Faster way to split a string and count characters using R?

Question

I\'m looking for a faster way to calculate GC content for DNA strings read in from a FASTA file. This boils down to taking a string and counting the number of times that the let

Answer 1

Better to not split at all, just count the matches:

gcCount2 <-  function(line, st, sp){
  sum(gregexpr('[GCgc]', substr(line, st, sp))[[1]] > 0)
}

That's an order of magnitude faster.

A small C function that just iterates over the characters would be yet another order of magnitude faster.