使用正则表达式拆分 header 和内容
Splitting header and content using regex
我在文件中有以下序列文本
每个 header 都以“>”开头
内容行数随机
>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
我想创建以下格式的嵌套字典:
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'
}
我被正则表达式卡住了,有人可以帮我吗?
你可以使用
^>
(?P<header>
[^\n()]*
(?:\((?P<name>[^\n()]+)\))?
[^()\n]*
)
[\n\r]
(?P<content>[\s\S]+?)(?=^>|\Z)
带有 multiline
和 verbose
标志,参见 a demo on regex101.com。
在 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)
这会产生
{'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}}
我在文件中有以下序列文本
每个 header 都以“>”开头 内容行数随机
>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
我想创建以下格式的嵌套字典:
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'
}
我被正则表达式卡住了,有人可以帮我吗?
你可以使用
^>
(?P<header>
[^\n()]*
(?:\((?P<name>[^\n()]+)\))?
[^()\n]*
)
[\n\r]
(?P<content>[\s\S]+?)(?=^>|\Z)
带有 multiline
和 verbose
标志,参见 a demo on regex101.com。
在
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)
这会产生
{'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}}