view smart_toolShed/SMART/Java/Python/ @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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
# "".
# 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.
import sys
from optparse import OptionParser
from commons.core.parsing.SequenceListParser import SequenceListParser
from SMART.Java.Python.misc.Progress import Progress

Transform qual and fasta files to a single fastq file

if __name__ == "__main__":
    # parse command line
    description = "Qual To FastQ v1.0.2: Convert a file in FASTA/Qual format to FastQ format. [Category: Conversion]"

    parser = OptionParser(description = description)
    parser.add_option("-f", "--fasta",     dest="fastaFileName",  action="store",               type="string", help="input fasta file [compulsory] [format: file in FASTA format]")
    parser.add_option("-q", "--qual",      dest="qualFileName",   action="store",               type="string", help="input qual file [compulsory] [format: file in TXT format]")
    parser.add_option("-o", "--output",    dest="outputFileName", action="store", default=None, type="string", help="output file [compulsory] [format: output file in FASTQ format]")
    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store", default=1,    type="int",    help="trace level [format: int]")
    (options, args) = parser.parse_args()
    fastaFile = open(options.fastaFileName)
    qualFile  = open(options.qualFileName)
    fastqFile = open(options.outputFileName, "w")
    fastaLine = fastaFile.readline().strip()
    qualLine  = qualFile.readline().strip()
    header    = None
    cpt       = 0
    while fastaLine:
        if not qualLine:
            raise Exception("Qual file is shorter!")
        if fastaLine[0] == ">":
            header = fastaLine[1:]
            if qualLine[0] != ">":
                raise Exception("Discrepencies around %s!" % (header))
            fastqFile.write("@%s\n" % (header))
            if qualLine[0] == ">":
                raise Exception("Discrepencies around %s!" % (qualLine[1:]))
            intQualities = qualLine.split()
            if len(intQualities) != len(fastaLine):
                raise Exception("Sizes of read and quality diverge in %s!" % (header))
            chrQualities = [chr(min(int(quality), 93) + 33) for quality in intQualities]
            fastqFile.write("%s\n+\n%s\n" % (fastaLine, "".join(chrQualities)))
        fastaLine = fastaFile.readline().strip()
        qualLine  = qualFile.readline().strip()
        if cpt % 1000 == 0 and options.verbosity > 1:
            sys.stdout.write("%d lines read\r" % (cpt))
        cpt += 1
    if options.verbosity > 0:
        print "%d lines read" % (cpt)
    if qualLine:
        raise Exception("Qual file is longer!")