gfa_to_fa.py

import sys
import os


gfa_file_path = str(sys.argv[1])

if not os.path.exists(gfa_file_path):
    print("the gfa file path you gave does not exists, pleast try again!")
    sys.exit()

sequences = []
with open(gfa_file_path, "r") as lines:
    for line in lines:
        if line.startswith("S"):
            line = line.split()
            sequences.append("\n>\n")
            sequences.append(line[2])


output_f_name = str(sys.argv[2])
fasta_f = open(output_f_name, "w")
for l in sequences:
    fasta_f.write(l)