Tracking CVS commits

CVS commits for biopython

biopython/DEPRECATED modified

revision 1.60
date: 2009/06/22 13:02:30; author: peterc; state: Exp; lines: +5 -0
Deprecating psycopg support in BioSQL code (use psycopg2 instead)

biopython/MANIFEST.in modified

revision 1.33
date: 2009/06/23 13:30:05; author: peterc; state: Exp; lines: +1 -0
Include the biopython.jpg file in the manifest

biopython/NEWS modified

revision 1.86
date: 2009/06/23 11:36:58; author: peterc; state: Exp; lines: +4 -0
Adding a note that the tutorial and unit tests have also seen updates

biopython/README modified

revision 1.51
date: 2009/06/23 10:50:47; author: peterc; state: Exp; lines: +22 -22
Updated dependencies in README file, and mentioned the application note

biopython/Bio/Seq.py modified

revision 1.81
date: 2009/06/23 11:13:50; author: peterc; state: Exp; lines: +35 -19
Implement __contains__ for using the in keyword with a Seq object (Bug 2853). Added comment about comparison methods (see also section in the tutorial)

biopython/Bio/SeqFeature.py modified

revision 1.20
date: 2009/06/22 15:44:10; author: chapmanb; state: Exp; lines: +7 -7
Allow annotations, letter_annotations in SeqRecords. Allow qualifiers and sub_features to SeqFeatures: Bug 2841.

biopython/Bio/SeqRecord.py modified

revision 1.37
date: 2009/06/22 15:44:10; author: chapmanb; state: Exp; lines: +18 -13
Allow annotations, letter_annotations in SeqRecords. Allow qualifiers and sub_features to SeqFeatures: Bug 2841.

biopython/Bio/__init__.py modified

revision 1.36
date: 2009/06/23 11:03:19; author: peterc; state: Exp; lines: +1 -1
Bumping version number to Biopython 1.51b

biopython/Bio/Application/__init__.py modified

revision 1.22
date: 2009/06/22 12:50:37; author: peterc; state: Exp; lines: +5 -5
Removed trailing space from command line wrapper output

biopython/Bio/Blast/NCBIWWW.py modified

revision 1.57
date: 2009/06/19 16:25:53; author: peterc; state: Exp; lines: +4 -0
Cope with newline-newline place holder page while waiting for BLAST results, report and fix from Cymon Cox via mailing list

biopython/Bio/Clustalw/__init__.py modified

revision 1.30
date: 2009/06/22 18:08:38; author: peterc; state: Exp; lines: +11 -2
Bio.Clustalw is now effectively obsolete

biopython/Bio/GFF/__init__.py modified

revision 1.10
date: 2009/06/23 14:05:26; author: peterc; state: Exp; lines: +3 -5
Use Seq object translate method instead of deprecated Bio.Translate

biopython/Bio/Restriction/Restriction.py modified

revision 1.12
date: 2009/06/23 11:08:45; author: peterc; state: Exp; lines: +1 -1
Fix from Frédéric Sohm for Bug 2856

biopython/Bio/SeqIO/QualityIO.py modified

revision 1.27
date: 2009/06/23 14:24:35; author: peterc; state: Exp; lines: +16 -4
Fixed a typo, added another doctest

biopython/Bio/SeqIO/__init__.py modified

revision 1.54
date: 2009/06/22 13:21:32; author: peterc; state: Exp; lines: +1 -1
Fixed stupid error mapping output formats

biopython/BioSQL/BioSeqDatabase.py modified

revision 1.26
date: 2009/06/22 13:02:30; author: peterc; state: Exp; lines: +8 -0
Deprecating psycopg support in BioSQL code (use psycopg2 instead)

biopython/Doc/Tutorial.tex modified

revision 1.262
date: 2009/06/23 12:08:57; author: peterc; state: Exp; lines: +2 -2
Fix for hevea, already worked on pdflatex

biopython/Tests/test_Dialign_tool.py modified

revision 1.6
date: 2009/06/22 12:50:37; author: peterc; state: Exp; lines: +6 -4
Removed trailing space from command line wrapper output

biopython/Tests/test_Emboss.py modified

revision 1.25
date: 2009/06/22 12:50:37; author: peterc; state: Exp; lines: +2 -2
Removed trailing space from command line wrapper output

biopython/Tests/test_Mafft_tool.py modified

revision 1.4
date: 2009/06/22 12:50:37; author: peterc; state: Exp; lines: +11 -4
Removed trailing space from command line wrapper output

biopython/Tests/test_Muscle_tool.py modified

revision 1.10
date: 2009/06/22 12:50:37; author: peterc; state: Exp; lines: +10 -9
Removed trailing space from command line wrapper output

biopython/Tests/test_NCBITextParser.py modified

revision 1.4
date: 2009/06/21 04:55:00; author: mdehoon; state: Exp; lines: +594 -0
Adding a test for plain-text Blast output with multiple records.

biopython/Tests/test_Prank_tool.py modified

revision 1.8
date: 2009/06/22 12:50:37; author: peterc; state: Exp; lines: +4 -3
Removed trailing space from command line wrapper output

biopython/Tests/test_Probcons_tool.py modified

revision 1.2
date: 2009/06/23 11:41:19; author: peterc; state: Exp; lines: +6 -7
Updates reflecting trimmed command line strings

biopython/Tests/test_SeqIO.py modified

revision 1.58
date: 2009/06/19 17:25:04; author: peterc; state: Exp; lines: +2 -2
Sort the format dictionaries for consist ordering across platforms

biopython/Tests/test_SeqIO_features.py modified

revision 1.18
date: 2009/06/22 15:44:10; author: chapmanb; state: Exp; lines: +38 -0
Allow annotations, letter_annotations in SeqRecords. Allow qualifiers and sub_features to SeqFeatures: Bug 2841.

biopython/Tests/test_TCoffee_tool.py modified

revision 1.2
date: 2009/06/23 11:41:19; author: peterc; state: Exp; lines: +4 -4
Updates reflecting trimmed command line strings

biopython/Tests/test_translate.py modified

revision 1.6
date: 2009/06/19 17:16:46; author: peterc; state: Exp; lines: +18 -53
Use Seq methods instead of deprecated Bio.Translate, all old tests retained except for the back translation

biopython/Tests/Blast/bt103 added

revision 1.1
date: 2009/06/21 04:55:01; author: mdehoon; state: Exp;
Adding a test for plain-text Blast output with multiple records.

biopython/Tests/output/test_SeqIO modified

revision 1.42
date: 2009/06/22 13:53:40; author: peterc; state: Exp; lines: +191 -191
Updating after some FASTQ tweaks

biopython/Tests/output/test_translate modified

revision 1.2
date: 2009/06/19 17:16:46; author: peterc; state: Exp; lines: +0 -2
Use Seq methods instead of deprecated Bio.Translate, all old tests retained except for the back translation