I'd like to extract everything after "-" in vector of strings in R.
For example in :
test = c("Pierre-Pomme","Jean-Poire","Michel-Fraise")
I'd like to get
c("Pomme","Poire","Fraise")
Thanks !
With str_extract. \\b is a zero-length token that matches a word-boundary. This includes any non-word characters:
library(stringr)
str_extract(test, '\\b\\w+$')
# [1] "Pomme" "Poire" "Fraise"
We can also use a back reference with sub. \\1 refers to string matched by the first capture group (.+), which is any character one or more times following a - at the end:
sub('.+-(.+)', '\\1', test)
# [1] "Pomme" "Poire" "Fraise"
This also works with str_replace if that is already loaded:
library(stringr)
str_replace(test, '.+-(.+)', '\\1')
# [1] "Pomme" "Poire" "Fraise"
Third option would be using strsplit and extract the second word from each element of the list (similar to word from #akrun's answer):
sapply(strsplit(test, '-'), `[`, 2)
# [1] "Pomme" "Poire" "Fraise"
stringr also has str_split variant to this:
str_split(test, '-', simplify = TRUE)[,2]
# [1] "Pomme" "Poire" "Fraise"
We can use sub to match characters (.*) until the - and in the replacement specify ""
sub(".*-", "", test)
Or another option is word
library(stringr)
word(test, 2, sep="-")
I think the other answers might be what you're looking for, but if you don't want to lose the original context you can try something like this:
library(tidyverse)
tibble(test) %>%
separate(test, c("first", "last"), remove = F)
This will return a dataframe containing the original strings plus components, which might be more useful down the road:
# A tibble: 3 x 3
test first last
<chr> <chr> <chr>
1 Pierre-Pomme Pierre Pomme
2 Jean-Poire Jean Poire
3 Michel-Fraise Michel Fraise
For some reason the responses here didn't work for my particular string. I found this response more helpful (i.e., using Stringr's lookbehind function): stringr str_extract capture group capturing everything.
Related
Is there an R function to get only the part of a string before the 2nd capital character appears?
For example:
Example <- "MonkeysDogsCats"
Expected output should be:
"Monkeys"
Maybe something like
stringr::str_extract("MonkeysDogsCats", "[A-Z][a-z]*")
#[1] "Monkeys"
Here is an alternative approach:
Here we first put a space before all uppercase and then extract the first word:
library(stringr)
word(gsub("([a-z])([A-Z])","\\1 \\2", Example), 1)
[1] "Monkeys"
A base solution with sub():
x <- "MonkeysDogsCats"
sub("(?<=[a-z])[A-Z].*", "", x, perl = TRUE)
# [1] "Monkeys"
Another way using stringr::word():
stringr::word(x, 1, sep = "(?=[A-Z])\\B")
# [1] "Monkeys"
If the goal is strictly to capture any string before the 2nd capital character, one might want pick a solution it'll also work with all types of strings including numbers and special characters.
strings <- c("MonkeysDogsCats",
"M4DogsCats",
"M?DogsCats")
stringr::str_remove(strings, "(?<=.)[A-Z].*")
Output:
[1] "Monkeys" "M4" "M?"
It depends on what you want to allow to match. You can for example match an uppercase char [A-Z] optionally followed by any character that is not an uppercase character [^A-Z]*
If you don't want to allow whitespace chars, you can exclude them [^A-Z\\s]*
library(stringr)
str_extract("MonkeysDogsCats", "[A-Z][^A-Z]*")
Output
[1] "Monkeys"
R demo
If there should be an uppercase character following, and there are only lowercase characters allowed:
str <- "MonkeysDogsCats"
regmatches(str, regexpr("[A-Z][a-z]*(?=[A-Z])", str, perl = TRUE))
Output
[1] "Monkeys"
R demo
I am in R and would like to extract a two digit number 38y from the following string:
"/Users/files/folder/file_number_23a_version_38y_Control.txt"
I know that _Control always comes after the 38y and that 38y is preceded by an underscore. How can I use strsplit or other R commands to extract the 38y?
You could use
regmatches(x, regexpr("[^_]+(?=_Control)", x, perl = TRUE))
# [1] "38y"
or equivalently
stringr::str_extract(x, "[^_]+(?=_Control)")
# [1] "38y"
Using gsub.
gsub('.*_(.*)_Control.*', '\\1', x)
# [1] "38y"
See demo with detailed explanation.
A possible solution:
library(stringr)
text <- "/Users/files/folder/file_number_23a_version_38y_Control.txt"
str_extract(text, "(?<=_)\\d+\\D(?=_Control)")
#> [1] "38y"
You can find an explanation of the regex part at:
https://regex101.com/r/PQSZHX/1
I want to extract strings using rm_between function from the library(qdapRegex)
I need to extract the string between the second "|" and the word "_HUMAN".
