I have a string from which I want to extract certain words and I have used Python's regular expression but unfortunately I am only getting one word from all the matches.
Here is my input string
go = "GO:0030054^cellular_component^cell junction`GO:0005813^cellular_component^centrosome`GO:0036064^cellular_component^ciliary basal body`GO:0005737^cellular_component^cytoplasm"
Here is my regular expression I tried
go_search = re.search(r'(GO:\d+)', go, re.MULTILINE|re.IGNORECASE)
But the only output I got is
go_search.group(1)
'GO:0030054'
How can I get all the 4 GO'id's (GO:0005813, GO:0036064, and GO:0005737) and not just one which I am just getting now
You need re.findall instead of re.search:
re.findall(r'GO:\d+', go, re.MULTILINE|re.IGNORECASE)
# ['GO:0030054', 'GO:0005813', 'GO:0036064', 'GO:0005737']
Replace re.search() with re.finditer(). This gives you an iterator over the matches.
go = "GO:0030054^cellular_component^cell junction`GO:0005813^cellular_component^centrosome`GO:0036064^cellular_component^ciliary basal body`GO:0005737^cellular_component^cytoplasm"
go_search_iter = re.finditer(r'(GO:\d+)', go, re.MULTILINE|re.IGNORECASE)
for go_search in go_search_iter:
print(go_search.group(1))
# do stuff with go_search
Related
I have the following file names that exhibit this pattern:
000014_L_20111007T084734-20111008T023142.txt
000014_U_20111007T084734-20111008T023142.txt
...
I want to extract the middle two time stamp parts after the second underscore '_' and before '.txt'. So I used the following Python regex string split:
time_info = re.split('^[0-9]+_[LU]_|-|\.txt$', f)
But this gives me two extra empty strings in the returned list:
time_info=['', '20111007T084734', '20111008T023142', '']
How do I get only the two time stamp information? i.e. I want:
time_info=['20111007T084734', '20111008T023142']
I'm no Python expert but maybe you could just remove the empty strings from your list?
str_list = re.split('^[0-9]+_[LU]_|-|\.txt$', f)
time_info = filter(None, str_list)
Don't use re.split(), use the groups() method of regex Match/SRE_Match objects.
>>> f = '000014_L_20111007T084734-20111008T023142.txt'
>>> time_info = re.search(r'[LU]_(\w+)-(\w+)\.', f).groups()
>>> time_info
('20111007T084734', '20111008T023142')
You can even name the capturing groups and retrieve them in a dict, though you use groupdict() rather than groups() for that. (The regex pattern for such a case would be something like r'[LU]_(?P<groupA>\w+)-(?P<groupB>\w+)\.')
If the timestamps are always after the second _ then you can use str.split and str.strip:
>>> strs = "000014_L_20111007T084734-20111008T023142.txt"
>>> strs.strip(".txt").split("_",2)[-1].split("-")
['20111007T084734', '20111008T023142']
Since this came up on google and for completeness, try using re.findall as an alternative!
This does require a little re-thinking, but it still returns a list of matches like split does. This makes it a nice drop-in replacement for some existing code and gets rid of the unwanted text. Pair it with lookaheads and/or lookbehinds and you get very similar behavior.
Yes, this is a bit of a "you're asking the wrong question" answer and doesn't use re.split(). It does solve the underlying issue- your list of matches suddenly have zero-length strings in it and you don't want that.
>>> f='000014_L_20111007T084734-20111008T023142.txt'
>>> f[10:-4].split('-')
['0111007T084734', '20111008T023142']
or, somewhat more general:
>>> f[f.rfind('_')+1:-4].split('-')
['20111007T084734', '20111008T023142']
I am trying to sort through a some files using regex expression.
I have a file which contains the two following lines
NET "MBC_ADR_I1<1>" LOC = "R2";
NET "GP_O<7>" LOC = "R20";
I am using the following expression to get one of the lines only
f2MatchLoc = re.search('(LOC)[ ]+=[ ]+["]?({})'.format(f1LocValue), f2Line, re.IGNORECASE)
where f1LocValue = R2. However I'm getting a match on both lines.
I've tried to enter the same expression here
regex101.com
which shows that my argument should be correctly formatted
f2MatchLoc = re.search(r'(LOC)[ ]+=[ ]+["]?({}\b)'.format(f1LocValue), f2Line, re.IGNORECASE)
^^
You need to use \b after R2 so that there are no partial matches. See demo. Also use r or raw mode.
Because you have no conditions how the string should end.
'(LOC)[ ]+=[ ]+["]?({})'
^??
