October 2008 Archives by date

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Starting: Wed Oct 1 00:24:18 UTC 2008
Ending: Fri Oct 31 10:03:28 UTC 2008
Messages: 182

• [Biopython-dev] Numpy conversion   Michiel de Hoon
• [Biopython-dev] Numpy conversion   Peter
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2601] Seq find() method: proposal   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2596] Add string like split, strip, rstrip and lstrip methods to the Seq object   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] determining the version   Peter
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Versions of numpy/Numeric   Peter
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Versions of numpy/Numeric   Bruce Southey
• [Biopython-dev] Versions of numpy/Numeric   Bruce Southey
• [Biopython-dev] [Bug 2604] New: test_Restriction failure with Python 2.6 (also cause error in test_CAPS)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2605] New: test_PDB failure with Python 2.6   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Versions of numpy/Numeric   Bruce Southey
• [Biopython-dev] Versions of numpy/Numeric   Peter
• [Biopython-dev] [Bug 2605] test_PDB failure with Python 2.6   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2605] test_PDB failure with Python 2.6   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Python 2.6   Peter
• [Biopython-dev] [Bug 2607] New: Gcc "differ in signedness" warning with cstringfnsmodule.c   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2608] New: Gcc "differ in signedness" warnings with trie.c   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2609] New: Gcc 4.3.2 'initialization from incompatible pointer type' warning with triemodule.c   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2608] Gcc "differ in signedness" warnings with trie.c   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Versions of numpy/Numeric   Bruce Southey
• [Biopython-dev] [Bug 2611] New: Message corrections when tests are skipped   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2611] Message corrections when tests are skipped   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Python 2.6   Peter
• [Biopython-dev] [Bug 2604] test_Restriction failure with Python 2.6 (also cause error in test_CAPS)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2608] Gcc "differ in signedness" warnings with trie.c   Andrew Dalke
• [Biopython-dev] Bio.MarkovModel   Michiel de Hoon
• [Biopython-dev] Bio.MarkovModel   Peter
• [Biopython-dev] Bio.MarkovModel; Bio.Popgen, Bio.PDB documentation   Michiel de Hoon
• [Biopython-dev] [Bug 2604] test_Restriction failure with Python 2.6 (also cause error in test_CAPS)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Bio.MarkovModel; Bio.Popgen, Bio.PDB documentation   Peter
• [Biopython-dev] Fwd: Biopython - Bio.Restriction problem with super on python 2.6   Peter
• [Biopython-dev] Python 2.6   Peter
• [Biopython-dev] [Bug 2604] test_Restriction failure with Python 2.6 (also cause error in test_CAPS)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2613] New: test_Wise and test_psw fail under Python 2.3   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2613] test_Wise and test_psw fail under Python 2.3   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2604] test_Restriction failure with Python 2.6 (also cause error in test_CAPS)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] taxonomic labels   Zac Brown
• [Biopython-dev] taxonomic labels   Peter
• [Biopython-dev] Python 2.6   Frank Kauff
• [Biopython-dev] Python 2.6   Peter
• [Biopython-dev] [Bug 2601] Seq find() method: proposal   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2596] Add string like split, strip, rstrip and lstrip methods to the Seq object   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 2613] test_Wise and test_psw fail under Python 2.3   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 2613] test_Wise and test_psw fail under Python 2.3   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2613] test_Wise and test_psw fail under Python 2.3   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 2583] small bug in NCBIXML.py   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2528] NCBIStandalone.blastall(): Replace os.popen3 with subprocess.Popen   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2589] Errors in running tests in 1.48   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2600] enhance Seq and SeqRecord to new style classes   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2475] BioSQL.Loader should reuse existing taxon entries in lineage   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2592] numpy migration for Bio.PDB.Vector   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Time to deprecate Bio.Transcribe?   Peter
