如何提取P匹配结果中的坐标？

Question

从这个 link http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p-match.cgi 产生的结果我需要处理以便只获得序列 ID、开始和结束位置。我可以通过哪些方式从结果中提取坐标信息？下面是示例结果。

Scanning sequence ID:   BEST1_HUMAN

              150 (-)  1.000  0.997  GGAAAggccc                                   R05891
              354 (+)  0.988  0.981  gtgtAGACAtt                                  R06227
V$CREL_01c-RelV$EVI1_05Evi-1

Scanning sequence ID:   4F2_HUMAN

              365 (+)  1.000  1.000  gggacCTACA                                   R05884
               789 (-)  1.000  1.000  gcgCGAAA                                       R05828; R05834; R05835; R05838; R05839
V$CREL_01c-RelV$E2F_02E2F

预期输出：

Sequence ID start end
（end site是添加到start site的短序列GGAAAggccc的个数）。

BEST1_HUMAN 150 160
BEST1_HUMAN 354 365
4F2_HUMAN   365 375
4F2_HUMAN   789 797

谁能帮帮我？

Answer 1

使用 this answer 中的代码段将您的结果分成大小均匀的块并提取所需数据：

def chunks(l, n):
    #Generator to yield n sized chunks from l
    for i in xrange(0, len(l), n):
        yield l[i: i + n]

with open('p_match.txt') as f:
    for chunk in chunks(f.readlines(), 6):
        sequence_id = chunk[0].split()[-1].strip()
        for i in (2,3):
            start = int(chunk[i].split()[0].strip())
            sequence = chunk[i].split()[-2].strip()
            stop = start + len(sequence)
            print sequence_id, start, stop

编辑：显然结果可以包含可变数量的起始位置，因此上述拆分为大小均匀的块的解决方案不起作用。然后您可以使用正则表达式路由或逐行浏览文件：

with open('p_match.txt') as f:
    text = f.read()
    chunks = text.split('Scanning sequence ID:')
    for chunk in chunks:
        if chunk:
            lines = chunk.split('\n')
            sequence_id = lines[0].strip()
            for line in lines:
                if line.startswith('              '):
                    start = int(line.split()[0].strip())
                    sequence = line.split()[-2].strip()
                    stop = start + len(sequence)
                    print sequence_id, start, stop

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