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Asked: 2026-06-06T09:18:35+00:00

How can I use regex in python to capture something between two strings or

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How can I use regex in python to capture something between two strings or phrases, and removing everything else on the line?

For example, the following is a protein sequence preceded by a one-line header. 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 “,” ?

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).

This is what each protein sequence entry looks like – a header followed by a sequence:

>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

This is the desired output:

CG33289-PC
MEMLKYVISDNNYSWWIKLYFAIIFALVLFVAVNLAVGIYNKWDSTPVII
GISSKMTPIDQIPFPTITVCNMNQAKKSKVEHLMPGSIRYAMLQKTCYKE
SNFSQYMDTQHRNETFSNFILDVSEKCADLIVSCIFHQQRIPCTDIFRET
FVDEGLCCIFNVLHPYYLYKFKSPYIRDFTSSDRFADIAVDWDPISGYPQ
RLPSSYYPRPGVGVGTSMGLQIVLNGHVDDYFCSSTNGQGFKILLYNPID
QPRMKESGLPVMIGHQTSFRIIARNVEATPSIRNIHRTKRQCIFSDEQEL
LFYRYYTRRNCEAECDSMFFLRLCSCIPYYLPLIYPNASVCDVFHFECLN
RAESQIFDLQSSQCKEFCLTSCHDLIFFPDAFSTPFSQKDVKAQTNYLTN
FSRAV

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1 Answer

  1. Editorial Team

    Using regexps:

    >>> 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
>>>
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