R/packsToFasta.R

In packFinder: de novo Annotation of Pack-TYPE Transposable Elements

#' @title
#' Save packFinder Results in FASTA Format (.fasta)
#'
#' @description
#' Saves a dataframe of potential Pack-TYPE elements, 
#' usually generated via \code{\link{packSearch}}. 
#' May be retrieved using \code{\link{getPacksFromFasta}}.
#'
#' @param file
#' FASTA file save path.
#'
#' @param packMatches
#' taframe containing genomic ranges and names referring 
#' to sequences to be extracted. Can be obtained from 
#' \code{\link{packSearch}} or generated from a 
#' \code{\link[GenomicRanges:GRanges-class]{GRanges}} object, 
#' after conversion to a dataframe. Must contain the 
#' following features:
#' \itemize{
#'     \item start - the predicted element's start base 
#'     sequence position.
#'     \item end - the predicted element's end 
#'     base sequence position.
#'     \item seqnames - character string 
#'     referring to the sequence name in \code{Genome} to 
#'     which \code{start} and \code{end} refer to.
#' }
#'
#' @param Genome
#' A DNAStringSet object containing sequences referred to 
#' in \code{packMatches} (the object originally used to 
#' predict the transposons \code{\link{packSearch}}).
#'
#' @return
#' Save location of Fasta file.
#'
#' @seealso 
#' \code{\link{getPacksFromFasta}}, \code{\link{packSearch}}
#' 
#' @examples
#' data(arabidopsisThalianaRefseq)
#' data(packMatches)
#' 
#' packsToFasta(
#'     packMatches, 
#'     system.file("extdata", "packMatches.fasta", package = "packFinder"), 
#'     arabidopsisThalianaRefseq
#' )
#' 
#' @author
#' Jack Gisby
#'
#' @export

packsToFasta <- function(packMatches, file, Genome) {
    
    file.create(file)
    
    # create package-specific FASTA file
    for (match in seq_len(length(packMatches[, 1]))) {
        seq <- Genome[names(Genome) == packMatches$seqnames[match]][[1]]
        seq <- seq[packMatches$start[match]:packMatches$end[match]]
        write(c(
            paste0(
                ">", packMatches$seqnames[match],
                " | start = ", packMatches$start[match],
                " | end = ", packMatches$end[match],
                " | width = ", packMatches$width[match],
                " | strand = ", packMatches$strand[match],
                " | TSD = ", packMatches$TSD[match]
            ),
            as.character(seq)
        ),
        file = file,
        append = TRUE
        )
    }
    
    return(print(paste0("FASTA written to ", file)))
}