compiling a fuzzy regexp with python regex

Question

When I found out that the python regex module allows fuzzy matching I was increasingly happy as it seemed as a simple solution to many of my problems. But now I am having a problem for which I did not find any answers from documentation.

How could I compile Strings into regexps using also the new fuzziness value feature?

To illustrate my usual needs and give a sample a little piece of code

import regex
f = open('liner.fa', 'r')
nosZ2f='TTCCGACTACCAAGGCAAATACTGCTTCTCGAC'
nosZ2r='AGGTCACATCAACGTCAACG'

#nini=regex.compile(nosZ2r{e<=3})

nimekiri=list(f)
pikkus=len(nimekiri)

count = 0
while (count < pikkus):
    line = nimekiri[count].rstrip('\n')
    m=regex.findall("(TTCCGACTACCAAGGCAAATACTGCTTCTCGAC){e<=3}", line)
    n=regex.findall("AGGTCACATCAACGTCAACG{e<=3}", line) 
    if bool(m) & bool(n):
        print nimekiri[count-1].rstrip('\n')
        print line
    count = count + 1

f.close()

As you can see the regexps with fuzzyness of 3 errors work fine. But I was forced to enter the whole string (nosZ2f/r) manually into the findall. I was not able to compile a regexp with error/fuzzyness values.

What would be correct syntax of turning a string (line nosZ2f/r) to a regexp pattern with fuzzyness value of 3 errors? (failed attempt seen at commented line)

Possibility to use input strings as source for regexp would be critical for any actually useful script I have in mind. (not much automation going on otherwise) So it'd delight me if I could frex. replace

m=regex.findall("(TTCCGACTACCAAGGCAAATACTGCTTCTCGAC){e<=3}", line)

with

m=regex.findall(nini, line) etc.

Or

m=regex.findall("string{e<=3}", line)

Spencer Rathbun · Accepted Answer · 2014-01-14 13:26:02Z

3

You need to put your strings together correctly.

import regex
testString = 'some phrase'
r = regex.compile('('+testString+'){e<=5}')
r.match('phrase')

If you want to build a regex pattern, you'll need to use various string manipulation techniques to build up the appropriate pattern to use.

answered Jan 14, 2014 at 13:26

Spencer Rathbun

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