Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/splitMultiFasta.py @ 22:1e3f2c2657a3
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:26:07 -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. # """Split a Multi-Fasta file to several Fasta files""" import os from optparse import OptionParser from SMART.Java.Python.structure.TranscriptContainer import * from commons.core.writer.Gff3Writer import * from SMART.Java.Python.misc.Progress import * from SMART.Java.Python.misc import Utils if __name__ == "__main__": # parse command line description = "Split Multi-Fasta v1.0.1: Split a Multi-Fasta file to several Fasta files. [Category: Personnal]" parser = OptionParser(description = description) parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file 1 [compulsory] [format: file in FASTA format]") parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in FASTA format]") (options, args) = parser.parse_args() inputHandle = open(options.inputFileName) outputHandle = None for line in inputHandle: line = line.strip() if line[0] == ">": if outputHandle != None: outputHandle.close() name = line[1:].split(" ")[0] outputHandle = open("%s%s.fasta" % (options.outputFileName, name), "w") outputHandle.write("%s\n" % (line)) inputHandle.close() outputHandle.close()