Python regex: re.search() is extremely slow on large text files - python

My code does the following:
Take a large text file (i.e. a legal document that is 300 pages as a PDF).
Find a certain keyword (e.g. "small").
Return n words to the left and n words to the right of the keyword.
NOTE: In this context, a "word" is any string of non-space characters. "$cow123" would be a word, but "health care" would be two words.
Here is my problem:
The code takes an extremely long time to run on the 300 pages, and that time tends to increase very quickly as n increases.
Here is my code:
fileHandle = open('test_pdf.txt', mode='r')
document = fileHandle.read()
def search(searchText, doc, n):
#Searches for text, and retrieves n words either side of the text, which are returned separately
surround = r"\s*(\S*)\s*"
groups = re.search(r'{}{}{}'.format(surround*n, searchText, surround*n), doc).groups()
return groups[:n],groups[n:]
Here is the nasty culprit:
print search("\$27.5 million", document, 10)
Here's how you can test this code:
Copy the function definition from the code block above and run the following:
t = "The world is a small place, we $.205% try to take care of it."
print search("\$.205", t, 3)
I suspect that I have a nasty case of catastrophic backtracking, but I'm too new to regex to point my finger on the problem.
How do I speed up my code?


How about using re.search (or even string.find if you're only searching for fixed strings) to find the string, without any surrounding capturing groups. Then you use the position and length of the match (.start and .end on a re matchobject, or the return value of find plus the length of the search string). Get the substring before the match and do /\s*(\S*)\s*\z/ etc. on it, and get the substring after the match and do /\A\s*(\S*)\s*/ etc. on it.
Also, for help with your backtracking: you can use a pattern like \s+\S+\s+ instead of \s*\S*\s* (two chunks of whitespace have to be separated by a non-zero amount of non-whitespace, or else they wouldn't be two chunks), and you shouldn't butt up two consecutive \s*s like you do. I think r'\S+'.join([[r'\s+']*(n)) would give the right pattern for capturing n previous words (but my Python is rusty, so check that).


I see several problems here. The First, and probably worst, is that everything in your "surround" regex is, not just optional but independently optional. Given this string:
"Lorem ipsum tritani impedit civibus ei pri"
...when searchText = "tritani" and n = 1, this is what it has to go through before it finds the first match:
regex: \s* \S* \s* tritani
offset 0: '' 'Lorem' ' ' FAIL
'' 'Lorem' '' FAIL
'' 'Lore' '' FAIL
'' 'Lor' '' FAIL
'' 'Lo' '' FAIL
'' 'L' '' FAIL
'' '' '' FAIL
...then it bumps ahead one position and starts over:
offset 1: '' 'orem' ' ' FAIL
'' 'orem' '' FAIL
'' 'ore' '' FAIL
'' 'or' '' FAIL
'' 'o' '' FAIL
'' '' '' FAIL
... and so on. According to RegexBuddy's debugger, it takes almost 150 steps to reach the offset where it can make the first match:
position 5: ' ' 'ipsum' ' ' 'tritani'
And that's with just one word to skip over, and with n=1. If you set n=2 you end up with this:
\s*(\S*)\s*\s*(\S*)\s*tritani\s*(\S*)\s*\s*(\S*)\s*
I sure you can see where this is is going. Note especially that when I change it to this:
(?:\s+)(\S+)(?:\s+)(\S+)(?:\s+)tritani(?:\s+)(\S+)(?:\s+)(\S+)(?:\s+)
...it finds the first match in a little over 20 steps. This is one of the most common regex anti-patterns: using * when you should be using +. In other words, if it's not optional, don't treat it as optional.
Finally, you may have noticed the \s*\s* the auto-generated regex