• [Biopython-dev] [Bug 2509] Deprecating the .data property of the Seq and MutableSeq objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2600] enhance Seq and SeqRecord to new style classes   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2613] test_Wise and test_psw fail under Python 2.3   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2589] Errors in running tests in 1.48   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2589] Errors in running tests in 1.48   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] Modules to be removed from Biopython   Peter
• [Biopython-dev] Bio.Ndb obsolete?   Peter
• [Biopython-dev] Python 2.6   Peter
• [Biopython-dev] Bio.Ndb obsolete?   Peter
• [Biopython-dev] Bio.mathfns obsolete? And Bio.clistfns too?   Peter
• [Biopython-dev] Bio.mathfns obsolete? And Bio.clistfns too? And Bio.stringfns?   Peter
• [Biopython-dev] Python 2.6   Peter
• [Biopython-dev] Python 2.6   Peter
• [Biopython-dev] [Bug 2528] NCBIStandalone.blastall(): Replace os.popen3 with subprocess.Popen   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2600] enhance Seq and SeqRecord to new style classes   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2509] Deprecating the .data property of the Seq and MutableSeq objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2525] The unit tests GUI run_tests.py does not track skipped tests   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2524] Handle missing libraries like numpy or reportlab in run_tests.py   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] Python 2.6   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] [Bug 2616] New: BioSQL support for Psycopg2   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2616] BioSQL support for Psycopg2   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2616] BioSQL support for Psycopg2   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2616] BioSQL support for Psycopg2   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Bio.Graphics and GenomeDiagram   Leighton Pritchard
• [Biopython-dev] Bio.Graphics and GenomeDiagram   Peter
• [Biopython-dev] Bio.Graphics and GenomeDiagram   Leighton Pritchard
• [Biopython-dev] Sequences and simple plots   Peter
• [Biopython-dev] [Bug 2616] BioSQL support for Psycopg2   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2616] BioSQL support for Psycopg2   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Sequences and simple plots   Leighton Pritchard
• [Biopython-dev] [Bug 2616] BioSQL support for Psycopg2   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Sequences and simple plots   Peter
• [Biopython-dev] Sequences and simple plots   Leighton Pritchard
• [Biopython-dev] Biopython with python 2.6 on Windows   Peter
• [Biopython-dev] [Bug 2551] Adding advanced __getitem__ to generic alignment, e.g. align[1:2, 5:-5]   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2591] GenBank files misparsed for long organism names   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2509] Deprecating the .data property of the Seq and MutableSeq objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Bio.Graphics and GenomeDiagram   Robert Cadena
• [Biopython-dev] Bio.Graphics and GenomeDiagram   Leighton Pritchard
• [Biopython-dev] [Bug 2616] BioSQL support for Psycopg2   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2616] BioSQL support for Psycopg2   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2616] BioSQL support for Psycopg2   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2618] New: back_translate method for the Seq object (in Bio.Seq)?   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2618] back_translate method for the Seq object (in Bio.Seq)?   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] What would we gain by dropping python 2.3?   Peter
• [Biopython-dev] What would we gain by dropping python 2.3?   Peter
• [Biopython-dev] What would we gain by dropping python 2.3?   Bruce Southey
• [Biopython-dev] What would we gain by dropping python 2.3?   Peter
• [Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2616] BioSQL support for Psycopg2   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] [Bug 2619] New: Bio.PDB.MMCIFParser component MMCIFlex commented out in setup.py   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2619] Bio.PDB.MMCIFParser component MMCIFlex commented out in setup.py   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 2381] translate and transcibe methods for the Seq object (in Bio.Seq)   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 2381] translate and transcibe methods for the Seq object (in Bio.Seq)   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 2509] Deprecating the .data property of the Seq and MutableSeq objects   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2622] New: Parsing between position locations like 5933^5934 in GenBank/EMBL files   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2622] Parsing between position locations like 5933^5934 in GenBank/EMBL files   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2622] Parsing between position locations like 5933^5934 in GenBank/EMBL files   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2619] Bio.PDB.MMCIFParser component MMCIFlex commented out in setup.py   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2619] Bio.PDB.MMCIFParser component MMCIFlex commented out in setup.py   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] flex, setup.py and Bio.PDB.mmCIF (Bug 2619)   Peter
