How to extract substring between patterns "_" and "." in R

Question

I have many filenames which look like:

txt= "MA0051_IRF2.xml"

I want to extract IRF2 which is between "_" and ".". How do I do this in R?

Frank Schmitt · Accepted Answer · 2014-05-07T13:41:52.813

31

To achieve this, you need a regexp that

matches an (optional) arbitrary string in front of the _ : .*
matches a literal _ : [_]
matches everything up to (but not including) the next . and stores it in capturing group no. 1 : ([^.]+)
matches a literal . : [.]
matches an (optional) arbitrary string after the . : .*

In your call to gsub, you then

use the regular expression we built in the previous step
replace the whole string with the contents of the first capturing group: \\1 (we need to escape the backslash, hence the double backslash)

Example:

gsub(".*[_]([^.]+)[.].*", "\\1", "MA0051_IRF2.xml")

edited May 07 '14 at 13:41

answered May 07 '14 at 12:59

Frank Schmitt

1

excellent explanation! Could you please explain what "\\1" does in gsub()? – Paul.j May 07 '14 at 13:34
`_` isn't special and doesn't need to be escaped or put in a character class. +1 for `[.]`. – Matthew Lundberg May 07 '14 at 13:50
@MatthewLundberg You're right about the _, of course. – Frank Schmitt May 07 '14 at 14:24
what if txt= "MA0051_IRF2.xml MA0051_IRF3.xml". I need IRF2 ans IRF3. – Shalini Baranwal Sep 06 '18 at 07:50

score 6 · Answer 2 · answered May 07 '14 at 13:15

6

an other possibility with the stringr package:

 str_extract(x, perl("(?<=_)(.+)(?=\\.)"))

answered May 07 '14 at 13:15

droopy

1

If I am not wrong, current versions of `stringr` do not longer use the function `perl`, the syntax for stringr v>1.4 would be `str_extract(x, "(?<=_)(.+)(?=\\.)")`. – Alf Pascu Mar 28 '22 at 15:26

David Arenburg · Answer 3 · 2014-05-07T13:12:48.380

4

gsub(".*_(.*)\\..*", "\\1", txt)
##"IRF2"

edited May 07 '14 at 13:12

answered May 07 '14 at 12:56

David Arenburg

score 4 · Answer 4 · answered May 07 '14 at 14:04

4

Here's a possible solution that doesn't require regex knowledge:

txt <- "MA0051_IRF2.xml"

library(qdap)
genXtract(txt, "_", ".")

## _  :  . 
##  "IRF2"

answered May 07 '14 at 14:04

Tyler Rinker

This is cool, but you can make sure you can extract as a character to add it in mutate? For example `mutate(extract=genXtract(txt,"-",".")` – LDT Oct 19 '22 at 07:41

4 Answers4