Search kmers of one file in kmers of an other file and count occurences in Python

Question

Got this function, which generates all possible kmers over the four Bases in python:

def generate_kmers(k):

    bases = ['A', 'C', 'T', 'G']  # in task (a) we only should wirte a function that generates k-mers of the four Bases
    kmer = [''.join(p) for p in itertools.product(bases, repeat=length_kmer)]
    # itertools.product returns a Cartesian product of input iterables, in our case it generates over bases and joined
    # all string combinations together over a length of k-mers
    return kmer

now what I want is, to look over a list of Sequences of a fastq file (e.g. ['GTATACACTAGTCCAGGATGTGCTTCTTGTAGAAAAGTAAAACAATGGTTAAAAGATCACAATCTTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN', 'CCTGTAGAGTCATAAAGACCTCTTGGGTCCATCCTAGAAATTTTTCAGCTGAGAATAACGGGTCTGTTTCAGTTATTGCTTCTACTATNNNNNNNNNNNNNNNNNNNNNNNNNNN']) and count the occurences of all my kmers of the function generate_kmer in my list of Sequences and to save it in a dictionary. (e.g. {AAAA: 2, AAAC: 1...}) First I tried to modify generate_kmer, so that it gives all k-mers of the sequence file, and iterate over kmerSequences and kmerBases but that doesn't worked.

Does somebody has any ideas on how I can do it?

Answer 1

You could try this with count:

import itertools

def generate_kmers(k):

    bases = ['A', 'C', 'T', 'G']  # in task (a) we only should wirte a function that generates k-mers of the four Bases
    kmer = [''.join(p) for p in itertools.product(bases, repeat=k)]
    # itertools.product returns a Cartesian product of input iterables, in our case it generates over bases and joined
    # all string combinations together over a length of k-mers
    return kmer

seqs=['GTATACACTAGTCCAGGATGTGCTTCTTGTAGAAAAGTAAAACAATGGTTAAAAGATCACAATCTTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN', 'CCTGTAGAGTCATAAAGACCTCTTGGGTCCATCCTAGAAATTTTTCAGCTGAGAATAACGGGTCTGTTTCAGTTATTGCTTCTACTATNNNNNNNNNNNNNNNNNNNNNNNNNNN']
k=4
mers4= generate_kmers(k)
dcts=[{kmer:seq.count(kmer) for kmer in mers4}for seq in seqs]
print(dcts)

Edit:

import itertools
import re
def generate_kmers(k):

    bases = ['A', 'C', 'T', 'G']  # in task (a) we only should wirte a function that generates k-mers of the four Bases
    kmer = [''.join(p) for p in itertools.product(bases, repeat=k)]
    # itertools.product returns a Cartesian product of input iterables, in our case it generates over bases and joined
    # all string combinations together over a length of k-mers
    return kmer

k=4
mers4= generate_kmers(k)

#given sequence
s='GTATACACTAGTCCAGGATGTGCTTCTTGTAGAAAAGTAAAACAATGGTTAAAAGATCACAATCTTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN'

#function that returns the dictionary with ocurrences
def dct_count(seq):
    return {mer:len(re.findall(mer, s)) for mer in mers4}

dc=dct_count(s)
print(dc)