Get gap positions in a fasta file

get_gap_postions.py

#!/usr/bin/env python
# Script to identify gaps regions in an assembly
# input : fasta 
# output : bed
# usage : get_gap_postions.py fasta bed
# Import necessary packages
import argparse
import re
from Bio import SeqIO

# Parse command-line arguments
parser = argparse.ArgumentParser()
parser.add_argument("fasta")
parser.add_argument("bed")
args = parser.parse_args()
f = open(args.bed,'wa')
# Open FASTA, search for masked regions, print in BED3 format
with open(args.fasta) as handle:
    for record in SeqIO.parse(handle, "fasta"):
        for match in re.finditer('N+', str(record.seq)):
            f.write('{0}\t{1}\t{2}\n'.format(record.id, match.start(), match.end()))

f.close()