python.bio.devel (thread)

[Bug 2560] New: Adding BLAST support to Bio.AlignIO, bugzilla-daemon
- [Bug 2560] Adding BLAST support to Bio.AlignIO, bugzilla-daemon
[Bug 2558] New: AlignIO nexus parsing chokes on superfluous comma, bugzilla-daemon
- [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] New: AlignIO::write fails when delegating to SeqIO::write, bugzilla-daemon
- [Bug 2557] AlignIO::write fails when delegating to SeqIO::write, bugzilla-daemon
[Bug 2554] New: 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 2554] Creating an Alignment from a list of SeqRecord objects, bugzilla-daemon
[Bug 2553] New: Adding SeqRecord objects to an alignment (append or extend), bugzilla-daemon
- [Bug 2553] 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 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
- [Bug 1944] Align.Generic adding iterator and more, bugzilla-daemon
[Bug 2550] New: 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] Alphabet problems when adding sequences, bugzilla-daemon
Updating the installation instructions, Peter
Removing the deprecated Bio.WWW modules, Peter
- Re: Removing the deprecated Bio.WWW modules, Michiel de Hoon
  - Re: Removing the deprecated Bio.WWW modules, Peter
Bio.KDTree, Michiel de Hoon
- Re: Bio.KDTree, Peter
[Bug 2548] New: 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 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 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] New: Translation of ambiguous codons like NNN and TAN, 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
- [Bug 2547] Translation of ambiguous codons like NNN and TAN, 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
[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 2530] Bio.Seq.translate() treats invalid codons as stops, 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 1999] new frame translation method, bugzilla-daemon
Biopython presentation at BOSC2008, Tiago Antão
- Re: Biopython presentation at BOSC2008, Peter
- Re: Biopython presentation at BOSC2008, Tiago Antão
Re: Modules to be removed from Biopython, Peter
- Re: Modules to be removed from Biopython, Peter
[Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq), bugzilla-daemon
- [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq), bugzilla-daemon
- [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq), bugzilla-daemon
- [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq), bugzilla-daemon
Dump file in Bio/Saf/__init__.py, Peter
- Re: Dump file in Bio/Saf/__init__.py, Michiel de Hoon
  - Re: Dump file in Bio/Saf/__init__.py, Peter
    - Re: Dump file in Bio/Saf/__init__.py, Peter
[Bug 2544] New: Bio.SeqIO improvements, bugzilla-daemon
- [Bug 2544] Bio.GenBank and SeqFeature improvements, bugzilla-daemon
- [Bug 2544] Bio.GenBank and SeqFeature improvements, bugzilla-daemon
[Bug 2351] Make Seq more like a string, even subclass string?, bugzilla-daemon
[Bug 2543] New: Bio.Nexus.Trees can't handle named ancestors, bugzilla-daemon
- [Bug 2543] Bio.Nexus.Trees can't handle named ancestors, bugzilla-daemon
- [Bug 2543] Bio.Nexus.Trees can't handle named ancestors, bugzilla-daemon
Deprecating the HTML parser in Bio.Blast.NCBIWWW, Peter
[Bug 2443] Specifying the alphabet in Bio.SeqIO and Bio.AlignIO, bugzilla-daemon
Checking alphabet argument in alignments, Peter
[Bug 2542] New: AlignInfo.py fails a test, bugzilla-daemon
- [Bug 2542] AlignInfo.py fails a test, bugzilla-daemon
- [Bug 2542] AlignInfo.py fails a test, bugzilla-daemon
- [Bug 2542] AlignInfo.py fails a test, bugzilla-daemon
- [Bug 2542] AlignInfo.py fails a test, 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 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
- [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
Bio.Sequencing, Michiel de Hoon
- Re: Bio.Sequencing, Frank Kauff
- Re: Bio.Sequencing, Peter
Alignment problem. bug?, Sebastian Bassi
- Re: Alignment problem. bug?, Peter
  - Re: Alignment problem. bug?, Peter
    - Re: Alignment problem. bug?, Sebastian Bassi
    - Re: Alignment problem. bug?, Peter
    - Re: Alignment problem. bug?, Sebastian Bassi
[Bug 2538] New: _security_check_parameters assumes all arguments are strings, bugzilla-daemon
- [Bug 2538] _security_check_parameters assumes all arguments are strings, bugzilla-daemon
- [Bug 2538] _security_check_parameters assumes all arguments are strings, bugzilla-daemon
[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 2448] Bio.EUtils can't handle accented author names, bugzilla-daemon
[Bug 2447] EUtils cannot parse PubMed XML for ACS journals, bugzilla-daemon
NCBIStandalon not compatible with previous versions, is this a bug?, Sebastian Bassi
- Re: NCBIStandalon not compatible with previous versions, is this a bug?, Peter
Biopython release 1.47, Michiel de Hoon
CVS freeze for release 1.47, Michiel de Hoon
What happened to Biopython 1.46?, Peter
[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
- [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
- [Bug 2227] Writing Nexus files with Bio.SeqIO, bugzilla-daemon
- [Bug 2227] Writing Nexus files with Bio.SeqIO, 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 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 2535] New: Support for PIR / NBRF format in Bio.SeqIO, 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 2469] requires_wise.py fails on Windows (test suite), bugzilla-daemon
[Bug 2524] Handle missing libraries like TextTools in run_tests.py, bugzilla-daemon
Bio.IntelliGenetics, Michiel de Hoon
- Re: Bio.IntelliGenetics, Peter
  - Re: Bio.IntelliGenetics, Peter
  - Bio.IntelliGenetics, Peter
  - Re: Bio.IntelliGenetics, Michiel de Hoon
    - Re: Bio.IntelliGenetics, Peter
- Re: Bio.IntelliGenetics, Michiel de Hoon
- Re: Bio.IntelliGenetics, Michiel de Hoon
  - Re: Bio.IntelliGenetics, Peter
Questions about the NEXUS format, Peter
- Re: Questions about the NEXUS format, Frank Kauff
  - Re: Questions about the NEXUS format, Peter
Bug 2533 - Support for simple "tab" format in Bio.SeqIO, 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
Catching more error conditions in Bio.Entrez, Peter
- Re: Catching more error conditions in Bio.Entrez, Sean Davis
  - Re: Catching more error conditions in Bio.Entrez, Peter
[Bug 2533] New: Support for simple "tab" format in Bio.SeqIO, bugzilla-daemon
- [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] Support for simple "tab" format in Bio.SeqIO, bugzilla-daemon
[Bug 2532] Using IUPAC alphabets in mixed case Seq objects, 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
- [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