You could try using mmap and appropriate regex flags, eg (untested):
import re
import mmap
with open('your file') as fin:
mf = mmap.mmap(fin.fileno(), 0, access=mmap.ACCESS_READ)
for match in re.finditer(your_re, mf, flags=re.DOTALL):
print match.group() # do something with your match
This'll only keep memory usage lower though...
The alternative is to have a sliding window of words (simple example of just single word before and after)...:
import re
import mmap
from itertools import islice, tee, izip_longest
with open('testingdata.txt') as fin:
mf = mmap.mmap(fin.fileno(), 0, access=mmap.ACCESS_READ)
words = (m.group() for m in re.finditer('\w+', mf, flags=re.DOTALL))
grouped = [islice(el, idx, None) for idx, el in enumerate(tee(words, 3))]
for group in izip_longest(*grouped, fillvalue=''):
if group[1] == 'something': # check criteria for group
print group


I think you are going about this completely backwards (I'm a little confused as to what you are doing in the first place!)
I would recommend checking out the re_search function I developed in the textools module of my cloud toolbox
with re_search you could solve this problem with something like:
from cloudtb import textools
data_list = textools.re_search('my match', pdf_text_str) # search for character objects
# you now have a list of strings and RegPart objects. Parse through them:
for i, regpart in enumerate(data_list):
if isinstance(regpart, basestring):
words = textools.re_search('\w+', regpart)
# do stuff with words
else:
# I Think you are ignoring these? Not totally sure
Here is a link on how to use and how it works:
http://cloudformdesign.com/?p=183
In addition to this, your regular expressions would also be printed out in more readable format.
You might also want to check out my tool Search The Sky or the similar tool Kiki to help you build and understand your regular expressions.

Related

Regex to exclude words followed by space

I tried a lot of solutions but can't get this Regex to work.
The string-
"Flow Control None"
I want to exclude "Flow Control" plus the blank space, and only return whatever is on the right.

Since you have tagged your question with #python and #regex, I'll outline a simple solution to your problem using these tools. Furthermore, the other two answers don't really tackle the exact problem of matching "whatever is on the right" of your "Flow Control " prefix.
First, start by importing the re builtin module (read the docs).
import re
Define the pattern you want to match. Here, we're matching "whatever is on the right" ((?P<suffix>.+)$) of ^Flow Control .
pattern = re.compile(r"^Flow Control (?P<suffix>.+)$")
Grab the match for a given string (e.g. "Flow Control None")
suffix = pattern.search("Flow Control None").group("suffix")
print(suffix) # Out: None
Hopefully, this complete working example will also help you
import re
def get_suffix(text: str):
pattern = re.compile(r"^Flow Control (?P<suffix>.+)$")
matches = pattern.search(text)
return matches.group("suffix") if matches else None
examples = [
"Flow Control None",
"Flow Control None None",
"Flow Control None",
"Flow Control ",
]
for example in examples:
suffix = get_suffix(text=example)
if suffix:
print(f"Matched: {repr(suffix)}")
else:
print(f"No matches for: {repr(example)}")

Use split like so:
my_str = 'Flow Control None'
out_str = my_str.split()[-1]
# 'None'
Or use re.findall:
import re
out_str = re.findall(r'^.*\s(\S+)$', my_str)[0]

If you really want a purely regex solution try this: (?<= )[a-zA-Z]*$
The (?<= ) matches a single ' ' but doesn't include it in the match. [a-zA-Z]* matches anything from a to z or A to Z any number of times. $ matches the end of the line.
You could also try replacing the * with a + if you want to ensure that your match has at least one letter (* will produce a 0-length match if your string ends in a space, + will match nothing).
But it may be clearer to do something like
data = "Flow Control None"
split = data.split(' ')
split[len(split) - 1] # returns "None"
EDIT data.split(' ')[-1] also returns "None"
or
data[data.rfind(' ') + 1:] # returns "None"
that don't involve regexes at all.

