FIndingMotifinDNA.py

# Given two strings ss and tt, tt is a substring of ss if tt is contained as a contiguous collection of symbols in
#  ss (as a result, tt must be no longer than ss).
# The position of a symbol in a string is the total number of symbols found to its left, including itself
# (e.g., the positions of all occurrences of 'U' in "AUGCUUCAGAAAGGUCUUACG" are 2, 5, 6, 15, 17, and 18).
# The symbol at position ii of ss is denoted by s[i]s[i].
#
# A substring of ss can be represented as s[j:k]s[j:k], where jj and kk represent the starting and ending
# positions of the substring in ss; for example, if ss = "AUGCUUCAGAAAGGUCUUACG", then s[2:5]s[2:5] = "UGCU".
#
# The location of a substring s[j:k]s[j:k] is its beginning position jj; note that tt will have multiple
# locations in ss if it occurs more than once as a substring of ss (see the Sample below).
#
# Given: Two DNA strings ss and tt (each of length at most 1 kbp).
# Return: All locations of tt as a substring of ss.

import re
def findMotif(ss,tt):
    # motifs = [m.start()+1 for m in re.finditer(tt,ss, overlapped= True)]
    motifs = []
    k = 0
    while k < len(ss):
        k = ss.find(tt, k)
        if k == -1:
            return motifs
        else:
            motifs.append(k+1)
            k += 1  # change to k += len(sub) to not search overlapping results

    return motifs


ss ='TTGCATAGGTTGCATAGGTGCATAGGGCATAGGGCATCGCATAGGAAGCATAGGGCATAGGACTACCTGCATAGGAGCATAGGATGAATGAGGTCTTGTGCATAGGCCGGGCATAGGGTGTGTCCGCGCATAGGGCATAGGGCATAGGACAACCCGCTCGCCGCATAGGCGCATAGGGCGCATAGGAGCATAGGGCATAGGAGGAAAGTGTCTAGCATAGGGACTAGTATGGGGCATAGGGCATAGGGCATAGGGGCATAGGTGTGCATAGGAGTAGCATAGGCGCATAGGGCTGTCGCATAGGGCATAGGCTGCATAGGTGGCATAGGGCTCTCTTAAATAAATAGCATAGGACTTATATTGGCATAGGAGCTTTTAAAGCATAGGGACGCATAGGTGCATAGGAGCATAGGGCATAGGTTTCCGCATAGGTTGACATGCATAGGGAGGGCATAGGTTTGCATAGGCCTTAGTGCATAGGGCATAGGGCGCATAGGGCATAGGGGCATAGGTGGAGGCATAGGACTGCATAGGGGCATAGGGCATAGGGCATAGGCACGGCATAGGAGCATAGGAAGCATAGGGCATAGGCGCATAGGCCATGCATAGGGCATAGGAACGCATAGGAAAGCATAGGGCATAGGCGTTAACGGGCATAGGCGCATAGGCTGCATAGGATCGCATAGGTGGAGAGCATAGGCGGCATAGGTTGCAGCATAGGAGGCATAGGGCATAGGCGCATAGGAGCCATCGCGCATAGGCTGTCACTTAGTTCGGGGCCGCATAGGGCATAGGCAGGCATAGGGGCATAGGCAGCGGGGATTGGCGGGCATAGGGGCGAGCATAGGGCATAGGTGTTAGCATAGGTGGCATAGGGTAGCATAGGACGCATAGGCGCATAGGCACAGCGATTGCATAGGTAGCATAGGGCATAGGGGGAGCAAACGCATAGGAAGCATAGGAATGCATAGG'
tt = 'GCATAGGGC'
print(findMotif(ss,tt))