Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/wrongFastqToQual.py @ 58:5f5c9b74c2dd
Uploaded
author | m-zytnicki |
---|---|
date | Fri, 07 Feb 2014 11:53:36 -0500 |
parents | 769e306b7933 |
children |
line wrap: on
line source
#! /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. # """Convert a pseudo-FASTQ file to QUAL files""" import os from optparse import OptionParser from SMART.Java.Python.misc.Progress import * from math import * if __name__ == "__main__": # parse command line description = "Wrong FastQ to Qual v1.0.1: Convert a pseudo-FastQ (i.e. a FastQ file with a wrong format) into a Qual file. [Category: Personnal]" parser = OptionParser(description = description) parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in FASTQ format]") parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in QUAL format]") parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]") (options, args) = parser.parse_args() inputFile = open(options.inputFileName) outputFastaFile = open("%s.fasta" % (options.outputFileName), "w") outputQualFile = open("%s.qual" % (options.outputFileName), "w") inSequence = False inQuality = True sequenceName = None for line in inputFile: line = line.strip() if line[0] == "@": if inQuality == False: sys.exit("Quality of %s is missing" % (sequenceName)) inSequence = True inQuality = False sequenceName = line[1:] outputFastaFile.write(">%s\n" % (sequenceName)) elif line[0] == "+": if inSequence == False: sys.exit("Sequence of %s is missing" % (line[1:])) inSequence = False inQuality = True if sequenceName != line[1:]: sys.exit("Names in sequence and qual are different (%s, %s)" % (sequenceName, line[1:])) outputQualFile.write(">%s\n" % (sequenceName)) else: if inSequence: outputFastaFile.write("%s\n" % (line)) elif inQuality: outputQualFile.write("%s\n" % (line)) inputFile.close() outputFastaFile.close() outputQualFile.close()