R regex - splitting between parentheses

Question

Suppose I have a string x and I want to split it like so:

x <- "(A|C|T)AG(C|T)(A|C|G|T)(A|C|G|T)(A|C|G|T)(A|C|G|T)(A|C|G|T)GCC(C|T)(A|C|G|T)(A|C|G|T)(A|C|G)"

# Desired output
[1]  "(A|C|T)"  "A"  "G"  "(C|T)"  "(A|C|G|T)"  "(A|C|G|T)"  "(A|C|G|T)"  
[8]  "(A|C|G|T)"  "(A|C|G|T)"  "G"  "C"  "C"  "(C|T)"  "(A|C|G|T)"  
[15] "(A|C|G|T)"  "(A|C|G)"

I am using this splitting function, but I'm unable to split the strings not in the parenthesis. What would be the best way to approach this regex problem?

splitme <- function(x) {
  x <- unlist(strsplit(x, "(?=\\()", perl=TRUE))
  x <- unlist(strsplit(x, "(?<=\\))", perl=TRUE))
  for (i in which(x=="(")) {
    x[i+1] <- paste(x[i], x[i+1], sep="")
  }
  x[-which(x=="(")]
}

splitme(x)
 [1] "(A|C|T)"   "AG"        "(C|T)"     "(A|C|G|T)" "(A|C|G|T)" "(A|C|G|T)" "(A|C|G|T)" "(A|C|G|T)" "GCC"      
[10] "(C|T)"     "(A|C|G|T)" "(A|C|G|T)" "(A|C|G)"

`regmatches(x,gregexpr("\\(([^\\)]+)\\)|[^\\(\\)\\|]",x))[[1]]` — A. Webb, Aug 18 '15 at 18:09

zero323 · Answer 1 · 2015-08-18T18:01:19.670

3

Something like this should work:

> library(stringi)

> unlist(stri_extract_all_regex(x, "\\([ACGT\\|]*\\)|[ACGT]"))
 [1] "(A|C|T)"   "A"         "G"         "(C|T)"     "(A|C|G|T)" "(A|C|G|T)"
 [7] "(A|C|G|T)" "(A|C|G|T)" "(A|C|G|T)" "G"         "C"         "C"        
[13] "(C|T)"     "(A|C|G|T)" "(A|C|G|T)" "(A|C|G)"

\\([ACGT\\|]*\\) will match everything enclosed in parentheses and [ACGT] the remaining bases.

edited Aug 18 '15 at 18:01

answered Aug 18 '15 at 17:59

zero323

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It's indeed a better approach than absolutely trying to use a split way. – Casimir et Hippolyte Aug 18 '15 at 23:10

score 2 · Accepted Answer · answered Aug 18 '15 at 18:05

It looks like you'd like to split the string after each ), and after each letter that's followed by either another letter or by a (. If that's the behavior you'd like, you can use this:

pat <- "(?<=\\))|(?<=[[:alpha:]])(?=[[:alpha:]\\(])"
strsplit(x, pat, perl=TRUE)[[1]]
#  [1] "(A|C|T)"   "A"         "G"         "(C|T)"     "(A|C|G|T)" "(A|C|G|T)"
#  [7] "(A|C|G|T)" "(A|C|G|T)" "(A|C|G|T)" "G"         "C"         "C"        
# [13] "(C|T)"     "(A|C|G|T)" "(A|C|G|T)" "(A|C|G)"

score 1 · Answer 3 · answered Aug 18 '15 at 18:01

1

To split single letters, you can just run strsplit(x, ""). All you have to do is just make sure not to apply that to "finished" strings (i.e. the ones with parentheses).

y = splitme(x)
Indices = !which(grepl(y, "\\("))
y[Indices] = strsplit(y[Indices], "")
unlist(y)
 [1] "(A|C|T)"   "A"         "G"         "(C|T)"     "(A|C|G|T)" "(A|C|G|T)" "(A|C|G|T)" "(A|C|G|T)"
 [9] "(A|C|G|T)" "G"         "C"         "C"         "(C|T)"     "(A|C|G|T)" "(A|C|G|T)" "(A|C|G)"

answered Aug 18 '15 at 18:01

Señor O

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4

I think we posted the same approach. :\ Rock, paper, scissors for who deletes – Pierre L Aug 18 '15 at 18:02
1

`sample(c("rock", "paper", "scissors"), 1)` – Señor O Aug 18 '15 at 18:06
Paper (need more characters) – Señor O Aug 18 '15 at 18:21
I got "rock". you win – Pierre L Aug 18 '15 at 18:24
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SO should implement this as an official policy ;) – Señor O Aug 18 '15 at 18:25
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Random seed could be made out of the date of the question. The paradigm could be expanded to include [lizard and Spock](http://www.samkass.com/theories/RPSSL.html). – Roman Luštrik Aug 19 '15 at 10:48

R regex - splitting between parentheses

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