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comparison edge_pro.py @ 0:7af33315bc5e draft

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author crs4
date Mon, 09 Sep 2013 06:11:47 -0400
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children f77ce4f92b46
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-1:000000000000 0:7af33315bc5e
1 # -*- coding: utf-8 -*-
2 """
3 Wrapper for EDGE - Gene expression in Prokaryotes
4 Author: Paolo Uva paolo dot uva at crs4 dot it
5 Date: March 18, 2013
6 """
7
8 import glob
9 import optparse
10 import os
11 import shutil
12 import subprocess
13 import tempfile
14 import sys
15
16 def __main__():
17 # Parse Command Line
18 parser = optparse.OptionParser()
19 # Input
20 parser.add_option('-g', '--genome', dest="genome")
21 parser.add_option('-p', '--ptt', dest="ptt")
22 parser.add_option('-r', '--rnt', dest="rnt")
23 parser.add_option('-u', '--input1', dest="input1")
24 parser.add_option('-v', '--input2', dest="input2")
25 parser.add_option('-t', '--num-threads', dest="num_threads", type='int')
26 parser.add_option('-m', '--minInsertSize', dest="minInsertSize", type='int')
27 parser.add_option('-M', '--maxInsertSize', dest="maxInsertSize", type='int')
28 parser.add_option('-w', '--window', dest="window", type='int')
29 parser.add_option('-i', '--utrSize', dest="utrSize", type='int')
30 parser.add_option('-x', '--similarity', dest="similarity", type='float')
31 parser.add_option('-c', '--minCoverage', dest="minCoverage", type='int')
32 parser.add_option('-l', '--readLength', dest="readLength", type='int')
33 # Output
34 parser.add_option('--out-aln', dest="out_aln")
35 parser.add_option('--out-rpkm', dest="out_rpkm")
36 parser.add_option('--out-log', dest="out_log")
37 (options, args) = parser.parse_args()
38 if len(args) > 0:
39 parser.error('Wrong number of arguments')
40
41 # Build command
42 if options.input2:
43 input2_flag = '-v %s' % (options.input2)
44 else:
45 input2_flag = ''
46 if options.num_threads is not None:
47 num_threads_flag = '-t %d' % options.num_threads
48 else:
49 num_threads_flag = ''
50 if options.minInsertSize is not None:
51 minInsertSize_flag = '-m %d' % options.minInsertSize
52 else:
53 minInsertSize_flag = ''
54 if options.maxInsertSize is not None:
55 maxInsertSize_flag = '-M %d' % options.maxInsertSize
56 else:
57 maxInsertSize_flag = ''
58 if options.window is not None:
59 window_flag = '-w %d' % options.window
60 else:
61 window_flag = ''
62 if options.utrSize is not None:
63 utrSize_flag = '-i %d' % options.utrSize
64 else:
65 utrSize_flag = ''
66 if options.similarity is not None:
67 similarity_flag = '-x %s' % options.similarity
68 else:
69 similarity_flag = ''
70 if options.readLength is not None:
71 readLength_flag = '-l %d' % (options.readLength)
72 else:
73 readLength_flag = ''
74 if options.minCoverage is not None:
75 minCoverage_flag = '-c %d' % options.minCoverage
76 else:
77 minCoverage_flag = ''
78
79 wd = tempfile.mkdtemp()
80 try:
81 prefix = os.path.join(wd, 'out')
82 cl = 'edge.pl -g %s -p %s -r %s -u %s -o %s %s %s %s %s %s %s %s %s %s' % (options.genome, options.ptt, options.rnt, options.input1, prefix, input2_flag, num_threads_flag, minInsertSize_flag, maxInsertSize_flag, window_flag, utrSize_flag, similarity_flag, readLength_flag, minCoverage_flag)
83 print cl
84
85 if options.out_log:
86 sout = open(options.out_log, 'w')
87 else:
88 sout = sys.stdout
89 try:
90 subprocess.check_call(cl, stdout=sout, stderr=subprocess.STDOUT, shell=True) # need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there
91 finally:
92 if sout != sys.stdout:
93 sout.close()
94
95 # Move alignment file
96 shutil.move(prefix + '.alignments', options.out_aln)
97 # Concatenate multiple RPKM files together
98 with open(options.out_rpkm, 'wb') as destination:
99 for filename in glob.iglob(prefix + '.rpkm_*'):
100 with open(filename, 'rb') as source:
101 shutil.copyfileobj(source, destination)
102 finally:
103 shutil.rmtree(wd)
104
105
106 if __name__ == "__main__":
107 __main__()