What is a correct regular expression to extract the string "(procedure)" -or in general text from inside the parenthesis - from the strings below
input string examples are
Positron emission tomography using flutemetamol (18F) with computed
tomography of brain (procedure)
another example
Urinary tract infection prophylaxis (procedure)
Possible approaches are:
Go to end of the text, and look for first opening parenthesis and take subset from that position to the end of the text
from beginning of text, identify last '(' char and do that position to end as substring
Other strings can be (different "tag" is extracted)
[1] "Xanthoma of eyelid (disorder)" "Ventricular tachyarrhythmia (disorder)"
[3] "Abnormal urine odor (finding)" "Coloboma of iris (disorder)"
[5] "Macroencephaly (disorder)" "Right main coronary artery thrombosis (disorder)"
(general regex is sought) (or a solution in R is even better)
If it is the last part of the string then this regex will do it:
/\(([^()]*)\)$/
Explaination: Look for an open ( and match everything in between it that isn't ( or ) and then has a ) at the end of the string.
https://regex101.com/r/cEsQtf/1
sub can do that with the right regex
Text = c("Positron emission tomography using flutemetamol (18F)
with computed tomography of brain (procedure)",
"Urinary tract infection prophylaxis (procedure)",
"Xanthoma of eyelid (disorder)",
"Ventricular tachyarrhythmia (disorder)",
"Abnormal urine odor (finding)",
"Coloboma of iris (disorder)",
"Macroencephaly (disorder)",
"Right main coronary artery thrombosis (disorder)")
sub(".*\\((.*)\\).*", "\\1", Text)
[1] "procedure" "procedure" "disorder" "disorder" "finding" "disorder"
[7] "disorder" "disorder"
Addendum: Detailed explanation of the regex
The question asks to find the content of the final set of parentheses in the strings. This expression is slightly confusing because it includes two different uses of parentheses, One is to represent parentheses in the string being processed and the other is to set up a "capturing group", the way that we specify what part should be returned by the expression. The expression is made up of five basic units:
1. Initial .* - matches everything up to the final open parenthesis.
Note that this is relying on "greedy matching"
2. \\( ... \\) - matches the final set of parentheses.
Because ( by itself means something else, we need to "escape" the
parentheses by preceding them with \. That is we want the regular
expression to say \( ... \). However, the way R interprets strings,
if we just typed \( and \), R would interpret the \ as escaping the (
and so interpret this as just ( ... ). So we escape the backslash.
R will interpret \\( ... \\) as \( ... \) meaning the literal
characters ( & ).
3. ( ... ) Inside the pair in part 2
This is making use of the special meaning of parentheses. When we
enclose an expression in parentheses, whatever value is inside them
will be stored in a variable for later use. That variable is called
\1, which is what was used in the substitution pattern. Again, is
we just wrote \1, R would interpret it as if we were trying to escape
the 1. Writing \\1 is interpreted as the character \ followed by 1,
i.e. \1.
4. Central .* Inside the pair in part 3
This is what we are looking for, all characters inside the parentheses.
5. Final .*
This is in the expression to match any characters that may follow the
final set of parentheses.
The sub function will use this to replace the matched pattern (in this case, all characters in the string) with the substitution pattern \1 i.e. the contents of the variable containing whatever was in the first (in our case only) capturing group - the stuff inside the final parentheses.
You can actually use the following to extract the text inside nested parentheses at the end of string:
x <- c("FELON IN POSSESSION OF AMMUNITION (ACTUAL POSSESSION) (79023)",
"FAIL TO DISPLAY REGISTRATION - POSSESSION REQUIRED (320.0605(1))")
sub(".*(\\(((?:[^()]++|(?1))*)\\))$", "\\2", x, perl=TRUE)
See the online R demo and the regex demo.
Details:
.* - any zero or more chars other than line break chars, as many as possible
(\(((?:[^()]++|(?1))*)\)) - Capturing group 1 (necessary for recursion to take place):
\( - a ( char
((?:[^()]++|(?1))*) - Capturing group 2 (our value): zero or more occurrences of any one or more chars other than ( and ), or the whole Group 1 pattern
\) - a ) char
$ - end of string.
The whole string is thus, when matched, replaced with the value of Group 2. If there is no match, the string remains what it was.
Related
I have some errors in some numbers showing numbers like "59.34343.23". I know the first dot is correct but the second one (or any after the first) should be remove. How can I remove those?
