alignment.py 文件源码

def get_percent_identity(a_aln_seq, b_aln_seq):
    """Get the percent identity between two alignment strings"""

    if len(a_aln_seq) != len(b_aln_seq):
        raise ValueError('Sequence lengths not equal - was an alignment run?')

    count = 0
    gaps = 0
    for n in range(0, len(a_aln_seq)):
        if a_aln_seq[n] == b_aln_seq[n]:
            if a_aln_seq[n] != "-":
                count += 1
            else:
                gaps += 1

    return count / float((len(a_aln_seq) - gaps))