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+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2010
+ − 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 """Remove all dirty sequences"""
+ − 32
+ − 33 import os
+ − 34 import sys
+ − 35 from optparse import OptionParser
+ − 36 from commons.core.parsing.FastaParser import *
+ − 37 from commons.core.writer.FastaWriter import *
+ − 38 from commons.core.parsing.FastqParser import *
+ − 39 from commons.core.writer.FastqWriter import *
+ − 40 from SMART.Java.Python.misc.Progress import *
+ − 41 from SMART.Java.Python.misc.RPlotter import *
+ − 42
+ − 43
+ − 44 if __name__ == "__main__":
+ − 45
+ − 46 # parse command line
+ − 47 description = "Restrict from nucleotide v1.0.1: Remove the sequences with ambiguous nucleotides. [Category: Personal]"
+ − 48
+ − 49 parser = OptionParser(description = description)
+ − 50 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in sequence format given by -f]")
+ − 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]")
+ − 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]")
+ − 53 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 54 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
+ − 55 (options, args) = parser.parse_args()
+ − 56
+ − 57 # treat items
+ − 58 if options.format == "fasta":
+ − 59 parser = FastaParser(options.inputFileName, options.verbosity)
+ − 60 writer = FastaWriter(options.outputFileName, options.verbosity)
+ − 61 elif options.format == "fastq":
+ − 62 parser = FastqParser(options.inputFileName, options.verbosity)
+ − 63 writer = FastqWriter(options.outputFileName, options.verbosity)
+ − 64 else:
+ − 65 sys.exit("Do not understand '%s' format." % (options.format))
+ − 66 nbSequences = parser.getNbSequences()
+ − 67 print "sequences: %d" % (nbSequences)
+ − 68
+ − 69 progress = Progress(nbSequences, "Analyzing sequences of %s" % (options.inputFileName), options.verbosity)
+ − 70 nbKept = 0
+ − 71 for sequence in parser.getIterator():
+ − 72 if not sequence.containsAmbiguousNucleotides():
+ − 73 writer.addSequence(sequence)
+ − 74 nbKept += 1
+ − 75 progress.inc()
+ − 76 progress.done()
+ − 77
+ − 78 print "%d items, %d kept (%.2f%%)" % (nbSequences, nbKept, float(nbKept) / nbSequences * 100)