python regex for finding all matches - python

I have a sequence
seq = 'CCGATGACCTCACAGCCGCCTCCTGCCTTGAGGAAAGGAACTGCAATTCC'
I am try to get sequences of length 23bp ending with NGG where N = A or C or T or G`
I use p = re.compile('([ACGT]{21}GG)') and when I say
for m in p.finditer(seq):
print m.group()
I get only CACAGCCGCCTCCTGCCTTGAGG.
But clearly CCGCCTCCTGCCTTGAGGAAAGG also matches. Why is it not reported?

Put your regex inside a lookahead assertion in-order to do overlapping matches. Your regex fails to match the two strings because by one match contains another match . Regex by default won't do overlapping match. You need to put the pattern inside lookarounds in-order to capture the overlapping matches.
(?=([ACGT]{21}GG))
Code:
>>> seq = 'CCGATGACCTCACAGCCGCCTCCTGCCTTGAGGAAAGGAACTGCAATTCC'
>>> p = re.compile(r'(?=([ACGT]{21}GG))')
>>> for m in p.finditer(seq):
print m.group(1)
CACAGCCGCCTCCTGCCTTGAGG
CCGCCTCCTGCCTTGAGGAAAGG
See the captures at the right side in this demo.

Related

See which component in regex alternation was captured

In regex alternation, is there a way to retrieve which alternation was matched? I just need the first alternation match, not all the alternations that match.
For example, I have a regex like this
pattern = r'(abc.*def|mno.*pqr|mno.*pqrt|.....)'
string = 'mnoxxxpqrt'
I want the output to be 'mno.*pqr'
How should I write the regex statement? Python language is preferred.
To do this efficiently without any iterations, you can put your desired sub-patterns in a list and join them into one alternation pattern with each sub-pattern enclosed in a capture group (so the resulting pattern looks like (abc.*def)|(mno.*pqr) instead of (abc.*def|mno.*pqr)). You can then obtain the group number of the sub-pattern with the Match object's lastindex attribute and in turn obtain the matching sub-pattern from the original list of sub-patterns:
import re
patterns = [r'abc.*def', r'mno.*pqr', r'mno.*pqrt']
pattern = '|'.join(map('({})'.format, patterns))
string = 'mno_foobar_pqrt'
print(pattern)
print(patterns[re.search(pattern, string).lastindex - 1])
This outputs:
(abc.*def)|(mno.*pqr)|(mno.*pqrt)
mno.*pqr
Demo: https://replit.com/#blhsing/JointBruisedMention
You can use capture groups:
import re
string = 'abcxxxdef'
patterns = ['abc.*def', 'mno.*pqr']
match = re.match(r'((abc.*def)|(mno.*pqr))',string)
groups = match.groups()
alternations = []
for i in range(1, len(groups)):
if (groups[i] != None):
pattern = patterns[i-1]
break
print(pattern)
Result: mno.*pqr
Expressions inside round brackets are capture groups, they correspond to the 1st to last index of the response. The 0th index is the whole match.
Then you would need to find the index which matched. Except your patterns would need to be fined before hand.
Well you could iterate the terms in the regex alternation:
string = 'abcxxxdef'
pattern = r'(abc.*def|mno.*pqr)'
terms = pattern[1:-1].split("|")
for term in terms:
if re.search(term, string):
print("MATCH => " + term)
This prints:
MATCH => abc.*def
The right answer to the question How should I write the regex statement? should actually be:
There is no known way to write the regex statement using the provided regex pattern which will allow to extract from the regex search result the information which of the alternatives have triggered the match.
And as there is no way to do it using the given pattern it is necessary to change the regex pattern which then makes it possible to extract from the match the requested information.
A possible way around this regex engine limitation is proposed below, but it requires an additional regex pattern search and has the disadvantage that there is a chance that it fails for some special search pattern alternatives.
The below provided code allows usage of simpler regex patterns without defining groups and works the "other way around" by checking which of the alternate patterns triggers a match in the found match for the entire regex:
import re
pattern = r'abc.*def|mno.*pqr|mno.*pqrt'
text = 'mnoxxxpqrt'
match = re.match(pattern,text)[0]
print(next(p for p in pattern.split('|') if re.match(p, match)))
It might fail in case when in the text found match string fails to be also a match for the single regex pattern what can happen for example if a non-word boundary \B requirement is used in the search pattern ( as mentioned in the comments by Kelly Bundy ).
A not failing alternative solution is to perform the regex search using a modified regex pattern. Below an approach using a dictionary for defining the alternatives and a function returning the matched group:
import re
dct_alts = {1:r'(abc.*def)',2:r'(mno.*pqr)',3:r'(mno.*pqrt)'}
# ^-- the dictionary index is the index of the matching group in the found match.
text = 'mnoxxxpqrt'
def get_matched_group(dct_alts, text):
pattern = '|'.join(dct_alts.values())
re_match = re.match(pattern, text)
return(dct_alts[re_match.lastindex])
print(get_matched_group(dct_alts, text))
prints
(mno.*pqr)
For the sake of completeness a function returning a list of all of the alternatives which give a match (not only the first one which matches):
import re
lst_alts = [r'abc.*def', r'mno.*pqr', r'mno.*pqrt']
text = 'mnoxxxpqrt'
def get_all_matched_groups(lst_alts, text):
matches = []
for pattern in lst_alts:
re_match = re.match(pattern, text)
if re_match:
matches.append(pattern)
return matches
print(get_all_matched_groups(lst_alts, text))
prints
['mno.*pqr', 'mno.*pqrt']