So it matches anything that starts with LOC = "R2. Following are all valid search results
LOC = "R2
LOC = "R2asd
LOC = "R2121
LOC = "R2 "
Simply, you can use double quotes or semicolon to identify end of search string. Also you can replace \s for white-space capturing and you can remove [] around single element lists
r'(LOC)\s+=\s+"?({})"?;'
I'm tackling a python challenge problem to find a block of text in the format xXXXxXXXx (lower vs upper case, not all X's) in a chunk like this:
jdskvSJNDfbSJneSfnJDKoJIWhsjnfakjn
I have tested the following RegEx and found it correctly matches what I am looking for from this site (http://www.regexr.com/):
'([a-z])([A-Z]){3}([a-z])([A-Z]){3}([a-z])'
However, when I try to match this expression to the block of text, it just returns the entire string:
In [1]: import re
In [2]: example = 'jdskvSJNDfbSJneSfnJDKoJIWhsjnfakjn'
In [3]: expression = re.compile(r'([a-z])([A-Z]){3}([a-z])([A-Z]){3}([a-z])')
In [4]: found = expression.search(example)
In [5]: print found.string
jdskvSJNDfbSJneSfnJDKoJIWhsjnfakjn
Any ideas? Is my expression incorrect? Also, if there is a simpler way to represent that expression, feel free to let me know. I'm fairly new to RegEx.
You need to return the match group instead of the string attribute.
>>> import re
>>> s = 'jdskvSJNDfbSJneSfnJDKoJIWhsjnfakjn'
>>> rgx = re.compile(r'[a-z][A-Z]{3}[a-z][A-Z]{3}[a-z]')
>>> found = rgx.search(s).group()
>>> print found
nJDKoJIWh
The string attribute always returns the string passed as input to the match. This is clearly documented:
string
The string passed to match() or search().
The problem has nothing to do with the matching, you're just grabbing the wrong thing from the match object. Use match.group(0) (or match.group()).
Based on xXXXxXXXx if you want upper letters with len 3 and lower with len 1 between them this is what you want :
([a-z])(([A-Z]){3}([a-z]))+
also you can get your search function with group()
print expression.search(example).group(0)
I'm trying to match a pattern against strings that could have multiple instances of the pattern. I need every instance separately. re.findall() should do it but I don't know what I'm doing wrong.
pattern = re.compile('/review: (http://url.com/(\d+)\s?)+/', re.IGNORECASE)
match = pattern.findall('this is the message. review: http://url.com/123 http://url.com/456')
I need 'http://url.com/123', http://url.com/456 and the two numbers 123 & 456 to be different elements of the match list.
I have also tried '/review: ((http://url.com/(\d+)\s?)+)/' as the pattern, but no luck.
Use this. You need to place 'review' outside the capturing group to achieve the desired result.
pattern = re.compile(r'(?:review: )?(http://url.com/(\d+))\s?', re.IGNORECASE)
This gives output
>>> match = pattern.findall('this is the message. review: http://url.com/123 http://url.com/456')
>>> match
[('http://url.com/123', '123'), ('http://url.com/456', '456')]
You've got extra /'s in the regex. In python the pattern should just be a string. e.g. instead of this:
pattern = re.compile('/review: (http://url.com/(\d+)\s?)+/', re.IGNORECASE)
It should be:
pattern = re.compile('review: (http://url.com/(\d+)\s?)+', re.IGNORECASE)
Also typically in python you'd actually use a "raw" string like this:
pattern = re.compile(r'review: (http://url.com/(\d+)\s?)+', re.IGNORECASE)
The extra r on the front of the string saves you from having to do lots of backslash escaping etc.
Use a two-step approach: First get everything from "review:" to EOL, then tokenize that.
msg = 'this is the message. review: http://url.com/123 http://url.com/456'
review_pattern = re.compile('.*review: (.*)$')
urls = review_pattern.findall(msg)[0]
url_pattern = re.compile("(http://url.com/(\d+))")
url_pattern.findall(urls)
Assume I have a string which includes some data fields that are separated by "|", like
|1|2|3|4|5|6|7|8|
My purpose is to get the 8th field. This is what I'm doing:
pattern = re.compile(r'^\s+(\|.*?\|){8}')
match = pattern.match(test_line)
if match:
print:match.group(8)
But looks like it can not match. I know in this case I need to use ? for non-greedy match, but why I can not get the 8th field?
Thanks
Regex might be complicating this problem rather than simplifying it. A simple way to get an eighth item from a | delimited string is using split():
a = '|here|is|some|data|separated|by|bars|hooray!|'
print a.split('|')[8]
RETURNS
hooray!
Using regex, one way to get it would be:
import re
a = '|here|is|some|data|separated|by|bars|hooray!|'
pattern = re.compile(r'([^\|]+)')
match = pattern.findall(a)
print match[7]
RETURNS
hooray!