R/dnastring2aln.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 dnastring2aln
#' @name dnastring2aln
#' @description This function converts a \code{DNAStringSet} into an
#' \code{seqinr} \code{alignment}.
#' @param dna \code{DNAStringSet} [mandatory]
#' @return An object of class \code{alignment} which is a list with the
#' following components:\cr
#' \code{nb} the number of aligned sequences\cr
#' \code{nam} a vector of strings containing the names of the aligned
#' sequences\cr
#' \code{seq} a vector of strings containing the aligned sequences\cr
#' \code{com} a vector of strings containing the commentaries for each sequence
#' or \code{NA} if there are no comments
#' @importFrom Biostrings DNAString DNAStringSet AAString AAStringSet
#' readDNAStringSet readAAStringSet writeXStringSet width subseq
#' @importFrom seqinr as.alignment
#' @seealso \code{\link[seqinr]{as.alignment}}
#' @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()
#' @export dnastring2aln
#' @author Kristian K Ullrich

dnastring2aln <- function(dna){
    stopifnot("Error: input needs to be a DNAStringSet"=
        methods::is(dna, "DNAStringSet"))
    alignment.nb <- length(dna)
    alignment.nam <- names(dna)
    alignment.seq <- tolower(as.character(dna))
    names(alignment.seq) <- NULL
    alignment.com <- NA
    alignment <- list(alignment.nb, alignment.nam, alignment.seq, alignment.com)
    names(alignment) <- c("nb", "nam", "seq", "com")
    attr(alignment, "class") <- "alignment"
    return(alignment)
}