Trypsin Digest (cleavage) Does Not Work Using Regular Expression
I have trying to code the theoretical tryptic cleavage of protein sequences in Python. The cleavage rule for trypsin is: after R or K, but not before P. (i.e. the trypsin cleaves (
Solution 1:
regexes are nice, but here's a solution that uses regular python. Since you're looking for subsequences in the bases, it makes sense to build this as a generator, which yields the fragments.
example = 'MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK'
def trypsin(bases):
sub = ''while bases:
k, r = bases.find('K'), bases.find('R')
cut = min(k, r)+1if k > 0and r > 0elsemax(k, r)+1sub += bases[:cut]
bases = bases[cut:]
ifnot bases or bases[0] != 'P':
yieldsubsub = ''print list(trypsin(example))
Solution 2:
EDIT With a slight modification your regex works well:
In your comment you mentioned you have multiple sequences in a file (let's call it sequences.dat):
$ cat sequences.dat
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK
>>> withopen('sequences.dat') as f:
s = f.read()
>>> print(s)
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK
MVPPPPSRGGAAKPGQLGRSLGPLLLLLRPEEPEDGDREICSESK
>>> protein = re.sub(r'(?<=[RK])(?=[^P])','\n', s, re.DOTALL)
>>> protein.split()
['MVPPPPSR', 'GGAAKPGQLGR', 'SLGPLLLLLRPEEPEDGDR', 'EICSESK', 'MVPPPPSR', 'GGAAKPGQLGR', 'SLGPLLLLLRPEEPEDGDR', 'EICSESK', 'MVPPPPSR', 'GGAAKPGQLGR', 'SLGPLLLLLRPEEPEDGDR', 'EICSESK']
>>> print protein
MVPPPPSR
GGAAKPGQLGR
SLGPLLLLLRPEEPEDGDR
EICSESK
MVPPPPSR
GGAAKPGQLGR
SLGPLLLLLRPEEPEDGDR
EICSESK
MVPPPPSR
GGAAKPGQLGR
SLGPLLLLLRPEEPEDGDR
EICSESK
Solution 3:
I believe the following regexp will do as you have described:
([KR]?[^P].*?[KR](?!P))
Result below from pythonregexp
>>> regex = re.compile("([KR]?[^P].*?[KR](?!P))")
>>> r = regex.search(string)
>>> r
<_sre.SRE_Match object at 0xb1a9f49eb4111980>
>>> regex.match(string)
<_sre.SRE_Match object at 0xb1a9f49eb4102980>
# List the groups found>>> r.groups()
(u'MVPPPPSR',)
# List the named dictionary objects found>>> r.groupdict()
{}
# Run findall>>> regex.findall(string)
[u'MVPPPPSR', u'GGAAKPGQLGR', u'SLGPLLLLLRPEEPEDGDR', u'EICSESK']
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