R/chop_fasta.R

In adsteen/genomechop:

##' Reads a fasta & chops it
##'
##' @param fasta_list contents of a single fasta file (a list of SeqFastadna objects) as read by read.fasta
##' @param len length of pieces to chop
##' @param random Whether to chop at random. At present only this method is implemented
##' @param n The number of pieces to chop into (as an integer), or "complete", in which case len * n = the length of the sequence
##' @export

chop_fasta <- function(fasta_list, len=1000, method = "random", n = "complete") {
  st <- system.time({
    # This function is really just a wrapper for everything else

    browser()
    chops <- lapply(fasta_list, chop_sequence)
    # chop_sequence will just cut the sequence n times and return (I guess a list)
  })
  print(st)

  chops
}