Bug for `AlignmentReadsStats.define_allele(base, ref=None)`

[soh-i]

base = ['T', 'T', 'T', 'T', 'T', 'G', 'G', 'G', 'G']
allele = AlignmentReadsStats.define_allele(base, ref='T')
print allele

=> ('G', 4) はOK

ところが、先頭の要素をAにしてみると、

base = ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'G', 'G']
allele = AlignmentReadsStats.define_allele(base, ref='T')
print allele

=> ('A', 1) バグ。

正しくは、('G', 4)

[soh-i]

from  collections import Counter

def define_allele(base, ref=None):
    data = Counter(base)
    common = data.most_common()

    found_allele = {}
    for i in common:
        b_type = i[0]
        count = i[1]
        if b_type != ref:
            found_allele.update({b_type: count})

    if len(found_allele):
        # Mismatch is found
        max_val= max(found_allele.values())
    else:
        # Mismatch base is not found
        return '.'

    result = []
    for value in found_allele.values():
        if value == max_val:
            for itm in found_allele.items():
                if itm[1] == value:
                    result.append(itm)
            break
    return result

でどうでしょう。

[soh-i]

if __name__ == '__main__':
    base = ['A', 'A', 'A', 'T', 'T', 'G', 'G', 'G', 'C', 'C', 'C']
    print "base: {0}".format(base)

    for r in ['A', 'T', 'G', 'C']:
        print "ref: {0}".format(r),
        print define_allele(base, ref=r)

    base = ['A', 'A', 'A', 'A']
    print define_allele(base, ref='A')

base: ['A', 'A', 'A', 'T', 'T', 'G', 'G', 'G', 'C', 'C', 'C']
ref: A [('C', 3), ('G', 3)]
ref: T [('A', 3), ('C', 3), ('G', 3)]
ref: G [('A', 3), ('C', 3)]
ref: C [('A', 3), ('G', 3)]
.

[soh-i]

新年あけましておめでとうございます。今年も宜しくお願いします。2014年、初仕事は、最も高いアレル頻度を持つ塩基の種類を決定するメソッドのバグ修正になっております。pileup branchにpushさせて頂きましたので、masterへ順次mergeして頂ければ幸いに思います。卒論まで残り19日です、、、、