Package Bio :: Package AlignAce :: Module CompareAceStandalone
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Source Code for Module Bio.AlignAce.CompareAceStandalone

 1  # Copyright 2003 by Bartek Wilczynski.  All rights reserved. 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5   
 6  """ 
 7   
 8  This module provides code to work with the standalone version of CompareAce,  
 9  for motif comparison 
10   
11  CompareACE homepage: 
12   
13  http://atlas.med.harvard.edu/ 
14   
15  functions: 
16  CompareAce - runs the AlignACE standalone prgram and returns the ApplicationResult object 
17  """ 
18   
19  import os 
20  import re 
21   
22  from Bio import File 
23  from Applications import CompareAceCommandline 
24   
25  import Scanner 
26  import Parser 
27   
28   
29 -def CompareAce( cmd="CompareACE", **keywds):
30 """Runs CompareACE and returns data. 31 32 motif1, motif2 == files containing AlignACE motifs 33 """ 34 35 if not os.path.exists(cmd): 36 raise IOError("Executable does not exist at %s" % cmd) 37 38 CompareCmd = CompareAceCommandline(cmd) 39 40 for (par,val) in keywds.iteritems(): 41 CompareCmd.set_parameter(par,val) 42 43 return CompareCmd.run()
44