July 2008 Archives by thread

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Starting: Tue Jul 1 04:36:33 EDT 2008
Ending: Thu Jul 31 12:00:23 EDT 2008
Messages: 166

• [Biopython-dev] [Bug 2531] Nexus and fasta parsers have a problem with identical taxa names   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2531] Nexus and fasta parsers have a problem with identical taxa names   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2531] Nexus and fasta parsers have a problem with identical taxa names   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2532] Using IUPAC alphabets in mixed case Seq objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2533] New: Support for simple "tab" format in Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2533] Support for simple "tab" format in Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2533] Support for simple "tab" format in Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2533] Support for simple "tab" format in Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Catching more error conditions in Bio.Entrez   Peter
  • [Biopython-dev] Catching more error conditions in Bio.Entrez   Sean Davis
    • [Biopython-dev] Catching more error conditions in Bio.Entrez   Peter
• [Biopython-dev] Bug 2533 - Support for simple "tab" format in Bio.SeqIO   Peter
  • [Biopython-dev] Bug 2533 - Support for simple "tab" format in Bio.SeqIO   Peter
    • [Biopython-dev] Bug 2533 - Support for simple "tab" format in Bio.SeqIO   Leighton Pritchard
      • [Biopython-dev] Bug 2533 - Support for simple "tab" format in Bio.SeqIO   Peter
• [Biopython-dev] Questions about the NEXUS format   Peter
  • [Biopython-dev] Questions about the NEXUS format   Frank Kauff
    • [Biopython-dev] Questions about the NEXUS format   Peter
• [Biopython-dev] Bio.IntelliGenetics   Michiel de Hoon
  • [Biopython-dev] Bio.IntelliGenetics   Peter
    • [Biopython-dev] Bio.IntelliGenetics   Peter
    • [Biopython-dev] Bio.IntelliGenetics   Michiel de Hoon
      • [Biopython-dev] Bio.IntelliGenetics   Peter
• [Biopython-dev] Bio.IntelliGenetics   Peter
• [Biopython-dev] [Bug 2524] Handle missing libraries like TextTools in run_tests.py   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2469] requires_wise.py fails on Windows (test suite)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Bio.IntelliGenetics   Michiel de Hoon
• [Biopython-dev] [Bug 2535] New: Support for PIR / NBRF format in Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2535] Support for PIR / NBRF format in Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2535] Support for PIR / NBRF format in Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2508] NCBIStandalone.blastall: provide support for '-F F' and make it safe   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2531] Nexus and fasta parsers have a problem with identical taxa names   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2531] Nexus and fasta parsers have a problem with identical taxa names   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2531] Nexus and fasta parsers have a problem with identical taxa names   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] What happened to Biopython 1.46?   Peter
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Bio.IntelliGenetics   Michiel de Hoon
  • [Biopython-dev] Bio.IntelliGenetics   Peter
• [Biopython-dev] CVS freeze for release 1.47   Michiel de Hoon
• [Biopython-dev] Biopython release 1.47   Michiel de Hoon
• [Biopython-dev] NCBIStandalon not compatible with previous versions, is this a bug?   Sebastian Bassi
  • [Biopython-dev] NCBIStandalon not compatible with previous versions, is this a bug?   Peter
• [Biopython-dev] [Bug 2447] EUtils cannot parse PubMed XML for ACS journals   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2448] Bio.EUtils can't handle accented author names   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2448] Bio.EUtils can't handle accented author names   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2538] New: _security_check_parameters assumes all arguments are strings   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2538] _security_check_parameters assumes all arguments are strings   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2538] _security_check_parameters assumes all arguments are strings   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Alignment problem. bug?   Sebastian Bassi
  • [Biopython-dev] Alignment problem. bug?   Peter
    • [Biopython-dev] Alignment problem. bug?   Peter
      • [Biopython-dev] Alignment problem. bug?   Sebastian Bassi
      • [Biopython-dev] Alignment problem. bug?   Peter
      • [Biopython-dev] Alignment problem. bug?   Sebastian Bassi
• [Biopython-dev] Bio.Sequencing   Michiel de Hoon
  • [Biopython-dev] Bio.Sequencing   Frank Kauff
  • [Biopython-dev] Bio.Sequencing   Peter
• [Biopython-dev] Simple __getitem__ for Alignments   Peter
• [Biopython-dev] [Bug 2454] Iterators can't use file-like objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2454] Iterators can't use file-like objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2454] Iterators can't use file-like objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2454] Iterators can't use file-like objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2508] NCBIStandalone.blastall: provide support for '-F F' and make it safe   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2508] NCBIStandalone.blastall: provide support for '-F F' and make it safe   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2508] NCBIStandalone.blastall: provide support for '-F F' and make it safe   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2454] Iterators can't use file-like objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2542] New: AlignInfo.py fails a test   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2542] AlignInfo.py fails a test   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2542] AlignInfo.py fails a test   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2542] AlignInfo.py fails a test   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2542] AlignInfo.py fails a test   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2542] AlignInfo.py fails a test   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2542] AlignInfo.py fails a test   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Checking alphabet argument in alignments   Peter
