使用正则表达式拆分标题和内容

Question

我在文件中有以下序列文本

每个标题以“>”开头，内容行数是随机的

>XM_024446048.1 PREDICTED: Homo sapiens mannosidase alpha class 2A member 1 (MAN2A1), transcript variant X2, mRNA
CAGCCCCC
TGAGCGAC
TCCCTAATGTG
ACAGTAAAGAA
>NM_001308028.1 Homo sapiens FER tyrosine kinase (FER), transcript variant 2, mRNA
CAGCCC
CCGTGACGC
GGGGTGGTGACT
GGCTC
GGTGGT
GTGAC
>NM_0013082323028.1 H STZ mRSN1A
CAGCCC
CCGTGACGC
GGG
GTGGTGA
CTGGCTCCGGAGT
CTGAGGGGTTCGG

我想以下列格式创建一个嵌套的dict：

nested_dict = { 'sequence1': {

'header': 'XM_024446048.1 PREDICTED: Homo sapiens mannosidase alpha class 2A member 1 (MAN2A1), transcript variant X2, mRNA',
'content': 'CAGCCCCCTGAGCGACTCCCTAATGTGACAGTAAAGAA'


},
               'sequence2': {

'header': 'NM_001308028.1 Homo sapiens FER tyrosine kinase (FER), transcript variant 2, mRNA',
'content': 'CAGCCCCCGTGACGCGGGGTGGTGACTGGCTCGGTGGTGTGAC'


},

               'sequence3': {

'header': 'NM_0013082323028.1 H STZ mRSN1A',
'content': 'CAGCCCCCGTGACGCGGGGTGGTGACTGGCTCCGGAGTCTGAGGGGTTCGG'


}

我坚持使用正则表达式，任何人都可以帮助我吗？

Answer 1

你可以用

^>
(?P<header>
[^\n()]*
    (?:\((?P<name>[^\n()]+)\))?
[^()\n]*
)
[\n\r]
(?P<content>[\s\S]+?)(?=^>|\Z)

与multiline和verbose旗帜，请参阅a demo on regex101.com。

---

In Python:

rx = re.compile(r'''
    ^>
    (?P<header>
    [^\n()]*
        (?:\((?P<name>[^\n()]+)\))?
    [^()\n]*
    )
    [\n\r]
    (?P<content>[\s\S]+?)(?=^>|\Z)''', re.M | re.X)

sequences = {"sequence{}".format(idx):
                 {"header": m.group('header'),
                  "content": m.group("content"),
                  "name": m.group('name')
                  }
             for idx, m in enumerate(rx.finditer(data), 1)}
print(sequences)

这产生了

{'sequence1': {'header': 'XM_024446048.1 PREDICTED: Homo sapiens mannosidase alpha class 2A member 1 (MAN2A1), transcript variant X2, mRNA', 'content': 'CAGCCCCC\nTGAGCGAC\nTCCCTAATGTG\nACAGTAAAGAA\n', 'name': 'MAN2A1'}, 'sequence2': {'header': 'NM_001308028.1 Homo sapiens FER tyrosine kinase (FER), transcript variant 2, mRNA', 'content': 'CAGCCC\nCCGTGACGC\nGGGGTGGTGACT\nGGCTC\nGGTGGT\nGTGAC\n', 'name': 'FER'}, 'sequence3': {'header': 'NM_0013082323028.1 H STZ mRSN1A', 'content': 'CAGCCC\nCCGTGACGC\nGGG\nGTGGTGA\nCTGGCTCCGGAGT\nCTGAGGGGTTCGG', 'name': None}}

见a demo on ideone.com。