• [Biopython-dev] [Bug 2619] Bio.PDB.MMCIFParser component MMCIFlex commented out in setup.py   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2176] XML Blast parser: miscellaneous bug fixes and cleanup   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2618] back_translate method for the Seq object (in Bio.Seq)?   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2176] XML Blast parser: miscellaneous bug fixes and cleanup   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2176] XML Blast parser: miscellaneous bug fixes and cleanup   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Deprecating Bio.mathfns, Bio.stringfns and their C code?   Peter
• [Biopython-dev] Deprecating Bio.mathfns, Bio.stringfns and their C code?   Bruce Southey
• [Biopython-dev] Deprecating Bio.mathfns, Bio.stringfns and their C code?   Peter
• [Biopython-dev] Deprecating Bio.mathfns, Bio.stringfns and their C code?   Bruce Southey
• [Biopython-dev] Deprecating Bio.mathfns, Bio.stringfns and their C code?   Peter
• [Biopython-dev] [Bug 2626] New: Bio.PDB mmCIFParser parse exceptions   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2627] New: Updated Bio.MarkovModel to remove oldnumeric and listfns imports   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2627] Updated Bio.MarkovModel to remove oldnumeric and listfns imports   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2627] Updated Bio.MarkovModel to remove oldnumeric and listfns imports   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Deprecating Bio.mathfns, Bio.stringfns and their C code?   Bruce Southey
• [Biopython-dev] [Bug 2628] New: Have Bio.SeqIO.write(...) and Bio.AlignIO.write(...) return number of records   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2629] New: Updated Bio.NaiveBayes to listfns import   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2629] Updated Bio.NaiveBayes to listfns import   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2629] Updated Bio.NaiveBayes to listfns import   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] CE implementation in Python   Iddo Friedberg
• [Biopython-dev] CE implementation in Python   Peter
• [Biopython-dev] [Bug 2631] New: Updated Bio.MaxEntropy to remove listfns import   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2631] Updated Bio.MaxEntropy to remove listfns import   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2631] Updated Bio.MaxEntropy to remove listfns import   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] Deprecating Bio.mathfns, Bio.stringfns and their C code?   Bruce Southey
• [Biopython-dev] [Bug 2631] Updated Bio.MaxEntropy to remove listfns import   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2631] Updated Bio.MaxEntropy to remove listfns import   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2634] New: PAM30 Matrix doesn't work with   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2634] PAM30 Matrix doesn't work with qblast   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2634] PAM30 Matrix doesn't work with qblast   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 2381] translate and transcibe methods for the Seq object (in Bio.Seq)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2628] Have Bio.SeqIO.write(...) and Bio.AlignIO.write(...) return number of records   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2622] Parsing between position locations like 5933^5934 in GenBank/EMBL files   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 1492] Martel Parser fails on Bio.db["protein-genbank-cgi"] entry   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 1589] Parsing fails at "operon" tag with RecordParser or FeatureParser   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 1758] genbank parser chokes on /transl_except   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2072] GenBank parser breaks: LOCUS line does not contain valid sequence type (DNA, RNA, ...)   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2076] EMBL to GenBank converter should fix unterminated lines   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 1920] Bio.Geo does not support recent GEO files   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 1773] Martel.Parser.ParserPositionException   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [Bug 2361] Test Suite Failures from Martel/Sax with egenix mxTextTools 3.0   bugzilla-daemon at portal.open-bio.org
• [Biopython-dev] [BioPython] calculate F-Statistics from SNP data   Tiago Antão
• [Biopython-dev] Statistics in population genetics module - Part I   Tiago Antão
• [Biopython-dev] Statistics in population genetics module - Part I   Bruce Southey
• [Biopython-dev] Statistics in population genetics module - Part I   Tiago Antão

Last message date: Fri Oct 31 10:03:28 UTC 2008
Archived on: Mon Jun 16 03:55:13 UTC 2014

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