Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/launchPrank.py @ 31:0ab839023fe4

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
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30:5677346472b5 31:0ab839023fe4
1 #!/usr/bin/env python
2
3 import os
4 import sys
5 import getopt
6
7 from pyRepet.launcher.programLauncher import programLauncher
8
9
10 def help():
11 print
12 print "usage: launchPrank.py [ options ]"
13 print "options:"
14 print " -h: this help"
15 print " -i: name of the input file (format=fasta)"
16 print " -o: name of the output file (format=aligned fasta, default='inFileName'+fa_aln)"
17 print " -P: Prank's parameters"
18 print " -c: clean"
19 print " -v: verbose (default=0/1)"
20 print
21
22
23 def main():
24 """
25 Launch PRANK.
26 """
27 inFileName = ""
28 outFileName = ""
29 parameters = ""
30 clean = False
31 verbose = 0
32
33 try:
34 opts, args = getopt.getopt( sys.argv[1:], "hi:o:P:cv:" )
35 except getopt.GetoptError, err:
36 print str(err)
37 help()
38 sys.exit(1)
39 for o,a in opts:
40 if o == "-h":
41 help()
42 sys.exit(0)
43 elif o == "-i":
44 inFileName = a
45 elif o == "-o":
46 outFileName = a
47 elif o == "-P":
48 parameters = a
49 elif o == "-c":
50 clean = True
51 elif o == "-v":
52 verbose = int(a)
53
54 if inFileName == "":
55 print "ERROR: missing input file (-i)"
56 help()
57 sys.exit(1)
58
59 if not os.path.exists( inFileName ):
60 print "ERROR: can't find file '%s'" % ( inFileName )
61 help()
62 sys.exit(1)
63
64 if verbose > 0:
65 print "START %s" % ( sys.argv[0].split("/")[-1] )
66 sys.stdout.flush()
67
68 if outFileName == "":
69 outFileName = "%s.fa_aln" % ( inFileName )
70
71 pL = programLauncher( inFileName )
72 returnStatus = pL.launchPrank( outFileName, parameters, "yes", verbose )
73 if returnStatus != 0:
74 print "ERROR: launchPrank() returned '%i'" % ( returnStatus )
75 sys.exit(1)
76
77 if verbose > 0:
78 print "END %s" % ( sys.argv[0].split("/")[-1] )
79 sys.stdout.flush()
80
81 return 0
82
83
84 if __name__ == "__main__":
85 main()