在具有汉明距离的较大字符串中搜索子字符串的存在

Question

I have 2 files, file1 and file2 file 1 has all the 4-mer,5-mer and 6-mer substrings of the full string "abcdef"

file2 has longer strings like

ddghtgabcdtttfwe

ddghtgabdatttfwe

hhttaaddsbcdeggd

etc. I want to see if the strings in file2 have matches in the strings in file1 allowing for some mismatches (maximum Hamming distance 2). For example ddghtgabcdtttfwe and ddghtgabcdatttfwe are hits for substring abcd and abcd,abcde respectively. Can you suggest a good way of doing this in python

Answer 1

Partial solution:

def hamming(s1,s2):
    return len([(c1,c2) for (c1,c2) in zip(s1,s2) if c1 != c2])

and then:

def almostIn(s1,s2):
    n = len(s1)
    for s in (s2[i:i+n] for i in range(1 + len(s2)-n)):
        if hamming(s1,s) <= 2: return True
    return False

This later function will return True if s1 occurs in s2 with Hamming distance <= 2. There is a certain amount of rescanning the same characters, so this is probably not optimal, but might be good enough for your intended application.