Extract a string between patterns/delimiters in R

Question

I have variable names in the form:

PP_Sample_12.GT

or

PP_Sample-17.GT

I\'m trying to use string split to

Answer 1

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"

Answer 2

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)

Answer 3

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)

Answer 4

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