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#' @title Retrieve NCBI GENOME_REPORTS file
#' @description Retrieves NCBI GENOME_REPORTS file from
#' ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/overview.txt.
#' @param local_file character, file path, default: file.path(cachedir(), "_ncbi_downloads", "overview.txt")
#' @return a tibble object with the report
#' @author Hajk-Georg Drost
#' @examples
#' \dontrun{
#' report <- getGENOMEREPORT()
#' report
#' }
#' @export
getGENOMEREPORT <- function(local_file = file.path(cachedir(), "_ncbi_downloads", "overview.txt")) {
if (!dir.exists(dirname(local_file))) {
dir.create(dirname(local_file), recursive = TRUE, showWarnings = FALSE)
}
custom_download_check_local("ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/overview.txt",
local_file, rest_api_status = NULL, db = "refgen",
notify_exist = FALSE)
suppressWarnings(
ncbi_overview <-
readr::read_tsv(
local_file,
comment = "#",
col_names = c(
"organism_name",
"kingdoms",
"group",
"subgroup",
"file_size_MB",
"chrs",
"organelles",
"plasmids",
"bio_projects"
),
col_types = readr::cols(
organism_name = readr::col_character(),
kingdoms = readr::col_character(),
group = readr::col_character(),
subgroup = readr::col_character(),
file_size_MB = readr::col_double(),
chrs = readr::col_integer(),
organelles = readr::col_integer(),
plasmids = readr::col_integer(),
bio_projects = readr::col_integer()
)
)
)
return(ncbi_overview)
}
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