I have a list of fasta sequences, each of which look like this:
>>> sequence_list[0]
'gi|13195623|ref|NM_024197.1| Mus musculus NADH dehydrogenase (ubiquinone) 1 alp
ha subcomplex 10 (Ndufa10), mRNAGCCGGCGCAGACGGCGAAGTCATGGCCTTGAGGTTGCTGAGACTCGTC
CCGGCGTCGGCTCCCGCGCGCGGCCTCGCGGCCGGAGCCCAGCGCGTGGG (etc)
I'd like to be able to extract the gene names from each of the fasta entries in my list, but I'm having difficulty finding the right regular expression. I thought this one would work: "^/(.+/),$". Start with a parentheses, then any number of any character, then end with a parentheses followed by a comma. Unfortunately: this returns None:
test = re.search(r"^/(.+/),$", sequence_list[0])
print(test)
Can someone point out the error in this regex?
Without any capturing groups,
>>> import re
>>> str = """
... gi|13195623|ref|NM_024197.1| Mus musculus NADH dehydrogenase (ubiquinone) 1 alp
... ha subcomplex 10 (Ndufa10), mRNAGCCGGCGCAGACGGCGAAGTCATGGCCTTGAGGTTGCTGAGACTCGTC
... CCGGCGTCGGCTCCCGCGCGCGGCCTCGCGGCCGGAGCCCAGCGCGTGGG (etc)"""
>>> m = re.findall(r'(?<=\().*?(?=\),)', str)
>>> m
['Ndufa10']
It matches only the words which are inside the parenthesis only when the closing bracket is followed by a comma.
DEMO
Explanation:
(?<=\() In regex (?<=pattern) is called a lookbehind. It actually looks after a string which matches the pattern inside lookbehind . In our case the pattern inside the lookbehind is \( means a literal (.
.*?(?=\),) It matches any character zero or more times. ? after the * makes the match reluctant. So it does an shortest match. And the characters in which the regex engine is going to match must be followed by ),
you need to escape parenthesis:
>>> re.findall(r'\([^)]*\),', txt)
['(Ndufa10),']
Can someone point out the error in this regex? r"^/(.+/),$"
regex escape character is \ not / (do not confuse with python escape character which is also \, but is not needed when using raw strings)
=> r"^\(.+\),$"
^ and $ match start/end of the input string, not what you want to output
=> r"\(.+\),"
you need to match "any" characters up to 1st occurence of ), not to the last one, so you need lazy operator +?
=> r"\(.+?\),"
in case gene names could not contain ) character, you can use a faster regex that avoids backtracking
=> r"\([^)]+\),"
Related
I have a text like this;
[Some Text][1][Some Text][2][Some Text][3][Some Text][4]
I want to match [Some Text][2] with this regex;
/\[.*?\]\[2\]/
But it returns [Some Text][1][Some Text][2]
How can i match only [Some Text][2]?
Note : There can be any character in Some Text including [ and ] And the numbers in square brackets can be any number not only 1 and 2. The Some Text that i want to match can be at the beginning of the line and there can be multiple Some Texts
JSFiddle
The \[.*?\]\[2\] pattern works like this:
\[ - finds the leftmost [ (as the regex engine processes the string input from left to right)
.*? - matches any 0+ chars other than line break chars, as few as possible, but as many as needed for a successful match, as there are subsequent patterns, see below
\]\[2\] - ][2] substring.
So, the .*? gets expanded upon each failure until it finds the leftmost ][2]. Note the lazy quantifiers do not guarantee the "shortest" matches.
Solution
Instead of a .*? (or .*) use negated character classes that match any char but the boundary char.
\[[^\]\[]*\]\[2\]
See this regex demo.
Here, .*? is replaced with [^\]\[]* - 0 or more chars other than ] and [.
Other examples:
Strings between angle brackets: <[^<>]*> matches <...> with no < and > inside
Strings between parentheses: \([^()]*\) matches (...) with no ( and ) inside
Strings between double quotation marks: "[^"]*" matches "..." with no " inside
Strings between curly braces: \{[^{}]*} matches "..." with no " inside
In other situations, when the starting pattern is a multichar string or complex pattern, use a tempered greedy token, (?:(?!start).)*?. To match abc 1 def in abc 0 abc 1 def, use abc(?:(?!abc).)*?def.
You could try the below regex,
(?!^)(\[[A-Z].*?\]\[\d+\])
DEMO
s = "[abc]abx[abc]b"
s = re.sub("\[([^\]]*)\]a", "ABC", s)
'ABCbx[abc]b'
In the string, s, I want to match 'abc' when it's enclosed in [], and followed by a 'a'. So in that string, the first [abc] will be replaced, and the second won't.
I wrote the pattern above, it matches:
match anything starting with a '[', followed by any number of characters which is not ']', then followed by the character 'a'.
