1
2
3
4
5
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
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
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