Nothing
#' @inherit getBio
#' @title RNA Sequence Retrieval
#' @description Main retrieval function for RNA sequences of an organism
#' of interest. By specifying the scientific name of an organism of interest the
#' corresponding fasta-file storing the RNA information for the organism
#' of interest can be downloaded and stored locally.
#' RNA files can be retrieved from several databases.
#'
#' @param path a character string specifying the location (a folder) in which
#' the corresponding
#' CDS file shall be stored. Default is
#' \code{path} = \code{file.path("_ncbi_downloads","RNA")}.
#' @examples
#' \dontrun{
#' # download the RNA of Arabidopsis thaliana from refseq
#' # and store the corresponding RNA file in '_ncbi_downloads/RNA'
#' file_path <- getRNA( db = "refseq",
#' organism = "Arabidopsis thaliana",
#' path = file.path("_ncbi_downloads","RNA"))
#'
#' Ath_RNA <- read_rna(file_path, format = "fasta")
#' }
#' @family getBio
#' @family rna
#' @export
getRNA <-
function(db = "refseq",
organism,
reference = FALSE,
skip_bacteria = TRUE,
release = NULL,
assembly_type = "toplevel",
path = file.path("_ncbi_downloads", "RNA"),
gunzip = FALSE,
mute_citation = FALSE) {
if (!is.element(db, c("refseq", "genbank", "ensembl")))
stop(
"Please select one of the available data bases:
'refseq', 'genbank', or 'ensembl'.",
call. = FALSE
)
if (db == "ensemblgenomes") {
organism_name <- is.genome.available(db = db, organism = organism, details = TRUE)$display_name[1]
if (!is.na(organism_name))
message("-> Starting RNA retrieval of '", organism_name, "' from ", db, " ...")
if (is.na(organism_name))
message("-> Starting RNA retrieval of '", organism, "' from ", db, " ...")
} else {
message("-> Starting RNA retrieval of '", organism, "' from ", db, " ...")
message("\n")
}
if (!file.exists(path)) {
dir.create(path, recursive = TRUE)
}
if (is.element(db, c("refseq", "genbank"))) {
info <- get_file_refseq_genbank(db, organism, reference, skip_bacteria,
release, gunzip, path, assembly_type,
type = "rna")
refseq_genbank_download_post_processing(info, organism, db, path,
gunzip,
remove_annotation_outliers = FALSE,
format = "rna",
mute_citation = mute_citation)
} else if (db %in% c("ensembl", "ensemblgenomes")) {
rna.path <- getENSEMBL.Seq(
organism,
type = "ncrna",
id.type = "none",
release = release,
path = path
)
ensembl_download_post_processing(rna.path, organism,
format = "ncrna",
gunzip = gunzip,
mute_citation = mute_citation)
}
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.