Mercurial > repos > yufei-luo > s_mart

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

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