UCSC BLAT输出python

是否有一种方法可以使用Python从以下BLAT结果中获得不匹配的位置号

00000001 taaaagatgaagtttctatcatccaaaaaatgggctacagaaacc 00000045
<<<<<<<< |||||||||||||||||||||||||||  |||||||||||||||| <<<<<<<<
41629392 taaaagatgaagtttctatcatccaaagtatgggctacagaaacc 41629348

00000001 TAAAAGATGAAGTTTCATCATCCAAAAAAATGGGCTACAGAAACC 00000045
您可以使用字符串的
.find
方法查找不匹配项。不匹配由空间（′）表示，因此我们在BLAT输出的中线寻找。我个人不认识布拉特，所以我不确定输出是否总是以三行的形式出现，但假设是这样，下面的函数将返回一个位置不匹配列表，每个位置在顶部序列中表示为不匹配位置的元组，在底部序列中表示为相同的位置

blat_src = """00000001 taaaagatgaagtttctatcatccaaaaaatgggctacagaaacc 00000045
<<<<<<<< |||||||||||||||||||||||||||  |||||||||||||||| <<<<<<<<
41629392 taaaagatgaagtttctatcatccaaagtatgggctacagaaacc 41629348"""

def find_mismatch(blat):
    #break the blat input into lines
    lines = blat.split("\n")

    #give some firendly names to the different lines
    seq_a = lines[0]
    seq_b = lines[2]

    #We're not interested in the '<' and '>' so we strip them out with a slice
    matchstr = lines[1][9:-9]

    #Get the integer values of the starts of each sequence segment
    pos_a = int(seq_a[:8])
    pos_b = int(seq_b[:8])

    results = []

    #find the index of first space character, mmpos = mismatch position
    mmpos = matchstr.find(" ")
    #if a space exists (-1 if none found)
    while mmpos != -1:
        #the position of the mismatch is the start position of the
        #sequence plus the index within the segment
        results.append((posa+mmpos, posb+mmpos))
        #search the rest of the string (from mmpos+1 onwards)
        mmpos = matchstr.find(" ", mmpos+1)
    return results

print find_mismatch(blat_src)

告诉我们位置28和29（根据顶部序列索引）或位置41629419和41629420（根据底部序列索引）不匹配
 您想在顶部或底部序列中显示该位置吗？两者都有？我要从最下面的顺序。
[(28, 41629419), (29, 41629420)]