get_best_motif.py

# parses arguments using argparse
# @return args list of all parameters
def parse_arguments():
    parser = argparse.ArgumentParser()
    parser.add_argument("meme", help="Path to meme file")
    parser.add_argument("output", help="Output file")
    parser.add_argument("num", help="Number of motifs parsed from file")
    args = parser.parse_args()
    return args

# write lines of file till certain line (MOTIF + [num])
def main():
    args = parse_arguments()
    out = open(args.output, "w+")
    number = int(args.num) + 1
    motif = "MOTIF " + str(number)
    with open(args.meme) as f:
        for line in f:
            if motif in line:
                break
            out.write(line)


if __name__ == "__main__":
    import argparse
    main()