R/translateORFs.r

In rfctbio-bsu/ORFhunteR: Predict open reading frames in nucleotide sequences

#' Translate open reading frames to proteins
#' @description Translate the identified open reading frames to proteins.
#' @param seqORFs character string giving the name of FASTA/FA file with
#'     sequences of identified open reading frames.
#' @param aaSymbol type of amino acid symbols (one- or three-letter coding).
#'     Default value is 1.
#' @param workDir character string giving the path to and name of work
#'     directory. NULL by default that mean the current working directory.
#' @return AAStringSet object with protein sequences.
#' @author Vasily V. Grinev
#' @examples
#' seq_orf_path <- system.file("extdata",
#'                             "Set.trans_ORFs.sequences.fasta",
#'                             package="ORFhunteR")
#' prot_seqs <- translateORFs(seqORFs=seq_orf_path)
#' @export

translateORFs <- function(seqORFs, aaSymbol=1, workDir=NULL){
  ### Internal calling of codon table.
  codon_table_path <- system.file("extdata",
                                  "codon.table.txt",
                                  package="ORFhunteR")
  codon_table <- read.table(file=codon_table_path,
                            sep="\t",
                            header=TRUE,
                            quote="\"",
                            as.is=TRUE)
  ### Loading of the open reading frame sequences
  #   as an object of class DNAStringSet.
  if (!is.null(workDir)){
    seqORFs <- paste(workDir, seqORFs, sep="/")
  }
  seq_orfs <- readDNAStringSet(filepath=seqORFs)
  ### Open reading frames to proteins translation.
  seq_prts <- lapply(X=seq_orfs,
                     FUN=function(y){
                       y <- as.character(x=y)
                       prt <- sapply(X=seq(from=1,
                                           to=nchar(x=y) - 3,
                                           by=3),
                                     FUN=function(z){
                                       substr(x=y,
                                              start=z,
                                              stop=z + 2)
                                     }
                       )
                       prt <- paste(codon_table[match(x=prt,
                                                      table=codon_table[, 1]),
                                                if (aaSymbol == 1){
                                                  4
                                                }else{
                                                  3
                                                }],
                                    collapse="")
                     }
  )
  seq_prts <- AAStringSet(x=unlist(x=seq_prts), use.names=TRUE)
  ### Returning a final object.
  return(seq_prts)
}