Package Bio :: Package Motif :: Package Applications :: Module _AlignAce
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Source Code for Module Bio.Motif.Applications._AlignAce

 1  # Copyright 2003-2009 by Bartek Wilczynski.  All rights reserved. 
 2  # Revisions copyright 2009 by Peter Cock. 
 3  # This code is part of the Biopython distribution and governed by its 
 4  # license.  Please see the LICENSE file that should have been included 
 5  # as part of this package. 
 6  """This module provides code to work with the standalone version of AlignACE,  
 7  for motif search in DNA sequences. 
 8   
 9  AlignACE homepage: 
10   
11  http://atlas.med.harvard.edu/ 
12   
13  AlignACE Citations: 
14   
15  Computational identification of cis-regulatory elements associated with  
16  groups of functionally related genes in Saccharomyces cerevisiae,  
17  Hughes, JD, Estep, PW, Tavazoie S, & GM Church, Journal of Molecular  
18  Biology 2000 Mar 10;296(5):1205-14. 
19   
20  Finding DNA Regulatory Motifs within Unaligned Non-Coding Sequences  
21  Clustered by Whole-Genome mRNA Quantitation,  
22  Roth, FR, Hughes, JD, Estep, PE & GM Church, Nature Biotechnology  
23  1998 Oct;16(10):939-45.  
24   
25  """ 
26  from Bio.Application import AbstractCommandline, _Option, _Argument 
27   
28   
29 -class AlignAceCommandline(AbstractCommandline):
30 """Create a commandline for the AlignAce program. 31 32 XXX This could use more checking for valid paramters to the program. 33 """
34 - def __init__(self, cmd="AlignACE", **kwargs):
35 self.parameters = \ 36 [ 37 _Option(["-i","input"],["input"],lambda x : x.__class__== str,1, 38 "Input Sequence file in FASTA format."), 39 40 _Option(["-numcols","numcols"],["input"],lambda x : x.__class__== int,0, 41 "Number of columns to align"), 42 43 _Option(["-expect","expect"],["input"],lambda x : x.__class__== int,0, 44 "number of sites expected in model "), 45 46 _Option(["-gcback","gcback"],["input"],lambda x : x.__class__== float,0, 47 "background fractional GC content of input sequence"), 48 49 _Option(["-minpass","minpass"],["input"],lambda x : x.__class__== int,0, 50 "minimum number of non-improved passes in phase 1"), 51 52 _Option(["-seed","seed"],["input"],lambda x : x.__class__== int,0, 53 "set seed for random number generator (time)"), 54 55 _Option(["-undersample","undersample"],["input"],lambda x : x.__class__== int,0, 56 "possible sites / (expect * numcols * seedings)"), 57 58 _Option(["-oversample","oversample"],["input"],lambda x : x.__class__== int,0, 59 "1/undersample"), 60 ] 61 AbstractCommandline.__init__(self, cmd, **kwargs)
62 63
64 -class CompareAceCommandline(AbstractCommandline):
65 """Create a commandline for the CompareAce program. 66 67 XXX This could use more checking for valid paramters to the program. 68 """
69 - def __init__(self, cmd="CompareACE", **kwargs):
70 import os.path 71 self.parameters = \ 72 [ 73 _Argument(["motif1"],["input","file"], os.path.exists,1,"name of file containing motif 1"), 74 _Argument(["motif2"],["input","file"], os.path.exists,1,"name of file containing motif 2"), 75 ] 76 AbstractCommandline.__init__(self, cmd, **kwargs)
77