July 2010 Archives by author

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Starting: Thu Jul 1 11:56:54 EDT 2010
Ending: Sat Jul 31 16:59:41 EDT 2010
Messages: 159

• [Bioperl-guts-l] [bioperl/bioperl-run] 749ab0: contigs off with Ubuntu packaged MAQ   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] b984f4: fix edge case when adding gaps   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 718cad: algorithm can be SSEARCH as well; use test_output_...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 97f73d: move to tempfiles for cleanup   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] fe1195: move tests over to tempfile use (tmpdir not being ...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 8fefbb: test commit for org setup   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 2c4036: updated for SeqXML v0.2   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] c41d7f: Merge branch 'topic/species_proxy'   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] e785d8: add some significant milestones   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 03e09b: small fixes, but the previous code does work when ...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 4908bb: remove samtool cruft from MANIFEST   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 51c937: added summary mode to bio::db::gff mysql adaptor   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 58bde5: added interval statistics gathering to Pg adaptor   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 0fe064: Clarify warnings when defaulting the value of end(...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 3f8e73: added Dan Bolser's patches to fix inconsistent nam...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] fb81d7: adding optional -type parameter (and support for i...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] cb475a: adding a bioperl commandline netinstaller based on...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 39652b: fix POD   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 2a240f: [bug 3107] pass strand info to alns   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 566e13: [bug 3095] doc changes to indicate difference betw...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] bcd98d: Merge branch 'master' of github.com:bioperl/bioper...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 3819ef: interpro parser now throws an error when it cannot...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d1d9d1: added a little defensive error checking when addin...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 3cde0b: Bio::Root::IO->_insert() special case when inserti...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] f1f67a: more perltidy   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] c08e27: more perltidy   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 12aa17: Add tests for the exceptions thrown by invalid Bio...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] cfafb2: Fix some failing InterPro tests, since the number ...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 244ba4: Fix bug which prevents the parsing of the InterPro...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] be8dd8: Removed warning when Bio::Assembly::IO::ace parsin...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 783e04: Bio::Root::IO insert() with no backup file   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] bcde3b: Update MANIFEST and MANIFEST.SKIP   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 29cf23: allow POST for ID lists longer than 200 or terms l...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 29cf23: allow POST for ID lists longer than 200 or terms l...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 19d5b7: Refactor some tests in t/Ontology/IO/interpro.t   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 7314af: Add Conserved_site as an InterPro root term and up...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 7c6739: Add a test to show that there is a bug with get_db...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 19d5b7: Refactor some tests in t/Ontology/IO/interpro.t   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 505452: squash warnings popping up with uninit data; marke...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 09f5f0: Add a test for each kind of InterPro dbxref contex...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 09f5f0: Add a test for each kind of InterPro dbxref contex...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 22c410: reimplement various methods in terms of get_dbxref...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 3a817b: Add some tests for get_members and protein_count a...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 6c2c95: Add tests for class_list, get_examples and get_ext...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] c495ed: Add a test for get_references and to_string   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 846480: a bit o' debugging; alias add_dbxrefs to add_dbxre...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 42712c: Add some tests for get_members and protein_count a...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] aee9fe: move Bio::Assembly::IO tests into their own direct...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] a30498: cleanup tests, passing but file cleanup not in pla...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] a7be37: clean up generated index files   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 8a8d14: test count off on skip (ID mapper appears to be ha...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 424905: remote db ID change causing fail   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 605c9d: Merge branch 'topic/cjfields_interpro_get_dbxref'   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] d58682: [RT 58464] patching to allow file names with space...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 2bfc2c: [RT 58464] patching to allow file names with space...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-db] 98d2a0: [RT 44466] remove corba-related scripts, now obsol...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 3a03b2: silence exception that happens with -y option   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] f63896: added interval stats support to pg - untested   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] fb68a0: whitespace cleanup in WrapperBase.pm code   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 3997d7: StandAloneBlast.t should allow different types of ...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 95f860: Add a failing test for <cite> elements in term def...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] ffb03e: phiX174 sequence, for is_circular SF tests   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 589130: * add tests for circular sequences   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] ffb03e: phiX174 sequence, for is_circular SF tests   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d752a4: allow looping ranges for circular genomes. See Re...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 6672d9: more informative err msf   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 14cccb: fixed interval stats table for postgres--used with...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 6ded08: Fixed sql syntax error in creation of interval_sta...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 34a985: fixed a problem where the loader tried to create t...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] a3ee8b: Introspect feature objects and call apporpriate GF...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 40eb18: Merge branch 'master' into branch-1-6   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 4b125a: first alpha   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] f69a78: domain flag borking the request; fix courtesy John...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] a6d919: strip keyword substitution from perl modules   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 1d4985: strip keyword substitution from perl modules   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] f69a78: domain flag borking the request; fix courtesy John...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 4ee526: [bug 3122] catch seek calls on the unseekable (tha...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] b31f53: [bug 3126] catch description (patch courtesy Toshi...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 15aad7: [bug 3039] added Dave's changes to a branch; these...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] b0b52c: dir in maint for working on dynamiting the monolit...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] c1abbd: Force ID field for all gb files converted to gff3   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 4ee526: [bug 3122] catch seek calls on the unseekable (tha...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 56ba53: return the first note (scalar context of array, wa...   noreply at github.com
