January 2007 Archives by thread
Starting: Mon Jan 1 15:49:40 EST 2007
Ending: Wed Jan 31 13:07:36 EST 2007
Messages: 253
- [Bioperl-guts-l] [Bug 2172] New: genbank.pm: parsing of RefSeq NC_004822 crashes
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2173] New: Bio::Graphics::Glyph::stackedplot always generates homogenous histogram
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run RepeatMasker.pm, 1.25, 1.26
Senduran Balasubramaniam
- [Bioperl-guts-l] [Bug 2127] Add Amap, Kalign and Probcon Quiet option
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph dna.pm,1.29,1.30
Lincoln Stein
- [Bioperl-guts-l] [Bug 2127] Add Amap, Kalign and Probcon Quiet option
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2168] "no data for midline" exception thrown
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-live/t/data testaln.list,NONE,1.1
Weigang Qiu
- [Bioperl-guts-l] bioperl-live/Bio SimpleAlign.pm,1.123,1.124
Weigang Qiu
- [Bioperl-guts-l] bioperl-live/t SimpleAlign.t,1.48,1.49
Weigang Qiu
- [Bioperl-guts-l] bioperl-live/Bio/Tools/Run WrapperBase.pm, 1.25, 1.26
Senduran Balasubramaniam
- [Bioperl-guts-l] [Bug 2178] New: Bio::Enzyme's cutter() is wrong for V, H, D, B amibuities
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2179] New: bug in Bio::Restriction::IO::withrefm
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-live/Bio/Annotation Collection.pm, 1.24, 1.25
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/Tools Infernal.pm,1.2,1.3
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/SeqIO genbank.pm,1.160,1.161
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio SimpleAlign.pm,1.124,1.125
Weigang Qiu
- [Bioperl-guts-l] bioperl-live AUTHORS,1.52,1.53
Malcom Cook
- [Bioperl-guts-l] bioperl-live/Bio/DB/Taxonomy flatfile.pm, 1.19, 1.20
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/Bio/FeatureIO bed.pm,1.8,1.9
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/Bio/Annotation Tree.pm,NONE,1.1
Weigang Qiu
- [Bioperl-guts-l] bioperl-live/t Annotation.t,1.20,1.21
Weigang Qiu
- [Bioperl-guts-l] bioperl-live/Bio RangeI.pm,1.51,1.52
Malcom Cook
- [Bioperl-guts-l] bioperl-live/t Range.t,1.11,1.12
Malcom Cook
- [Bioperl-guts-l] [Bug 2180] New: Bio::SearchIO SearchIO can't parse fasta output fileMSG: Did not specify a Query End or Query Begin
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2181] New: Bio::SearchIO SearchIO can't parse fasta output file MSG: Did not specify a Query End or Query Begin
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2182] New: t/DB.t update - (swissprot data changed)
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-live/t rnamotif.t,1.5,1.6
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t DB.t,1.71,1.72
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/Root RootI.pm,1.74,1.75
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/t RootI.t,1.8,1.9
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/t rnamotif.t,1.6,1.7
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t DB.t,1.72,1.73
Christopher John Fields
- [Bioperl-guts-l] [Bug 1244] Invalid species name 'Oryza' in Bio::Species
Christian Phillips
- [Bioperl-guts-l] bioperl-live/Bio/Tools/Run WrapperBase.pm, 1.26, 1.27
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/t WrapperBase.t,NONE,1.1
Senduran Balasubramaniam
- [Bioperl-guts-l] [Bug 2183] New: Bio::Tools::Run::WrapperBase::cleanup doesn't work?
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2184] New: segmentation error during BioPerl 1.5.2 installation
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phast PhyloFit.pm, 1.1, 1.2
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phast PhastCons.pm, 1.2, 1.3
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/t/data/taxdump - New directory
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/t PhastCons.t,NONE,1.1
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/t/data/taxdump names.dmp, NONE, 1.1 nodes.dmp, NONE, 1.1
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo PhyloBase.pm, NONE, 1.1
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo PhyloBase.pm, 1.1, 1.2
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/t/data apes.newick, NONE, 1.1 apes.multi_fasta, NONE, 1.1
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/t SeqBoot.t, 1.2, 1.3 Neighbor.t, 1.8, 1.9 ProtDist.t, 1.15, 1.16 ProtPars.t, 1.8, 1.9
Weigang Qiu
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phylip SeqBoot.pm, 1.12, 1.13 ProtPars.pm, 1.24, 1.25 ProtDist.pm, 1.30, 1.31 Consense.pm, 1.14, 1.15 Neighbor.pm, 1.27, 1.28
Weigang Qiu
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run Simprot.pm,NONE,1.1
Albert Vilella
- [Bioperl-guts-l] bioperl-live/Bio/Graphics Glyph.pm,1.132,1.133
Brian Osborne
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run Simprot.pm,1.1,1.2
Albert Vilella
- [Bioperl-guts-l] [Bug 2185] New: It is not possible to read phylip alignment file via a new file handle in AlignIO.