in regex how to match multiple Or conditions but exclude one condition

If I need to match a string "a" with any combination of symbols ##$ before and after it, such as #a#, #a#, $a$ etc, but not a specific pattern #a$. How can I exclude this? Suppose there're too many combinations to manually spell out one-by-one. And it's not negative lookahead or behind cases as seen in other SO answers.
import re
pattern = "[#|#|&]a[#|#|&]"
string = "something#a&others"
re.findall(pattern, string)
Currently the pattern returns results like '#a&' as expected, but also wrongly return on the string to be excluded. The correct pattern should return [] on re.findall(pattern,'#a$')
You can use the character class to list all the possible characters, and use a single negative lookbehind after the match to assert not #a$ directly to the left.
Note that you don't need the | in the character class, as it would match a pipe char and is the same as [#|#&]
[##&$]a[##&$](?<!#a\$)
Regex demo | Python demo
import re
pattern = r"[##&$]a[##&$](?<!#a\$)"
print(re.findall(pattern,'something#a&others#a$'))
Output
['#a&']
I was going to suggest a fairly ugly and complex regex pattern with lookarounds. But instead, you could just proceed with your current pattern and then use a list comprehension to remove the false positive case:
inp = "something#a&others #a$"
matches = re.findall(r'[##&$]+a[##&$]+', inp)
matches = [x for x in matches if x != '#a$']
print(matches) # ['#a&']

Extract a string between two set of patterns in Python

I am trying to extract a substring between two set of patterns using re.search().
On the left, there can be either 0x or 0X, and on the right there can be either U, , or \n. The result should not contain boundary patterns. For example, 0x1234U should result in 1234.
I tried with the following search pattern: (0x|0X)(.*)(U| |\n), but it includes the left and right patterns in the result.
What would be the correct search pattern?
You could use also use a single group using .group(1)
0[xX](.*?)[U\s]
The pattern matches:
0[xX] Match either 0x or 0X
(.*?) Capture in group 1 matching any character except a newline, as least as possible
[U\s] Match either U or a whitespace characters (which could also match a newline)
Regex demo | Python demo
import re
s = r"0x1234U"
pattern = r"0[xX](.*?)[U\s]"
m = re.search(pattern, s)
if m:
print(m.group(1))
Output
1234
You could use a combination of lookbehind and lookahead with a non-greedy match pattern in between:
import re
pattern = r"(?<=0[xX])(.*?)(?=[U\s\n])"
re.findall(pattern,"---0x1234U...0X456a ")
['1234', '456a']

