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)