Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/modifyFasta.py @ 38:2c0c0a89fad7
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author | m-zytnicki |
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date | Thu, 02 May 2013 09:56:47 -0400 |
parents | 769e306b7933 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/modifyFasta.py Thu May 02 09:56:47 2013 -0400 @@ -0,0 +1,62 @@ +#! /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. +# +"""Modify the content of a FASTA file""" + +from optparse import OptionParser +from commons.core.parsing.FastaParser import FastaParser +from commons.core.writer.FastaWriter import FastaWriter +from SMART.Java.Python.misc.Progress import Progress + + +if __name__ == "__main__": + + # parse command line + description = "Modify Sequence List v1.0.1: Extend or shring a list of sequences. [Category: Data Modification]" + + 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", default=None, type="string", help="output file [compulsory] [format: output file in FASTA format]") + parser.add_option("-s", "--start", dest="start", action="store", default=None, type="int", help="keep first nucleotides [format: int]") + parser.add_option("-e", "--end", dest="end", action="store", default=None, type="int", help="keep last nucleotides [format: int]") + parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") + (options, args) = parser.parse_args() + + parser = FastaParser(options.inputFileName, options.verbosity) + writer = FastaWriter(options.outputFileName, options.verbosity) + progress = Progress(parser.getNbSequences(), "Reading file %s" % (options.inputFileName), options.verbosity) + for sequence in parser.getIterator(): + if options.start != None: + sequence.shrinkToFirstNucleotides(options.start) + if options.end != None: + sequence.shrinkToLastNucleotides(options.end) + writer.addSequence(sequence) + progress.inc() + progress.done()