Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/trimSequence.py @ 9:1eb55963fe39
Updated CompareOverlappingSmall*.py
author | m-zytnicki |
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date | Thu, 14 Mar 2013 05:23:05 -0400 |
parents | 769e306b7933 |
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#! /usr/bin/env python # # Copyright INRA-URGI 2009-2010 # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. # """Remove sequences with low reliability""" from optparse import OptionParser from commons.core.parsing.SequenceListParser import * from commons.core.writer.FastaWriter import * from SMART.Java.Python.misc.Progress import * if __name__ == "__main__": # parse command line description = "Trim Sequences v1.0.1: Remove sequences with low reliability: low occurrences and highly repeted. [Category: Personnal]" parser = OptionParser(description = description) parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in FASTA format]") parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in FASTA format]") parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]") (options, args) = parser.parse_args() parser = SequenceListParser(options.inputFileName, options.verbosity) nbSequences = parser.getNbSequences() progress = Progress(nbSequences, "Parsing file %s" % (options.inputFileName), options.verbosity) writer = FastaWriter(options.outputFileName, options.verbosity) if options.log: logHandle = open("log.txt", "w") letters = ("A", "C", "G", "T") nbLowComplexity = 0 nbTooManyOccurrences = 0 for sequence in parser.getIteractor(): halfSize = len(sequence.sequence) / 2 occurrences = set() nbOccurrences = dict(zip(letters, [0 for letter in letters])) tooManyOccurrences = False good = True for char in sequence.sequence: if char in letters: occurrences.add(char) nbOccurrences[char] += 1 if len(occurrences) < 4: nbLowComplexity += 1 if options.log: logHandle.write("Low complexity for %s\n" % (sequence.sequence)) good = False if good: for letter, nbOccurrence in nbOccurrences.iteritems(): if nbOccurrence > halfSize: if not tooManyOccurrences: nbTooManyOccurrences += 1 if options.log: logHandle.write("Too many occurrences for %s\n" % (sequence.sequence)) tooManyOccurrences = True good = False if good: writer.addSequence(sequence) progress.inc() progress.done() if options.log: logHandle.close() print "%d out of %d have low complexity (%f%%)" % (nbLowComplexity, nbSequences, (float(nbLowComplexity) / nbSequences * 100)) print "%d out of %d have too many occurrences (%f%%)" % (nbTooManyOccurrences, nbSequences, (float(nbTooManyOccurrences) / nbSequences * 100))