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Commits on Jan 20, 2017
  1. Use our standard doctest invocation

    peterjc committed Jan 20, 2017
  2. Remove Python 3.1 workaround

    peterjc committed Jan 20, 2017
  3. Test on Python 3.6

    peterjc committed Jan 20, 2017
Commits on Jan 19, 2017
  1. More explicit testing instructions in README

    This should help where test failures are due to not having compiled our C code, see #1010 and #1024.
    peterjc committed on GitHub Jan 19, 2017
Commits on Jan 8, 2017
  1. Tidy up GenBank processing code

    Squashed commit of pull request #1031 
    
    - Remove redundant parentheses
    - Decorate static methods as such
    - Alpha-order long lists of attributes
    - Define 'constant' attributes during object instantiation, instead of repeatedly setting them in methods
    - Fix line indents
    biologyguy committed with peterjc Jan 8, 2017
Commits on Jan 7, 2017
  1. XML submittedName allowed in Uniprot. Fixes #1028 (#1034)

    Fixes #1028 by adding "submittedName" to the allowed name tags in UniprotIO
    
    Test added to test_Uniprot.py
    
    Squashed commit of pull request #1034.
    OscarMaestre committed with peterjc Jan 7, 2017
  2. Remove duplicated entry for Bertrand in CONTRIB

    peterjc committed Jan 7, 2017
Commits on Jan 2, 2017
  1. Non-descriptive failure in python 3 Affy.CelFile.read_v4

    A piece of code like this:
    
    import Bio.Affy.CelFile as CELFile
    with open("CELFileV4.CEL"), "r") as f:
        record = CELFile.read_v4(f)
    
    fails in a non-descriptive way with UnicodeDecodeError in python 3. Instead, an error should be raised, which informs the user what went wrong, in this case, opening the file in a wrong mode.
    
    This has already been in place with the version-detecting function read.
    
    This pull request proposes a unified approach, which shares error handling between read and read_v4.
    
    In python 2 there is no problem, the record is read in correctly.
    picrin committed with peterjc Jan 1, 2017
Commits on Dec 28, 2016
  1. Updated the docstring for parse, as the previous example now requires…

    … read
    mdehoon committed Dec 28, 2016
  2. Updated documentation for current Entrez.efetch data returned by NCBI…

    … for db=pubmed; see issue #1027
    mdehoon committed Dec 28, 2016
Commits on Dec 22, 2016
  1. Write structured GenBank comments; robust parsing

    Squashed commit of pull request #1029, itself a replacement of pull request #945.
    
    The original implementation was not robust against malformed structured comments, causing crashes.
    
    Any structured comment information was previously discarded from the record when written.
    
    Adding output files for unit tests as well.
    biologyguy committed with peterjc Dec 22, 2016
Commits on Dec 12, 2016
  1. Update names in NEWS file for next release

    Bow and Michiel have contributed pull requests and/or reviewing and merging.
    peterjc committed on GitHub Dec 12, 2016
  2. Partial codons for SearchIO when parsing Exonerate

    Squashed commit of pull request #815.
    
    Fix for handling protein to nucleic acid mapping in Exonerate, with tests for exonerate protein2genome mode.
    bow committed with peterjc Dec 12, 2016
  3. Ensure PWM calculations work even without C code. (#1019)

    In order that our test suite passes even on  C Python when
    if built without NumPy (e.g. testing new releases of Python
    where NumPy is not readily available), always use the pure
    Python fallback (previously used for non-C-Python only),
    but issue a warning.
    
    Closes #851.
    peterjc committed with mdehoon Dec 12, 2016
Commits on Dec 9, 2016
  1. Thank Milind for test updates.

    See pull request #1020 which closes #1006.
    peterjc committed Dec 9, 2016
  2. Replace assertTrue with assertIn/assertNotIn when suitable

    This closes issue 1006
    assertTrue(a in b) is now assertIn(a, b)
    assertTrue(a in b, b) is assertIn(a, b)
    assertTrue(a in b, message) is assertIn(a, b, message)
    The same for 'not in', by using assertNotIn
    milindl committed with peterjc Dec 9, 2016
  3. Parser for Affy CEL file version 4

    Backwards compatibility with version 3 is maintained.
    
    Test cases for package Affy are added. Both new and old code is now tested.
    
    affy_v4_example.CEL is added. It is artifically generated and small.
    
