How to extract substrings in R using stringr::str_match

Question

I have the following two strings:

x <- "chr1:625000-635000.BB_162.Adipose"
y <- "chr1:625000-635000.BB_162.combined.HMSC-ad"

With this regex I have no problem capturing parts of x

> stringr::str_match(x,"(\\w+):(\\d+)-(\\d+)\\.(\\w+)\\.(\\w+)")
     [,1]                                [,2]   [,3]     [,4]     [,5]     [,6]     
[1,] "chr1:625000-635000.BB_162.Adipose" "chr1" "625000" "635000" "BB_162" "Adipose"

What I want to do is with y to obtain this

     [,1]                                [,2]   [,3]     [,4]     [,5]     [,6]     
[1,] "chr1:625000-635000.BB_162.combined.HMSC-ad"  "chr1" "625000" "635000" "BB_162" "HMSC-ad"

With my current regex and apply for y I get this instead:

   [,1]                                 [,2]   [,3]     [,4]     [,5]     [,6]      
[1,] "chr1:625000-635000.BB_162.combined" "chr1" "625000" "635000" "BB_162" "combined"

How can I generalize my regex so that it can deal with both x and y?

Update

S.Kalbar, your regex gave this:

> stringr::str_match(y,"(\\w+):(\\d+)-(\\d+)\\.(\\w+)\\.(\\w+)(?:\\.([A-Za-z-]+))?")
     [,1]                                         [,2]   [,3]     [,4]     [,5]     [,6]       [,7]     
[1,] "chr1:625000-635000.BB_162.combined.HMSC-ad" "chr1" "625000" "635000" "BB_162" "combined" "HMSC-ad"
> stringr::str_match(x,"(\\w+):(\\d+)-(\\d+)\\.(\\w+)\\.(\\w+)(?:\\.([A-Za-z-]+))?")
     [,1]                                [,2]   [,3]     [,4]     [,5]     [,6]      [,7]
[1,] "chr1:625000-635000.BB_162.Adipose" "chr1" "625000" "635000" "BB_162" "Adipose" NA

What' I'd like to get is this for y:

                                          [,1]     [,2]   [,3]     [,4]     [,5]     [,6]        
[1,] "chr1:625000-635000.BB_162.combined.HMSC-ad" "chr1" "625000" "635000" "BB_162" "HMSC-ad"

And this for x:

                                   [,1]  [,2]   [,3]     [,4]     [,5]     [,6]      
[1,] "chr1:625000-635000.BB_162.Adipose" "chr1" "625000" "635000" "BB_162" "Adipose"

For general regex problems it can help to play with your examples on regex 101. — twedl
– twedl, Commented Jan 25, 2018 at 2:30

Srdjan M. · Accepted Answer · 2018-01-25 03:01:42Z

1

Regex: (\w+):(\d+)-(\d+)\.(\w+)(?:\.\w+)?(?:\.([A-Za-z-]+))

RegEx demo

edited Jan 25, 2018 at 3:01

answered Jan 25, 2018 at 2:30

Srdjan M.

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2 Comments

pdubois Over a year ago

@S.Kalbar It's seems that the answer is incorrect for x, it get Adipos without ending e. Beside please give example in R code.

pdubois Over a year ago

@S.Kalbar as pointed in my OP. I look for one regex that can take care for both x and y.

Jan · Accepted Answer · 2018-01-25 07:47:36Z

1

You could give the engines some tokens to split on:

(?:(?<=\\d)-(?=\\d))|(?:\\.combined\\.)|[.:]+

Broken down, this says:

(?:(?<=\\d)-(?=\\d))  # a dash between numbers
|                     # or
(?:\\.combined\\.)    # .combined. literally
|                     # or
[.:]+                 # one of . or :

In R using str_split():

library(stringr)

x <- c("chr1:625000-635000.BB_162.Adipose", "chr1:625000-635000.BB_162.combined.HMSC-ad")
str_split(x, '(?:(?<=\\d)-(?=\\d))|(?:\\.combined\\.)|[.:]+', simplify = TRUE)

Which yields

     [,1]   [,2]     [,3]     [,4]     [,5]     
[1,] "chr1" "625000" "635000" "BB_162" "Adipose"
[2,] "chr1" "625000" "635000" "BB_162" "HMSC-ad"

answered Jan 25, 2018 at 7:47

Jan

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