How to add variable error to regex fuzzy search. Python

Question

import regex,re


sequence = 'aaaaaaaaaaaabbbbbbbbbbbbcccccccccccc' #being searched
query = 'aaabbbbbbbbbbbbccc' #100% coverage
query_1 = 'aaaabbbbbbbbcbbbcccc' #95% coverage
query_2 = 'aaabbbbcbbbbbcbccc' #90% coverage

threshold = .95
error = len(query_1) - (len(query_1)*threshold) #for query_1 errors must be <= 1

print regex.search(query_1 + '{e<={}}'.format(error),sequence).group(0)

Im trying to add additional parameters to a regex search so it only works if a certain percentage of the query is in sequence being searched.

For example, if I wanted it to be at least 95% coverage it would work for query_1 but it would not work for query_2

The fuzzy matching capabilities of the regex module might be what you are looking for. — Martin Ender
– Martin Ender, Commented Jul 2, 2013 at 22:21

perreal · Accepted Answer · 2013-07-03 20:58:28Z

1

Using the regex module:

import regex
sequence = 'aaaaaaaaaaaabbbbbbbbbbbbcccccccccccc' #being searched
query = 'aaabbbbbbbbbbbbccc' #100% coverage
query_1 = 'aaaabbbbbbbbcbbbcccc' #95% coverage
query_2 = 'aaabbbbcbbbbbcbccc' #90% coverage
threshold = 0.97
queries = (query, query_1, query_2)
for q in queries:
    error = int(len(q) - (len(q)*threshold))
    m = regex.search(r'(%s){e<=%d}'%(q,error), sequence)
    print 'match' if m else 'nomatch'

answered Jul 3, 2013 at 20:58

perreal

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2 Comments

O.rka Over a year ago

what is it called when you add (%s)(%d)%(variable1,variable2) ? i want to look at the documentation because i've seen that before @perreal

perreal Over a year ago

it's called old style string format: docs.python.org/2/library/stdtypes.html#string-formatting

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