I have a column within a data frame containing long text sequences (often in the thousands of characters) of the format:
abab(VR) | ddee(NR) | def(NR) | fff(VR) | oqq | pqq | ppf(VR)
i.e. a string, a suffix in brackets, then a delimiter
I'm trying to work out the syntax in R to delete the items that end in (VR), including the trailing pipe if present, so that I'm left with:
ddee(NR) | def(NR) | oqq | pqq
I cannot work out the regular expression (or gsub) that will remove these entries and would like to request if anyone could help me please.
If you want to use gsub, you can remove the pattern in two stages:
gsub(" \\| $", "", gsub("\\w+\\(VR\\)( \\| )?", "", s))
# firstly remove all words ending with (VR) and optional | following the pattern and
# then remove the possible | at the end of the string
# [1] "ddee(NR) | def(NR) | oqq | pqq"
regular expression \\w+\\(VR\\) will match words ending with (VR), parentheses are escaped by \\;
( \\| )? matches optional delimiter |, this makes sure it will match the pattern both in the middle and at the end of the string;
possible | left out at the end of the string can be removed by a second gsub;
Here is a method using strsplit and paste with the collapse argument:
paste(sapply(strsplit(temp, split=" +\\| +"),
function(i) { i[setdiff(seq_along(i), grep("\\(VR\\)$", i))] }),
collapse=" | ")
[1] "ddee(NR) | def(NR) | oqq | pqq"
We split on the pipe and spaces, then feed the resulting list to sapply which uses the grep function to drop any elements of the vector that end with "(VR)". Finally, the result is pasted together.
I added a subsetting method with setdiff so that vectors without any "(VR)" will return without any modification.
Related
I would like to use R to remove all underlines expect those between words. At the end the code removes underlines at the end or at the beginning of a word.
The result should be
'hello_world and hello_world'.
I want to use those pre-built classes. Right know I have learn to expect particular characters with following code but I don't know how to use the word boundary sequences.
test<-"hello_world and _hello_world_"
gsub("[^_[:^punct:]]", "", test, perl=T)
You can use
gsub("[^_[:^punct:]]|_+\\b|\\b_+", "", test, perl=TRUE)
See the regex demo
Details:
[^_[:^punct:]] - any punctuation except _
| - or
_+\b - one or more _ at the end of a word
| - or
\b_+ - one or more _ at the start of a word
One non-regex way is to split and use trimws by setting the whitespace argument to _, i.e.
paste(sapply(strsplit(test, ' '), function(i)trimws(i, whitespace = '_')), collapse = ' ')
#[1] "hello_world and hello_world"
We can remove all the underlying which has a word boundary on either of the end. We use positive lookahead and lookbehind regex to find such underlyings. To remove underlying at the start and end we use trimws.
test<-"hello_world and _hello_world_"
gsub("(?<=\\b)_|_(?=\\b)", "", trimws(test, whitespace = '_'), perl = TRUE)
#[1] "hello_world and hello_world"
You could use:
test <- "hello_world and _hello_world_"
output <- gsub("(?<![^\\W])_|_(?![^\\W])", "", test, perl=TRUE)
output
[1] "hello_world and hello_world"
Explanation of regex:
(?<![^\\W]) assert that what precedes is a non word character OR the start of the input
_ match an underscore to remove
| OR
_ match an underscore to remove, followed by
(?![^\\W]) assert that what follows is a non word character OR the end of the input
I’m still new to R and regexes, but I’m trying to achieve the following; suppose I have a data table of the following sort:
Title | URL
stackoverflow.com | https://stackoverflow.com
google.com | http://
youtube.com | https://youtube.com
overclock.net | https://
I want to append the cells in column URL with their corresponding value in column Title, in case URL consists only of either http:// or https://, so the desired output would look as follows:
Title | URL
stackoverflow.com | https://stackoverflow.com
google.com | http://google.com
youtube.com | https://youtube.com
overclock.net | https://overclock.net
To do so, I tried using the sub function in conjunction with a lookahead regex as follows:
dt$URL <- sub("(?:^|\\W)https?://(?:$|\\W)", "\\1", dt$Title, perl = TRUE)
or
dt$URL <- sub("\\s(https?://)", "\\1", dt$Title, perl = TRUE)
or
dt$URL <- sub("\\b(https?://\\b)", "\\1", dt$Title, perl = TRUE)
But none of the above produces the desired output. The issue is that it doesn’t append/replace anything at all, possibly because the regex doesn’t match anything, or it also matches if there is more data than just http:// or https:// present, i.e. it will also match on a full domain name (which I do not want). How should I adjust my code so that it produces the desired output, given the example input above?
Thank you!
url.col <- c("https://stackoverflow.com",
"http://",
"https://youtube.com",
"https://")
title.col <- c("stackoverflow.com",
"google.com",
"youtube.com",
"overclock.net")
ifelse(grepl("^(\\w*http(s)?://)$", url.col), # if pattern matches url.col elem:
paste0(url.col, title.col), # join content of cols together and return!
url.col) # but if not return url.col element 'as is'
[1] "https://stackoverflow.com"
[2] "http://google.com"
[3] "https://youtube.com"
[4] "https://overclock.net"
I have a data frame with strings under a variable with the | character. What I want is to remove anything downstream of the | character.