I cant figure out how to select the second "|" and not the first.
example <- c("sp|B5ME19|EIFCL_HUMAN", "sp|Q99613|EIF3C_HUMAN")
prots <- rm_between(example, '|', 'HUMAN', extract=TRUE)
Thank you!!
Another alternative using regmatches, regexpr and using perl=TRUE to make use of \K
^(?:[^|]*\|){2}\K[^|_]+(?=_HUMAN)
Regex demo
For example
regmatches(example, regexpr("^(?:[^|]*\\|){2}\\K[^|_]+(?=_HUMAN)", example, perl=TRUE))
Output
[1] "EIFCL" "EIF3C"
In your rm_between(example, '|', 'HUMAN', extract=TRUE) command, the | is used to match the leftmost | and HUMAN is used to match the left most HUMAN right after.
Note the default value for the FIXED argument is TRUE, so | and HUMAN are treated as literal chars.
You need to make the pattern a regex pattern, by setting fixed=FALSE. However, the ^(?:[^|]*\|){2} as the left argument regex will not work because the qdap package creates an ICU regex with lookarounds (since you use extract=TRUE that sets include.markers to FALSE), which is (?<=^(?:[^|]*\|){2}).*?(?=HUMAN).
As a workaround, you could use a constrained-width lookbehind, by replacing * with a limiting quantifier with a reasonably large max parameter. Say, if you do not expect more than a 1000 chars between each pipe, you may use {0,1000}:
rm_between(example, '^(?:[^|]{0,1000}\\|){2}', '_HUMAN', extract=TRUE, fixed=FALSE)
# => [[1]]
# [1] "EIFCL"
#
# [[2]]
# [1] "EIF3C"
However, you really should think of using simpler approaches, like those described in other answers. Here is another variation with sub:
sub("^(?:[^|]*\\|){2}(.*?)_HUMAN.*", "\\1", example)
# => [1] "EIFCL" "EIF3C"
Details
^ - startof strig
(?:[^|]*\\|){2} - two occurrences of any 0 or more non-pipe chars followed with a pipe char (so, matching up to and including the second |)
(.*?) - Group 1: any 0 or more chars, as few as possible
_HUMAN.* - _HUMAN and the rest of the string.
\1 keeps only Group 1 value in the result.
A stringr variation:
stringr::str_match(example, "^(?:[^|]*\\|){2}(.*?)_HUMAN")[,2]
# => [1] "EIFCL" "EIF3C"
With str_match, the captures can be accessed easily, we do it with [,2] to get Group 1 value.
this is not exactly what you asked for, but you can achieve the result with base R:
sub("^.*\\|([^\\|]+)_HUMAN.*$", "\\1", example)
This solution is an application of regular expression.
"^.*\\|([^\\|]+)_HUMAN.*$" matches the entire character string.
\\1 matches whatever was matched inside the first parenthesis.
Using regular gsub:
example <- c("sp|B5ME19|EIFCL_HUMAN", "sp|Q99613|EIF3C_HUMAN")
gsub(".*?\\|.*?\\|(.*?)_HUMAN", "\\1", example)
#> [1] "EIFCL" "EIF3C"
The part (.*?) is replaced by itself as the replacement contains the back-reference \\1.
If you absolutely prefer qdapRegex you can try:
rm_between(example, '.{0,100}\\|.{0,100}\\|', '_HUMAN', fixed = FALSE, extract = TRUE)
The reason why we have to use .{0,100} instead of .*? is that the underlying stringi needs a mamixmum length for the look-behind pattern (i.e. the left argument in rm_between).
Just saying that you could easily just use sapply()/strsplit():
example <- c("sp|B5ME19|EIFCL_HUMAN", "sp|Q99613|EIF3C_HUMAN")
unlist(sapply(strsplit(example, "|", fixed = T),
function(item) strsplit(item[3], "_HUMAN", fixed = T)))
# [1] "EIFCL" "EIF3C"
It just splits on | in the first list and on _HUMAN on every third element within that list.
I have a column as below.
9453, 55489, 4588, 18893, 4457, 2339, 45489HQ, 7833HQ
I would like to add leading zero if the number is less than 5 digits. However, some numbers have "HQ" in the end, some don't.(I did check other posts, they dont have similar problem in the "HQ" part)
so the finally desired output should be:
09453, 55489, 04588, 18893, 04457, 02339, 45489HQ, 07833HQ
any idea how to do this? Thank you so much for reading my post!
A one-liner using regular expressions:
my_strings <- c("9453", "55489", "4588",
"18893", "4457", "2339", "45489HQ", "7833HQ")
gsub("^([0-9]{1,4})(HQ|$)", "0\\1\\2",my_strings)
[1] "09453" "55489" "04588" "18893"
"04457" "02339" "45489HQ" "07833HQ"
Explanation:
^ start of string
[0-9]{1,4} one to four numbers in a row
(HQ|$) the string "HQ" or the end of the string
Parentheses represent capture groups in order. So 0\\1\\2 means 0 followed by the first capture group [0-9]{1,4} and the second capture group HQ|$.
