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comparison smart_toolShed/SMART/Java/Python/wigExploder.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 #! /usr/bin/env python
2 #
3 # Copyright INRA-URGI 2009-2010
4 #
5 # This software is governed by the CeCILL license under French law and
6 # abiding by the rules of distribution of free software. You can use,
7 # modify and/ or redistribute the software under the terms of the CeCILL
8 # license as circulated by CEA, CNRS and INRIA at the following URL
9 # "http://www.cecill.info".
10 #
11 # As a counterpart to the access to the source code and rights to copy,
12 # modify and redistribute granted by the license, users are provided only
13 # with a limited warranty and the software's author, the holder of the
14 # economic rights, and the successive licensors have only limited
15 # liability.
16 #
17 # In this respect, the user's attention is drawn to the risks associated
18 # with loading, using, modifying and/or developing or reproducing the
19 # software by the user in light of its specific status of free software,
20 # that may mean that it is complicated to manipulate, and that also
21 # therefore means that it is reserved for developers and experienced
22 # professionals having in-depth computer knowledge. Users are therefore
23 # encouraged to load and test the software's suitability as regards their
24 # requirements in conditions enabling the security of their systems and/or
25 # data to be ensured and, more generally, to use and operate it in the
26 # same conditions as regards security.
27 #
28 # The fact that you are presently reading this means that you have had
29 # knowledge of the CeCILL license and that you accept its terms.
30 #
31 """Explode wig files into several files, one for each chromosome"""
32
33 import os, re, sys
34 from optparse import OptionParser
35
36
37 if __name__ == "__main__":
38
39 # parse command line
40 description = "Wig Exploder v1.0.1: Explode a big WIG file into several smaller WIG files (one per chromosome). [Category: Personal]"
41
42 parser = OptionParser(description = description)
43 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in WIG format]")
44 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output directory [compulsory] [format: directory]")
45 parser.add_option("-s", "--strand", dest="strand", action="store", default=None, type="string", help="strand of the input WIG file (if any) [format: choice (+, -)]")
46 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
47 (options, args) = parser.parse_args()
48
49 inputFile = open(options.inputFileName)
50
51 files = {}
52 file = None
53 trackLine = None
54 strand = ""
55 if options.strand != None:
56 strand = options.strand
57
58 for line in inputFile:
59 line = line.strip()
60
61 if line.startswith("track"):
62 trackLine = line
63 continue
64
65 m1 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=\d+\s+step=\d+\s*$", line)
66 m2 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=\d+\s+step=\d+\s+span=\d+\s*$", line)
67 m3 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s*$", line)
68 m4 = re.search(r"^\s*variableStep\s+chrom=(\S+)span=\d+\s*$", line)
69
70 m = None
71 if m1 != None:
72 m = m1
73 elif m2 != None:
74 m = m2
75 elif m3 != None:
76 m = m3
77 elif m4 != None:
78 m = m4
79
80 if m != None:
81 chromosome = m.group(1)
82
83 if chromosome in files:
84 file = files[chromosome]
85 else:
86 file = open("%s%s%s%s.wig" % (options.output, os.sep, chromosome, strand), "w")
87 files[chromosome] = file
88 if trackLine != None:
89 file.write("%s\n" % (trackLine))
90
91 if file == None:
92 sys.exit("Header is missing (current first line is '%s')! Aborting..." % (line))
93
94 file.write("%s\n" % (line))
95
96 inputFile.close()
97
98 for chromosome in files:
99 files[chromosome].close()