python.bio.devel (thread)

[Bug 2532] New: Using IUPAC alphabets in mixed case Seq objects, bugzilla-daemon
- [Bug 2532] Using IUPAC alphabets in mixed case Seq objects, bugzilla-daemon
Bug 2531 - Bio.Nexus problem with file with repeated id, Peter
[Bug 2531] New: 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
- [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
  - Re: [Bug 2531] Nexus and fasta parsers have a problem with identical taxa names, Frank Kauff
- [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
New release 1.46, Michiel de Hoon
- Re: New release 1.46, Peter
CVS freeze for release 1.46, Michiel de Hoon
Failing unit tests under Windows, Peter
[Bug 2530] New: 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
Bio.GenBank.NCBIDictionary, Bio.PubMed.Dictionary, Michiel de Hoon
[BioPython] Entrez, Peter
Recent Bio.Nexus updates, Peter
- Re: Recent Bio.Nexus updates, Frank Kauff
  - Re: Recent Bio.Nexus updates, Peter
Modules to be removed from Biopython, Michiel de Hoon
- Re: Modules to be removed from Biopython, Peter
  - Re: Modules to be removed from Biopython, Peter
Removing obsolete bits of the Tutorial, Peter
- Re: Removing obsolete bits of the Tutorial, Michiel de Hoon
  - Re: Removing obsolete bits of the Tutorial, Peter
    - Re: Removing obsolete bits of the Tutorial, Michiel de Hoon
Bio.AlignIO and Bio.Entrez documentation, Peter
[Bug 2090] Blast.NCBIStandalone BlastParser fails with blastall 2.2.14, bugzilla-daemon
[BioPython] Bio.ECell, anybody?, Michiel de Hoon
New release, Michiel de Hoon
- Re: New release, Peter
  - Re: New release, Peter
  - Re: New release, Michiel de Hoon
- New release, Michiel de Hoon
  - Re: New release, Peter Cock
Re: [BioPython] Fwd: NCBI Abuse Activity with BioPython, Peter
- Re: [BioPython] Fwd: NCBI Abuse Activity with BioPython, Peter
  - Re: [BioPython] Fwd: NCBI Abuse Activity with BioPython, Peter
[Bug 2499] Bio.Blast.NCBIXML cannot handle XML without date in BlastOutput_version, bugzilla-daemon
NCBI Abuse activity with Biopython, Michiel de Hoon
- Re: NCBI Abuse activity with Biopython, Andrew Dalke
  - Re: NCBI Abuse activity with Biopython, Peter Cock
    - Re: NCBI Abuse activity with Biopython, Andrew Dalke
    - Re: NCBI Abuse activity with Biopython, Michiel de Hoon
    - Re: NCBI Abuse activity with Biopython, Peter
    - Re: NCBI Abuse activity with Biopython, Michiel de Hoon
    - Re: NCBI Abuse activity with Biopython, Michiel de Hoon
    - Re: NCBI Abuse activity with Biopython, Peter
    - Re: NCBI Abuse activity with Biopython, Michiel de Hoon
    - Re: NCBI Abuse activity with Biopython, Peter
    - Re: NCBI Abuse activity with Biopython, Andrew Dalke
    - Re: NCBI Abuse activity with Biopython, Peter
    - Re: NCBI Abuse activity with Biopython, Michiel de Hoon
    - Re: NCBI Abuse activity with Biopython, Peter
    - Re: NCBI Abuse activity with Biopython, Michiel de Hoon
    - Re: NCBI Abuse activity with Biopython, Peter
[Bug 2529] New: NCBI BLAST XML parser does not support the online blast version 2.2.18+, bugzilla-daemon
- [Bug 2529] NCBI BLAST XML parser does not support the online blast version 2.2.18+, bugzilla-daemon
- [Bug 2529] NCBI BLAST XML parser does not support the online blast version 2.2.18+, bugzilla-daemon
- [Bug 2529] NCBI BLAST XML parser does not support the online blast version 2.2.18+, bugzilla-daemon
[BioPython] Bio.SCOP.FileIndex, Michiel de Hoon