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-live/Bio/Graphics Glyph.pm,1.133,1.134
Lincoln Stein
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Lagan.pm, 1.15, 1.16
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run Simprot.pm,1.2,1.3
Albert Vilella
- [Bioperl-guts-l] bioperl-run/t/data longnames.aln,NONE,1.1
Weigang Qiu
- [Bioperl-guts-l] bioperl-run/t/data simprot_tree.nh,NONE,1.1
Albert Vilella
- [Bioperl-guts-l] bioperl-run/t Simprot.t,NONE,1.1
Albert Vilella
- [Bioperl-guts-l] bioperl-live/Bio/Tree TreeFunctionsI.pm, 1.32, 1.33
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/Bio/AlignIO phylip.pm,1.38,1.39
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/AlignIO arp.pm, 1.1, 1.2 mase.pm, 1.14, 1.15 metafasta.pm, 1.8, 1.9
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t AlignIO.t,1.71,1.72
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/AlignIO nexus.pm,1.29,1.30
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t AlignIO.t,1.72,1.73
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph generic.pm, 1.45, 1.46
Lincoln Stein
- [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature NormalizedFeature.pm, 1.23, 1.24
Lincoln Stein
- [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph generic.pm, 1.46, 1.47
Lincoln Stein
- [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph generic.pm, 1.47, 1.48
Lincoln Stein
- [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph fixedwidth.pm, NONE, 1.1
Lincoln Stein
- [Bioperl-guts-l] bioperl-live/Bio/SearchIO blast.pm,1.110,1.111
Senduran Balasubramaniam
- [Bioperl-guts-l] [Bug 2189] New: parsing of BLAST v2.2.15 multiquery reports does not generate Hits
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2190] New: Bio::Biblio::IO breaks with some PubMed entries
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-live/Bio/DB/Biblio eutils.pm,1.12,1.13
Brian Osborne
- [Bioperl-guts-l] bioperl-live/Bio/SearchIO SearchResultEventBuilder.pm, 1.43, 1.44
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/SearchIO blast.pm,1.111,1.112
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t/data test.infernal,NONE,1.1
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t rnamotif.t,1.7,1.8
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/Tools Infernal.pm,1.3,1.4
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/Tools RNAMotif.pm,1.14,1.15
Christopher John Fields
- [Bioperl-guts-l] [Bug 2191] New: Bio::Tree::Node is missing delete_edge function
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-live/Bio/Tools/Run WrapperBase.pm, 1.27, 1.28
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t WrapperBase.t,1.1,1.2
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/Tools/Run WrapperBase.pm, 1.28, 1.29
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t WrapperBase.t,1.2,1.3
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t/data sprintf.rnamotif,1.1,1.2
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t/data trna.strict.rnamotif,1.1,1.2
Christopher John Fields
- [Bioperl-guts-l] bioperl-run MANIFEST.SKIP,1.2,NONE
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run Njtree.t,1.1,NONE
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/t Njtree.t,NONE,1.1
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run Makefile.PL,1.23,1.24
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run Build.PL,1.2,1.3
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-db MANIFEST.SKIP,1.1,NONE
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-db Build.PL,1.4,1.5
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-db Makefile.PL,1.14,1.15
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-network Build.PL,1.2,1.3
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-network Makefile.PL,1.13,1.14
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph xyplot.pm, 1.31, 1.32
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/Bio/Tools/Run WrapperBase.pm, 1.29, 1.30
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/Tools/Run WrapperBase.pm, 1.30, 1.31
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/Bio/Align Utilities.pm,1.23,1.24
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/Align Utilities.pm,1.24,1.25
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t alignUtilities.t,1.3,1.4
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/SeqFeature Annotated.pm, 1.36, 1.37
Malcom Cook
- [Bioperl-guts-l] bioperl-live/t SeqFeature.t,1.47,1.48
Malcom Cook
- [Bioperl-guts-l] bioperl-network/Bio/Network/IO psi.pm,1.13,1.14
Brian Osborne
- [Bioperl-guts-l] bioperl-network/t/data human_small-01.xml, NONE, 1.1
Brian Osborne
- [Bioperl-guts-l] bioperl-live/t/data longnames.aln, NONE, 1.1 longnames.dnd, NONE, 1.1
Weigang Qiu
- [Bioperl-guts-l] bioperl-live ModuleBuildBioperl.pm,1.24,1.25
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-network/t IO_psi10.t, NONE, 1.1 IO_psi25.t, NONE, 1.1 ProteinNet.t, 1.7, 1.8 IO_psi.t, 1.3, NONE
Brian Osborne
- [Bioperl-guts-l] bioperl-network/Bio/Network/IO psi10.pm, NONE, 1.1 psi.pm, 1.14, NONE
Brian Osborne
- [Bioperl-guts-l] bioperl-network/t/data horse_small.xml,NONE,1.1
Brian Osborne
