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#' @inherit getBio
#' @title Genome Retrieval
#' @description Main genome retrieval function for an organism of interest.
#' By specifying the scientific name of an organism of interest the
#' corresponding fasta-file storing the genome of the organism of interest
#' can be downloaded and stored locally. Genome files can be retrieved from
#' several databases. In addition, the genome summary statistics for the
#' retrieved species is stored locally to provide users with
#' insights regarding the genome assembly quality (see \code{\link{summary_genome}} for details).
#' This is useful when comparing genomes with large difference in genome assembly qualities.
#' @family getBio
#' @family genome
#' @export
getGenome <- function(db = "refseq",
organism,
reference = FALSE,
skip_bacteria = TRUE,
release = NULL,
gunzip = FALSE,
path = file.path("_ncbi_downloads", "genomes"),
assembly_type = "toplevel",
mute_citation = FALSE,
analyse_genome = 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 (!all(assembly_type %in% c("toplevel", "primary_assembly")))
stop("Please specify valid assembly types: \ntoplevel, primary_assembly")
if (!is.logical(reference))
stop("Please specify 'reference' as either TRUE or FALSE.", call. = FALSE)
message("-> Starting genome retrieval of '", organism, "' from ", db, " ...")
message("\n")
# create result folder
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 = "genome")
refseq_genbank_download_post_processing(info, organism, db, path,
gunzip,
remove_annotation_outliers = FALSE,
format = "genome",
analyse_genome = analyse_genome,
mute_citation = mute_citation)
} else if (db %in% c("ensembl", "ensemblgenomes")) {
genome.path <- getENSEMBL.Seq(organism, type = "dna",
id.type = assembly_type,
release = release,
path = path)
ensembl_download_post_processing(genome.path, organism,
format = "genome",
gunzip = gunzip,
mute_citation = mute_citation)
}
}
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