annotate smart_toolShed/SMART/Java/Python/getSequence.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2010
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"""Get a given sequence in a multi-Fasta file"""
import sys
from optparse import OptionParser
from commons.core.parsing.FastaParser import FastaParser
from SMART.Java.Python.misc.Progress import Progress
from commons.core.writer.FastaWriter import FastaWriter

if __name__ == "__main__":
    
    # parse command line
    description = "Get Sequence v1.0.1: Get a single sequence in a FASTA file. [Category: Data Selection]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input", dest="inputFileName",action="store",type="string", help="multi-FASTA file [compulsory] [format: file in FASTA format]")
    parser.add_option("-n", "--name",dest="name",action="store",type="string", help="name of the sequence [compulsory] [format: string]")
    parser.add_option("-o", "--output",dest="outputFileName",action="store",type="string", help="output sequence file (FASTA) [compulsory] [format: file in FASTA format]")
    parser.add_option("-v", "--verbosity", dest="verbosity",action="store",default=1,type="int",help="trace level [format: int]")
    (options, args) = parser.parse_args()

    # read Fasta file
    sequenceListParser = FastaParser(options.inputFileName, options.verbosity)
    for sequence in sequenceListParser.getIterator():
        name = sequence.name.split(" ")[0]
        if name == options.name:
            writer = FastaWriter(options.outputFileName, options.verbosity)
            writer.addSequence(sequence)
            print sequence.printFasta(),
            sys.exit(0)
    writer.close()
    print "No sequence found"