    See also:
    
    http://www.affymetrix.com/estore/support/developer/powertools/changelog/gcos-agcc/cel.html.affx
    
    Which explains:
    
        Version 3 is generated by the MAS software. This was also
        known as the ASCII version.
    
        Version 4 is generated by the GCOS software. This was also
        known as the binary or XDA version.
    
        Command Console version 1 is generated by the Command
        Console software. This is stored in the Command Console
        "generic" data file format.
    
    (Squashed commit of pull reqesut #1011)
    picrin committed with peterjc Nov 27, 2016
  4. Mark residues as disordered when parsing MMCIF

    Squashed commit of pull request #1014.
    
    This commit updates MMCIFParser to match the behaviour of PDBParser (and
    the documentation) when parsing point mutations. This is done by calling
    the "init_residue" of StructureBuilder when the residue name changes, as
    well as when the residue ID changes.
    
    None of the existing MMCIF files contain point mutations, so I have
    added 3JQH.cif for parsing.
    StefansM committed with peterjc Dec 9, 2016
  5. Stefans worked on the MMCIF code

    peterjc committed Dec 9, 2016
  6. Fix QUIET parameter for FastMMCIFParser

    The `_build_structure` method was called outside of the
    `warnings.catch_warnings` context manager, so warnings were not actually
    suppressed.
    StefansM committed with peterjc Nov 29, 2016
  7. Improve parsing and error checking and reporting for TRANSFAC motifs:

    Improve parsing and error checking and reporting for TRANSFAC motifs:
      - Add help messages for asserts.
      - allow parsing of TRANSFAC matrices, which use something else
        than 2 spaces as whitespace separator
        (raise BiopythonParserWarning)
      - Check if each line contains a key of 2 characters, else assert
      - Use line.split(None, 1) to split each line in two fields on
        whitespace to allow parsing of TRANSFAC matrices, which use
        something else than 2 spaces as whitespace separator between
        key and value.
      - Allow parsing slightly wrong TRANSFAC matrix lines:
         - Allow numbers of only 1 character as start of a matrix line
           instead of only numbers of 2 digits
           (raise BiopythonParserWarning).
         - Allow parsing of TRANSFAC matrix if it starts with "00"
           instead of "01" (raise BiopythonParserWarning).
         - Check if a matrix line contains values for each nucleotide.
         - Allow a number of only 1 character, instead of zero prefixed
    ghuls committed with peterjc Dec 2, 2016
Commits on Nov 29, 2016
  1. Added ExPASy Cellosaurus parser with tests

    Squashed commit from pull request #983 with merge conflict
    fixed and NEWS entry reworded (by Peter).
    stevemmarshall committed with peterjc Nov 7, 2016
  2. Fill in a couple of GitHub URLs in CONTRIB file

    peterjc committed Nov 29, 2016
  3. Thank Adrian and Brandon for PAML fix.

    See pull request #1012 and issue #483.
    peterjc committed Nov 29, 2016
  4. Record missing data in Bio.Phylo.PAML.codeml

    Squashed commit from pull request #1012, fixes #483.
    
    The codeml parser parses now all site parameters of a pairwise codeml analysis.
    
    Thanks to Brandon Invergo for his input and review.
    alpae committed with peterjc Nov 29, 2016
  5. Avoid writing output files under Tests/ directory.

    Partly addresses issue #1013
    peterjc committed Nov 29, 2016
  6. Avoid accidentally checking in Doc/examples/other_trees.nwk

    peterjc committed Nov 29, 2016
Commits on Nov 28, 2016
Commits on Nov 25, 2016
  1. Remove left-over handle.close()

    peterjc committed Nov 25, 2016
  2. Can now use context manager with gzip and bz2

    We've dropped Python 2.6 since I first wrote these examples.
    peterjc committed Nov 25, 2016
  3. Fix bzip2 SeqIO example under Python 3

    Note bz2.open was added in Python 3.3
    peterjc committed Nov 25, 2016
  4. Fix example inconsistency

    peterjc committed Nov 25, 2016
  5. Fix gzip file mode

    This closes issue #1009.
    peterjc committed Nov 25, 2016
Commits on Nov 24, 2016
  1. Thank Aaron for KEGG documentation update

    See pull request #660 (overdue for merging), and preceeding
    commits turning these examples into Tutorial doctests.
    peterjc committed Nov 24, 2016