• [Bioperl-guts-l] [Bug 3107] New: column_from_residue_number() provides weird position translation on BLAST minus strand   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3107] column_from_residue_number() provides weird position translation on BLAST minus strand   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3107] column_from_residue_number() provides weird position translation on BLAST minus strand   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3108] New: Bio::SearchIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3108] Bio::SearchIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3110] New: Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3111] New: Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3112] New: Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3113] New: Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3114] New: Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3115] New: Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3111] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3110] New: Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3112] New: Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3110] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3114] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3110] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3113] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3110] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3115] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3110] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2899] problem with t/LocalDB/SeqFeature.t when host ne localhost   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3116] New: tr/// warning with Bio::Range in Perl 5.12   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3117] New: Bio::Tree::TreeFunctionsI use()ing UNIVERSAL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3117] Bio::Tree::TreeFunctionsI use()ing UNIVERSAL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3116] tr/// warning with Bio::Range in Perl 5.12   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3108] Bio::SearchIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3107] column_from_residue_number() provides weird position translation on BLAST minus strand   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3104] Bio::Species::classification() unhappy with single node "hierarchies"   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2594] Bio::Species memory leak   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3110] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3095] seq_version() in Bio::PrimarySeq not found   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3110] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3110] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3110] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3017] use threads to get genbank file error   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3120] New: Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy?   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy?   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3121] New: Bio::OntologyIO cannot parse the full InterPro XML file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full InterPro XML file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full InterPro XML file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full InterPro XML file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full InterPro XML file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full InterPro XML file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full InterPro XML file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full InterPro XML file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full InterPro XML file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3121] Bio::OntologyIO cannot parse the full InterPro XML file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy?   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy?   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3122] New: Bio::SeqIO ignores first line of piped Fasta sequence when no format parameter is set   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3122] Bio::SeqIO ignores first line of piped Fasta sequence when no format parameter is set   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3122] Bio::SeqIO ignores first line of piped Fasta sequence when no format parameter is set   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3122] Bio::SeqIO ignores first line of piped Fasta sequence when no format parameter is set   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3123] New: get_dbxrefs does not work on InterPro terms   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3123] get_dbxrefs does not work on InterPro terms   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3123] get_dbxrefs does not work on InterPro terms   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3123] get_dbxrefs does not work on InterPro terms   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3123] get_dbxrefs does not work on InterPro terms   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3125] New: bioperl-run LVB.pm and LVB.t require updates for LVB version 2.3   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3126] New: description() method returns nothing in Bio::DB::Fasta   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3126] description() method returns nothing in Bio::DB::Fasta   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3122] Bio::SeqIO ignores first line of piped Fasta sequence when no format parameter is set   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3125] bioperl-run LVB.pm and LVB.t require updates for LVB version 2.3   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3126] description() method returns nothing in Bio::DB::Fasta   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3028] Bio::TreeIO::nexus Fails to correctly output FigTree Formatting tags   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3039] TreeIO::newick writes root node branch length incorrectly   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3039] TreeIO::newick writes root node branch length incorrectly   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3056] Bio::Tools::Run::Primer3 has not updated for Primer3 versions 2 and above   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3125] bioperl-run LVB.pm and LVB.t require updates for LVB version 2.3   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3108] Bio::SearchIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2691] Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency   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] [Bug 2691] Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2673] original fields not inherited by seq objects in alignment slices   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

Last message date: Sat Jul 31 16:59:41 EDT 2010
Archived on: Sat Jul 31 16:59:46 EDT 2010

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