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comparison long-orfs_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 --> long-orfs
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 Long-ORFs input options...'
14 parser = optparse.OptionParser()
15 parser.add_option('--loSequence', dest='sequence', help='')
16 parser.add_option('--loStartCodons', dest='start_codons', help='')
17 parser.add_option('--loEntropy', dest='entropy', help='')
18 parser.add_option('--loFixed', action='store_true', dest='fixed', help='')
19 parser.add_option('--loMinLen', dest='min_len', type='int', help='')
20 parser.add_option('--loIgnore', dest='ignore', help='')
21 parser.add_option('--loLinear', action='store_true', dest='linear', help='')
22 parser.add_option('--loLengthOpt', action='store_true', dest='length_opt', help='')
23 parser.add_option('--loNoHeader', action='store_true', dest='no_header', help='')
24 parser.add_option('--loMaxOverlap', dest='max_olap', type='int', help='')
25 parser.add_option('--loCutoff', dest='cutoff', type='float', help='')
26 parser.add_option('--loWithoutStops', action='store_true', dest='without_stops', help='')
27 parser.add_option('--loTransTable', dest='trans_table', type='int', help='')
28 parser.add_option('--loStopCodons', dest='stop_codons', help='')
29 parser.add_option('--loOutput', dest='output', help='')
30 parser.add_option('--logfile', dest='logfile', help='')
31 (options, args) = parser.parse_args()
32 if len(args) > 0:
33 parser.error('Wrong number of arguments')
34
35 # build Long-ORFs command to be executed
36 sequence = options.sequence
37 if options.start_codons:
38 start_codons = '--start_codons %s' % (options.start_codons)
39 else:
40 start_codons = ''
41 if options.entropy:
42 entropy = '--entropy %s' % (options.entropy)
43 else:
44 entropy = ''
45 if options.fixed:
46 fixed = '--fixed'
47 else:
48 fixed = ''
49 if options.min_len is not None:
50 min_len = '--min_len %d' % (options.min_len)
51 else:
52 min_len = ''
53 if options.ignore:
54 ignore = '--ignore %s' % (options.ignore)
55 else:
56 ignore = ''
57 if options.linear:
58 linear = '--linear'
59 else:
60 linear = ''
61 if options.length_opt:
62 length_opt = '--length_opt'
63 else:
64 length_opt = ''
65 if options.no_header:
66 no_header = '--no_header'
67 else:
68 no_header = ''
69 if options.max_olap is not None:
70 max_olap = '--max_olap %d' % (options.max_olap)
71 else:
72 max_olap = ''
73 if options.cutoff is not None:
74 cutoff = '--cutoff %s' % (options.cutoff)
75 else:
76 cutoff = ''
77 if options.without_stops:
78 without_stops = '--without_stops'
79 else:
80 without_stops = ''
81 if options.trans_table is not None:
82 trans_table = '--trans_table %s' % (options.trans_table)
83 else:
84 trans_table = ''
85 if options.stop_codons:
86 stop_codons = '--stop_codons %s' % (options.stop_codons)
87 else:
88 stop_codons = ''
89 output = options.output
90 logfile = options.logfile
91
92 # Build Long-ORFs command
93 cmd = 'long-orfs %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s' % (sequence, start_codons, entropy, fixed, min_len, ignore, linear, length_opt, no_header, max_olap, cutoff, without_stops, trans_table, stop_codons, output)
94 print '\nLong-ORFs command to be executed: \n %s' % (cmd)
95
96 print 'Executing Long-ORFs...'
97 if logfile:
98 log = open(logfile, 'w')
99 else:
100 log = sys.stdout
101 try:
102 subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True)
103 finally:
104 if log != sys.stdout:
105 log.close()
106 print 'Long-ORFs executed!'
107
108
109 if __name__ == "__main__":
110 __main__()