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comparison anomaly_wrapper.py @ 0:9c8ffce71f7c draft default tip

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author crs4
date Mon, 09 Sep 2013 12:16:17 -0400
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-1:000000000000 0:9c8ffce71f7c
1 # -*- coding: utf-8 -*-
2 """
3 Glimmer --> anomaly
4 version 0.2 (andrea.pinna@crs4.it)
5 """
6
7 import optparse
8 import subprocess
9 import sys
10
11 def __main__():
12 # load arguments
13 print 'Parsing Anomaly input options...'
14 parser = optparse.OptionParser()
15 parser.add_option('--anSequence', dest='sequence', help='')
16 parser.add_option('--anCoords', dest='coords', help='')
17 parser.add_option('--anCheckFirstCodon', action='store_true', dest='check_first_codon', help='')
18 parser.add_option('--anCheckStopCodon', action='store_true', dest='check_stop_codon', help='')
19 parser.add_option('--anStartCodons', dest='start_codons', help='')
20 parser.add_option('--anStopCodons', dest='stop_codons', help='')
21 parser.add_option('--anOutput', dest='output', help='')
22 parser.add_option('--logfile', dest='logfile', help='')
23 (options, args) = parser.parse_args()
24 if len(args) > 0:
25 parser.error('Wrong number of arguments')
26
27 # build Anomaly command to be executed
28 # sequence file
29 sequence = options.sequence
30 coords = options.coords
31 if options.start_codons:
32 start_codons = '-A %s' % (options.start_codons)
33 else:
34 start_codons = ''
35 if options.stop_codons:
36 stop_codons = '-Z %s' % (options.stop_codons)
37 else:
38 stop_codons = ''
39 if options.check_first_codon:
40 check_first_codon = '-s'
41 else:
42 check_first_codon = ''
43 if options.check_stop_codon:
44 check_stop_codon = '-t'
45 else:
46 check_stop_codon = ''
47 output = options.output
48 logfile = options.logfile
49
50 # Build Anomaly command
51 cmd = 'anomaly %s %s %s %s %s %s > %s' % (start_codons, check_first_codon, check_stop_codon, stop_codons, sequence, coords, output)
52 print '\nAnomaly command to be executed: \n %s' % (cmd)
53
54 print 'Executing Anomaly...'
55 if logfile:
56 log = open(logfile, 'w')
57 else:
58 log = sys.stdout
59 try:
60 subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True)
61 finally:
62 if log != sys.stdout:
63 log.close()
64 print 'Anomaly executed!'
65
66
67 if __name__ == "__main__":
68 __main__()