kmer_count.py

#!/usr/bin/env python

from collections import Counter, defaultdict
from PatternsNumbers import NumberToPattern, PatternToNumber

def main():
    #dna = open("E-coli.txt").read()
    #print count_kmers_v2(s=dna, k=9, t=3, L=500)
   
    f = open("dataset_2994_5.txt")
    text = f.readline().strip()
    k = int(f.readline())
    f.close()

    freqs = ComputingFrequencies(text, k)
    
    #f = open("result.txt", "w")
    #for el in freqs:
    #    f.write("{} ".format(el))
    #f.close()



def count_kmers_v2(s, k, t, L):

    c = defaultdict(int)
    kmers_pass = set()
    
    for i in range(L - k + 1):
        kmer = s[i:i + k]
        c[kmer] += 1
        if c[kmer] == t:
            kmers_pass.add(kmer)
            
    for i in range(1,len(s) - L + 1):
        
        old = s[i - 1:i + k - 1]
        c[old] -= 1
        new = s[i + L - k:i + L]
        c[new] += 1
        if c[new] == t:
            kmers_pass.add(new)
    
    return len(kmers_pass)


def count_kmers(s, k, t, L):

    window = s[:L]
    kmers = [window[i : i + k] for i in range(0, L, k)]
    c = Counter(kmers)
    kmers_pass = set()
    
    for kmer, count in c.most_common():
        if count >= t:
            kmers_pass.add(kmer)
        else:
            break
                
    for i in range(1,len(s) - L):
        
        old = s[i - 1:i + k - 1]
        c[old] -= 1
        new = s[i + L - k + 1:i + L + 1 ]
        c[new] += 1
        if c[new] >= t:
            kmers_pass.add(new)
    
    return len(kmers_pass)


def ComputingFrequencies(text, k):
    FrequencyArray = [0]*(4**k)

    for i in range(len(text) - k + 1):
        Pattern = text[i:i + k]
        j = PatternToNumber(Pattern)
        FrequencyArray[j] += 1

    return FrequencyArray


if __name__ == "__main__":
    main()