Complex string filtering with python

I have a long string that is a phylogenetic tree and I want to do a very specific filtering.
(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;
Basically every x#y is a species#gene_id information. What I am trying to do is trimming this down so that I will only have x instead of x#y.
(Esy, Aar,(Spa,Cpl))...
I tried splitting the string first but the problem is string has different 'split points' for what I want to achieve i.e. some parts x#y is ending with a , and others with a ). I searched for a solution and saw regular expression operations, but I am new to Python and I couldn't be sure if that is what I should be focusing on. I also thought about strip() but it seems like I need to specify the characters to be stripped for this.
Main problem is there is no 'pattern' for me to tell Python to follow. Only thing is that all species ids are 3 letters and they are before an # character.
Is there a method that can do what I want? I will be really glad if you can help me out with my problem. Thanks in advance.

Give this a try:
import re:
pat = re.compile(r'(\w{3})#')
txt = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
pat.findall(t)
Result:
['Esy', 'Aar', 'Spa', 'Cpl', 'Bst', 'Aly', 'Ath', 'Chi', 'Cru', 'Hco', 'Hlo', 'Hla', 'Hse', 'Esa', 'Aal']
If you need the structure intact, we can try to remove the unnecessary parts instead:
pat = re.compile(r'(#|:)[^/),]*')
pat.sub('',t).replace(',', ', ')
Result:
'(Esy, Aar, ((Spa, Cpl), (((Bst, ((Aly, Ath), (Chi, Cru))), (((Hco, Hlo), Hla), Hse)), (Esa, Aal))))'
Regex demo

How about this kind of function:
def parse_string(string):
new_string = ''
skip = False
for char in string:
if char == '#':
skip = True
if char == ',':
skip = False
if not skip or char in ['(', ')']:
new_string += char
return new_string
Calling it on your string:
string = '(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;'
parse_string(string)
> '(Esy,Aar,((Spa,Cpl),(((Bst,((Aly,Ath),(Chi,Cru))),(((Hco,Hlo),Hla),Hse)),(Esa,Aal))))'

you can use regex:
import re
s = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
p = "...?(?=#)|\(|\)"
result = re.findall(p, s)
and you have your result as a list, so you can make it string or do anything with it
for explaining what is happening :
p is regular expression pattern
so in this pattern:
. means matching any word
...?(?=#) means match any word until I get to a word ? wich ? is #, so this whole pattern means that you get any three words before #
| is or statement, I used it here to find another pattern
and the rest of them is to find ) and (

Try this regex if you need the brackets in the output:
import re
regex = r"#[A-Za-z0-9_\.:]+|[0-9:\.;e-]+"
phylogenetic_tree = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
print(re.sub(regex,"",phylogenetic_tree))
Output:
(Esy,Aar,((Spa,Cpl),(((Bst,((Aly,Ath),(Chi,Cru))),(((Hco,Hlo),Hla),Hs)),(Esa,Aal))))