For example, considering the string
heat-shock protein hsp70, putative | location=Ld28_v01s1:1091329-1093293(-) | length=654 | sequence_SO=chromosome | SO=protein_coding
I wish to have only:
heat-shock protein hsp70, putative
Do I need any escape character for the | character?
If I do:
a <- c("foo_5", "bar_7")
gsub("*_.", "", a)
I get:
[1] "foo" "bar"
i.e. I am removing anything downstream of the _ character.
However, If I repeat the same task with a | instead of the _:
b <- c("foo|5", "bar|7")
gsub("*|.", "", a)
I get:
[1] "" ""
You have to scape | by adding \\|. Try this
> gsub("\\|.*$", "", string)
[1] "heat-shock protein hsp70, putative "
where string is
string <- "heat-shock protein hsp70, putative | location=Ld28_v01s1:1091329-1093293(-) | length=654 | sequence_SO=chromosome | SO=protein_coding"
This alternative remove the space at the end of line in the output
gsub("\\s+\\|.*$", "", string)
[1] "heat-shock protein hsp70, putative"
Maybe a better job for strsplit than for a gsub
And yes, it looks like the pipe does need to be escaped.
string <- "heat-shock protein hsp70, putative | location=Ld28_v01s1:1091329-1093293(-) | length=654 | sequence_SO=chromosome | SO=protein_coding"
strsplit(string, ' \\| ')[[1]][1]
That outputs
"heat-shock protein hsp70, putative"
Note that I'm assuming you only want the text from before the first pipe, and that you want to drop the space that separates the pipe from the piece of the string you care about.
Months ago I ended up with a sub statement that originally worked with my input data. It has since stopped working causing me to re-examine my ugly process. I hate to share it but it accomplished several things at once:
active$id[grep("CIR",active$description)] <- sub(".*CIR0*(\\d+).*","\\1",active$description[grep("CIR",active$description)],perl=TRUE)
This statement created a new id column by finding rows that had an id embedded in the description column. The sub statement would find the number following a "CIR0" and populate the id column iff there was an id within a row's description. I recognize it is inefficient with the embedded grep subsetting either side of the assignment.
Is there a way to have a 'sub' replacement be NA or empty if the pattern does not match? I feel like I'm missing something very simple but ask for the community's assistance. Thank you.
Example with the results of creating an id column:
| name | id | description |
|------+-----+-------------------|
| a | 343 | Here is CIR00343 |
| b | | Didn't have it |
| c | 123 | What is CIR0123 |
| d | | CIR lacks a digit |
| e | 452 | CIR452 is next |
I was struggling with the same issue a few weeks ago. I ended up using the str_match function from the stringr package. It returns NA if the target string is not found. Just make sure you subset the result correctly. An example:
library(stringr)
str = "Little_Red_Riding_Hood"
sub(".*(Little).*","\\1",str) # Returns 'Little'
sub(".*(Big).*","\\1",str) # Returns 'Little_Red_Riding_Hood'
str_match(str,".*(Little).*")[1,2] #Returns 'Little'
str_match(str,".*(Big).*")[1,2] # Returns NA
I think in this case you could try using ifelse(), i.e.,
active$id[grep("CIR",active$description)] <- ifelse(match, replacement, "")
where match should evaluate to true if there's a match, and replacement is what that element would be replaced with in that case. Likewise, if match evaluates to false, that element's replaced with an empty string (or NA if you prefer).
I would like to split a string of character at pattern "|"
but
unlist(strsplit("I am | very smart", " | "))
[1] "I" "am" "|" "very" "smart"
or
gsub(pattern="|", replacement="*", x="I am | very smart")
[1] "*I* *a*m* *|* *v*e*r*y* *s*m*a*r*t*"
The problem is that by default strsplit interprets " | " as a regular expression, in which | has special meaning (as "or").
Use fixed argument:
unlist(strsplit("I am | very smart", " | ", fixed=TRUE))
# [1] "I am" "very smart"
Side effect is faster computation.
stringr alternative:
unlist(stringr::str_split("I am | very smart", fixed(" | ")))
| is a metacharacter. You need to escape it (using \\ before it).
> unlist(strsplit("I am | very smart", " \\| "))
[1] "I am" "very smart"
> sub(pattern="\\|", replacement="*", x="I am | very smart")
[1] "I am * very smart"
Edit: The reason you need two backslashes is that the single backslash prefix is reserved for special symbols such as \n (newline) and \t (tab). For more information look in the help page ?regex. The other metacharacters are . \ | ( ) [ { ^ $ * + ?
If you are parsing a table than calling read.table might be a better option. Tiny example:
> txt <- textConnection("I am | very smart")
> read.table(txt, sep='|')
V1 V2
1 I am very smart
So I would suggest to fetch the wiki page with Rcurl, grab the interesting part of the page with XML (which has a really neat function to parse HTML tables also) and if HTML format is not available call read.table with specified sep. Good luck!
Pipe '|' is a metacharacter, used as an 'OR' operator in regular expression.
try
unlist(strsplit("I am | very smart", "\s+\|\s+"))