def main():
# TODO docs
parser = argparse.ArgumentParser()
parser.add_argument("-i", dest="input", type=str)
parser.add_argument("-o", dest="output", type=str)
args = parser.parse_args()
input_file = os.path.abspath(args.input) if args.input else raiser()
output_file = os.path.abspath(args.output) if args.output else raiser()
sequences = Sequences(input_file)
with open(output_file, "w") as op:
for position, entropy in enumerate(query_position_entropy(sequences)):
print(position, entropy, sep="\t", file=op)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("-v", dest="variants", type=str)
parser.add_argument("-r", dest="reference", type=str)
parser.add_argument("-f", dest="feature_table", type=str)
parser.add_argument("-o", dest="output", type=str)
parser.add_argument("-m", dest="reference_metadata", type=str)
args = parser.parse_args()
var_file = os.path.abspath(args.variants) if args.variants else raiser()
ref_file = os.path.abspath(args.reference) if args.reference else raiser()
aa_table = os.path.abspath(args.feature_table) if args.feature_table else raiser()
output_file = os.path.abspath(args.output) if args.output else raiser()
metadata = map(os.path.abspath, args.reference_metadata.split(",")) \
if args.reference_metadata else []
#print(metadata)
reference_seq = Sequences(ref_file).sequences[0]
variant_stream = stream_variants(var_file)
process_variants(reference_seq,
variant_stream,
aa_table,
output_file,
*metadata)
