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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
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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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,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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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
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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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
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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
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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 """Remove all dirty sequences"""
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32
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33 import os
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34 import sys
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35 from optparse import OptionParser
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36 from commons.core.parsing.FastaParser import *
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37 from commons.core.writer.FastaWriter import *
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38 from commons.core.parsing.FastqParser import *
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39 from commons.core.writer.FastqWriter import *
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40 from SMART.Java.Python.misc.Progress import *
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41 from SMART.Java.Python.misc.RPlotter import *
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42
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43
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44 if __name__ == "__main__":
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45
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46 # parse command line
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47 description = "Restrict from nucleotide v1.0.1: Remove the sequences with ambiguous nucleotides. [Category: Personal]"
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48
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49 parser = OptionParser(description = description)
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50 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in sequence format given by -f]")
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51 parser.add_option("-f", "--format", dest="inputFileName", action="store", default="fasta", type="string", help="format of the input and output files [compulsory] [format: sequence file format]")
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52 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in sequence format given by -f]")
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53 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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54 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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55 (options, args) = parser.parse_args()
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56
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57 # treat items
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58 if options.format == "fasta":
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59 parser = FastaParser(options.inputFileName, options.verbosity)
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60 writer = FastaWriter(options.outputFileName, options.verbosity)
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61 elif options.format == "fastq":
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62 parser = FastqParser(options.inputFileName, options.verbosity)
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63 writer = FastqWriter(options.outputFileName, options.verbosity)
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64 else:
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65 sys.exit("Do not understand '%s' format." % (options.format))
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66 nbSequences = parser.getNbSequences()
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67 print "sequences: %d" % (nbSequences)
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68
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69 progress = Progress(nbSequences, "Analyzing sequences of %s" % (options.inputFileName), options.verbosity)
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70 nbKept = 0
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71 for sequence in parser.getIterator():
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72 if not sequence.containsAmbiguousNucleotides():
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73 writer.addSequence(sequence)
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74 nbKept += 1
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75 progress.inc()
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76 progress.done()
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77
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78 print "%d items, %d kept (%.2f%%)" % (nbSequences, nbKept, float(nbKept) / nbSequences * 100)
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