python.bio.devel (date)

July 31, 2008

[Bug 2560] Adding BLAST support to Bio.AlignIO, bugzilla-daemon
[Bug 2560] New: Adding BLAST support to Bio.AlignIO, bugzilla-daemon

July 30, 2008

[Bug 2558] Bio.Nexus chokes on TRANSLATE block with superfluous comma, bugzilla-daemon
[Bug 2558] Bio.Nexus chokes on TRANSLATE block with superfluous comma, bugzilla-daemon
[Bug 2557] AlignIO::write fails when delegating to SeqIO::write, bugzilla-daemon
[Bug 2558] New: AlignIO nexus parsing chokes on superfluous comma, bugzilla-daemon
[Bug 2557] New: AlignIO::write fails when delegating to SeqIO::write, bugzilla-daemon

July 28, 2008

[Bug 2554] Creating an Alignment from a list of SeqRecord objects, bugzilla-daemon
[Bug 2554] Creating an Alignment from a list of SeqRecord objects, bugzilla-daemon
[Bug 2553] Adding SeqRecord objects to an alignment (append or extend), bugzilla-daemon
[Bug 2554] New: Creating an Alignment from a list of SeqRecord objects, bugzilla-daemon
[Bug 2507] Adding __getitem__ to SeqRecord for element access and slicing, bugzilla-daemon
[Bug 1944] Align.Generic adding iterator and more, bugzilla-daemon
[Bug 2553] New: Adding SeqRecord objects to an alignment (append or extend), bugzilla-daemon
[Bug 2552] New: Adding alignments, bugzilla-daemon
[Bug 2507] Adding __getitem__ to SeqRecord for element access and slicing, bugzilla-daemon
[Bug 2551] New: Adding advanced __getitem__ to generic alignment, e.g. align[1:2, 5:-5], bugzilla-daemon
[Bug 1944] Align.Generic adding iterator and more, bugzilla-daemon

July 27, 2008

[Bug 2550] Alphabet problems when adding sequences, bugzilla-daemon
[Bug 2550] Alphabet problems when adding sequences, bugzilla-daemon
[Bug 2550] Alphabet problems when adding sequences, bugzilla-daemon
[Bug 2550] Alphabet problems when adding sequences, bugzilla-daemon
[Bug 2550] New: Alphabet problems when adding sequences, bugzilla-daemon

July 26, 2008

[Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O, bugzilla-daemon

July 25, 2008

Re: Removing the deprecated Bio.WWW modules, Peter
Updating the installation instructions, Peter
Re: Removing the deprecated Bio.WWW modules, Michiel de Hoon

July 24, 2008

Removing the deprecated Bio.WWW modules, Peter

July 23, 2008

[Bug 2543] Bio.Nexus.Trees can't handle named ancestors, bugzilla-daemon
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon

July 22, 2008

[Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq), bugzilla-daemon
Re: Bio.KDTree, Peter
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
Re: Modules to be removed from Biopython, Peter
Bio.KDTree, Michiel de Hoon
[Bug 2454] Iterators can't use file-like objects, bugzilla-daemon

July 21, 2008

[Bug 2547] Translation of ambiguous codons like NNN and TAN, bugzilla-daemon
[Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq), bugzilla-daemon
[Bug 2547] Translation of ambiguous codons like NNN and TAN, bugzilla-daemon
[Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O, bugzilla-daemon
[Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O, bugzilla-daemon
[Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O, bugzilla-daemon
[Bug 2547] Translation of ambiguous codons like NNN and TAN, bugzilla-daemon
[Bug 2547] Translation of ambiguous codons like NNN and TAN, bugzilla-daemon

July 20, 2008

[Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O, bugzilla-daemon
[Bug 2547] Translation of ambiguous codons like NNN and TAN, bugzilla-daemon
[Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O, bugzilla-daemon
[Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O, bugzilla-daemon
[Bug 2548] New: Updating IUPACData and ExtendedIUPACProtein for U and O, bugzilla-daemon
Re: [Bug 2530] Bio.Seq.translate() treats invalid codons as stops, Peter
[Bug 2530] Bio.Seq.translate() treats invalid codons as stops, bugzilla-daemon
[Bug 2547] New: Translation of ambiguous codons like NNN and TAN, bugzilla-daemon