However, in the replacement, I want the string to be like:
[ABC]abx[abc]b . // NOT ABCbx[abc]b
Namely, I don't want the whole matched pattern to be replaced, but only anything with the bracket []. How to achieve that?
match.group(1) will return the content in []. But how to take advantage of this in re.sub?
Why not simply include [ and ] in the substitution?
s = re.sub("\[([^\]]*)\]a", "[ABC]a", s)
There exist more than 1 method, one of them is exploting groups.
import re
s = "[abc]abx[abc]b"
out = re.sub('(\[)([^\]]*)(\]a)', r'\1ABC\3', s)
print(out)
Output:
[ABC]abx[abc]b
Note that there are 3 groups (enclosed in brackets) in first argument of re.sub, then I refer to 1st and 3rd (note indexing starts at 1) so they remain unchanged, instead of 2nd group I put ABC. Second argument of re.sub is raw string, so I do not need to escape \.
This regex uses lookarounds for the prefix/suffix assertions, so that the match text itself is only "abc":
(?<=\[)[^]]*(?=\]a)
Example: https://regex101.com/r/NDlhZf/1
So that's:
(?<=\[) - positive look-behind, asserting that a literal [ is directly before the start of the match
[^]]* - any number of non-] characters (the actual match)
(?=\]a) - positive look-ahead, asserting that the text ]a directly follows the match text.
I am basically trying to match string pattern(wildcard match)
Please carefully look at this -
*(star) - means exactly one word .
This is not a regex pattern...it is a convention.
So,if there patterns like -
*.key - '.key.' is preceded by exactly one word(word containing no dots)
*.key.* - '.key.' is preceded and succeeded by exactly one word having no dots
key.* - '.key' preceeds exactly one word .
So,
"door.key" matches "*.key"
"brown.door.key" doesn't match "*.key".
"brown.key.door" matches "*.key.*"
but "brown.iron.key.door" doesn't match "*.key.*"
So, when I encounter a '*' in pattern, I have replace it with a regex so that it means it is exactly one word.(a-zA-z0-9_).Can anyone please help me do this in python?
To convert your pattern to a regexp, you first need to make sure each character is interpreted literally and not as a special character. We can do that by inserting a \ in front of any re special character. Those characters can be obtained through sre_parse.SPECIAL_CHARS.
Since you have a special meaning for *, we do not want to escape that one but instead replace it by \w+.
Code
import sre_parse
def convert_to_regexp(pattern):
special_characters = set(sre_parse.SPECIAL_CHARS)
special_characters.remove('*')
safe_pattern = ''.join(['\\' + c if c in special_characters else c for c in pattern ])
return safe_pattern.replace('*', '\\w+')
Example
import re
pattern = '*.key'
r_pattern = convert_to_regexp(pattern) # '\\w+\\.key'
re.match(r_pattern, 'door.key') # Match
re.match(r_pattern, 'brown.door.key') # None
And here is an example with escaped special characters
pattern = '*.(key)'
r_pattern = convert_to_regexp(pattern) # '\\w+\\.\\(key\\)'
re.match(r_pattern, 'door.(key)') # Match
re.match(r_pattern, 'brown.door.(key)') # None
Sidenote
If you intend looking for the output pattern with re.search or re.findall, you might want to wrap the re pattern between \b boundary characters.
The conversion rules you are looking for go like this:
* is a word, thus: \w+
. is a literal dot: \.
key is and stays a literal string
plus, your samples indicate you are going to match whole strings, which in turn means your pattern should match from the ^ beginning to the $ end of the string.
Therefore, *.key becomes ^\w+\.key$, *.key.* becomes ^\w+\.key\.\w+$, and so forth..
Online Demo: play with it!
^ means a string that starts with the given set of characters in a regular expression.
$ means a string that ends with the given set of characters in a regular expression.
\s means a whitespace character.
\S means a non-whitespace character.
+ means 1 or more characters matching given condition.
Now, you want to match just a single word meaning a string of characters that start and end with non-spaced string. So, the required regular expression is:
^\S+$
You could do it with a combination of "any characters that aren't period" and the start/end anchors.
*.key would be ^[^.]*\.key, and *.key.* would be ^[^.]*\.key\.[^.]*$
EDIT: As tripleee said, [^.]*, which matches "any number of characters that aren't periods," would allow whitespace characters (which of course aren't periods), so using \w+, "any number of 'word characters'" like the other answers is better.
Somehow puzzled by the way regular expressions work in python, I am looking to replace all commas inside strings that are preceded by a letter and followed either by a letter or a whitespace. For example:
2015,1674,240/09,PEOPLE V. MICHAEL JORDAN,15,15
2015,2135,602832/09,DOYLE V ICON, LLC,15,15
The first line has effectively 6 columns, while the second line has 7 columns. Thus I am trying to replace the comma between (N, L) in the second line by a whitespace (N L) as so:
2015,2135,602832/09,DOYLE V ICON LLC,15,15
This is what I have tried so far, without success however:
new_text = re.sub(r'([\w],[\s\w|\w])', "", text)
Any ideas where I am wrong?
