Reputation: 617
HI I am working on antibodies where I have to find a specific pattern for it's antigen specificity using python. I am puzzling over to find a match pattern with predefined numbers of substitution.
I tried regex (re.findall/re.search) with possible permutation/combination but this couldn't solve my problem. Also, searching on internet didn't help.
Not sure though if it needs an AI/ML algorithm to match specific pattern.
condition:-
I want to match any given string with the pattern with maximum 4 possible substitutions from substitution_list at any position without changing its original frame.
substitution_list='A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y']
pattern="AVTLDPQRSTSTRP"
e.g:-
string_1="AV**A**LDPQRSTSTRP" --> matched
string_2="AV**A**LDPQ**C**STSTRP" --> matched
string_3="AV**V**L**P**PQ**L**ST**L**TRP" --> matched
string_4="**L**V**V**L**P**PQ**L**STS**C**RP" --> NOT matched (5 substitution)
string_5="TRPAVQRSTLDPTS" --> NOT matched (original frame has changed)
Thanks.
Upvotes: 2
Views: 80
Reputation: 617
I have find a way (dirty though) which helps me in this particular case.
def match_pattern(string):
pattern='AVTLDPQRSTSTRP' ### standard template
max_subs=4 ### maximum allowed substitutions
score=0
for i in range(len(string)):
if string[i]!=pattern[i]:
score+=1
# print(score)
if score <=max_subs:
print('String matched')
else:
print('Not matched')
test_strings=["AVALDPQRSTSTRP" ,"AVALDPQCSTSTRP" ,"AVVLPPQLSTLTRP" ,"LVVLPPQLSTSCRP" ,"TRPAVQRSTLDPTS"]
for string in test_strings:
match_pattern(string)
String matched
String matched
String matched
Not matched
Not matched
Upvotes: 1