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Commits on Aug 31, 2015
  1. @peterjc

    Hack for calling subprocess on Windows 8.1

    peterjc authored
    Thanks to Ben Fulton for testing this, problem found by
    test_Applicaion.py failing to call the echo command.
Commits on Aug 20, 2015
  1. @peterjc
Commits on Aug 19, 2015
  1. @peterjc

    Don't append empty lineage '.' onto GenBank ORGANISM field

    peterjc authored
    Also fixed two cases of PEP8 spacing.
  2. @peterjc
Commits on Aug 11, 2015
  1. @mdehoon

    Merge pull request #596 from bneron/fix_motifs_write

    mdehoon authored
    Fix motifs write
Commits on Aug 10, 2015
  1. @peterjc

    Thank Lucas

    peterjc authored
    Also correct Fabio Madeira's name in NEWS file, although without
    accented "a" which seems to really confuse my editor (thus two
    failed edits previously).
  2. @peterjc
  3. @xapple
  4. @bneron

    replace assertRaisesRegexp by a assertRaises

    bneron authored
    as assertRaisesRegexp does not exist in 2.6
  5. @bneron

    usee a more pythonic way to test the presence of attribute

    bneron authored
    instead to use hasattr to test the attribute matrix_id
    I use the block try ... except
  6. @bneron
  7. @bneron

    fix bug #573

    bneron authored
    test if matrix_id is an attribute of the instance
    if not put None in the header inestead of martix_id value
  8. @xapple

    Added a test for issue #594

    xapple authored
  9. @xapple

    Fix TypeError instead of CorruptedXMLError

    xapple authored
    Truncated XML in Entrez should raise CorruptedXMLError not a TypeError. See issue #594
Commits on Aug 5, 2015
  1. @kblin @peterjc

    GenBank: Improve error message from EMBL parser

    kblin authored peterjc committed
    When there is content in an EMBL file after SQ or CO lines that is not // or whitespace, the
    parser throws an AssertionError. Unfortunately, the error message is less than helpful.
    Improve the error message.
    
    This fixes issue #431
    
    Signed-off-by: Kai Blin <kblin@biosustain.dtu.dk>
Commits on Aug 3, 2015
  1. @bow

    Fix issue #588

    bow authored
    The bug is caused by phmmer outputing an unexpected line at the end
    of the output hmmer3-text file when the `-A` flag is set. This commit
    ensures the line is ignored and adds a test case to check for this
    behavior.
Commits on Aug 2, 2015
  1. @bow

    Fix hmmer3-text bug where table hit description has preference over f…

    bow authored
    …ull descriptions
    
    Previously, the hit description in the hit table always overwrites the full
    description. This doesn't matter when they are the same, but the description
    in the tables has a maximum length. If the full description exceeds the length,
    a truncated version is shown in the table.
    
    This change ensures that the full description is always used.
Commits on Jul 31, 2015
  1. @mdehoon

    these three are properties

    mdehoon authored
Commits on Jul 22, 2015
  1. @peterjc

    Thank Franco Caramia for disordered residue fix

    peterjc authored
    See GitHub issue #302
  2. @fcaramia @peterjc

    Fixed disordered residue issue #302

    fcaramia authored peterjc committed
Commits on Jul 20, 2015
  1. @kblin

    SeqFeature: Fix a typo in the ValueError message

    kblin authored
    Signed-off-by: Kai Blin <kblin@biosustain.dtu.dk>
  2. @kblin

    SeqFeature: Reword the ValueError message on None .locations

    kblin authored
    Signed-off-by: Kai Blin <kblin@biosustain.dtu.dk>
Commits on Jul 17, 2015
  1. @kblin

    GenBank: Don't use assertIsNone in the test

    kblin authored
    assertIsNone is not available in Python 2.6
    
    Signed-off-by: Kai Blin <kblin@biosustain.dtu.dk>
  2. @kblin

    SeqFeature: raise a ValueError in extract() if location is None

    kblin authored
    If the FeatureLocation is None, instead of creating a somewhat obscure AttributeError,
    explicitly fail with a ValueError.
    This fixes issue #584
    
    Signed-off-by: Kai Blin <kblin@biosustain.dtu.dk>
  3. @kblin

    GenBank: Explicitly check for current behaviour on negative location …

    kblin authored
    …coordinates
    
    To make sure we notice if we ever change the behaviour discussed in issue #584, explicitly test for this.
    
    Signed-off-by: Kai Blin <kblin@biosustain.dtu.dk>
Commits on Jul 16, 2015
  1. @peterjc

    Fix for strand issue in CompoundLocation from EMBL/GenBank

    peterjc authored
    See GitHub issue #570, complement(join(...)) as used by NCBI worked,
    but join(complement(...),complement(...),...) as used by EMBL/ENSEMBL
    did not.
    
    Mention this and recent CompoundLocation reverse complement bug fix
    in the NEWS file.
  2. @peterjc
  3. @peterjc

    Test join(complement(...),complement(...)) versus complement(join(...…

    peterjc authored
    …,...))
    
    See GitHub issue #570, seems this wasn't covered by a unit test.
    
    Test added to test_SeqIO_features.py using existing template approach.
Commits on Jul 15, 2015
  1. @peterjc

    Fix subtle bug in reverse complement of CompoundLocation

    peterjc authored
    This was discovered while working on GitHub issue #570.
  2. @peterjc

    Check GenBank/EMBL location string via sub_features and CompoundLocation

    peterjc authored
    This reveals a subtle bug in the CompoundLocation._flip(...)
    method wrongly reversing the order of the parts. Since they
    are listed in biological order, changing our frame of reference
    to the other strand coordindates should not change this.
  3. @peterjc

    Remove stray whitespace

    peterjc authored
  4. @mdehoon
Commits on Jul 8, 2015
  1. @bow @peterjc

    Fix for issue #525, HmmerIO text parser bug fix.

    bow authored peterjc committed
    HmmerIO text parser broke on sequence hits without individual domain hits
    
    Also with additional tests to ensure the bug does not happen again.
  2. @bow

    Fix for issue #556.

    bow authored
    Instead of relying on raw string splits, we now use regex splits
    to have the parser more robust. We should be able to handle
    cases where descriptions are not present, provided each ID starts
    with the '>' character.
Commits on Jul 7, 2015
  1. @mdehoon

    Update to Bio/motifs/jaspar/db.py received from David Arenillas, Univ…

    mdehoon authored
    …ersity of British Columbia
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