- Re: [BioPython] Bio.SCOP.FileIndex, Peter
  - Re: [BioPython] Bio.SCOP.FileIndex, Michiel de Hoon
    - Re: [BioPython] Bio.SCOP.FileIndex, Michiel de Hoon
[Bug 2528] New: NCBIStandalone.blastall(): Replace os.popen3 with subprocess.Popen, bugzilla-daemon
- [Bug 2528] NCBIStandalone.blastall(): Replace os.popen3 with subprocess.Popen, bugzilla-daemon
- [Bug 2528] NCBIStandalone.blastall(): Replace os.popen3 with subprocess.Popen, bugzilla-daemon
- [Bug 2528] NCBIStandalone.blastall(): Replace os.popen3 with subprocess.Popen, bugzilla-daemon
- [Bug 2528] NCBIStandalone.blastall(): Replace os.popen3 with subprocess.Popen, bugzilla-daemon
- [Bug 2528] NCBIStandalone.blastall(): Replace os.popen3 with subprocess.Popen, bugzilla-daemon
[Bug 2527] New: Bug in NCBIXML.py in _end_BlastOutput_version(), bugzilla-daemon
- [Bug 2527] Bug in NCBIXML.py in _end_BlastOutput_version(), bugzilla-daemon
- [Bug 2527] Bug in NCBIXML.py in _end_BlastOutput_version(), bugzilla-daemon
- [Bug 2527] Bug in NCBIXML.py in _end_BlastOutput_version(), bugzilla-daemon
- [Bug 2527] Bug in NCBIXML.py in _end_BlastOutput_version(), bugzilla-daemon
- [Bug 2527] Bug in NCBIXML.py in _end_BlastOutput_version(), bugzilla-daemon
Bio.SCOP, Michiel de Hoon
- Re: Bio.SCOP, Peter
[Bug 2375] Coalescent support through Simcoal2, bugzilla-daemon
- [Bug 2375] Coalescent support through Simcoal2, bugzilla-daemon
- [Bug 2375] Coalescent support through Simcoal2, bugzilla-daemon
[Bug 2526] New: SeqFeature's .id property is not preserved in BioSQL, bugzilla-daemon
[Bug 2525] New: The unit tests GUI run_tests.py does not track skipped tests, bugzilla-daemon
- [Bug 2525] The unit tests GUI run_tests.py does not track skipped tests, bugzilla-daemon
[Bug 2524] New: Handle missing libraries like TextTools in run_tests.py, bugzilla-daemon
- [Bug 2524] Handle missing libraries like TextTools in run_tests.py, bugzilla-daemon
test_Entrez.py fails on Linux?, Peter
- Re: test_Entrez.py fails on Linux?, Peter
  - Re: test_Entrez.py fails on Linux?, Michiel de Hoon
    - Re: test_Entrez.py fails on Linux?, Peter
    - Re: test_Entrez.py fails on Linux?, Peter
Bio.CDD, anyone?, Michiel de Hoon
- Re: [BioPython] Bio.CDD, anyone?, Peter
  - Re: [BioPython] Bio.CDD, anyone?, Michiel de Hoon
    - Re: [BioPython] Bio.CDD, anyone?, Bruce Southey
    - Re: [BioPython] Bio.CDD, anyone?, Michiel de Hoon
  - Re: [BioPython] Bio.CDD, anyone?, Chris Fields
[Bug 2408] GenBank records do not contain U's, bugzilla-daemon
BioPax parser, Yair Benita
- Re: BioPax parser, Peter
Re: SeqRecord to file format as string, Peter
- Re: SeqRecord to file format as string, Jared Flatow
  - Re: SeqRecord to file format as string, Jared Flatow
  - Re: SeqRecord to file format as string, Peter
    - Re: SeqRecord to file format as string, Jared Flatow
[Bug 2497] Unit tests do not cover Bio.Blast.NCBIWWW.qblast(), bugzilla-daemon
[Bug 2520] New: Reading ACE assembly contig files in Bio.SeqIO, bugzilla-daemon
- [Bug 2520] Reading ACE assembly contig files in Bio.SeqIO, bugzilla-daemon
- [Bug 2520] Reading ACE assembly contig files in Bio.SeqIO, bugzilla-daemon
Iterating over Ace contig files, Peter
- Re: Iterating over Ace contig files, Frank Kauff
  - Re: Iterating over Ace contig files, Peter
    - Re: Iterating over Ace contig files, Michiel de Hoon
Re: [BioPython] Ace contig files in Bio.SeqIO or Bio.AlignIO, Jose Blanca
