R/getGENOMEREPORT.R

In HajkD/biomartr: Genomic Data Retrieval

#' @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)
}