Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/sequenceListSplitter.py @ 4:1fc014126d55

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Uploaded
author yufei-luo
date Fri, 18 Jan 2013 04:45:50 -0500
parents e0f8dcca02ed
children
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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 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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30 #
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31 """Split a FASTA file into several shorter ones"""
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32
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33 from optparse import OptionParser
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34 from commons.core.parsing.SequenceListParser import *
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35 from commons.core.writer.FastaWriter import *
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36 from SMART.Java.Python.misc.Progress import *
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37
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38
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39 if __name__ == "__main__":
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40
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41 # parse command line
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42 description = "Sequence List Splitter v1.0.1: Split a list of big sequences into small chunks. [Category: Personnal]"
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43
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44 parser = OptionParser(description = description)
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45 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in FASTA format]")
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46 parser.add_option("-o", "--output", dest="outputFileNames", action="store", type="string", help="output files [compulsory] [format: output file in FASTA format]")
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47 parser.add_option("-n", "--number", dest="number", action="store", default=10, type="int", help="number of splits [compulsory] [format: int] [default: 10]")
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48 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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49 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
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50 (options, args) = parser.parse_args()
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51
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52 if options.log:
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53 logHandle = open(options.outputFileNames + ".log", "w")
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54
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55 # split file
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56 sequenceListParser = SequenceListParser(options.inputFileName, options.verbosity)
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57 nbSequences = sequenceListParser.getNbSequences()
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58 nbSequencesByFile = math.ceil(nbSequences / options.number)
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59
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60 # write into files
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61 currentFileNumber = 1
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62 writer = FastaWriter("%s%i.fasta" % (options.outputFileNames, currentFileNumber), options.verbosity)
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63 nbSequencesHere = 0
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64 progress = Progress(nbSequences, "Writing files", options.verbosity)
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65 for sequence in sequenceListParser.getIterator():
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66 writer.addSequence(sequence)
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67 nbSequencesHere += 1
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68 if nbSequencesHere == nbSequencesByFile:
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69 currentFileNumber += 1
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70 writer = FastaWriter("%s%i.fasta" % (options.outputFileNames, currentFileNumber), options.verbosity)
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71 nbSequencesHere = 0
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72 progress.inc()
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73 progress.done()