1
2
3
4
5 """Command line wrapper for the multiple alignment program PROBCONS.
6
7 http://probcons.stanford.edu/
8
9 Citations:
10 Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS:
11 Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15:
12 330-340.
13
14 Last checked agains version: 1.12
15 """
16 import types
17 from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline
18
20 """Command line wrapper for the multiple alignment program PROBCONS."""
21 - def __init__(self, cmd="probcons", **kwargs):
22 self.parameters = \
23 [
24
25
26
27
28
29 _Switch(["-clustalw", "clustalw"], ["input"],
30 "Use CLUSTALW output format instead of MFA"),
31 _Option(["-c", "c", "--consistency", "consistency" ], ["input"],
32 lambda x: x in range(0,6),
33 0,
34 "Use 0 <= REPS <= 5 (default: 2) passes of consistency transformation",
35 0),
36 _Option(["-ir", "--iterative-refinement", "iterative-refinement", "ir"], ["input"],
37 lambda x: x in range(0,1001),
38 0,
39 "Use 0 <= REPS <= 1000 (default: 100) passes of iterative-refinement",
40 0),
41 _Option(["-pre", "--pre-training", "pre-training", "pre"], ["input"],
42 lambda x: x in range(0,21),
43 0,
44 "Use 0 <= REPS <= 20 (default: 0) rounds of pretraining",
45 0),
46 _Switch(["-pairs", "pairs"], ["input"],
47 "Generate all-pairs pairwise alignments"),
48 _Switch(["-viterbi", "viterbi"], ["input"],
49 "Use Viterbi algorithm to generate all pairs (automatically enables -pairs)"),
50 _Switch(["-verbose", "verbose"], ["input"],
51 "Report progress while aligning (default: off)"),
52 _Option(["-annot", "annot"], ["input"],
53 None,
54 0,
55 "Write annotation for multiple alignment to FILENAME",
56 0),
57 _Option(["-t", "t", "--train", "train"], ["input"],
58 None,
59 0,
60 "Compute EM transition probabilities, store in FILENAME (default: no training)",
61 0),
62 _Switch(["-e", "e", "--emissions", "emissions"], ["input"],
63 "Also reestimate emission probabilities (default: off)"),
64 _Option(["-p", "p", "--paramfile", "paramfile"], ["input"],
65 None,
66 0,
67 "Read parameters from FILENAME",
68 0),
69 _Switch(["-a", "--alignment-order", "alignment-order", "a"], ["input"],
70 "Print sequences in alignment order rather than input order (default: off)"),
71
72 _Argument(["input"], ["input", "file"], None, 1,
73 "Input file name. Must be multiple FASTA alignment "+ \
74 "(MFA) format"),
75 ]
76 AbstractCommandline.__init__(self, cmd, **kwargs)
77