these functions take a DNA sequence and return the coordinates (python syntax) of the contigs

contig_coords_from_DNA_sequence

#!/usr/bin/env python

myseq = "ACNNNNNNNNNNNNNCATGTACTTGGATCTATCGGTGATCGGATCGGTATGCGTACGAGTGTCAGTCNNNNNNNNNNNNNNNACGTGGTATGCGGCATGCGTAGCGTCAGCTAGCTGATATTGCGTAGCNNNNNNNNNNGGTATGCGTG"

def contig_ranges(seq, sub):
    indices = list(find_all(seq, sub))
    gap_starts = []
    gap_stops  = []
    gap_ranges = []
    prev = -1

    # get the starts of the gaps
    for i in range(len(indices)):
        if prev != indices[i] - 1:
            gap_starts.append(indices[i])
        prev = indices[i]

    # get the indices of the ends of the gaps
    prev = 999999999999
    for i in range(len(indices) - 1, -1, -1):
        if prev != indices[i] + 1:
            gap_stops.append(indices[i])
        prev = indices[i]
    gap_stops = [x + len(sub) for x in gap_stops[::-1]]

    contigs = []
    # now get the ranges
    for i in range(len(gap_stops)):
        gap_ranges.append([gap_starts[i], gap_stops[i]])
        if i == 0:
            contigs.append([0, gap_starts[i]])
            contigs.append([gap_stops[i], gap_starts[i+1]])
        elif i == (len(gap_stops) -1):
            contigs.append([gap_stops[i], len(seq)])
        else:
            contigs.append([gap_stops[i], gap_starts[i+1]])
    return contigs

def find_all(seq, sub):
    start = 0
    indices = []
    while True:
        start = seq.find(sub, start)
        if start == -1: return
        yield start
        #start += len(sub) # use start += 1 to find overlapping matches
        start += 1 # use start += 1 to find overlapping matches
    return indices

# first argument is the sequence
# second sequence is the minimum number of Ns in a gap
ranges = contig_ranges(myseq, "NNNN")

print(ranges)
print(myseq)

for start, stop in ranges:
    print(myseq)
    print("{}{}".format("".join([" "] * start), myseq[start:stop]))