如何在python中使用正则表达式来捕获两个字符串或短语之间的某些内容,并删除该行的其他所有内容?
例如,下面是一个蛋白质序列,前面有一个单行标题。 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"?
我需要用这个简化的结果"CG33289-PC"替换标题,而不是破坏蛋白质序列(在所有大写字母的标题行下方找到)。
这是每个蛋白质序列条目的样子 - 一个标题后跟一个序列:
>FBpp0293870 type=protein;loc=3L:join(21527760..21527913,21527977..21528076,21528130..21528390,21528443..21528653,21528712..21529192,21529254..21529264);ID=FBpp0293870;名称=CG33289-PC;父=FBgn0053289,FBtr0305327;dbxref=FlyBase:FBpp0293870,FlyBase_Annotation_IDs:CG33289-PC;MD5=478485a27487608aa2b6c35d39a3295c;长度=405;释放=R5.45;物种=德梅尔; MEMLKYVISDNNYSWWIKLYFAIIFALVLFVAVNLAVGIYNKWDSTPVII GISSKMTPIDQIPFPTITVCNMNQAKKSKVEHLMPGSIRYAMLQKTCYKE SNFSQYMDTQHRNETFSNFILDVSEKCADLIVSCIFHQQRIPCTDIFRET FVDEGLCCIFNVLHPYYLYKFKSPYIRDFTSSDRFADIAVDWDPISGYPQ RLPSSYYPRPGVGVGTSMGLQIVLNGHVDDYFCSSTNGQGFKILLYNPID QPRMKESGLPVMIGHQTSFRIIARNVEATPSIRNIHRTKRQCIFSDEQEL LFYRYYTRRNCEAECDSMFFLRLCSCIPYYLPLIYPNASVCDVFHFECLN RAESQIFDLQSSQCKEFCLTSCHDLIFFPDAFSTPFSQKDVKAQTNYLTN 弗拉夫
这是所需的输出:
CG33289电脑
MEMLKYVISDNNYSWWIKLYFAIIFALVLFVAVNLAVGIYNKWDSTPVII GISSKMTPIDQIPFPTITVCNMNQAKKSKVEHLMPGSIRYAMLQKTCYKE SNFSQYMDTQHRNETFSNFILDVSEKCADLIVSCIFHQQRIPCTDIFRET FVDEGLCCIFNVLHPYYLYKFKSPYIRDFTSSDRFADIAVDWDPISGYPQ RLPSSYYPRPGVGVGTSMGLQIVLNGHVDDYFCSSTNGQGFKILLYNPID QPRMKESGLPVMIGHQTSFRIIARNVEATPSIRNIHRTKRQCIFSDEQEL LFYRYYTRRNCEAECDSMFFLRLCSCIPYYLPLIYPNASVCDVFHFECLN RAESQIFDLQSSQCKEFCLTSCHDLIFFPDAFSTPFSQKDVKAQTNYLTN 弗拉夫
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'1n', s)
CG33289-PC
MEMLKYVISDNNYSWWIKLYFAIIFALVLFVAVNLAVGIYNKWDSTPVII
GISSKMTPIDQIPFPTITVCNMNQAKKSKVEHLMPGSIRYAMLQKTCYKE
SNFSQYMDTQHRNETFSNFILDVSEKCADLIVSCIFHQQRIPCTDIFRET
FVDEGLCCIFNVLHPYYLYKFKSPYIRDFTSSDRFADIAVDWDPISGYPQ
RLPSSYYPRPGVGVGTSMGLQIVLNGHVDDYFCSSTNGQGFKILLYNPID
QPRMKESGLPVMIGHQTSFRIIARNVEATPSIRNIHRTKRQCIFSDEQEL
LFYRYYTRRNCEAECDSMFFLRLCSCIPYYLPLIYPNASVCDVFHFECLN
RAESQIFDLQSSQCKEFCLTSCHDLIFFPDAFSTPFSQKDVKAQTNYLTN
FSRAV
>>>
不是一个优雅的解决方案,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])
假设FlyBase_Annotation_IDs
只能在数据中出现一次。
我不确定文件的格式,但此正则表达式将捕获示例中的数据:
"FlyBase_Annotation_IDs:([A-Z0-9a-z-]*);"
使用findall
函数获取匹配项。
假设标题后面有一个换行符:
>>> import re
>>> protein = "..."
>>> r = re.compile(r"^.*FlyBase_Annotation_IDs:([A-Z0-9a-z-]*);.*$", re.MULTILINE)
>>> r.sub(r"1", protein)
正则表达式中的组([A-Z0-9a-z-]*)
提取任何字母数字字符和短划线。如果 id 可以包含其他字符,只需添加它们即可。