1 """Definitions for interacting with AlignAce.
2 """
3 from Bio.Application import _Option,_Argument, AbstractCommandline
4 from Bio.Application import generic_run
5
7 """Create a commandline for the AlignAce program.
8
9 XXX This could use more checking for valid paramters to the program.
10 """
11 - def __init__(self, cmd="AlignACE", **kwargs):
12 self.parameters = \
13 [
14 _Option(["-i","input"],["input"],lambda x : x.__class__== str,1,
15 "Input Sequence file in FASTA format."),
16
17 _Option(["-numcols","numcols"],["input"],lambda x : x.__class__== int,0,
18 "Number of columns to align"),
19
20 _Option(["-expect","expect"],["input"],lambda x : x.__class__== int,0,
21 "number of sites expected in model "),
22
23 _Option(["-gcback","gcback"],["input"],lambda x : x.__class__== float,0,
24 "background fractional GC content of input sequence"),
25
26 _Option(["-minpass","minpass"],["input"],lambda x : x.__class__== int,0,
27 "minimum number of non-improved passes in phase 1"),
28
29 _Option(["-seed","seed"],["input"],lambda x : x.__class__== int,0,
30 "set seed for random number generator (time)"),
31
32 _Option(["-undersample","undersample"],["input"],lambda x : x.__class__== int,0,
33 "possible sites / (expect * numcols * seedings)"),
34
35 _Option(["-oversample","oversample"],["input"],lambda x : x.__class__== int,0,
36 "1/undersample"),
37 ]
38 AbstractCommandline.__init__(self, cmd, **kwargs)
39
42
43
45 """Create a commandline for the CompareAce program.
46
47 XXX This could use more checking for valid paramters to the program.
48 """
49 - def __init__(self, cmd="CompareACE", **kwargs):
50 import os.path
51 self.parameters = \
52 [
53 _Argument(["motif1"],["input","file"], os.path.exists,1,"name of file containing motif 1"),
54 _Argument(["motif2"],["input","file"], os.path.exists,1,"name of file containing motif 2"),
55 ]
56 AbstractCommandline.__init__(self, cmd, **kwargs)
57
60