Mercurial > repos > yufei-luo > s_mart

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

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Uploaded
author yufei-luo
date Thu, 17 Jan 2013 11:01:51 -0500
parents e0f8dcca02ed
children
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 """Restrict a sequence list with some names"""
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32
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33 from optparse import OptionParser
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34 from commons.core.parsing.ParserChooser import ParserChooser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 from commons.core.writer.WriterChooser import WriterChooser
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36 from SMART.Java.Python.misc.Progress import Progress
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37 from SMART.Java.Python.misc import Utils
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38
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39 class RestrictSequenceList(object):
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40
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41 def __init__(self, verbosity):
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42 self.verbosity = verbosity
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43 self.exclude = False
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44
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45 def setInputFileName(self, fileName, format):
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46 chooser = ParserChooser(self.verbosity)
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47 chooser.findFormat(format)
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48 self.parser = chooser.getParser(fileName)
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49
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50 def setExclusion(self, boolean):
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51 self.exclude = boolean
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52
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53 def setOutputFileName(self, fileName, format):
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54 chooser = WriterChooser(self.verbosity)
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55 chooser.findFormat(format)
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56 self.writer = chooser.getWriter(fileName)
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57
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58 def setNamesFileName(self, fileName):
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59 self.namesFileName = fileName
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60
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61 def _readNames(self):
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62 self.names = []
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63 handle = open(self.namesFileName)
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64 for name in handle:
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65 self.names.append(name.strip())
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66 handle.close()
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67
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68 def _write(self):
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69 nbElements = self.parser.getNbItems()
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70 progress = Progress(nbElements, "Parsing input file", self.verbosity)
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71 nbRead = 0
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72 nbWritten = 0
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73 for element in self.parser.getIterator():
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74 name = element.getName()
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75 nbRead += 1
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76 if Utils.xor(name in self.names, self.exclude):
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77 self.writer.addElement(element)
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78 nbWritten += 1
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79 if name in self.names:
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80 self.names.remove(name)
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81 progress.inc()
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82 progress.done()
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83 if self.verbosity > 0:
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84 print "%d read" % (nbRead)
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85 print "%d written (%d%%)" % (nbWritten, 0 if nbRead == 0 else round(float(nbWritten) / nbRead * 100))
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86
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87 def run(self):
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88 self._readNames()
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89 self._write()
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90 if self.names:
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91 print "Some names are not present in the file: %s" % ", ".join(self.names)
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92
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93
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94
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95 if __name__ == "__main__":
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96
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97 description = "Restrict Sequence List v1.0.1: Keep the elements of a list of sequences whose name is mentionned in a given file. [Category: Data Selection]"
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98
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99 parser = OptionParser(description = description)
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100 parser.add_option("-i", "--input", dest="inputFile", action="store", type="string", help="input file [compulsory] [format: file in sequence format given by -f]")
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101 parser.add_option("-f", "--format", dest="format", action="store", default="fasta", type="string", help="format of the input and output files [compulsory] [format: sequence file format] [default: fasta]")
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102 parser.add_option("-n", "--name", dest="names", action="store", type="string", help="names of the transcripts [compulsory] [format: file in TXT format]")
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103 parser.add_option("-o", "--output", dest="outputFile", action="store", type="string", help="output file [format: output file in sequence format given by -f]")
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104 parser.add_option("-x", "--exclude", dest="exclude", action="store_true", default=False, help="output all those whose name is NOT on the list [format: boolean]")
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105 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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106 (options, args) = parser.parse_args()
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107
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108 rsl = RestrictSequenceList(options.verbosity)
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109 rsl.setInputFileName(options.inputFile, options.format)
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110 rsl.setOutputFileName(options.outputFile, options.format)
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111 rsl.setNamesFileName(options.names)
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112 rsl.setExclusion(options.exclude)
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113 rsl.run()