def sbhfast(k=20): graph = C_DeBrujin.DeBruijnGraph([dna], k) res = graph.eulerianWalkOrCycle() answer = res[0] + ''.join(map(lambda x: x[-1], res[1:])) ld = float(levenshteinDistance(dna, answer)) l = float(len(dna)) s[-1].sbhfast_acc += ((l - ld) / l) * 100
def shotgunfast(): sequencer = Sequencer(dna) # Sequencer for the clone library dna_slices = sequencer.sequence_all() reads = [] for block in dna_slices: # QUICK'N'DIRTY for kmer in block: reads.append(kmer) ld = float(levenshteinDistance(dna, C_Shotgun.perform(reads))) l = float(len(dna)) s[-1].sfast_acc += ((l - ld) / l) * 100