Because you are trying to parse a phylogenetic tree, I highly suggest to let BioPython do the heavy lifting for you.
You can easily parse and display a phylogenetic with Bio.Phylo. Then it is just iterating over all tree elements and splitting the names at the 'at'-sign.
Because Phylo expects the input to be in a file, we create an in-memory file-like object with io.StringIO. Getting the complete tree is then as easy as
Phylo.read(io.StringIO(s), 'newick')
In order to check if the parsed tree looks sane, I print it once with print(tree).
Now we want to change all node names that contain a '#'. With tree.find_elements we get access to all nodes. Some nodes don't have a name and some might not contain a '#'. So to be extra careful, we first check if n.name and '#' in n.name. Only then do we split each node's name at the '#' and take just the first part (index 0) of it:
n.name = n.name.split('#')[0]
In order to recreate the initial string representation, we use Phylo.write:
out = io.StringIO()
Phylo.write(tree, out, "newick")
print(out.getvalue())
Again, write wants to get a file argument - if we just want to get a string, we can use a StringIO object again.
Full code:
import io
from Bio import Phylo
if __name__ == '__main__':
s = '(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;'
tree = Phylo.read(io.StringIO(s), 'newick')
print(' before '.center(20, '='))
print(tree)
for n in tree.find_elements():
if n.name and '#' in n.name:
n.name = n.name.split('#')[0]
print(' result '.center(20, '='))
out = io.StringIO()
Phylo.write(tree, out, "newick")
print(out.getvalue())
Output:
====== before ======
Tree(rooted=False, weight=1.0)
Clade(branch_length=0.0129090235079)
Clade(branch_length=0.0726396855636, name='Esy#ESY15_g64743_DN3_SP7_c0')
Clade(branch_length=0.137507902808, name='Aar#AA_maker7399_1')
Clade(branch_length=0.0129090235079)
Clade(branch_length=9.05326020871e-05)
Clade(branch_length=0.0318934795022, name='Spa#Tp2g18720')
Clade(branch_length=0.0273465005242, name='Cpl#CP2_g48793_DN3_SP8_c')
Clade(branch_length=0.00328120860999)
Clade(branch_length=0.00859075940423)
Clade(branch_length=0.0340484449097)
Clade(branch_length=0.0332592496158, name='Bst#Bostr_13083s0053_1')
Clade(branch_length=0.0150356382287)
Clade(branch_length=0.0205924636564)
Clade(branch_length=0.0328569260951, name='Aly#AL8G21130_t1')
Clade(branch_length=0.0391706378372, name='Ath#AT5G48370_1')
Clade(branch_length=0.00998579652059)
Clade(branch_length=0.0954469923893, name='Chi#CARHR183840_1')
Clade(branch_length=0.0570981548016, name='Cru#Carubv10026342m')
Clade(branch_length=0.0372829371381)
Clade(branch_length=0.0206478928557)
Clade(branch_length=0.0144626717872)
Clade(branch_length=0.00823215335663, name='Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100')
Clade(branch_length=0.0085462978729, name='Hlo#DN13684_c0_g1_i1_p1')
Clade(branch_length=0.0225079453622, name='Hla#DN22821_c0_g1_i1_p1')
Clade(branch_length=0.048590776459, name='Hse#DN23412_c0_g1_i3_p1')
Clade(branch_length=1.00000050003e-06)
Clade(branch_length=0.0378509854703, name='Esa#Thhalv10004228m')
Clade(branch_length=0.0712272454125, name='Aal#Aa_G102140_t1')
==== result =====
(Esy:0.07264,Aar:0.13751,((Spa:0.03189,Cpl:0.02735):0.00009,(((Bst:0.03326,((Aly:0.03286,Ath:0.03917):0.02059,(Chi:0.09545,Cru:0.05710):0.00999):0.01504):0.03405,(((Hco:0.00823,Hlo:0.00855):0.01446,Hla:0.02251):0.02065,Hse:0.04859):0.03728):0.00859,(Esa:0.03785,Aal:0.07123):0.00000):0.00328):0.01291):0.01291;
The default format of Phylo uses less digits than in your original tree. In order to keep the numbers unchanged, just override the branch length format string with a '%s':
Phylo.write(tree, out, "newick", format_branch_length="%s")

Parsing code can be hard to follow. Tatsu lets you write readable parsing code by combining grammars and python:
text = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
import sys
import tatsu
grammar = """
start = things ';'
;
things = thing [ ',' things ]
;
thing = x '#' y ':' number
| '(' things ')' ':' number
;
x = /\w+/
;
y = /\w+/
;
number = /[+-]?\d+\.?\d*(e?[+-]?\d*)/
;
"""
class Semantics:
def x(self, ast):
# the method name matches the rule name
print('X =', ast)
parser = tatsu.compile(grammar, semantics=Semantics())
parser.parse(text)