I tried using gsub in R:
gsub("(?<=\\..*)\\.", "", "59.34343.23", perl=T)
or
gsub("(?<!^[^.]*)\\.", "", "59.34343.23", perl=T)
However it gets the following error "invalid regular expression". But I have been trying the same code in a regex tester and it works.
What is my mistake here?
You can use
gsub("^([^.]*\\.)|\\.", "\\1", "59.34343.23")
gsub("^([^.]*\\.)|\\.", "\\1", "59.34343.23", perl=TRUE)
See the R demo online and the regex demo.
Details:
^([^.]*\.) - Capturing group 1 (referred to as \1 from the replacement pattern): any zero or more chars from the start of string and then a . char (the first in the string)
| - or
\. - any other dot in the string.
Since the replacement, \1, refers to Group 1, and Group 1 only contains a value after the text before and including the first dot is matched, the replacement is either this part of text, or empty string (i.e. the second and all subsequent occurrences of dots are removed).
We may use
gsub("^[^.]+\\.(*SKIP)(*FAIL)|\\.", "", str1, perl = TRUE)
[1] "59.3434323"
data
str1 <- "59.34343.23"
By specifying perl = TRUE you can convert matches of the following regular expression to empty strings:
^[^.]*\.[^.]*\K.|\.
Start your engine!
If you are unfamiliar with \K hover over it in the regular expression at the link to see an explanation of its effect.
There is always the option to only write back the dot if its the first in the line.
Key feature is to consume the other dots but don't write it back.
Effect is to delete trailing dots.
Below uses a branch reset to accomplish the goal (Perl mode).
(?m)(?|(^[^.\n]*\.)|()\.+)
Replace $1
https://regex101.com/r/cHcu4j/1
(?m)
(?|
( ^ [^.\n]* \. ) # (1)
| ( ) # (1)
\.+
)
The pattern that you tried does not match, because there is an infinite quantifier in the lookbehind (?<=\\..*) that is not supported.
Another variation using \G to get continuous matches after the first dot:
(?:^[^.]*\.|\G(?!^))[^.]*\K\.
In parts, the pattern matches:
(?: Non capture group for the alternation |
^[^.]*\. Start of string, match any char except ., then match .
| Or
\G(?!^) Assert the position at the end of the previous match (not at the start)
)[^.]* Optionally match any char except .
\K\. Clear the match buffer an match the dot (to be removed)
Regex demo | R demo
gsub("(?:^[^.]*\\.|\\G(?!^))[^.]*\\K\\.", "", "59.34343.23", perl=T)
Output
[1] "59.3434323"
I need to identify matching course number that have xx.3xxxxxx.
These are some examples of the course numbers.
26.3730004
27.0210000
26.3730009
26.7114001
23.9610071
26.0A34430
23.3670005
26.0B05430
I tried many patterns one example I used is the pattern below. It did not get any match.
"[^0-9]{2}\Q.\E3[^0-9]+$"
I tried using grep and grepl. I actually need the code to return indexes.
This code shows my attempt to tag the rows that have matches.
Teacher$virtual[
which(
grepl("[^0-9]{2}\\Q.\\E3[^0-9]+$",Teacher$CourseNumber))]
<- "1"
I need to remove any row from my dataframe that have the course number with that pattern. XX.3XXXXXX
But, my code did not find any match. Can you please help me?
You should use
grepl("^[0-9]{2}\\.3", Teacher$CourseNumber)
See the regex graph:
Details:
^ - start of a string
[0-9]{2} - two digits
\\. - a dot (note that a regex escape is a literal backslash, but inside a string literal, "...", a single backslash is used to form string escape sequences, hence the backslash must be double to obtain a literal backslash char necessary for a regex escape)
3 - a 3 char.
NOTE: If you want to use in-pattern quoting with \Q and \E (in between which all chars are treated literally) you need to use PCRE regex, add perl=TRUE and use
grepl("^[0-9]{2}\\Q.\\E3", Teacher$CourseNumber, perl=TRUE)
Now, the dot is treated as a literal dot, not a . metacharacter that matches any char but a line break char (in a PCRE regex, . does not match line break chars by default).
Here, this simple expression would likely cover that:
^[0-9]{2}\.[3].+$
which has a [3] boundary right after the .. It would probably work without start and end anchors:
[0-9]{2}\.[3].+
Demo
We can add or reduce the boundaries, if it'd be necessary.
I have the following string:
x = "marchTextIWantToDisplayWithSpacesmarch"
I would like to delete the 'march' portion at the beginning of the string and then add a space before each uppercase letter in the remainder to yield the following result:
"Text I Want To Display With Spacesmarch"
To insert whitepace, I used gsub("([a-z]?)([A-Z])", "\\1 \\2", x, perl= T) but I have no clue how to modify the pattern so that the first 'march' is excluded from the returned string. I'm trying to get better at this so any help would be greatly appreciated.
