R/read_rna.R

In biomartr: Genomic Data Retrieval

#' @title Import RNA as Biostrings or data.table object
#' @description This function reads an organism specific RNA stored in a
#' defined file format.
#' @param file a character string specifying the path to the file
#' storing the RNA.
#' @param format a character string specifying the file format used to store the
#'  genome, e.g. \code{format = "fasta"} (default) or \code{format = "gbk"}.
#' @param obj.type a character string specifying the object stype in which the
#' genomic sequence shall be represented.
#' Either as \code{obj.type = "Biostrings"} (default) or
#' as \code{obj.type = "data.table"}.
#' @param ... additional arguments that are used by
#' \code{\link[seqinr]{read.fasta}}.
#' @author Hajk-Georg Drost
#' @details This function takes a string specifying the path to the RNA file
#' of interest as first argument. It is possible to read in different proteome
#' file standards such as \emph{fasta} or \emph{genebank}.
#' @return A data.table storing the gene id in the first column and the
#' corresponding sequence as string in the second column.
#' @family rna
#' @family readers
#' @import Biostrings
#' @export

read_rna <-
    function(file,
             format = "fasta",
             obj.type = "Biostrings",
             ...) {
        if (!is.element(format, c("fasta", "gbk")))
            stop("Please choose a file format that is supported
                 by this function.",
                 call. = FALSE)

        if (!is.element(obj.type, c("Biostrings", "data.table")))
            stop(
                "Please specify a valid object type:
                obj.type = 'Biostrings' (default) or obj.type = 'data.table'.",
                call. = FALSE
            )

        geneids <- NULL

        if (obj.type == "Biostrings") {
            tryCatch({
                RNA_file <-
                    Biostrings::readDNAStringSet(filepath = file,
                                                 format = format, ...)
            }, error = function(e) {
                stop(
                    paste0(
                        "File ",
                        file,
                        " could not be read properly. \n",
                        "Please make sure that ",
                        file,
                        " contains only RNA sequences and is in ",
                        format,
                        " format."
                    ),
                    call. = FALSE
                )
            })

            return(RNA_file)
        }

        if (obj.type == "data.table") {
            tryCatch({
                RNA_file <-
                    Biostrings::readDNAStringSet(filepath = file,
                                                 format = format, ...)

                RNA_names <-
                    as.vector(unlist(lapply(RNA_file@ranges@NAMES, function(x) {
                        return(strsplit(x, " ")[[1]][1])
                    })))

                RNA.dt <-
                    data.table::data.table(geneids = RNA_names ,
                                           seqs =
                                               tolower(as.character(RNA_file)))


                data.table::setkey(RNA.dt, geneids)


            }, error = function(e) {
                stop(
                    paste0(
                        "File ",
                        file,
                        " could not be read properly. \n",
                        "Please make sure that ",
                        file,
                        " contains only RNA sequences and is in ",
                        format,
                        " format."
                    ),
                    call. = FALSE
                )
            })
                return(RNA.dt)
        }
    }