Exemplo n.º 1
0
def correct_errors(seqs):
    corrections = []
    c = Counter(seqs)

    correct = [item for item in c if c[item] >= 2]
    reverse = {reverse_complement(s) for s in correct}
    seqset = set(correct)

    for s in [item for item in c if c[item] < 2]:
        if s not in reverse:
            for fix in (f for f in seqset | reverse if hamming(s, f) == 1):
                corrections.append((s, fix))

    return corrections
Exemplo n.º 2
0
def correct_errors(seqs):
    corrections = []
    c = Counter(seqs)

    correct = [item for item in c if c[item] >= 2]
    reverse = {reverse_complement(s) for s in correct}
    seqset = set(correct)

    for s in [item for item in c if c[item] < 2]:
        if s not in reverse:
            for fix in (f for f in seqset | reverse if hamming(s, f) == 1):
                corrections.append((s, fix))

    return corrections
Exemplo n.º 3
0
def p_distance(s1, s2):
    return hamming(s1, s2) / len(s1)