Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/launchTCoffee.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 #!/usr/bin/env python
2
3 import os
4 import sys
5 import getopt
6 import exceptions
7
8 if not os.environ.has_key( "REPET_PATH" ):
9 print "ERROR: no environment variable REPET_PATH"
10 sys.exit(1)
11 sys.path.append( os.environ["REPET_PATH"] )
12
13 from pyRepet.launcher.programLauncher import programLauncher
14
15
16 def help():
17 print
18 print "usage: ",sys.argv[0],"[ options ]"
19 print "options:"
20 print " -h: this help"
21 print " -i: name of the input file (format='fasta')"
22 print " -P: parameters"
23 print " -o: name of the output file (format='aligned fasta', default='inFileName'+fa_aln)"
24 print " -c: clean"
25 print " -v: verbosity level (default=0/1)"
26 print
27
28
29 def main():
30
31 inFileName = ""
32 parameters = ""
33 outFileName = ""
34 clean = False
35 verbose = 0
36
37 try:
38 opts, args = getopt.getopt(sys.argv[1:],"hi:P:o:cv:")
39 except getopt.GetoptError, err:
40 print str(err); help(); sys.exit(1)
41 for o,a in opts:
42 if o == "-h":
43 help(); sys.exit(0)
44 elif o == "-i":
45 inFileName = a
46 elif o == "-P":
47 parameters = a
48 elif o == "-o":
49 outFileName = a
50 elif o == "-c":
51 clean = True
52 elif o == "-v":
53 verbose = "yes"
54
55 if inFileName == "" and parameters == "":
56 print "ERROR: missing compulsory options"
57 help()
58 sys.exit(1)
59
60 if outFileName == "":
61 outFileName = "%s.fa_aln" % ( inFileName )
62
63 if verbose > 0:
64 print "START %s" % (sys.argv[0].split("/")[-1])
65 sys.stdout.flush()
66
67 pL = programLauncher( inFileName )
68 pL.launchTcoffee( outFileName, parameters )
69
70 if verbose > 0:
71 print "END %s" % (sys.argv[0].split("/")[-1])
72 sys.stdout.flush()
73
74 return 0
75
76
77 if __name__ == "__main__":
78 main()