view SMART/Java/Python/splitMultiFasta.py @ 9:1eb55963fe39

Updated CompareOverlappingSmall*.py

#! /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.
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# In this respect, the user's attention is drawn to the risks associated
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# software by the user in light of its specific status of free software,
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# The fact that you are presently reading this means that you have had
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#
"""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()