Regular Expressions

Regular expressions in PERL -

$line= “ATGAAATGTGGTGGG”

if($line=_{/^ATG(\S\S\S).*(\S)G$/)
{
print "match.group(1): $1\n";
print "match.group(2): $2\n";
}}~~~

Regular expressions in Python -

import re

line = “ATGAAATGTGGTGGG”

match = re.match( r’^ATG(SSS).*(S)G$’, line)

if match:
print “match.group(1) : “, match.group(1)
print “match.group(2) : “, match.group(2)

Regular expression is a special sublanguage to make searches through strings easy. Python has a special library (‘re’) to facilitate the use of regular expressions.

Search

import re

S=re.search(‘[a-z]a[a-z]’, ‘a fat cat sat’)

if S:
print “yes”
else:
print “no”

The above code searches for three letter patterns within the sentence, where
the first and third letter can be ‘a-z’, but the middle letter is ‘a’.

import re
str = ‘I am flying from Seatttle to San Francisco’
match = re.search(r’[SF]’, str)
if match:
print ‘found S/F’, match.group()
else:
print ‘did not find S/F’

Search and Replace

import re

seq=”ATTCGATCT”

s= re.sub(‘A’, ‘’, seq)
diff=len(seq)-len(s)
print “count of A =”, diff

The sub command replaces “Seattle” with “London” in the following example.

import re
str = ‘I am flying from Seattle to San Francisco’
x = re.sub(r’Seattle’, ‘London’, str)
print x

References

For description of regular expression sublanguage, check here -

https://regexr.com/

https://regex101.com/

https://developers.google.com/edu/python/regular-expressions?hl=en