[R] Efficiency challenge: MANY subsets

[Johannes Graumann]

Hello,

I have a list of character vectors like this:

sequences <- list(
  c("M","G","L","W","I","S","F","G","T","P","P","S","Y","T","Y","L","L","I","M",
  "N","H","K","L","L","L","I","N","N","N","N","L","T","E","V","H","T","Y","F",
  "N","I","N","I","N","I","D","K","M","Y","I","H","*")
)

and another list of subset ranges like this:

indexes <- list(
  list(
    c(1,22),c(22,46),c(46, 51),c(1,46),c(22,51),c(1,51)
  )
)

What I now want to do is to subset each entry in "sequences" 
(sequences[[1]]) with all ranges in the corresponding low level list in 
"indexes" (indexes[[1]]). Here is what I came up with.

fragments <- list()
for(iN in seq(length(sequences))){
  cat(paste(iN,"\n"))
  tmpFragments <- sapply(
    indexes[[iN]],
    function(x){
      sequences[[iN]][seq.int(x[1],x[2])]
    }
  )
  fragments[[iN]] <- tmpFragments
}

This works fine, but "sequences" contains thousands of entries and the 
corresponding "indexes" are sometimes hundreds of ranges long, so this whole 
process is EXTREMELY inefficient.

Does somebody out there take the challenge and show me a way on how to speed 
this up?

Thanks for any hints,

Joh