Python Regular Expression - right-to-left

I am trying to use regular expressions in python to match the frame number component of an image file in a sequence of images. I want to come up with a solution that covers a number of different naming conventions. If I put it into words I am trying to match the last instance of one or more numbers between two dots (eg .0100.). Below is an example of how my current logic falls down:
import os
import re
def sub_frame_number_for_frame_token(path, token='#'):
folder = os.path.dirname(path)
name = os.path.basename(path)
pattern = r'\.(\d+)\.'
matches = list(re.finditer(pattern, name) or [])
if not matches:
return path
# Get last match.
match = matches[-1]
frame_token = token * len(match.group(1))
start, end = match.span()
apetail_name = '%s.%s.%s' % (name[:start], frame_token, name[end:])
return os.path.join(folder, apetail_name)
# Success
eg1 = 'xx01_010_animation.0100.exr'
eg1 = sub_frame_number_for_frame_token(eg1) # result: xx01_010_animation.####.exr
# Failure
eg2 = 'xx01_010_animation.123.0100.exr'
eg2 = sub_frame_number_for_frame_token(eg2) # result: xx01_010_animation.###.0100.exr
I realise there are other ways in which I can solve this issue (I have already implemented a solution where I am splitting the path at the dot and taking the last item which is a number) but I am taking this opportunity to learn something about regular expressions. It appears the regular expression creates the groups from left-to-right and cannot use characters in the pattern more than once. Firstly is there anyway to search the string from right-to-left? Secondly, why doesn't the pattern find two matches in eg2 (123 and 0100)?
Cheers

finditer will return an iterator "over all non-overlapping matches in the string".
In your example, the last . of the first match will "consume" the first . of the second. Basically, after making the first match, the remaining string of your eg2 example is 0100.exr, which doesn't match.
To avoid this, you can use a lookahead assertion (?=), which doesn't consume the first match:
>>> pattern = re.compile(r'\.(\d+)(?=\.)')
>>> pattern.findall(eg1)
['0100']
>>> pattern.findall(eg2)
['123', '0100']
>>> eg3 = 'xx01_010_animation.123.0100.500.9000.1234.exr'
>>> pattern.findall(eg3)
['123', '0100', '500', '9000', '1234']
# and "right to left"
>>> pattern.findall(eg3)[::-1]
['1234', '9000', '500', '0100', '123']

My solution uses a very simple hackish way of fixing it. It reverses the string path in the beginning of your function and reverses the return value at the end of it. It basically uses regular expressions to search the backwards version of your given strings. Hackish, but it works. I used the syntax shown in this question to reverse the string.
import os
import re
def sub_frame_number_for_frame_token(path, token='#'):
path = path[::-1]
folder = os.path.dirname(path)
name = os.path.basename(path)
pattern = r'\.(\d+)\.'
matches = list(re.finditer(pattern, name) or [])
if not matches:
return path
# Get last match.
match = matches[-1]
frame_token = token * len(match.group(1))
start, end = match.span()
apetail_name = '%s.%s.%s' % (name[:start], frame_token, name[end:])
return os.path.join(folder, apetail_name)[::-1]
# Success
eg1 = 'xx01_010_animation.0100.exr'
eg1 = sub_frame_number_for_frame_token(eg1) # result: xx01_010_animation.####.exr
# Failure
eg2 = 'xx01_010_animation.123.0100.exr'
eg2 = sub_frame_number_for_frame_token(eg2) # result: xx01_010_animation.123.####.exr
print(eg1)
print(eg2)

I believe the problem is that finditer returns only non-overlapping matches. Because both '.' characters are part of the regular expression, it doesn't consider the second dot as a possible start of another match. You can probably use the lookahead construct ?= to match the second dot without consuming it with "?=.".
Because of the way regular expressions work, I don't think there is an easy way to search right-to-left (though I suppose you could reverse the string and write the pattern backwards...).