An option would be to capture the upper case letter as a group ((...)) and in the replacement create a space followed by the backreference (\\1) of the captured group
gsub("([A-Z])", " \\1", x)
#[1] "march Text I Want To Display With Spacesmarch"
If we need to remove the 'march'
sub("\\b[a-z]\\w+\\s+", "", gsub("([A-Z])", " \\1", x))
[#1] "Text I Want To Display With Spacesmarch"
data
x <- "marchTextIWantToDisplayWithSpacesmarch"
No, you can't achieve your replacement using single gsub because in one of your requirement, you want to remove all lowercase letters starting from the beginning, and your second requirement is to introduce a space before every capital letter except the first capital letter of the resultant string after removing all lowercase letters from the beginning of text.
Doing it in single gsub call would have been possible in cases where somehow we can re-use some of the existing characters to make the conditional replace which can't be the case here. So in first step, you can use ^[a-z]+ regex to get rid of all lowercase letters only from the beginning of string,
sub('^[a-z]+', '', "marchTextIWantToDisplayWithSpacesmarch")
leaving you with this,
[1] "TextIWantToDisplayWithSpacesmarch"
And next step you can use this (?<!^)(?=[A-Z]) regex to insert a space before every capital letter except the first one as you might not want an extra space before your sentence. But you can combine both and write them as this,
gsub('(?<!^)(?=[A-Z])', ' ', sub('^[a-z]+', '', "marchTextIWantToDisplayWithSpacesmarch"), perl=TRUE)
which will give you your desired string,
[1] "Text I Want To Display With Spacesmarch"
Edit:
Explanation of (?<!^)(?=[A-Z]) pattern
First, let's just take (?=[A-Z]) pattern,
See the pink markers in this demo
As you can see, in the demo, every capital letter is preceded by a pink mark which is the place where a space will get inserted. But we don't want space to be inserted before the very first letter as that is not needed. Hence we need a condition in regex, which will not select the first capital letter which appears at the start of string. And for that, we need to use a negative look behind (?<!^) which means that Do not select the position which is preceded by start of string and hence this (?<!^) helps in discarding the upper case letter that is preceded by just start of string.
See this demo where the pink marker is gone from the very first uppercase letter
Hope this clarifies how every other capital letter is selected but not the very first. Let me know if you have any queries further.
You may use a single regex call to gsub coupled with trimws to trim the resulting string:
trimws(gsub("^\\p{Ll}+|(?<=.)(?=\\p{Lu})", " ", x, perl=TRUE))
## => [1] "Text I Want To Display With Spacesmarch"
It also supports all Unicode lowercase (\p{Ll}) and uppercase (\p{Lu}) letters.
See the R demo online and the regex demo.
Details
^\\p{Ll}+ - 1 or more lowercase letters at the string start
| - or
(?<=.)(?=\\p{Lu}) - any location between any char but linebreak chars and an uppercase letter.
Here is an altenative with a single call to gsubfn regex with some ifelse logic:
> gsubfn("^\\p{Ll}*(\\p{L})|(?<=.)(?=\\p{Lu})", function(n) ifelse(nchar(n)>0,n," "), x, perl=TRUE,backref=-1)
[1] "Text I Want To Display With Spacesmarch"
Here, the ^\\p{Ll}*(\\p{L}) part matches 0+ lowercase letters and captures the next uppercase into Group 1 that will be accessed by passing n argument to the anonymous function. If n length is non-zero, this alternative matched and the we need to replace with this value. Else, we replace with a space.
Since this is tagged perl, my 2 cents:
Can you chain together the substitutions inside sub() and gsub()? In newer perl versions an /r option can be added to the s/// substitution so the matched string can be returned "non-destructively" and then matched again. This allows hackish match/substitution/rematches without mastering advanced syntax, e.g.:
perl -E '
say "marchTextIWantToDisplayWithSpacesmarch" =~
s/\Amarch//r =~ s/([[:upper:]])/ $1/gr =~ s/\A\s//r;'
Output
Text I Want To Display With Spacesmarch
This seems to be what #pushpesh-kumar-rajwanshi and #akrun are doing by wrapping gsub inside sub() (and vice versa). In general I don't thinkperl = T captures the full magnificently advanced madness of perl regexps ;-) but gsub/sub must be fast operating on vectors, no?
This question already has an answer here:
Reference - What does this regex mean?
