Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/wigExploder.py @ 1:30c5431d8ce4

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Uploaded
author yufei-luo
date Thu, 17 Jan 2013 11:01:51 -0500
parents e0f8dcca02ed
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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4 #
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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.
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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.
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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.
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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.
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9 # "http://www.cecill.info".
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10 #
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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.
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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.
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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.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 # liability.
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16 #
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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.
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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.
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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.
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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.
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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.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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.
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24 # requirements in conditions enabling the security of their systems and/or
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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.
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26 # same conditions as regards security.
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27 #
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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.
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 """Explode wig files into several files, one for each chromosome"""
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32
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33 import os, re, sys
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34 from optparse import OptionParser
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35
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36
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37 if __name__ == "__main__":
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38
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39 # parse command line
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40 description = "Wig Exploder v1.0.1: Explode a big WIG file into several smaller WIG files (one per chromosome). [Category: Personal]"
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41
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42 parser = OptionParser(description = description)
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43 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in WIG format]")
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44 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output directory [compulsory] [format: directory]")
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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 (+, -)]")
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46 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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47 (options, args) = parser.parse_args()
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48
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49 inputFile = open(options.inputFileName)
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50
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51 files = {}
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52 file = None
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53 trackLine = None
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54 strand = ""
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55 if options.strand != None:
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56 strand = options.strand
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57
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58 for line in inputFile:
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59 line = line.strip()
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60
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61 if line.startswith("track"):
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62 trackLine = line
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63 continue
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64
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65 m1 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=\d+\s+step=\d+\s*$", line)
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66 m2 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=\d+\s+step=\d+\s+span=\d+\s*$", line)
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67 m3 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s*$", line)
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68 m4 = re.search(r"^\s*variableStep\s+chrom=(\S+)span=\d+\s*$", line)
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69
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70 m = None
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71 if m1 != None:
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72 m = m1
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73 elif m2 != None:
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74 m = m2
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75 elif m3 != None:
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76 m = m3
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77 elif m4 != None:
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78 m = m4
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79
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80 if m != None:
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81 chromosome = m.group(1)
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82
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83 if chromosome in files:
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84 file = files[chromosome]
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85 else:
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86 file = open("%s%s%s%s.wig" % (options.output, os.sep, chromosome, strand), "w")
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87 files[chromosome] = file
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88 if trackLine != None:
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89 file.write("%s\n" % (trackLine))
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90
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91 if file == None:
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92 sys.exit("Header is missing (current first line is '%s')! Aborting..." % (line))
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93
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94 file.write("%s\n" % (line))
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95
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96 inputFile.close()
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97
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98 for chromosome in files:
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99 files[chromosome].close()