- Re: [BioPython] Ace contig files in Bio.SeqIO or Bio.AlignIO, Peter
[Bug 2468] Tutorial needs a fix: Bio.WWW.NCBI, bugzilla-daemon
[Bug 2488] Adding XML parsers to Bio.Entrez, bugzilla-daemon
Bio.SCOP maintainer?, Michiel de Hoon
[BioPython] Bio.Rebase, Michiel de Hoon
Re: CVS access and developers web site, Frank Kauff
- Re: CVS access and developers web site, Peter Cock
[Bug 2516] New: Make it clear what is numeric and what is numpy, bugzilla-daemon
- [Bug 2516] Make it clear what is numeric and what is numpy, bugzilla-daemon
- [Bug 2516] Make it clear what is numeric and what is numpy, bugzilla-daemon
- [Bug 2516] Make it clear what is numeric and what is numpy, bugzilla-daemon
Giving the SeqRecord a length? Evaluating it as a boolean, Peter
- Re: Giving the SeqRecord a length? Evaluating it as a boolean, Michiel de Hoon
[Bug 2511] New: setup.py problem with del sys.modules["Martel"], bugzilla-daemon
- [Bug 2511] setup.py problem with del sys.modules["Martel"], bugzilla-daemon
- [Bug 2511] setup.py problem with del sys.modules["Martel"], bugzilla-daemon
- [Bug 2511] setup.py problem with del sys.modules["Martel"], bugzilla-daemon
- [Bug 2511] setup.py problem with del sys.modules["Martel"], bugzilla-daemon
[BioPython] Bio.Gobase, anybody?, Michiel de Hoon
- Re: [BioPython] Bio.Gobase, anybody?, Martin MOKREJŠ
[Bug 2494] _retrieve_taxon in BioSQL.py needs urgent optimization, bugzilla-daemon
- [Bug 2494] _retrieve_taxon in BioSQL.py needs urgent optimization, bugzilla-daemon
[Bug 2351] Make Seq more like a string, even subclass string?, bugzilla-daemon
[Bug 2509] New: Deprecating the .data property of the Seq and MutableSeq objects, bugzilla-daemon
- [Bug 2509] Deprecating the .data property of the Seq and MutableSeq objects, bugzilla-daemon
- [Bug 2509] Deprecating the .data property of the Seq and MutableSeq objects, bugzilla-daemon
[Bug 2508] New: 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 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 2508] NCBIStandalone.blastall: provide support for '-F F' and make it safe, bugzilla-daemon
[Bug 2446] Comments in CT tags cause Bio.Sequencing.Ace.ACEParser to fail., 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
- [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
Re: Bio.Entrez & Bio.EUtil, Michiel de Hoon
- Re: Bio.Entrez & Bio.EUtil, Michiel de Hoon
Re: sequence class proposal, Peter
- Fwd: Re: sequence class proposal, Blanca Postigo Jose Miguel
  - Re: Fwd: Re: sequence class proposal, Peter
    - Re: Fwd: Re: sequence class proposal, Peter
[Bug 2507] New: 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 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 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 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 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 1944] Align.Generic adding iterator and more, bugzilla-daemon
- [Bug 1944] Align.Generic adding iterator and more, bugzilla-daemon
- [Bug 1944] Align.Generic adding iterator and more, bugzilla-daemon
[Bug 2503] An error when parsing NCBIWWW Blast output, bugzilla-daemon
- [Bug 2503] An error when parsing NCBIWWW Blast output, bugzilla-daemon
[Bug 2502] PSIBlastParser fails with blastpgp 2.2.18 though works with blastpgp 2.2.15, bugzilla-daemon
- [Bug 2502] PSIBlastParser fails with blastpgp 2.2.18 though works with blastpgp 2.2.15, bugzilla-daemon