python正则表达式在两个字符串或短语之间查找内容
[英]python regular expression to find something in between two strings or phrases
问题描述
How can I use regex in python to capture something between two strings or phrases, and removing everything else on the line? 
如何在python中使用正则表达式捕获两个字符串或短语之间的内容，并删除行中的所有其他内容？
For example, the following is a protein sequence preceded by a one-line header. 例如，以下是一个单行标题后的蛋白质序列。 How can I sift off "CG33289-PC" from the header below based on the stipulation that is occurs after the phrase "FlyBase_Annotation_IDs:" and before the next comma "," ? 如何根据短语“ FlyBase_Annotation_IDs：”之后和下一个逗号“，”之前的规定从下面的标题中筛选出“ CG33289-PC”？
I need to substitute the header with this simplified result "CG33289-PC" and not destroy the protein sequence (found below the header-line in all caps). 我需要用简化的结果“ CG33289-PC”替换标题，而不破坏蛋白质序列（在所有大写字母的标题行下方找到）。
This is what each protein sequence entry looks like - a header followed by a sequence: 这是每个蛋白质序列条目的样子-标题后跟序列：
>FBpp0293870 type=protein;loc=3L:join(21527760..21527913,21527977..21528076,21528130..21528390,21528443..21528653,21528712..21529192,21529254..21529264);
This is the desired output: 这是所需的输出：
CG33289-PC
MEMLKYVISDNNYSWWIKLYFAIIFALVLFVAVNLAVGIYNKWDSTPVII GISSKMTPIDQIPFPTITVCNMNQAKKSKVEHLMPGSIRYAMLQKTCYKE SNFSQYMDTQHRNETFSNFILDVSEKCADLIVSCIFHQQRIPCTDIFRET FVDEGLCCIFNVLHPYYLYKFKSPYIRDFTSSDRFADIAVDWDPISGYPQ RLPSSYYPRPGVGVGTSMGLQIVLNGHVDDYFCSSTNGQGFKILLYNPID QPRMKESGLPVMIGHQTSFRIIARNVEATPSIRNIHRTKRQCIFSDEQEL LFYRYYTRRNCEAECDSMFFLRLCSCIPYYLPLIYPNASVCDVFHFECLN RAESQIFDLQSSQCKEFCLTSCHDLIFFPDAFSTPFSQKDVKAQTNYLTN FSRAV
4 个解决方案
解决方案1
2 已采纳 2012-06-26 08:06:39
Using regexps: 使用正则表达式：
>>> s = """>FBpp0293870 type=protein;loc=3L:join(21527760..21527913,21527977..21528076,21528130..21528390,21528443..21528653,21528712..21529192,21529254..21529264); ID=FBpp0293870; name=CG33289-PC; parent=FBgn0053289,FBtr0305327; dbxref=FlyBase:FBpp0293870,FlyBase_Annotation_IDs:CG33289-PC; MD5=478485a27487608aa2b6c35d39a3295c; length=405; release=r5.45; species=Dmel; MEMLKYVISDNNYSWWIKLYFAIIFALVLFVAVNLAVGIYNKWDSTPVII
GISSKMTPIDQIPFPTITVCNMNQAKKSKVEHLMPGSIRYAMLQKTCYKE
SNFSQYMDTQHRNETFSNFILDVSEKCADLIVSCIFHQQRIPCTDIFRET
FVDEGLCCIFNVLHPYYLYKFKSPYIRDFTSSDRFADIAVDWDPISGYPQ
RLPSSYYPRPGVGVGTSMGLQIVLNGHVDDYFCSSTNGQGFKILLYNPID
QPRMKESGLPVMIGHQTSFRIIARNVEATPSIRNIHRTKRQCIFSDEQEL
LFYRYYTRRNCEAECDSMFFLRLCSCIPYYLPLIYPNASVCDVFHFECLN
RAESQIFDLQSSQCKEFCLTSCHDLIFFPDAFSTPFSQKDVKAQTNYLTN
FSRAV"""
>>> import re
>>> print re.sub(r'.*FlyBase_Annotation_IDs:([\w-]+).*;', r'\1\n', s)
CG33289-PC
MEMLKYVISDNNYSWWIKLYFAIIFALVLFVAVNLAVGIYNKWDSTPVII
GISSKMTPIDQIPFPTITVCNMNQAKKSKVEHLMPGSIRYAMLQKTCYKE
SNFSQYMDTQHRNETFSNFILDVSEKCADLIVSCIFHQQRIPCTDIFRET
FVDEGLCCIFNVLHPYYLYKFKSPYIRDFTSSDRFADIAVDWDPISGYPQ
RLPSSYYPRPGVGVGTSMGLQIVLNGHVDDYFCSSTNGQGFKILLYNPID
QPRMKESGLPVMIGHQTSFRIIARNVEATPSIRNIHRTKRQCIFSDEQEL
LFYRYYTRRNCEAECDSMFFLRLCSCIPYYLPLIYPNASVCDVFHFECLN
RAESQIFDLQSSQCKEFCLTSCHDLIFFPDAFSTPFSQKDVKAQTNYLTN
FSRAV
>>>
解决方案2
1 2012-06-26 07:47:39
Not an elegant solution, but this should work for you: 这不是一个很好的解决方案，但这应该适合您：
>>> fly = 'FlyBase_Annotation_IDs'
>>> repl = 'CG33289-PC'
>>> part1, part2 = protein.split(fly)
>>> part2 = part2.replace(repl, "FooBar")
>>> protein = fly.join([part1, part2])
assuming FlyBase_Annotation_IDs can only appear once in the data. 假设FlyBase_Annotation_IDs只能在数据中出现一次。
解决方案3
1 2012-06-26 07:49:12
I'm not sure about the format of the file, but this regex will capture the data in your example: 我不确定文件的格式，但是此正则表达式将捕获示例中的数据：
"FlyBase_Annotation_IDs:([A-Z0-9a-z-]*);"
Use findall function to get the match. 使用findall函数获取匹配项。
解决方案4
1 2012-06-26 08:07:10
Assuming there is a newline after the header: 假设标题后有一个换行符：
>>> import re
>>> protein = "..."
>>> r = re.compile(r"^.*FlyBase_Annotation_IDs:([A-Z0-9a-z-]*);.*$", re.MULTILINE)
>>> r.sub(r"\1", protein)
The group ([A-Z0-9a-z-]*) in the regular expression extracts any alphanumeric character and the dash. 正则表达式中的组([A-Z0-9a-z-]*)提取任何字母数字字符和破折号。 If ids can have other characters, just add them. 如果ID可以包含其他字符，则只需添加它们即可。
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