Regex : matching integers inside of brackets

I am trying to take off bracketed ends of strings such as version = 10.9.8[35]. I am trying to substitute the integer within brackets pattern
(so all of [35], including brackets) with an empty string using the regex [\[+0-9*\]+] but this also matches with numbers not surrounded by brackets. Am I not using the + quantifier properly?
You could match the format of the number and then match one or more digits between square brackets.
In the replacement using the first capturing group r'\1'
\b([0-9]+(?:\.[0-9]+)+)\[[0-9]+\]
\b Word boundary
( Capture group 1
[0-9]+ Match 1+ digits
(?:\.[0-9]+)+ Match a . and 1+ digits and repeat that 1 or more times
) Close group
\[[0-9]+\] Match 1+ digits between square brackets
Regex demo
For example
import re
regex = r"\b([0-9]+(?:\.[0-9]+)+)\[[0-9]+\]"
test_str = "version = 10.9.8[35]"
result = re.sub(regex, r'\1', test_str)
print (result)
Output
version = 10.9.8
No need for regex
s = '10.9.8[35]'
t = s[:s.rfind("[")]
print(t)
But if you insist ;-)
import re
s = '10.9.8[35]'
t = re.sub(r"^(.*?)[[]\d+[]]$", r"\1", s)
print(t)
Breakdown of regex:
^ - begins with
() - Capture Group 1 you want to keep
.*? - Any number of chars (non-greedy)
[[] - an opening [
\d+ 1+ digit
[]] - closing ]
$ - ends with
\1 - capture group 1 - used in replace part of regex replace. The bit you want to keep.
Output in both cases:
10.9.8
Use regex101.com to familiarise yourself more. If you click on any of the regex samples at bottom right of the website, it will give you more info. You can also use it to generate regex code in a variety of languages too. (not good for Java though!).
There's also a great series of Python regex videos on Youtube by PyMoondra.
A simpler regex solution:
import re
pattern = re.compile(r'\[\d+\]$')
s = '10.9.8[35]'
r = pattern.sub('', s)
print(r) # 10.9.8
The pattern matches square brackets at the end of a string with one or more number inside. The sub then replaces the square brackets and number with an empty string.
If you wanted to use the number in the square brackets just change the sub expression such as:
import re
pattern = re.compile(r'\[(\d+)\]$')
s = '10.9.8[35]'
r = pattern.sub(r'.\1', s)
print(r) # 10.9.8.35
Alternatively as said by the other answer you can just find it and splice to get rid of it.

Stripping variable borders with python re

How does one replace a pattern when the substitution itself is a variable?
I have the following string:
s = '''[[merit|merited]] and [[eat|eaten]] and [[go]]'''
I would like to retain only the right-most word in the brackets ('merited', 'eaten', 'go'), stripping away what surrounds these words, thus producing:
merited and eaten and go
I have the regex:
p = '''\[\[[a-zA-Z]*\[|]*([a-zA-Z]*)\]\]'''
...which produces:
>>> re.findall(p, s)
['merited', 'eaten', 'go']
However, as this varies, I don't see a way to use re.sub() or s.replace().
s = '''[[merit|merited]] and [[eat|eaten]] and [[go]]'''
p = '''\[\[[a-zA-Z]*?[|]*([a-zA-Z]*)\]\]'''
re.sub(p, r'\1', s)
? so that for [[go]] first [a-zA-Z]* will match empty (shortest) string and second will get actual go string
\1 substitutes first (in this case the only) match group in a pattern for each non-overlapping match in the string s. r'\1' is used so that \1 is not interpreted as the character with code 0x1
well first you need to fix your regex to capture the whole group:
>>> s = '[[merit|merited]] and [[eat|eaten]] and [[go]]'
>>> p = '(\[\[(?:[a-zA-Z]*\|)*([a-zA-Z]*)\]\])'
>>> [('[[merit|merited]]', 'merited'), ('[[eat|eaten]]', 'eaten'), ('[[go]]', 'go')]
[('[[merit|merited]]', 'merited'), ('[[eat|eaten]]', 'eaten'), ('[[go]]', 'go')]
This matches the whole [[whateverisinhere]] and separates the whole match as group 1 and just the final word as group 2. You can than use \2 token to replace the whole match with just group 2:
>>> re.sub(p,r'\2',s)
'merited and eaten and go'
or change your pattern to:
p = '\[\[(?:[a-zA-Z]*\|)*([a-zA-Z]*)\]\]'
which gets rid of grouping the entire match as group 1 and only groups what you want. you can then do:
>>> re.sub(p,r'\1',s)
to have the same effect.
POST EDIT:
I forgot to mention that I actually changed your regex so here is the explanation:
\[\[(?:[a-zA-Z]*\|)*([a-zA-Z]*)\]\]
\[\[ \]\] #literal matches of brackets
(?: )* #non-capturing group that can match 0 or more of whats inside
[a-zA-Z]*\| #matches any word that is followed by a '|' character
( ... ) #captures into group one the final word
I feel like this is stronger than what you originally had because it will also change if there are more than 2 options:
>>> s = '[[merit|merited]] and [[ate|eat|eaten]] and [[go]]'
>>> p = '\[\[(?:[a-zA-Z]*\|)*([a-zA-Z]*)\]\]'
>>> re.sub(p,r'\1',s)
'merited and eaten and go'

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