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 Exception: 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))): # noqa: B007 maf = maf.reverse_complement() if species: maf = maf.limit_to_species(species) maf_writer.write(maf) except Exception: print("Your MAF file appears to be malformed.", file=sys.stderr) sys.exit() print("%i regions were reverse complemented." % count) maf_writer.close()
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()