[R] Substring replacement in string

[Hervé Pagès]

Hi Alrik,

With the Biostrings/IRanges infrastructure (Bioconductor packages), you
can do this with:

   library(Biostrings)
   x0 <- BString("pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1, 
z1))")
   donttouch_words <- c("pmin", "pmax")

   ## Extract the substrings to modify (target substrings).
   donttouch_regions <- reduce(do.call("c", lapply(donttouch_words, 
matchPattern, x0)))
   target_regions <- ranges(gaps(donttouch_regions))
   target_substrings <- extractAt(x0, target_regions)

   ## Modify them.
   old <- paste0(letters, collapse="")
   new <- paste0(LETTERS, collapse="")
   target_substrings <- chartr(old, new, target_substrings)

   ## Replace in original string.
   x1 <- replaceAt(x0, target_regions, target_substrings)

Then:

   > x1
     57-letter "BString" instance
   seq: pmin(pmax(pmin(X1, X2), pmin(X3, X4)) == Y, pmax(Z1, Z1))

   > as.character(x1)
   [1] "pmin(pmax(pmin(X1, X2), pmin(X3, X4)) == Y, pmax(Z1, Z1))"

Hope this helps,
H.

On 02/27/2015 02:19 PM, Alrik Thiem wrote:
> Dear R-help list,
>
> I would like to replace all lower-case letters in a string that are not part
> of certain fixed expressions. For example, I have the string:
>
> "pmin(pmax(pmin(x1, X2), pmin(X3, X4)) == Y, pmax(Z1, z1))"
>
> Where I would like to replace all lower-case letters that do not belong to
> the functions "pmin" and "pmax" by 1 - toupper(...) to get
>
> "pmin(pmax(pmin(1 - X1, X2), pmin(X3, X4)) == Y, pmax(Z1, 1 - Z1))"
>
> Any ideas on how I could achieve that?
>
> Many thanks and best wishes,
>
> Alrik
>
>
> ********************************
> Alrik Thiem
> Post-Doctoral Researcher
>
> Department of Philosophy
> University of Geneva
> Rue de Candolle 2
> CH-1211 Geneva
>
> +41 76 527 80 83
>
> http://www.alrik-thiem.net
> http://www.compasss.org
>
> ______________________________________________
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>

-- 
Hervé Pagès

Program in Computational Biology
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