Help would be much appreciated!
The pattern you use, ([\w],[\s\w|\w]), is consuming a word char (= an alphanumeric or an underscore, [\w]) before a ,, then matches the comma, and then matches (and again, consumes) 1 character - a whitespace, a word character, or a literal | (as inside the character class, the pipe character is considered a literal pipe symbol, not alternation operator).
So, the main problem is that \w matches both letters and digits.
You can actually leverage lookarounds:
(?<=[a-zA-Z]),(?=[a-zA-Z\s])
See the regex demo
The (?<=[a-zA-Z]) is a positive lookbehind that requires a letter to be right before the , and (?=[a-zA-Z\s]) is a positive lookahead that requires a letter or whitespace to be present right after the comma.
Here is a Python demo:
import re
p = re.compile(r'(?<=[a-zA-Z]),(?=[a-zA-Z\s])')
test_str = "2015,1674,240/09,PEOPLE V. MICHAEL JORDAN,15,15\n2015,2135,602832/09,DOYLE V ICON, LLC,15,15"
result = p.sub("", test_str)
print(result)
If you still want to use \w, you can exclude digits and underscore from it using an opposite class \W inside a negated character class:
(?<=[^\W\d_]),(?=[^\W\d_]|\s)
See another regex demo
\w matches a-z,A-Z and 0-9, so your regex will replace all commas. You could try the following regex, and replace with \1\2.
([a-zA-Z]),(\s|[a-zA-Z])
Here is the DEMO.
I have a large list of chemical data, that contains entries like the following:
1. 2,4-D, Benzo(a)pyrene, Dioxin, PCP, 2,4,5-TP
2. Lead,Paints/Pigments,Zinc
I have a function that is correctly splitting the 1st entry into:
['2,4-D', 'Benzo(a)pyrene', 'Dioxin', 'PCP', '2,4,5-TP']
based on ', ' as a separator. For the second entry, ', ' won't work. But, if i could easily split any string that contains ',' with only two non-numeric characters on either side, I would be able to parse all entries like the second one, without splitting up the chemicals in entries like the first, that have numbers in their name separated by commas (i.e. 2,4,5-TP).
Is there an easy pythonic way to do this?
I explain a little bit based on #eph's answer:
import re
data_list = ['2,4-D, Benzo(a)pyrene, Dioxin, PCP, 2,4,5-TP', 'Lead,Paints/Pigments,Zinc']
for d in data_list:
print re.split(r'(?<=\D),\s*|\s*,(?=\D)',d)
re.split(pattern, string) will split string by the occurrences of regex pattern.
(plz read Regex Quick Start if you are not familiar with regex.)
The (?<=\D),\s*|\s*,(?=\D) consists of two part: (?<=\D),\s* and \s*,(?=\D). The meaning of each unit:
The middle | is the OR operator.
\D matches a single character that is not a digit.
\s matches a whitespace character (includes tabs and line breaks).
, matches character ",".
* attempts to match the preceding token zero or more times. Therefore, \s* means the whitespace can be appear zero or more times. (see Repetition with Star and Plus)
(?<= ... ) and (?= ...) are the lookbebind and lookahead assertions.
For example, q(?=u) matches a q that is followed by a u, without making the u part of the match.
Therefore, \s*,(?=\D) matches a , that is preceded by zero or more whitespace and followed by non-digit characters. Similarly, (?<=\D),\s* matches a , that is preceded by non-digit characters and followed by zero or more whitespace. The whole regex will find , that satisfy either case, which is equivalent to your requirement: ',' with only two non-numeric characters on either side.
Some useful tools for regex:
Regex Cheat Sheet
Online regex tester: regex101 (with a tree structure explanation to your regex)
Use regex and lookbehind/lookahead assertion
>>> re.split(r'(?<=\D\D),\s*|,\s*(?=\D\D)', s)
['2,4-D', 'Benzo(a)pyrene', 'Dioxin', 'PCP', '2,4,5-TP']
>>> s1 = "2,4-D, Benzo(a)pyrene, Dioxin, PCP, 2,4,5-TP"
>>> s2 = "Lead,Paints/Pigments,Zinc"
>>> import re
>>> res1 = re.findall(r"\s*(.*?[A-Za-z])(?:,|$)", s1)
>>> res1
['2,4-D', 'Benzo(a)pyrene', 'Dioxin', 'PCP', '2,4,5-TP']
>>> res2 = re.findall(r"\s*(.*?[A-Za-z])(?:,|$)", s2)
>>> res2
['Lead', 'Paints/Pigments', 'Zinc']