def compareBIMfiles(beforeFileName, afterFileName, outputFileName):
    """Compare two BIM files for differences.

    :param beforeFileName: the name of the file before modification.
    :param afterFileName: the name of the file after modification.
    :param outputFileName: the name of the output file (containing the
                           differences between the ``before`` and the ``after``
                           files.

    :type beforeFileName: str
    :type afterFileName: str
    :type outputFileName: str

    :returns: the number of differences between the two files.

    The ``bim`` files contain the list of markers in a given dataset. The
    ``before`` file should have more markers than the ``after`` file. The
    ``after`` file should be a subset of the markers in the ``before`` file.

    """
    # Creating the options
    options = Dummy()
    options.before = beforeFileName
    options.after = afterFileName
    options.out = outputFileName

    # Checking the options
    CompareBIM.checkArgs(options)

    # Reading the BIM files
    beforeBIM = CompareBIM.readBIM(options.before)
    afterBIM = CompareBIM.readBIM(options.after)

    # Finding the differences
    CompareBIM.compareSNPs(beforeBIM, afterBIM, options.out)

    return beforeBIM - afterBIM
def compareBIMfiles ( beforeFileName , afterFileName , outputFileName ) : options = Dummy ( ) options . before = beforeFileName options . after = afterFileName options . out = outputFileName CompareBIM . checkArgs ( options ) beforeBIM = CompareBIM . readBIM ( options . before ) afterBIM = CompareBIM . readBIM ( options . after ) CompareBIM . compareSNPs ( beforeBIM , afterBIM , options . out ) return beforeBIM - afterBIM
Compare two BIM files for differences.

    :param beforeFileName: the name of the file before modification.
    :param afterFileName: the name of the file after modification.
    :param outputFileName: the name of the output file (containing the
                           differences between the ``before`` and the ``after``
                           files.

    :type beforeFileName: str
    :type afterFileName: str
    :type outputFileName: str

    :returns: the number of differences between the two files.

    The ``bim`` files contain the list of markers in a given dataset. The
    ``before`` file should have more markers than the ``after`` file. The
    ``after`` file should be a subset of the markers in the ``before`` file.