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comparison edena_ovl_wrapper.py @ 1:cd6cc6d76708 draft

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Simplify passing repeated params to Python script. Add more info to help sections.
author crs4
date Fri, 18 Oct 2013 14:09:11 -0400
parents 60609a9cef3b
children
comparison
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0:60609a9cef3b 1:cd6cc6d76708
11 11
12 def __main__(): 12 def __main__():
13 # load arguments 13 # load arguments
14 print 'Parsing Edena (overlapping) input options...' 14 print 'Parsing Edena (overlapping) input options...'
15 parser = optparse.OptionParser() 15 parser = optparse.OptionParser()
16 parser.add_option('--unpaired_input', dest='unpaired_input', help='') 16 parser.add_option('--unpaired_input', action='append', dest='unpaired_input', help='')
17 parser.add_option('--dr_pair_1', dest='dr_pair_1', help='') 17 parser.add_option('--dr_pair_1', action='append', dest='dr_pair_1', help='')
18 parser.add_option('--dr_pair_2', dest='dr_pair_2', help='') 18 parser.add_option('--dr_pair_2', action='append', dest='dr_pair_2', help='')
19 parser.add_option('--rd_pair_1', dest='rd_pair_1', help='') 19 parser.add_option('--rd_pair_1', action='append', dest='rd_pair_1', help='')
20 parser.add_option('--rd_pair_2', dest='rd_pair_2', 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='') 21 parser.add_option('--nThreads', dest='nThreads', type='int', help='')
22 parser.add_option('--minOlap', dest='minOlap', type='int', help='') 22 parser.add_option('--minOlap', dest='minOlap', type='int', help='')
23 parser.add_option('--readsTruncation', dest='readsTruncation', type='int', help='') 23 parser.add_option('--readsTruncation', dest='readsTruncation', type='int', help='')
24 parser.add_option('--output', dest='output', help='') 24 parser.add_option('--output', dest='output', help='')
25 parser.add_option('--logfile', dest='logfile', help='') 25 parser.add_option('--logfile', dest='logfile', help='')
26 (options, args) = parser.parse_args() 26 (options, args) = parser.parse_args()
27 if len(args) > 0: 27 if len(args) > 0:
28 parser.error('Wrong number of arguments') 28 parser.error('Wrong number of arguments')
29 29
30 # build Edena (overlapping) command to be executed 30 # build Edena (overlapping) command to be executed
31 # unpaired input(s) 31 # unpaired input(s)
32 if options.unpaired_input: 32 if options.unpaired_input:
33 unpaired_inputs = options.unpaired_input.split('+')[0:-1]
34 unpaired_input = '-r' 33 unpaired_input = '-r'
35 for item in unpaired_inputs: 34 for item in options.unpaired_input:
36 unpaired_input += ' %s' % (item) 35 unpaired_input += ' %s' % (item)
37 else: 36 else:
38 unpaired_input = '' 37 unpaired_input = ''
39 # direct-reverse paired-end files 38 # direct-reverse paired-end files
40 if options.dr_pair_1 and options.dr_pair_2: 39 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' 40 dr_pairs = '-DRpairs'
44 for i in xrange(len(dr_pairs_1)): 41 for i in range(len(options.dr_pair_1)):
45 dr_pairs += ' %s %s' % (dr_pairs_1[i], dr_pairs_2[i]) 42 dr_pairs += ' %s %s' % (options.dr_pair_1[i], options.dr_pair_2[i])
46 else: 43 else:
47 dr_pairs = '' 44 dr_pairs = ''
48 # reverse-direct paired-end files 45 # reverse-direct paired-end files
49 if options.rd_pair_1 and options.rd_pair_2: 46 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' 47 rd_pairs = '-RDpairs'
53 for i in xrange(len(rd_pairs_1)): 48 for i in range(len(options.rd_pair_1)):
54 rd_pairs += ' %s %s' % (rd_pairs_1[i], rd_pairs_2[i]) 49 rd_pairs += ' %s %s' % (options.rd_pair_1[i], options.rd_pair_2[i])
55 else: 50 else:
56 rd_pairs = '' 51 rd_pairs = ''
57 # nThreads 52 # nThreads
58 if options.nThreads is not None: 53 nThreads = '-nThreads %d' % (options.nThreads) if options.nThreads is not None else ''
59 nThreads = '-nThreads %d' % (options.nThreads)
60 else:
61 nThreads = ''
62 # minimum overlap 54 # minimum overlap
63 if options.minOlap is not None: 55 minOlap = '-M %d' % (options.minOlap) if options.minOlap is not None else ''
64 minOlap = '-M %d' % (options.minOlap)
65 else:
66 minOlap = ''
67 # 3' end reads truncation 56 # 3' end reads truncation
68 if options.readsTruncation is not None: 57 readsTruncation = '-t %d' % (options.readsTruncation) if options.readsTruncation is not None else ''
69 readsTruncation = '-t %d' % (options.readsTruncation)
70 else:
71 readsTruncation = ''
72 # output file(s) 58 # output file(s)
73 output = options.output 59 output = options.output
74 logfile = options.logfile 60 logfile = options.logfile
75 61
76 # Build Edena (overlapping) command 62 # 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) 63 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 ) 64 print '\nEdena (overlapping) command to be executed:\n %s' % (cmd)
79 65
80 # Execution of Edena 66 # Execution of Edena
81 print 'Executing Edena (overlapping)...' 67 print 'Executing Edena (overlapping)...'
82 if logfile: 68 log = open(logfile, 'w') if logfile else sys.stdout
83 log = open(logfile, 'w')
84 else:
85 log = sys.stdout
86 try: 69 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...") 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...")
88 finally: 71 finally:
89 if log != sys.stdout: 72 if log != sys.stdout:
90 log.close() 73 log.close()
91 print 'Edena (overlapping) executed!' 74 print 'Edena (overlapping) executed!'
92 75
93 shutil.move( "galaxy_output.ovl", output) 76 shutil.move('galaxy_output.ovl', output)
94 77
95 78
96 if __name__ == "__main__": 79 if __name__ == "__main__":
97 __main__() 80 __main__()