code_challenge_5.py

# given a sequence find kmers of a given length that occur equal to t or more
# times in a given length of window in the sequence

from collections import deque


def kmer_frequency(text, k, window, thresh=3):
    counts = dict()
    kmers = deque()
    for w in range(len(text)-window+1):
        win = text[w:w+window]
        freqs = set()
        if w == 0:
            for i in range(len(win)-k+1):
                word = win[i:i+k]
                kmers.append(word)
                counts[word] = counts.get(word, 0) + 1
                if counts[word] >= thresh:
                    freqs.add(word)
        else:
            word = win[-k:]
            kmers.append(word)
            counts[word] = counts.get(word, 0) + 1
            word_to_rm = kmers.popleft()
            counts[word_to_rm] -= 1
            if counts[word_to_rm] == 0:
                counts.pop(word_to_rm, None)
            if counts[word] >= thresh:
                freqs.add(word)
        yield freqs

with open("E-coli.txt", "r") as myfile:
    text = myfile.read().replace('\n', '')

# text = raw_input('Paste sequence: ')
k = raw_input('Paste kmer size: ')
L = raw_input('Paste length of window: ')
t = raw_input('Paste the min num times a kmer should be seen: ')

lenk = int(k)
window = int(L)
times = int(t)

uniq = set()
for freqs in kmer_frequency(text, lenk, window, times):
    uniq.update(freqs)
print len(uniq)