compare pairs of sequences

def compare_seqs(seqs):
    """
    compare pairs of sequences
    """
    A, B, ignore_gaps = seqs
    a, b = A[1], B[1] # actual sequences
    if len(a) != len(b):
        print('# reads are not the same length', file=sys.stderr)
        exit()
    if ignore_gaps is True:
        pident = calc_pident_ignore_gaps(a, b)
    else:
        pident = calc_pident(a, b)
    return A[0], B[0], pident