def search_matches(pattern, k, d): kmers = pattern_to_number.list_kmer(k) matches = [] for kmer in kmers: if score_kmer(kmer, pattern, d) == 1: matches.append(kmer) return matches
def mutate_bases(word, m): """returns every possible mutation of word with number of possible mutations m""" legal_mutations =[] possibilities = pattern_to_number.list_kmer(len(word)) for i in possibilities: if count_mismatches(i, word) <= m: legal_mutations.append(i) return legal_mutations
def median_string(dna, k): """ Iterates through every possible kmer of length k and returns a kmer that minimizes d(pattern, dna). This is a faster version of the motif_finding problem. """ kmers = pattern_to_number.list_kmer(k) best_pattern = kmers[0] for kmer in kmers: if d(kmer, dna) < d(best_pattern, dna): best_pattern = kmer return best_pattern
def number_to_pattern(index, k): list_of_kmers = pattern_to_number.list_kmer(k) return list_of_kmers[index]
