1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
|
import sys
def gfa_to_fa(gfa_file_name: str):
"""Prints genomic sequences from GFA nodes
Args:
gfa_file_name (str): File name of the input GFA
"""
with open(gfa_file_name) as gfa_file:
for gfa_line in gfa_file.readlines():
# S 13 ctagtgggggacaaccaatcactaattgtgataAgatgtggtgtacacacactggtactggtcaggcaat AS:37h; SP:0_70; BP:0_61; EV:1 FC:i:60 min:113 max:113 mean:113.0 AC:113;
if gfa_line[0] != "S":
continue
print(f">{gfa_line.split()[1]}\n{gfa_line.split()[2]}")
if __name__ == '__main__':
gfa_to_fa(sys.argv[1])
|