Very basic code to find gaps in a single FASTA record. Min gap size is 10bp

gap_finder.py

#!/usr/bin/python3

import gzip
import sys

filename = sys.argv[1]
file = gzip.open(filename, "rt")

position = 0
contigous_n = 0
start = 0
for line in file:
    if ">" in line:
        continue
    stripped_line = line.rstrip()
    for c in stripped_line:
        # If we have an N then record the start if it is the first one
        # and increment the counter
        if c == "N":
            if contigous_n == 0:
                start = position
            contigous_n += 1
        # Otherwise we are in a non-N, so that could mean stopping the gap
        # and recording it
        else:
            if contigous_n >= 10:
                print(
                    f"Found a gap from {start+1} to {position}. Length claims it was {contigous_n}"
                )
                contigous_n = 0
                start = 0
        position += 1

if contigous_n >= 10:
    print(
        f"Found a gap from {start+1} to {position}. Length claims it was {contigous_n}"
    )