Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/splitMultiFasta.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/splitMultiFasta.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,64 @@ +#! /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()