CODEWITHSUNDEEP
regexrstrsplit
user2726449
user2726449

Reputation: 627

Extract a string between patterns/delimiters in R

I have variable names in the form:

PP_Sample_12.GT

or

PP_Sample-17.GT

I'm trying to use string split to grep out the middle section: ie Sample_12 or Sample-17. However, when I do:

IDtmp <- sapply(strsplit(names(df[c(1:13)]),'_'),function(x) x[2])
IDs <- data.frame(sapply(strsplit(IDtmp,'.GT',fixed=T),function(x) x[1]))

I end up with Sample for PP_Sample_12.GT.

Is there another way to do this? Maybe using a pattern/replace kind of function ? Though, not sure if this exists in R (but I think this might work with gsub)

Upvotes: 6

Views: 8541

Answers (4)

MrFlick
MrFlick

Reputation: 206263

Here's a gsub that will extract everything after the first _ and before the last .

x<-c("PP_Sample-12.GT","PP_Sample-17.GT")
gsub(".*_(.*)\\..*","\\1", x, perl=T)

Upvotes: 5

hwnd
hwnd

Reputation: 70732

This grabs the 2nd element of each part of the list that was split and then simplifies it into a vector by subsetting the function [, using sapply to call this function for each element of the original list.

x <- c('PP_Sample_12.GT', 'PP_Sample-17.GT')
sapply(strsplit(x, '(?:_(?=\\D)|\\.GT)', perl = T), '[', 2)

[1] "Sample_12" "Sample-17"

Upvotes: 1

G. Grothendieck
G. Grothendieck

Reputation: 269704

Using this input:

x <- c("PP_Sample_12.GT", "PP_Sample-17.GT")

1) strsplit. Replace the first underscore with a dot and then split on dots:

spl <- strsplit(sub("_", ".", x), ".", fixed = TRUE)
sapply(spl, "[", 2)

2) gsub Replace the prefix (^[^_]*_) and the suffix (\\.[^.]*$") with the empty string:

gsub("^[^_]*_|\\.[^.]*$", "", x)

3) gsubfn::strapplyc extract everything between underscore and dot.

library(gsubfn)
strapplyc(x, "_(.*)\\.", simplify = TRUE)

Upvotes: 6

Thomas
Thomas

Reputation: 44535

If they all start and end with the same characters and those characters aren't anywhere in the middle part of your string, the gsub expression is simple:

> x <- c("PP_Sample-12.GT","PP_Sample-17.GT")
> gsub('[(PP_)|(.GT)]','',x)
[1] "Sample-12" "Sample-17

Upvotes: 0

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