【bioinfo】根据sam文件中的MD标签判断reads比对情况

sam文件可选区域字段(Optional Feild)含义

MD标签是值：比对上的相对位置信息和错误信息。请注意：MD中并不包含insertion的信息。

使用re正则匹配，获取MD标签的比对的情况：

import re
def md_match(md_strings):
    # mdlen = len(md_strings)
    mat_times = 0
    num_re = r"([0-9]+)"
    mis_num_re = r"([A-Z]+|\^[A-Z]+)*([0-9]+)*"
    
    while True:
        re_str = num_re + mis_num_re * int(mat_times)
        re_md = re.compile(re_str)
        re_str_lst = re_md.match(md_strings).groups()
        if not re_str_lst[-1]: 
            break
        mat_times += 1
    return re_str_lst

进一步判断，比对的reads是否有较多错配：

import re
def is_good_match(md_strings, mis_times=3):
    """
    mis_times: default 3, <=3 good; >3: not good(>=4)
    --------------
    MD tag match good or not:
    True: if MD tag with mismatch(SNP&Del) times <= 3
        > eg: MD:Z:100 (no mismatch)
        > eg: MD:Z:80A19 (one mismatch)
        > eg: MD:Z:70T9A10T8 (3 mismatch bases)
        > eg: MD:Z:69CT9A10T8 (3 mismatch, but with 4 mismatch bases, extension one mismatch[see as one])
        > eg: MD:Z:69^AG9A10T8 (3 mismatch, but with 'AC' deletion to ref, del extension one mismatch[see as one])
        NOTE: 'MD' info without insertion.
    False: mismatch times >= 4:
        > eg: MD:Z:20G48CT9^T10T8
    """
    # re_md = re.compile(r"([0-9]+)"
    #                     "([A-Z]+|\^[A-Z]+)*([0-9]+)*"
    #                     "([A-Z]+|\^[A-Z]+)*([0-9]+)*"
    #                     "([A-Z]+|\^[A-Z]+)*([0-9]+)*"
    #                     "([A-Z]+|\^[A-Z]+)*([0-9]+)*")  # with >=4 mistmatch

    num_re = r"([0-9]+)"
    mis_num_re = r"([A-Z]+|\^[A-Z]+)*([0-9]+)*"
    re_str = num_re + mis_num_re * (int(mis_times) + 1)  # NOTE: +1, match list with "None" if 'mis<=3'
    re_md = re.compile(re_str)
    # print(num_re+mis_num_re*int(mis_times))

    re_str_lst = re_md.match(md_strings).groups()
    if None in re_str_lst:  # match times <= mis_times [3]
        return True
    else:
        return False