# Copyright 2003 by Bartek Wilczynski.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""

This module provides code to work with the standalone version of CompareAce, 
for motif comparison (DEPRECATED).

CompareACE homepage:

http://atlas.med.harvard.edu/

functions:
CompareAce - runs the AlignACE standalone prgram and returns the ApplicationResult object
"""

import warnings
warnings.warn('Bio.AlignAce is deprecated. Please use Bio.Motif instead.',
              DeprecationWarning)


import os
import re

from Bio import File
from Applications import CompareAceCommandline

import Scanner
import Parser


def CompareAce( cmd="CompareACE", **keywds):
    """Runs CompareACE and returns data.

    motif1, motif2 == files containing AlignACE motifs
    """

    if not os.path.exists(cmd):
        raise IOError("Executable does not exist at %s" % cmd)
    
    CompareCmd = CompareAceCommandline(cmd)

    for (par,val) in keywds.iteritems():
        CompareCmd.set_parameter(par,val)

    return CompareCmd.run()