python - How to find the overlap between 2 sequences, and return it

Question

I am new in Python, and have already spend to many hours with this problem, hope somebody can help me. I need to find the overlap between 2 sequences. The overlap is in the left end of the first sequences and the right end of the second one. I want the function to find the overlap, and return it.

My sequences are:

s1 = "CGATTCCAGGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTC"
s2 = "GGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTCGTCCAGACCCCTAGC"

My function should be named

def getOverlap(left, right)

With s1 being the left sequence, and the s2 being the right one.

The outcome should be

‘GGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTC’

Any help is appreciated

Answer 1

Have a look at the difflib library and more precisely at find_longest_match():

import difflib

def get_overlap(s1, s2):
    s = difflib.SequenceMatcher(None, s1, s2)
    pos_a, pos_b, size = s.find_longest_match(0, len(s1), 0, len(s2)) 
    return s1[pos_a:pos_a+size]

s1 = "CGATTCCAGGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTC"
s2 = "GGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTCGTCCAGACCCCTAGC"

print(get_overlap(s1, s2)) # GGCTCCCCACGGGGTACCCATAACTTGACAGTAGATCTC