If all you care about is the last \.(\d+)\., then anchor your pattern from the end of the string and do a simple re.search(_):
\.(\d+)\.(?:.*?)$
where (?:.*?) is non-capturing and non-greedy, so it will consume as few characters as possible between your real target and the end of the string, and those characters will not show up in matches.
(Caveat 1: I have not tested this. Caveat 2: That is one ugly regex, so add a comment explaining what it's doing.)
UPDATE: Actually I guess you could just do a ^.*(\.\d\.) and let the implicitly greedy .* match as much as possible (including matches that occur earlier in the string) while still matching your group. That makes for a simpler regex, but I think it makes your intentions less clear.

Efficient way to search for invalid characters in python

I am building a forum application in Django and I want to make sure that users dont enter certain characters in their forum posts. I need an efficient way to scan their whole post to check for the invalid characters. What I have so far is the following although it does not work correctly and I do not think the idea is very efficient.
def clean_topic_message(self):
topic_message = self.cleaned_data['topic_message']
words = topic_message.split()
if (topic_message == ""):
raise forms.ValidationError(_(u'Please provide a message for your topic'))
***for word in words:
if (re.match(r'[^<>/\{}[]~`]$',topic_message)):
raise forms.ValidationError(_(u'Topic message cannot contain the following: <>/\{}[]~`'))***
return topic_message
Thanks for any help.

For a regex solution, there are two ways to go here:
Find one invalid char anywhere in the string.
Validate every char in the string.
Here is a script that implements both:
import re
topic_message = 'This topic is a-ok'
# Option 1: Invalidate one char in string.
re1 = re.compile(r"[<>/{}[\]~`]");
if re1.search(topic_message):
print ("RE1: Invalid char detected.")
else:
print ("RE1: No invalid char detected.")
# Option 2: Validate all chars in string.
re2 = re.compile(r"^[^<>/{}[\]~`]*$");
if re2.match(topic_message):
print ("RE2: All chars are valid.")
else:
print ("RE2: Not all chars are valid.")
Take your pick.
Note: the original regex erroneously has a right square bracket in the character class which needs to be escaped.
Benchmarks: After seeing gnibbler's interesting solution using set(), I was curious to find out which of these methods would actually be fastest, so I decided to measure them. Here are the benchmark data and statements measured and the timeit result values:
Test data:
r"""
TEST topic_message STRINGS:
ok: 'This topic is A-ok. This topic is A-ok.'
bad: 'This topic is <not>-ok. This topic is {not}-ok.'
MEASURED PYTHON STATEMENTS:
Method 1: 're1.search(topic_message)'
Method 2: 're2.match(topic_message)'
Method 3: 'set(invalid_chars).intersection(topic_message)'
"""
Results:
r"""
Seconds to perform 1000000 Ok-match/Bad-no-match loops:
Method Ok-time Bad-time
1 1.054 1.190
2 1.830 1.636
3 4.364 4.577
"""
The benchmark tests show that Option 1 is slightly faster than option 2 and both are much faster than the set().intersection() method. This is true for strings which both match and don't match.

You have to be much more careful when using regular expressions - they are full of traps.
in the case of [^<>/\{}[]~] the first ] closes the group which is probably not what you intended. If you want to use ] in a group it has to be the first character after the [ eg []^<>/\{}[~]
simple test confirms this
>>> import re
>>> re.search("[[]]","]")
>>> re.search("[][]","]")
<_sre.SRE_Match object at 0xb7883db0>
regex is overkill for this problem anyway
def clean_topic_message(self):
topic_message = self.cleaned_data['topic_message']
invalid_chars = '^<>/\{}[]~`$'
if (topic_message == ""):
raise forms.ValidationError(_(u'Please provide a message for your topic'))
if set(invalid_chars).intersection(topic_message):
raise forms.ValidationError(_(u'Topic message cannot contain the following: %s'%invalid_chars))
return topic_message

If efficiency is a major concern I would re.compile() the re string, since you're going to use the same regex many times.

re.match and re.search behave differently. Splitting words is not required to search using regular expressions.
import re
symbols_re = re.compile(r"[^<>/\{}[]~`]");
if symbols_re.search(self.cleaned_data('topic_message')):
//raise Validation error

I can't say what would be more efficient, but you certainly should get rid of the $ (unless it's an invalid character for the message)... right now you only match the re if the characters are at the end of topic_message because $ anchors the match to the right-hand side of the line.

