#' @title Save a proteome in fasta format
#' @description This function takes a proteome (in data.table notation) as returned by
#' \code{\link{read.proteome}} and saves it to your hard drive.
#' @param proteome a data.table object storing amino acid sequences in the first column
#' and gene ids in the second column. See \code{\link{read.proteome}} for details.
#' @param file.name a character string specifying the name of the fasta output file.
#' @param nbchar number of characters per line.
#' @param open mode to open the output file, you can choose from "w" to write into a new file, or "a" to append at the end of an already existing file.
#' @param as.string when set to TRUE sequences are in the form of strings instead of vectors of single characters.
#' @author Hajk-Georg Drost
#' @examples
#'
#' \dontrun{
#'
#' # read an example proteome
#' Ath.proteome <- read.proteome(
#' system.file('seqs/ortho_thal_aa.fasta', package = 'orthologr'),
#' format = "fasta")
#'
#' # use the write.proteome function to store it on your hard drive
#' write.proteome(Ath.proteome, "test_proteome.fasta")
#'
#' }
#'
#' @export
write.proteome <- function(proteome, file.name, nbchar = 80, open = "w", as.string = TRUE){
# define visible bindings for global variables
seqs <- geneids <- NULL
seqinr::write.fasta( sequences = as.list(proteome[ , seqs]),
names = proteome[ , geneids],
nbchar = nbchar,
open = open,
file.out = file.name,
as.string = as.string)
}
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