On Wed, Jan 1, 2014 at 10:55 PM, Joshua Banta <jba...@uttyler.edu> wrote:
> Dear Listserve,
>
> I have a data-parsing question for you. I recognize this is more in the
> domain of PERL/Python, but I don't know those languages! On the other hand, I
> am pretty good overall with R, so I'd rather get the job done within the R
> "ecosphere."
>
> Here is what I want to do. Consider the following data:
>
> string <- "ATCGCCCGTA[AGA]TAACCG"
>
> I want to alter string so that it looks like this:
>
> ATCGCCCGTA[A][G][A]TAACCG
>
> In other words, I want to design a piece of code that will scan a character
> string, find bracketed groups of characters, break up each character within
> the bracket into its own individual bracketed character, and then put the
> group of individually bracketed characters back into the character string.
> The lengths of the character strings enclosed by a bracket will vary, but in
> every case, I want to do the same thing: break up each character within the
> bracket into its own individual bracketed character, and then put the group
> of individually bracketed characters back into the character string.
>
> So, for example, another string may look like this:
>
> string2 <- "ATTATACGCA[AAATGCCCCA]GCTA[AT]GCATTA"
>
> I want to alter string so that it looks like this:
>
> "ATTATACGCA[A][A][A][T][G][C][C][C][C][A]GCTA[A][T]GCATTA"
>
Here is a one line solution:
library(gsubfn)
> gsubfn("\\[([^]]+)\\]", ~ paste(paste0("[", strsplit(x, "")[[1]], "]"),
> collapse = ""), string)
[1] "ATCGCCCGTA[A][G][A]TAACCG"
>
> gsubfn("\\[([^]]+)\\]", ~ paste(paste0("[", strsplit(x, "")[[1]], "]"),
> collapse = ""), string2)
[1] "ATTATACGCA[A][A][A][T][G][C][C][C][C][A]GCTA[A][T]GCATTA"
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