July 19, 2008

[Bug 2530] Bio.Seq.translate() treats invalid codons as stops, bugzilla-daemon
[Bug 2530] Bio.Seq.translate() treats invalid codons as stops, bugzilla-daemon
[Bug 2530] Bio.Seq.translate() treats invalid codons as stops, bugzilla-daemon
[Bug 2530] Bio.Seq.translate() treats invalid codons as stops, bugzilla-daemon
[Bug 2530] Bio.Seq.translate() treats invalid codons as stops, bugzilla-daemon
[Bug 2530] Bio.Seq.translate() treats invalid codons as stops, bugzilla-daemon
[Bug 2532] Using IUPAC alphabets in mixed case Seq objects, bugzilla-daemon
[Bug 2530] Bio.Seq.translate() treats invalid codons as stops, bugzilla-daemon
[Bug 2448] Bio.EUtils can't handle accented author names, bugzilla-daemon
[Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq), bugzilla-daemon
[Bug 1999] new frame translation method, bugzilla-daemon

July 17, 2008

Re: Biopython presentation at BOSC2008, Tiago Antão
Re: Biopython presentation at BOSC2008, Peter
Biopython presentation at BOSC2008, Tiago Antão

July 16, 2008

[Bug 2544] Bio.GenBank and SeqFeature improvements, bugzilla-daemon
[Bug 2454] Iterators can't use file-like objects, bugzilla-daemon
Re: Dump file in Bio/Saf/__init__.py, Peter
[Bug 2454] Iterators can't use file-like objects, bugzilla-daemon
Re: Dump file in Bio/Saf/__init__.py, Peter
Re: Dump file in Bio/Saf/__init__.py, Michiel de Hoon
Re: Modules to be removed from Biopython, Peter
[Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq), bugzilla-daemon
Dump file in Bio/Saf/__init__.py, Peter
[Bug 2544] Bio.GenBank and SeqFeature improvements, bugzilla-daemon
[Bug 2544] New: Bio.SeqIO improvements, bugzilla-daemon

July 15, 2008

[Bug 2351] Make Seq more like a string, even subclass string?, bugzilla-daemon

July 14, 2008

[Bug 2543] Bio.Nexus.Trees can't handle named ancestors, bugzilla-daemon

July 13, 2008

[Bug 2543] New: Bio.Nexus.Trees can't handle named ancestors, bugzilla-daemon

July 12, 2008

Deprecating the HTML parser in Bio.Blast.NCBIWWW, Peter

July 11, 2008

[Bug 2542] AlignInfo.py fails a test, bugzilla-daemon
[Bug 2443] Specifying the alphabet in Bio.SeqIO and Bio.AlignIO, bugzilla-daemon
[Bug 2542] AlignInfo.py fails a test, bugzilla-daemon
[Bug 2542] AlignInfo.py fails a test, bugzilla-daemon
[Bug 2454] Iterators can't use file-like objects, bugzilla-daemon
[Bug 2542] AlignInfo.py fails a test, bugzilla-daemon
Checking alphabet argument in alignments, Peter
[Bug 2542] AlignInfo.py fails a test, bugzilla-daemon
[Bug 2542] AlignInfo.py fails a test, bugzilla-daemon
[Bug 2542] New: AlignInfo.py fails a test, bugzilla-daemon

July 10, 2008

[Bug 2533] Support for simple "tab" format in Bio.SeqIO, bugzilla-daemon
[Bug 2454] Iterators can't use file-like objects, bugzilla-daemon

July 09, 2008

[Bug 2508] NCBIStandalone.blastall: provide support for '-F F' and make it safe, bugzilla-daemon
[Bug 2508] NCBIStandalone.blastall: provide support for '-F F' and make it safe, bugzilla-daemon
[Bug 2508] NCBIStandalone.blastall: provide support for '-F F' and make it safe, bugzilla-daemon
[Bug 2454] Iterators can't use file-like objects, bugzilla-daemon
[Bug 2454] Iterators can't use file-like objects, bugzilla-daemon
[Bug 2454] Iterators can't use file-like objects, bugzilla-daemon
[Bug 2454] Iterators can't use file-like objects, bugzilla-daemon
Simple __getitem__ for Alignments, Peter
Re: Bug 2533 - Support for simple "tab" format in Bio.SeqIO, Peter
Re: Bug 2533 - Support for simple "tab" format in Bio.SeqIO, Leighton Pritchard
Re: Bug 2533 - Support for simple "tab" format in Bio.SeqIO, Peter

