 2009
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