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comparison edena_ovl_wrapper.py @ 2:b8c6a38530eb draft default tip

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Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA _SITE_OPTIONS. Directly call edena, remove edena_ovl_wrapper.py and edena_ass_wrapper.py . Discard stderr instead of redirecting to stdout. Do not redirect stdout to logfile. Add readme.rst .
author crs4
date Fri, 31 Jan 2014 12:08:21 -0500
parents cd6cc6d76708
children
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1:cd6cc6d76708 2:b8c6a38530eb
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', action='append', dest='unpaired_input', help='')
17 parser.add_option('--dr_pair_1', action='append', dest='dr_pair_1', help='')
18 parser.add_option('--dr_pair_2', action='append', dest='dr_pair_2', help='')
19 parser.add_option('--rd_pair_1', action='append', dest='rd_pair_1', help='')
20 parser.add_option('--rd_pair_2', action='append', 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_input = '-r'
34 for item in options.unpaired_input:
35 unpaired_input += ' %s' % (item)
36 else:
37 unpaired_input = ''
38 # direct-reverse paired-end files
39 if options.dr_pair_1 and options.dr_pair_2:
40 dr_pairs = '-DRpairs'
41 for i in range(len(options.dr_pair_1)):
42 dr_pairs += ' %s %s' % (options.dr_pair_1[i], options.dr_pair_2[i])
43 else:
44 dr_pairs = ''
45 # reverse-direct paired-end files
46 if options.rd_pair_1 and options.rd_pair_2:
47 rd_pairs = '-RDpairs'
48 for i in range(len(options.rd_pair_1)):
49 rd_pairs += ' %s %s' % (options.rd_pair_1[i], options.rd_pair_2[i])
50 else:
51 rd_pairs = ''
52 # nThreads
53 nThreads = '-nThreads %d' % (options.nThreads) if options.nThreads is not None else ''
54 # minimum overlap
55 minOlap = '-M %d' % (options.minOlap) if options.minOlap is not None else ''
56 # 3' end reads truncation
57 readsTruncation = '-t %d' % (options.readsTruncation) if options.readsTruncation is not None else ''
58 # output file(s)
59 output = options.output
60 logfile = options.logfile
61
62 # Build Edena (overlapping) command
63 cmd = 'edena %s %s %s %s %s %s -p galaxy_output' % (unpaired_input, dr_pairs, rd_pairs, nThreads, minOlap, readsTruncation)
64 print '\nEdena (overlapping) command to be executed:\n %s' % (cmd)
65
66 # Execution of Edena
67 print 'Executing Edena (overlapping)...'
68 log = open(logfile, 'w') if logfile else sys.stdout
69 try:
70 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...")
71 finally:
72 if log != sys.stdout:
73 log.close()
74 print 'Edena (overlapping) executed!'
75
76 shutil.move('galaxy_output.ovl', output)
77
78
79 if __name__ == "__main__":
80 __main__()