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Commits on May 22, 2015
  1. @peterjc
  2. @maclandrol
  3. @maclandrol

    Add unit test

    maclandrol authored
Commits on May 21, 2015
  1. @maclandrol
  2. @maclandrol
Commits on May 12, 2015
  1. @peterjc

    Cope with FTP references in Entrez XML.

    peterjc authored
    This addresses GitHub issue #527, and should fix the UnboundLocalError
    where a URL scheme is not given at all.
  2. @peterjc
  3. @peterjc
  4. @peterjc

    Fix test

    peterjc authored
  5. @peterjc
  6. @danich1 @peterjc

    Fixed the Version Discrepancy

    danich1 authored peterjc committed
    I made the necessary changes for the code to work in python2.6, python
    2.7 and python 3. I believe everything should be in order now.
  7. @danich1 @peterjc

    Updating local storage with IPGReportSet.xsd

    danich1 authored peterjc committed
  8. @danich1 @peterjc

    Added Functionality for Parsing XML Schema Type Files

    danich1 authored peterjc committed
Commits on May 11, 2015
  1. @peterjc
  2. @peterjc
  3. @mdehoon

    Merge pull request #532 from aertslab/jaspar_motif_name_space_fix

    mdehoon authored
    Jaspar motif name space fix
Commits on May 7, 2015
  1. @peterjc
  2. @sunhwan @peterjc

    added docstring and unittest for MMCIFParser to use file handle as we…

    sunhwan authored peterjc committed
    …ll as filename.
  3. @sunhwan @peterjc

    added docstring

    sunhwan authored peterjc committed
  4. @sunhwan @peterjc

    Edited MMCIF2Dict to use both filename or file handler

    sunhwan authored peterjc committed
Commits on May 6, 2015
  1. @peterjc
  2. @mdehoon

    Merge pull request #534 from erasche/ecitmatch

    mdehoon authored
    Implement ECitMatch in Bio.Entrez
Commits on May 4, 2015
  1. @peterjc

    Thank Kian Ho for PDB h-bond work.

    peterjc authored
    See GitHub pull request 464, which was rebased to master.
  2. @peterjc
  3. @kianho @peterjc

    Corrected Python 3 incompatibility in test_PDB.py.

    kianho authored peterjc committed
    Switched from dict.itervalues() (not implemented in Python 3) to
    dict.values().
  4. @kianho @peterjc

    Changed test assertion to assertEquals(...)

    kianho authored peterjc committed
  5. @kianho @peterjc

    Corrected the tuple ordering of dssp_dict values.

    kianho authored peterjc committed
  6. @kianho @peterjc
  7. @kianho @peterjc
Commits on Apr 28, 2015
  1. @ghuls

    Fix _read_jaspar docstring: JASPAR PFMs format has TABs as separator.

    ghuls authored
    The JASPAR PFMs format has TABs as column separator instead of spaces.
    For JASPAR 2014 the matrix_only format seems not been used anymore.
  2. @ghuls

    Do not include leading space(s) in the JASPAR motif name.

    ghuls authored
    Do not include leading space(s) in the JASPAR motif name.
Commits on Apr 27, 2015
  1. @peterjc

    SwissProt/UniProt example with semi-colon in gene name

    peterjc authored
    $ wget http://www.uniprot.org/uniprot/F2CXE6.txt
    $ wget http://www.uniprot.org/uniprot/F2CXE6.xml
    
    See GitHub issue #416 about better handling the evidence codes
    which currently are left on the gene name field as it is (which
    on the bright side means the semi-colon doesn't break anything).
Commits on Apr 23, 2015
  1. @peterjc

    Fixed typo

    peterjc authored
Commits on Apr 20, 2015
  1. @erasche

    Implement test case

    erasche authored
  2. @erasche
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