view tools/maf/maf_reverse_complement.py @ 0:9071e359b9a3

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#!/usr/bin/env python

"""
Reads a MAF file. Produces a MAF file containing
the reverse complement for each block in the source file.

usage: %prog input_maf_file output_maf_file
"""
#Dan Blankenberg
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.align.maf
from galaxy.tools.util import maf_utilities
import sys

assert sys.version_info[:2] >= ( 2, 4 )

def __main__():
    #Parse Command Line
    input_file = sys.argv.pop( 1 )
    output_file = sys.argv.pop( 1 )
    species = maf_utilities.parse_species_option( sys.argv.pop( 1 ) )
    
    try:
        maf_writer = bx.align.maf.Writer( open( output_file, 'w' ) )
    except:
        print sys.stderr, "Unable to open output file"
        sys.exit()
    try:
        count = 0
        for count, maf in enumerate( bx.align.maf.Reader( open( input_file ) ) ):
            maf = maf.reverse_complement()
            if species:
                maf = maf.limit_to_species( species )
            maf_writer.write( maf )
    except:
        print >>sys.stderr, "Your MAF file appears to be malformed."
        sys.exit()
    print "%i regions were reverse complemented." % count
    maf_writer.close()

if __name__ == "__main__": __main__()