R/aln2dnastring.R

In kullrich/distSTRING: distSTRING calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

#' @title aln2dnastring
#' @name aln2dnastring
#' @description This function converts a \code{seqinr} \code{alignment} into
#' an \code{DNAStringSet}.
#' @param aln \code{seqinr} \code{alignment} [mandatory]
#' @return An object of class \code{DNAStringSet}
#' @importFrom Biostrings DNAString DNAStringSet AAString AAStringSet
#' readDNAStringSet readAAStringSet writeXStringSet width subseq
#' @importFrom seqinr as.alignment
#' @seealso \code{\link[seqinr]{as.alignment}}
#' \code{\link[Biostrings]{DNAStringSet}}
#' @examples
#' ## define two cds sequences
#' cds1 <- Biostrings::DNAString("ATGCAACATTGC")
#' cds2 <- Biostrings::DNAString("ATG---CATTGC")
#' cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
#'     Biostrings::DNAStringSet(cds2))
#' ## convert into alignment
#' #dnastring2aln(cds1.cds2.aln)
#' cds1.cds2.aln |> dnastring2aln()
#' ## convert back into DNAStringSet
#' #aln2dnastring(dnastring2aln(cds1.cds2.aln))
#' cds1.cds2.aln |> dnastring2aln() |> aln2dnastring()
#' @export aln2dnastring
#' @author Kristian K Ullrich

aln2dnastring <- function(aln){
    dna <- Biostrings::DNAStringSet(unlist(aln$seq))
    names(dna) <- aln$nam
    return(dna)
}