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comparison edena_ovl_wrapper.py @ 0:60609a9cef3b draft

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author crs4
date Mon, 09 Sep 2013 05:44:31 -0400
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children cd6cc6d76708
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-1:000000000000 0:60609a9cef3b
1 # -*- coding: utf-8 -*-
2 """
3 Edena (overlapping)
4 version 0.2.1 (andrea.pinna@crs4.it)
5 """
6
7 import optparse
8 import shutil
9 import subprocess
10 import sys
11
12 def __main__():
13 # load arguments
14 print 'Parsing Edena (overlapping) input options...'
15 parser = optparse.OptionParser()
16 parser.add_option('--unpaired_input', dest='unpaired_input', help='')
17 parser.add_option('--dr_pair_1', dest='dr_pair_1', help='')
18 parser.add_option('--dr_pair_2', dest='dr_pair_2', help='')
19 parser.add_option('--rd_pair_1', dest='rd_pair_1', help='')
20 parser.add_option('--rd_pair_2', dest='rd_pair_2', help='')
21 parser.add_option('--nThreads', dest='nThreads', type='int', help='')
22 parser.add_option('--minOlap', dest='minOlap', type='int', help='')
23 parser.add_option('--readsTruncation', dest='readsTruncation', type='int', help='')
24 parser.add_option('--output', dest='output', help='')
25 parser.add_option('--logfile', dest='logfile', help='')
26 (options, args) = parser.parse_args()
27 if len(args) > 0:
28 parser.error('Wrong number of arguments')
29
30 # build Edena (overlapping) command to be executed
31 # unpaired input(s)
32 if options.unpaired_input:
33 unpaired_inputs = options.unpaired_input.split('+')[0:-1]
34 unpaired_input = '-r'
35 for item in unpaired_inputs:
36 unpaired_input += ' %s' % (item)
37 else:
38 unpaired_input = ''
39 # direct-reverse paired-end files
40 if options.dr_pair_1 and options.dr_pair_2:
41 dr_pairs_1 = options.dr_pair_1.split('+')[0:-1]
42 dr_pairs_2 = options.dr_pair_2.split('+')[0:-1]
43 dr_pairs = '-DRpairs'
44 for i in xrange(len(dr_pairs_1)):
45 dr_pairs += ' %s %s' % (dr_pairs_1[i], dr_pairs_2[i])
46 else:
47 dr_pairs = ''
48 # reverse-direct paired-end files
49 if options.rd_pair_1 and options.rd_pair_2:
50 rd_pairs_1 = options.rd_pair_1.split('+')[0:-1]
51 rd_pairs_2 = options.rd_pair_2.split('+')[0:-1]
52 rd_pairs = '-RDpairs'
53 for i in xrange(len(rd_pairs_1)):
54 rd_pairs += ' %s %s' % (rd_pairs_1[i], rd_pairs_2[i])
55 else:
56 rd_pairs = ''
57 # nThreads
58 if options.nThreads is not None:
59 nThreads = '-nThreads %d' % (options.nThreads)
60 else:
61 nThreads = ''
62 # minimum overlap
63 if options.minOlap is not None:
64 minOlap = '-M %d' % (options.minOlap)
65 else:
66 minOlap = ''
67 # 3' end reads truncation
68 if options.readsTruncation is not None:
69 readsTruncation = '-t %d' % (options.readsTruncation)
70 else:
71 readsTruncation = ''
72 # output file(s)
73 output = options.output
74 logfile = options.logfile
75
76 # Build Edena (overlapping) command
77 cmd = 'edena %s %s %s %s %s %s -p galaxy_output' % (unpaired_input, dr_pairs, rd_pairs, nThreads, minOlap, readsTruncation)
78 print '\nEdena (overlapping) command to be executed: \n %s' % ( cmd )
79
80 # Execution of Edena
81 print 'Executing Edena (overlapping)...'
82 if logfile:
83 log = open(logfile, 'w')
84 else:
85 log = sys.stdout
86 try:
87 subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True) # need to redirect stderr because edena writes some logging info there (e.g. "Computing overlaps >=30...")
88 finally:
89 if log != sys.stdout:
90 log.close()
91 print 'Edena (overlapping) executed!'
92
93 shutil.move( "galaxy_output.ovl", output)
94
95
96 if __name__ == "__main__":
97 __main__()