July 08, 2008

Re: Alignment problem. bug?, Sebastian Bassi
Re: Alignment problem. bug?, Peter
Re: Alignment problem. bug?, Sebastian Bassi
Re: Bio.Sequencing, Peter
Re: Bio.Sequencing, Frank Kauff
Bio.Sequencing, Michiel de Hoon
Re: Alignment problem. bug?, Peter
[Bug 2538] _security_check_parameters assumes all arguments are strings, bugzilla-daemon
Re: Alignment problem. bug?, Peter
[Bug 2538] _security_check_parameters assumes all arguments are strings, bugzilla-daemon

July 07, 2008

Alignment problem. bug?, Sebastian Bassi
[Bug 2538] New: _security_check_parameters assumes all arguments are strings, bugzilla-daemon
Re: NCBIStandalon not compatible with previous versions, is this a bug?, Peter
[Bug 2448] Bio.EUtils can't handle accented author names, bugzilla-daemon
[Bug 2448] Bio.EUtils can't handle accented author names, bugzilla-daemon
[Bug 2447] EUtils cannot parse PubMed XML for ACS journals, bugzilla-daemon

July 06, 2008

NCBIStandalon not compatible with previous versions, is this a bug?, Sebastian Bassi
Biopython release 1.47, Michiel de Hoon

July 05, 2008

CVS freeze for release 1.47, Michiel de Hoon

July 04, 2008

Re: Bio.IntelliGenetics, Peter
Re: Bio.IntelliGenetics, Michiel de Hoon
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
What happened to Biopython 1.46?, Peter

July 03, 2008

[Bug 2531] Nexus and fasta parsers have a problem with identical taxa names, bugzilla-daemon
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
[Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
[Bug 2531] Nexus and fasta parsers have a problem with identical taxa names, bugzilla-daemon
[Bug 2531] Nexus and fasta parsers have a problem with identical taxa names, bugzilla-daemon

July 02, 2008

[Bug 2508] NCBIStandalone.blastall: provide support for '-F F' and make it safe, bugzilla-daemon
[Bug 2535] Support for PIR / NBRF format in Bio.SeqIO, bugzilla-daemon
[Bug 2535] Support for PIR / NBRF format in Bio.SeqIO, bugzilla-daemon
[Bug 2535] New: Support for PIR / NBRF format in Bio.SeqIO, bugzilla-daemon
Re: Bio.IntelliGenetics, Michiel de Hoon
Re: Bio.IntelliGenetics, Peter
[Bug 2469] requires_wise.py fails on Windows (test suite), bugzilla-daemon
[Bug 2524] Handle missing libraries like TextTools in run_tests.py, bugzilla-daemon
Re: Bio.IntelliGenetics, Michiel de Hoon
Re: Questions about the NEXUS format, Peter
Bio.IntelliGenetics, Peter
Re: Bio.IntelliGenetics, Peter
Re: Questions about the NEXUS format, Frank Kauff
Re: Bio.IntelliGenetics, Peter
Bio.IntelliGenetics, Michiel de Hoon
Questions about the NEXUS format, Peter
Bug 2533 - Support for simple "tab" format in Bio.SeqIO, Peter
Re: Catching more error conditions in Bio.Entrez, Peter
Re: Catching more error conditions in Bio.Entrez, Sean Davis
Catching more error conditions in Bio.Entrez, Peter

July 01, 2008

[Bug 2533] Support for simple "tab" format in Bio.SeqIO, bugzilla-daemon
[Bug 2533] Support for simple "tab" format in Bio.SeqIO, bugzilla-daemon
[Bug 2533] New: Support for simple "tab" format in Bio.SeqIO, bugzilla-daemon
[Bug 2532] Using IUPAC alphabets in mixed case Seq objects, bugzilla-daemon
[Bug 2531] Nexus and fasta parsers have a problem with identical taxa names, bugzilla-daemon
[Bug 2531] Nexus and fasta parsers have a problem with identical taxa names, bugzilla-daemon
[Bug 2531] Nexus and fasta parsers have a problem with identical taxa names, bugzilla-daemon