• [Biopython-dev] [Bug 2454] Iterators can't use file-like objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2443] Specifying the alphabet in Bio.SeqIO and Bio.AlignIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Deprecating the HTML parser in Bio.Blast.NCBIWWW   Peter
• [Biopython-dev] [Bug 2543] New: Bio.Nexus.Trees can't handle named ancestors   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2543] Bio.Nexus.Trees can't handle named ancestors   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2543] Bio.Nexus.Trees can't handle named ancestors   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2351] Make Seq more like a string, even subclass string?   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2544] New: Bio.SeqIO improvements   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2544] Bio.GenBank and SeqFeature improvements   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2544] Bio.GenBank and SeqFeature improvements   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Dump file in Bio/Saf/__init__.py   Peter
  • [Biopython-dev] Dump file in Bio/Saf/__init__.py   Michiel de Hoon
    • [Biopython-dev] Dump file in Bio/Saf/__init__.py   Peter
      • [Biopython-dev] Dump file in Bio/Saf/__init__.py   Peter
• [Biopython-dev] [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Modules to be removed from Biopython   Peter
  • [Biopython-dev] Modules to be removed from Biopython   Peter
• [Biopython-dev] [Bug 2454] Iterators can't use file-like objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2454] Iterators can't use file-like objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Biopython presentation at BOSC2008   Tiago Antão
  • [Biopython-dev] Biopython presentation at BOSC2008   Peter
  • [Biopython-dev] Biopython presentation at BOSC2008   Tiago Antão
• [Biopython-dev] [Bug 1999] new frame translation method   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2448] Bio.EUtils can't handle accented author names   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2532] Using IUPAC alphabets in mixed case Seq objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops   Peter
• [Biopython-dev] [Bug 2547] New: Translation of ambiguous codons like NNN and TAN   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2547] Translation of ambiguous codons like NNN and TAN   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2547] Translation of ambiguous codons like NNN and TAN   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2547] Translation of ambiguous codons like NNN and TAN   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2547] Translation of ambiguous codons like NNN and TAN   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2547] Translation of ambiguous codons like NNN and TAN   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2548] New: Updating IUPACData and ExtendedIUPACProtein for U and O   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2548] Updating IUPACData and ExtendedIUPACProtein for U and O   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2454] Iterators can't use file-like objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Bio.KDTree   Michiel de Hoon
  • [Biopython-dev] Bio.KDTree   Peter
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2227] Writing Nexus files with Bio.SeqIO   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Removing the deprecated Bio.WWW modules   Peter
  • [Biopython-dev] Removing the deprecated Bio.WWW modules   Michiel de Hoon
    • [Biopython-dev] Removing the deprecated Bio.WWW modules   Peter
• [Biopython-dev] Updating the installation instructions   Peter
• [Biopython-dev] [Bug 2550] New: Alphabet problems when adding sequences   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2550] Alphabet problems when adding sequences   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2550] Alphabet problems when adding sequences   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2550] Alphabet problems when adding sequences   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2550] Alphabet problems when adding sequences   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 1944] Align.Generic adding iterator and more   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2551] New: Adding advanced __getitem__ to generic alignment, e.g. align[1:2, 5:-5]   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2507] Adding __getitem__ to SeqRecord for element access and slicing   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2552] New: Adding alignments   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2553] New: Adding SeqRecord objects to an alignment (append or extend)   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2553] Adding SeqRecord objects to an alignment (append or extend)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 1944] Align.Generic adding iterator and more   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2507] Adding __getitem__ to SeqRecord for element access and slicing   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2554] New: Creating an Alignment from a list of SeqRecord objects   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2554] Creating an Alignment from a list of SeqRecord objects   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2554] Creating an Alignment from a list of SeqRecord objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2557] New: AlignIO::write fails when delegating to SeqIO::write   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2557] AlignIO::write fails when delegating to SeqIO::write   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2558] New: AlignIO nexus parsing chokes on superfluous comma   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2558] Bio.Nexus chokes on TRANSLATE block with superfluous comma   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2558] Bio.Nexus chokes on TRANSLATE block with superfluous comma   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2560] New: Adding BLAST support to Bio.AlignIO   bugzilla-daemon at portal.open-bio.org
  • [Biopython-dev] [Bug 2560] Adding BLAST support to Bio.AlignIO   bugzilla-daemon at portal.open-bio.org

Last message date: Thu Jul 31 12:00:23 EDT 2008
Archived on: Thu Jul 31 12:00:25 EDT 2008

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