- [Bioperl-guts-l] bioperl-network/t/data horse_small.xml,1.1,NONE
Brian Osborne
- [Bioperl-guts-l] bioperl-network/t/data sulso_small.xml,NONE,1.1
Brian Osborne
- [Bioperl-guts-l] bioperl-live Build.PL,1.16,1.17
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live ModuleBuildBioperl.pm, 1.5.2.14, 1.5.2.15 Build.PL, 1.5.2.6, 1.5.2.7
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/Bio/Root Version.pm,1.9.4.6,1.9.4.7
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/Bio/FeatureIO bed.pm,1.9,1.10
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature Store.pm, 1.26, 1.27
Lincoln Stein
- [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.26, 1.27
Lincoln Stein
- [Bioperl-guts-l] bioperl-live/Bio/Graphics Panel.pm,1.129,1.130
Lincoln Stein
- [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store berkeleydb.pm, 1.13, 1.14 memory.pm, 1.9, 1.10
Lincoln Stein
- [Bioperl-guts-l] [Bug 2192] New: Bio::Structure::Entry get_residues() method residue leak bug
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2159] parsing xml blast results hit-description
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-live/Bio/SeqIO strider.pm,1.10,1.11
Malcom Cook
- [Bioperl-guts-l] bioperl-live/t SearchIO.t,1.106,1.107
Christopher John Fields
- [Bioperl-guts-l] [Bug 2193] New: "Undefined sub-sequence" exception parsing NCBI blastp report
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phast PhastCons.pm, 1.3, 1.4
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/t PhastCons.t,1.1,1.2
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo PhyloBase.pm, 1.2, 1.3
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/t genbank.t,1.17,1.18
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature Segment.pm, 1.15, 1.16
Jason Stajich
- [Bioperl-guts-l] bioperl-live/Bio/Structure/IO pdb.pm,1.19,1.20
Christopher John Fields
- [Bioperl-guts-l] [Bug 2194] New: ModuleBuildBioperl.pm complains when
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-network/t/data 12082530.xls,NONE,1.1
Brian Osborne
- [Bioperl-guts-l] [Bug 2195] New: SeqIO : parse ORGANISM from GenBank and bracket on differents lines
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2196] New: Bug in scf.pm code that fails when no comments present
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-live ModuleBuildBioperl.pm,1.25,1.26
Senduran Balasubramaniam
- [Bioperl-guts-l] [Bug 2197] New: Bio::Species throws if species name is synonym of lineage
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-live/t scf.t,1.12,1.13
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t/data 13-pilE-F.scf,NONE,1.1
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/SeqIO scf.pm,1.40,1.41
Christopher John Fields
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Hyphy Modeltest.pm, 1.2, 1.3
Albert Vilella
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Hyphy FEL.pm, 1.2, 1.3
Albert Vilella
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Hyphy REL.pm, 1.2, 1.3
Albert Vilella
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Hyphy SLAC.pm, 1.4, 1.5
Albert Vilella
- [Bioperl-guts-l] [Bug 2198] New: Alignment sort method
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] bioperl-live/Bio/Tools Genomewise.pm,1.9,1.10
Jason Stajich
- [Bioperl-guts-l] bioperl-live/Bio SimpleAlign.pm,1.125,1.126
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio Species.pm,1.47,1.48
Christopher John Fields
- [Bioperl-guts-l] [Bug 2092] Can't store proteins with species using bioperl-db
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] [Bug 2199] New: SeqIO : parse ORGANISM from GenBank and bracket on differents lines
bugzilla-daemon at portal.open-bio.org
- [Bioperl-guts-l] bioperl-live/Bio/SeqIO genbank.pm,1.161,1.162
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t/data AF305198.gb,NONE,1.1
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t genbank.t,1.18,1.19
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/SeqIO genbank.pm,1.162,1.163
Christopher John Fields
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Lagan.pm, 1.16, 1.17
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phast PhastCons.pm, 1.4, 1.5
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/Bio/SeqIO chadoxml.pm,1.22,1.23
Scott Cain
- [Bioperl-guts-l] bioperl-live/t SimpleAlign.t,1.49,1.50
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/SearchIO blastxml.pm,1.45,1.46
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/t SearchIO.t,1.107,1.108
Christopher John Fields
- [Bioperl-guts-l] bioperl-live/Bio/Graphics FeatureBase.pm, 1.19, 1.20 Glyph.pm, 1.134, 1.135
Lincoln Stein
- [Bioperl-guts-l] bioperl-live/Bio/Graphics FeatureBase.pm, 1.20, 1.21
Lincoln Stein
- [Bioperl-guts-l] bioperl-live/Bio/Annotation SimpleValue.pm, 1.21, 1.22
Malcom Cook
- [Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.27, 1.28
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phast PhastCons.pm, 1.5, 1.6
Senduran Balasubramaniam
- [Bioperl-guts-l] bioperl-live/Bio SimpleAlign.pm,1.126,1.127
Jason Stajich
Last message date:
Wed Jan 31 13:07:36 EST 2007
Archived on: Wed Jan 31 13:07:38 EST 2007
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