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()