(1 answer)
Closed 4 years ago.
I'm trying to understand a regular expression someone has written in the gsub() function.
I've never used regular expressions before seeing this code, and i have tried to work out how it's getting the final result with some googling, but i have hit a wall so to speak.
gsub('.*(.{2}$)', '\\1',"my big fluffy cat")
This code returns the last two characters in the given string. In the above example it would return "at". This is the expected result but from my brief foray into regular expressions i don't understand why this code does what it does.
What i understand is the '.*' means look for any character 0 or more times. So it's going to look at the entire string and this is what will be replaced.
The part in brackets looks for any two characters at the end of the string. It would make more sense to me if this part in brackets was in place of the '\1'. To me it would then read look at the entire string and replace it with the last two characters of that string.
All that does though is output the actual code as the replacement e.g ".{2}$".
Finally i don't understand why '\1' is in the replace part of the function. To me this is just saying replace the entire string with a single backslash and the number one. I say a single backslash because it's my understanding the first backslash is just there to make the second backslash a none special character.
For gsub there are two ways of using the function. The most common way is probably.
gsub("-","TEST","This is a - ")
which would return
This is a TEST
What this does is simply finds the matches in the regular expression and replaces it with the replacement string.
The second way to use gsub is the method in which you described. using \\1, \\2 or \\3...
What this does is looks at the first, second or third capture group in your regular expression.
A capture group is defined by anything inside the circular brackets ex: (capture_group_1)(capture_group_2)...
Explanation
Your analysis is correct.
What i understand is the '.*' means look for any character 0 or more times. So it's going to look at the entire string and this is what will be replaced.
The part in brackets looks for any two characters at the end of the string
The last two characters are placed in a capture group and we are simply replace the whole string with this capture group. Not replacing them with anything.
if it helps, check out the result of this expression.
gsub('(.*)(.{2}$)', 'Group 1: \\1, Group 2: \\2',"my big fluffy cat")
hope the examples can help you to understand it better:
Say we have a string foobarabcabcdef
.* matches whole string.
.*abc it matches: from the beginning matches any chars till the last abc (greedy matching), thus, it matches foobarabcabc
.*(...)$ matches the whole string as well, however, the last 3 chars were groupped. Without the () , the matched string will have a default group, group0, the () will be group1, 2, 3.... think about .*(...)(...)(...)$ so we have:
group 0 : whole string
group 1 : "abc" the first "abc"
group 2 : "abc" the 2nd "abc"
group 3 : "def" the last 3 chars
So back to your example, the \\1 is a reference to group. What it does is: "replace the whole string by the matched text in group1" That is, the .{2}$ part is the replacement.
If you don't understand the backslashs, you have to reference the syntax of r, I cannot tell more. It is all about escaping.
Important part of that regular expression are brackets, that's something called "capturing group".
Regular expression .*(.{2}$) says - match anything and capture last 2 characters at the line. Replacement \\1 is referencing to that group, so it will replace whole match with captured group, which are last two characters in this case.
I would like to achieve this result : "raster(B04) + raster(B02) - raster(A10mB03)"
Therefore, I created this regex: B[0-1][0-9]|A[1,2,6]0m/B[0-1][0-9]"
I am now trying to replace all matches of the string "B04 + B02 - A10mB03" with gsub("B[0-1][0-9]]|[A[1,2,6]0mB[0-1][0-9]", "raster()", string)
How could I include the original values B01, B02, A10mB03?
PS: I also tried gsub("B[0-1][0-9]]|[A[1,2,6]0mB[0-1][0-9]", "raster(\\1)", string) but it did not work.
Basically, you need to match some text and re-use it inside a replacement pattern. In base R regex methods, there is no way to do that without a capturing group, i.e. a pair of unescaped parentheses, enclosing the whole regex pattern in this case, and use a \\1 replacement backreference in the replacement pattern.
However, your regex contains some issues: [A[1,2,6] gets parsed as a single character class that matches A, [, 1, ,, 2 or 6 because you placed a [ before A. Also, note that , inside character classes matches a literal comma, and it is not what you expected. Another, similar issue, is with [0-9]] - it matches any ASCII digit with [0-9] and then a ] (the ] char does not have to be escaped in a regex pattern).
So, a potential fix for you expression can look like
gsub("(B[0-1][0-9]|A[126]0mB[0-1][0-9])", "raster(\\1)", string)
Or even just matching 1 or more word chars (considering the sample string you supplied)
gsub("(\\w+)", "raster(\\1)", string)
might do.
See the R demo online.