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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
Commits on Jul 2, 2015
  1. @mdehoon
Commits on Jun 29, 2015
  1. @peterjc

    Helpful exception if switch handle/records in SeqIO.write(...)

    peterjc authored
    Previously would get e.g. AttributeError: 'str' object has no attribute 'id'
Commits on Jun 26, 2015
  1. @anderspitman
Commits on Jun 25, 2015
  1. @peterjc

    Remove trailing whitespace

    peterjc authored
  2. @peterjc

    Fixed typos in comments

    peterjc authored
  3. @peterjc
  4. @ctSkennerton @peterjc

    Don't alter the SeqRecord

    ctSkennerton authored peterjc committed
  5. @ctSkennerton @peterjc

    Added ability to change the seqfeature source

    ctSkennerton authored peterjc committed
    Added a new kwarg to BioSQL.Loader._load_seqfeature_basic that
    allows the source to be changed dynamically based on the value
    of the source qualifier found in the annotations of the SeqRecord
    
    Background:
    GFF files set aside column 2 for the source of the feature that
    is set to the value of the program/algorithm that generated that
    feature. Parsing a gff file using BCBio.GFF returns a SeqRecord
    object that contains the source as a qualifier key-value pair.
    Normally these key-value pairs are loaded into the
    seqfeature_qualifier_value table, but the BioSQL wiki suggests that the
    source should instead go into the term table.
    
    The current code in biopython sets the value of source for a
    seqfeature to be the same value regardless of whether the SeqRecord
    object contains the source qualifier. This change adds in code that
    will search for a source qualifier in the SeqRecord, set the value to
    the source of the seqfeature and remove the key from the SeqRecord
    qualifiers dict so that it is not mistakenly added to the
    seqfeature_qualifier_value table
Commits on Jun 18, 2015
  1. @peterjc

    Fail gracefully if extra genes present.

    peterjc authored
    Seems revised NC_003212 annotation has another five genes
    in the region of interest, so will have to revisit the
    manually assigned list of gene colours at some point...
    
    See also GitHub issue #563.
  2. @peterjc

    PEP8 white space

    peterjc authored
  3. @peterjc

    Annotation tags have changed in example file.

    peterjc authored
    NC_003212 now has new locus_tag entries, the names we
    expected are preserved under old_locus_tag.
    
    Something else has changed too... - see also GitHub issue #563.
Commits on Jun 12, 2015
  1. @peterjc

    EMBL missing XX line between features and sequence

    peterjc authored
    Should resolve GitHub issue #561.
Commits on Jun 4, 2015
  1. @peterjc
  2. @peterjc

    Test case for row of dashes in plain text BLAST

    peterjc authored
    Based on GitHub issue #554 reported by @breviata
Commits on Jun 3, 2015
  1. @peterjc
  2. @peterjc
  3. @peterjc

    Test GenBank locations not split at comma

    peterjc authored
    Something wrong with the (global) warnings filter (?) which
    is always a pain when testing warnings are triggered.
    Workaround by hacking the test method sort order...
  4. @peterjc

    Tolerate GenBank locations not split at comma

    peterjc authored
    (Spotting by mis-matched brackets; issues a warning)
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