6
+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2011
+ − 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 import random
+ − 32 from optparse import OptionParser
+ − 33 from commons.core.parsing.ParserChooser import ParserChooser
+ − 34 from commons.core.writer.TranscriptWriter import TranscriptWriter
+ − 35 from SMART.Java.Python.structure.Transcript import Transcript
+ − 36 from SMART.Java.Python.misc.Progress import Progress
+ − 37
+ − 38 class GetRandomSubset(object):
+ − 39
+ − 40 def __init__(self, verbosity):
+ − 41 self.verbosity = verbosity
+ − 42
+ − 43 def setInputFile(self, fileName, format):
+ − 44 chooser = ParserChooser(self.verbosity)
+ − 45 chooser.findFormat(format)
+ − 46 self.parser = chooser.getParser(fileName)
+ − 47
+ − 48 def setNumber(self, number, percent):
+ − 49 if number != None:
+ − 50 self.number = number
+ − 51 elif percent != None:
+ − 52 self.number = int(float(percent) / 100 * self.parser.getNbTranscripts())
+ − 53 else:
+ − 54 raise Exception("Error! Number of elements to output is not given!")
+ − 55
+ − 56 def setOutputFile(self, fileName):
+ − 57 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
+ − 58
+ − 59 def chooseElements(self):
+ − 60 self.randomIndices = random.sample(range(self.parser.getNbTranscripts()), self.number)
+ − 61
+ − 62 def run(self):
+ − 63 self.chooseElements()
+ − 64 progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
+ − 65 nbWritten = 0
+ − 66 for cpt1, transcript in enumerate(self.parser.getIterator()):
+ − 67 if cpt1 in self.randomIndices:
+ − 68 self.writer.addTranscript(transcript)
+ − 69 nbWritten += 1
+ − 70 progress.inc()
+ − 71 self.writer.write()
+ − 72 self.writer.close()
+ − 73 progress.done()
+ − 74 if self.verbosity > 1:
+ − 75 print "%d transcripts read" % (self.parser.getNbTranscripts())
+ − 76 print "%d transcripts written" % (nbWritten)
+ − 77
+ − 78
+ − 79 if __name__ == "__main__":
+ − 80
+ − 81 description = "Get Random Subset v1.0.1: Get a random sub-set of a list of genomic coordinates. [Category: Personal]"
+ − 82
+ − 83 parser = OptionParser(description = description)
+ − 84 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 85 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
+ − 86 parser.add_option("-n", "--number", dest="number", action="store", default=None, type="string", help="number of elements to output [format: int]")
+ − 87 parser.add_option("-p", "--percent", dest="percent", action="store", default=None, type="string", help="percentage of elements to output (between 0 and 100) [format: int]")
+ − 88 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
+ − 89 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 90 (options, args) = parser.parse_args()
+ − 91
+ − 92 grs = GetRandomSubset(options.verbosity)
+ − 93 grs.setInputFile(options.inputFileName, options.format)
+ − 94 grs.setNumber(options.number, options.percent)
+ − 95 grs.setOutputFile(options.outputFileName)
+ − 96 grs.run()