Fastest way to count instances of substrings in string Python3.6

Question

I have been working on a program which requires the counting of sub-strings (up to 4000 sub-strings of 2-6 characters located in a list) inside a main string (~400,000 characters). I understand this is similar to the question asked at Counting substrings in a string, however, this solution does not work for me. Since my sub-strings are DNA sequences, many of my sub-strings are repetitive instances of a single character (e.g. 'AA'); therefore, 'AAA' will be interpreted as a single instance of 'AA' rather than two instances if i split the string by 'AA'. My current solution is using nested loops, but I'm hoping there is a faster way as this code takes 5+ minutes for a single main string. Thanks in advance!

def getKmers(self, kmer):
    self.kmer_dict = {}
    kmer_tuples = list(product(['A', 'C', 'G', 'T'], repeat = kmer))
    kmer_list = []
    for x in range(len(kmer_tuples)):
        new_kmer = ''
        for y in range(kmer):
            new_kmer += kmer_tuples[x][y]
        kmer_list.append(new_kmer)
    for x in range(len(kmer_list)):
        self.kmer_dict[kmer_list[x]] = 0
    for x in range(len(self.sequence)-kmer):
        for substr in kmer_list:
            if self.sequence[x:x+kmer] == substr:
                self.kmer_dict[substr] += 1
                break
    return self.kmer_dict

Answer 1

For counting overlapping substrings of DNA, you can use Biopython:

>>> from Bio.Seq import Seq
>>> Seq('AAA').count_overlap('AA')
2

Disclaimer: I wrote this method, see commit 97709cc.

However, if you're looking for really high performance, Python probably isn't the right language choice (although an extension like Cython could help).