How to find substrings flanked by a specific character and replace with text of the same length in R?

Question

In R, what is the best way of finding dots flanked by asterisks and replace them with asterisks?

input:

"AG**...**GG*.*.G.*C.C"

desired output:

"AG*******GG***.G.*C.C"

I tried the following function, but it is not elegant to say the least.

    library(stringr)

    replac <- function(my_string) {

        m <- str_locate_all(my_string, "\\*\\.+\\*")[[1]]

        if (nrow(m) == 0) return(my_string)

        split_s <- unlist(str_split(my_string, "")) 

        for (i in 1:nrow(m)) {
            st <- m[i, 1]
            en <- m[i, 2] 
            split_s[st:en] <- rep("*", length(st:en))
        }

        paste(split_s, collapse = "")
    }

• I've have edited the input string and expected output after @TheForthBird answer below to make clear that dots not flanked by asterisks should not be changed, and that other letters other and "A" and "G" may occur.

Answer 1

You might use gsub with perl = TRUE and make use of the \G anchor to assert the position at the end of the previous match.

You could match AG or GG using a character class [AG]G or [A-Z]+ to match 1+ uppercase characters.

In the replacement use *

(?:[A-Z]+\*+|\G(?!^))\K\.(?=[^*]*\*)

That will match

• (?: Non capturing group
• [A-Z]+*+Match 1+ times uppercase char A-Z, then 1+ times*`
  • | Or
  • \G(?!^) Assert position at the end of previous match, not at the start
• ) Close non capturing group
• \K Forget what is currently matched
• \. Match literally
• (?= Positive lookahead, assert what is on the right is
  • [^*]*\* Match 0+ times any char except *, then match *
• ) Close lookahead

Regex demo | R demo

For example:

gsub("(?:[A-Z]+\\*+|\\G(?!^))\\K\\.(?=[^*]*\\*)", "*", "AG**...**GG*.*.G.*C.C", perl = TRUE)

Result

[1] "AG*******GG***.G.*C.C"

Answer 2

Try this code, it's still not wrapped, but at least is a bit shorter than yours and works for all the cases, not only the ones without other occurrences of dots in the string:

replac_v2 <- function(my_string){
    b <- my_string #Just a shorter name
    while(TRUE){
        df<-as.data.frame(str_locate(b,"\\*\\.+\\*"))
        add<-as.numeric(df[2]-df[1])+1
        if(is.na(add)){return(b)}
        b<-str_replace(b,"\\*\\.+\\*",paste(rep("*",add),collapse=""))
    }}