Package Bio :: Package AlignAce
[hide private]
[frames] | no frames]

Source Code for Package Bio.AlignAce

 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  Parser and code for dealing with the standalone version of AlignAce, a motif search program (DEPRECATED). 
 7   
 8  It also includes a very simple interface to CompareACE tool. 
 9  http://atlas.med.harvard.edu/ 
10   
11  Now superseded by Bio.Motif 
12   
13  Class mapping: 
14  Bio.AlignAce.AlignAceStandalone -> Bio.Motif.Applications.AlignAceCommandline 
15  Bio.AlignAce.CompareAceStandalone -> Bio.Motif.Applications.CompareAceCommandline 
16  Bio.Alignace.Motif -> Bio.Motif.Motif 
17  Bio.AlignAce.Parser.CompareAceParser -> Bio.Motif.CompareAceParser 
18   
19  Instead of using Bio.AlignAce.Parser.AlignAceParser class, you can use 
20  Bio.Motif.parse(handle,format="AlignAce") 
21   
22  """ 
23   
24  import warnings 
25  warnings.warn('Bio.AlignAce is deprecated. Please use Bio.Motif instead.', 
26                DeprecationWarning) 
27