|
0
|
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__()
|
