increment_gfa_ids.py

import sys

if len(sys.argv) == 1:
    print("Please give the name of the gfa file to increment then the output file name")
    sys.exit()

in_file = sys.argv[1]
out_file = sys.argv[2]

out_file = open(out_file, "w")

with open(in_file, "r") as in_lines:
    for line in in_lines:
        line = line.strip().split("\t")
        if line[0] == "S":
            line[1] = str(int(line[1]) + 1)
        elif line[0] == "L":
            line[1] = str(int(line[1]) + 1)
            line[3] = str(int(line[3]) + 1)
        out_file.write("\t".join(line))
        out_file.write("\n")

out_file.close()
print("Done!")