view SMART/Java/Python/ @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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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
# "".
# 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
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# The fact that you are presently reading this means that you have had
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"""Remove all dirty sequences"""

import os
import sys
from optparse import OptionParser
from commons.core.parsing.FastaParser import *
from commons.core.writer.FastaWriter import *
from commons.core.parsing.FastqParser import *
from commons.core.writer.FastqWriter import *
from SMART.Java.Python.misc.Progress import *
from SMART.Java.Python.misc.RPlotter import *

if __name__ == "__main__":
    # parse command line
    description = "Restrict from nucleotide v1.0.1: Remove the sequences with ambiguous nucleotides. [Category: Personal]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input",         dest="inputFileName",    action="store",                                                type="string", help="input file [compulsory] [format: file in sequence format given by -f]")
    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]")
    parser.add_option("-o", "--output",        dest="outputFileName", action="store",                                                type="string", help="output file [compulsory] [format: output file in sequence format given by -f]")
    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()

    # treat items
    if options.format == "fasta":
        parser     = FastaParser(options.inputFileName, options.verbosity)
        writer     = FastaWriter(options.outputFileName, options.verbosity)
    elif options.format == "fastq":
        parser     = FastqParser(options.inputFileName, options.verbosity)
        writer     = FastqWriter(options.outputFileName, options.verbosity)
        sys.exit("Do not understand '%s' format." % (options.format))
    nbSequences = parser.getNbSequences()
    print "sequences: %d" % (nbSequences)
    progress = Progress(nbSequences, "Analyzing sequences of %s" % (options.inputFileName), options.verbosity)
    nbKept     = 0
    for sequence in parser.getIterator():
        if not sequence.containsAmbiguousNucleotides():
            nbKept += 1

    print "%d items, %d kept (%.2f%%)" % (nbSequences, nbKept, float(nbKept) / nbSequences * 100)