1 """Definitions for interacting with AlignAce.
2 """
3 from Bio import Application
4 from Bio.Application import _Option,_Argument
5
7 """Create a commandline for the AlignAce program.
8
9 XXX This could use more checking for valid paramters to the program.
10 """
12
13 Application.AbstractCommandline.__init__(self)
14 self.program_name = cmd
15
16 self.parameters = \
17 [
18 _Option(["-i","input","Sequence File"],["input"],lambda x : x.__class__== str,1,
19 "Input Sequence file in FASTA format."),
20
21 _Option(["-numcols","numcols","number of columns to align"],["input"],lambda x : x.__class__== int,0,
22 "Number of columns to align"),
23
24 _Option(["-expect","expect","number of sites expected in model "],["input"],lambda x : x.__class__== int,0,
25 "number of sites expected in model "),
26
27 _Option(["-gcback","gcback","background fractional GC content of input sequence"],["input"],lambda x : x.__class__== float,0,
28 "background fractional GC content of input sequence"),
29
30 _Option(["-minpass","minpass","minimum number of non-improved passes in phase 1"],["input"],lambda x : x.__class__== int,0,
31 "minimum number of non-improved passes in phase 1"),
32
33 _Option(["-seed","seed","set seed for random number generator (time)"],["input"],lambda x : x.__class__== int,0,
34 "set seed for random number generator (time)"),
35
36 _Option(["-undersample","undersample","possible sites / (expect * numcols * seedings)"],["input"],lambda x : x.__class__== int,0,
37 "possible sites / (expect * numcols * seedings)"),
38
39 _Option(["-oversample","oversample","1/undersample"],["input"],lambda x : x.__class__== int,0,
40 "1/undersample"),
41 ]
42
45
46
47
49 """Create a commandline for the CompareAce program.
50
51 XXX This could use more checking for valid paramters to the program.
52 """
54
55 import os.path
56 Application.AbstractCommandline.__init__(self)
57 self.program_name = cmd
58
59 self.parameters = \
60 [
61 _Argument(["motif1"],["input","file"], os.path.exists,1,"name of file containing motif 1"),
62 _Argument(["motif2"],["input","file"], os.path.exists,1,"name of file containing motif 2"),
63 ]
64
67