Of course if there is 5 numbers, then the regex isn't matched, so it doesn't change.
I was going to use the sprintf approach, but found the the stringr package provides a very easy solution.
library(stringr)
x <- c("9453", "55489", "4588", "18893", "4457", "2339", "45489HQ", "7833HQ")
[1] "9453" "55489" "4588" "18893" "4457" "2339" "45489HQ" "7833HQ"
This can be converted with one simple stringr::str_pad() function:
stringr::str_pad(x, 5, side="left", pad="0")
[1] "09453" "55489" "04588" "18893" "04457" "02339" "45489HQ" "7833HQ"
If the number needs to be padded even if the total string width is >5, then the number and text need to be separated with regex.
The following will work. It combines regex matching with the very helpful sprintf() function:
sprintf("%05.0f%s", # this encodes the format and recombines the number with padding (%05.0f) with text(%s)
as.numeric(gsub("^(\\d+).*", "\\1", x)), #get the number
gsub("[[:digit:]]+([a-zA-Z]*)$", "\\1", x)) #get just the text at the end
[1] "09453" "55489" "04588" "18893" "04457" "02339" "45489HQ" "07833HQ"
Another attempt, which will also work in cases like "123" or "1HQR":
x <- c("18893","4457","45489HQ","7833HQ","123", "1HQR")
regmatches(x, regexpr("^\\d+", x)) <- sprintf("%05d", as.numeric(sub("\\D+$","",x)))
x
#[1] "18893" "04457" "45489HQ" "07833HQ" "00123" "00001HQR"
This basically finds any numbers at the start of the string (^\\d+) and replaces them with a zero-padded (via sprintf) string that was subset out by removing any non-numeric characters (\\D+$) from the end of the string.
We can use only sprintf() and gsub() by splitting up the parts then putting them back together.
sprintf("%05d%s", as.numeric(gsub("[^0-9]+", "", x)), gsub("[0-9]+", "", x))
# [1] "18893" "04457" "45489HQ" "07833HQ" "00123" "00001HQR"
Using #thelatemail's data:
x <- c("18893", "4457", "45489HQ", "7833HQ", "123", "1HQR")
How do I remove part of a string? For example in ATGAS_1121 I want to remove everything before _.
Use regular expressions. In this case, you can use gsub:
gsub("^.*?_","_","ATGAS_1121")
[1] "_1121"
This regular expression matches the beginning of the string (^), any character (.) repeated zero or more times (*), and underscore (_). The ? makes the match "lazy" so that it only matches are far as the first underscore. That match is replaced with just an underscore. See ?regex for more details and references
You can use a built-in for this, strsplit:
> s = "TGAS_1121"
> s1 = unlist(strsplit(s, split='_', fixed=TRUE))[2]
> s1
[1] "1121"
strsplit returns both pieces of the string parsed on the split parameter as a list. That's probably not what you want, so wrap the call in unlist, then index that array so that only the second of the two elements in the vector are returned.
Finally, the fixed parameter should be set to TRUE to indicate that the split parameter is not a regular expression, but a literal matching character.
If you're a Tidyverse kind of person, here's the stringr solution:
R> library(stringr)
R> strings = c("TGAS_1121", "MGAS_1432", "ATGAS_1121")
R> strings %>% str_replace(".*_", "_")
[1] "_1121" "_1432" "_1121"
# Or:
R> strings %>% str_replace("^[A-Z]*", "")
[1] "_1121" "_1432" "_1121"
Here's the strsplit solution if s is a vector:
> s <- c("TGAS_1121", "MGAS_1432")
> s1 <- sapply(strsplit(s, split='_', fixed=TRUE), function(x) (x[2]))
> s1
[1] "1121" "1432"
Maybe the most intuitive solution is probably to use the stringr function str_remove which is even easier than str_replace as it has only 1 argument instead of 2.
The only tricky part in your example is that you want to keep the underscore but its possible: You must match the regular expression until it finds the specified string pattern (?=pattern).
See example:
strings = c("TGAS_1121", "MGAS_1432", "ATGAS_1121")
strings %>% stringr::str_remove(".+?(?=_)")
[1] "_1121" "_1432" "_1121"
Here the strsplit solution for a dataframe using dplyr package
col1 = c("TGAS_1121", "MGAS_1432", "ATGAS_1121")
col2 = c("T", "M", "A")
df = data.frame(col1, col2)
df
col1 col2
1 TGAS_1121 T
2 MGAS_1432 M
3 ATGAS_1121 A
df<-mutate(df,col1=as.character(col1))
df2<-mutate(df,col1=sapply(strsplit(df$col1, split='_', fixed=TRUE),function(x) (x[2])))
df2
col1 col2
1 1121 T
2 1432 M
3 1121 A