In any case you need to scan the entire message. So wouldn't something simple like this work ?
def checkMessage(topic_message):
for char in topic_message:
if char in "<>/\{}[]~`":
return False
return True

is_valid = not any(k in text for k in '<>/{}[]~`')

I agree with gnibbler, regex is an overkiller for this situation. Probably after removing this unwanted chars you'll want to remove unwanted words also, here's a little basic way to do it:
def remove_bad_words(title):
'''Helper to remove bad words from a sentence based in a dictionary of words.
'''
word_list = title.split(' ')
for word in word_list:
if word in BAD_WORDS: # BAD_WORDS is a list of unwanted words
word_list.remove(word)
#let's build the string again
title2 = u''
for word in word_list:
title2 = ('%s %s') % (title2, word)
#title2 = title2 + u' '+ word
return title2

Example: just tailor to your needs.
### valid chars: 0-9 , a-z, A-Z only
import re
REGEX_FOR_INVALID_CHARS=re.compile( r'[^0-9a-zA-Z]+' )
list_of_invalid_chars_found=REGEX_FOR_INVALID_CHARS.findall( topic_message )

python regex for repeating string

I am wanting to verify and then parse this string (in quotes):
string = "start: c12354, c3456, 34526; other stuff that I don't care about"
//Note that some codes begin with 'c'
I would like to verify that the string starts with 'start:' and ends with ';'
Afterward, I would like to have a regex parse out the strings. I tried the following python re code:
regx = r"start: (c?[0-9]+,?)+;"
reg = re.compile(regx)
matched = reg.search(string)
print ' matched.groups()', matched.groups()
I have tried different variations but I can either get the first or the last code but not a list of all three.
Or should I abandon using a regex?
EDIT: updated to reflect part of the problem space I neglected and fixed string difference.
Thanks for all the suggestions - in such a short time.

In Python, this isn’t possible with a single regular expression: each capture of a group overrides the last capture of that same group (in .NET, this would actually be possible since the engine distinguishes between captures and groups).
Your easiest solution is to first extract the part between start: and ; and then using a regular expression to return all matches, not just a single match, using re.findall('c?[0-9]+', text).

You could use the standard string tools, which are pretty much always more readable.
s = "start: c12354, c3456, 34526;"
s.startswith("start:") # returns a boolean if it starts with this string
s.endswith(";") # returns a boolean if it ends with this string
s[6:-1].split(', ') # will give you a list of tokens separated by the string ", "

This can be done (pretty elegantly) with a tool like Pyparsing:
from pyparsing import Group, Literal, Optional, Word
import string
code = Group(Optional(Literal("c"), default='') + Word(string.digits) + Optional(Literal(","), default=''))
parser = Literal("start:") + OneOrMore(code) + Literal(";")
# Read lines from file:
with open('lines.txt', 'r') as f:
for line in f:
try:
result = parser.parseString(line)
codes = [c[1] for c in result[1:-1]]
# Do something with teh codez...
except ParseException exc:
# Oh noes: string doesn't match!
continue
Cleaner than a regular expression, returns a list of codes (no need to string.split), and ignores any extra characters in the line, just like your example.

import re
sstr = re.compile(r'start:([^;]*);')
slst = re.compile(r'(?:c?)(\d+)')
mystr = "start: c12354, c3456, 34526; other stuff that I don't care about"
match = re.match(sstr, mystr)
if match:
res = re.findall(slst, match.group(0))
results in
['12354', '3456', '34526']

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