R/getMetaGenomeSummary.R

In biomartr: Genomic Data Retrieval

#' @title Retrieve the assembly_summary.txt file from NCBI genbank metagenomes
#' @description Retrieval function of the assembly_summary.txt file
#' from NCBI genbank metagenomes.
#' This files stores all available metagenome projects on NCBI Genbank.
#' @param local_file where to store this backend file, default:
#' file.path(cachedir(), "assembly_summary_metagenomes_genbank.txt")
#' @author Hajk-Georg Drost
#' @examples
#' \dontrun{
#' meta.summary <- getMetaGenomeSummary()
#' meta.summary
#' }
#' @seealso \code{\link{getKingdomAssemblySummary}},
#' \code{\link{getSummaryFile}}
#' @export

getMetaGenomeSummary <- function(local_file = file.path(cachedir(), "assembly_summary_metagenomes_genbank.txt")) {
    url <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/metagenomes/assembly_summary.txt"
    custom_download_check_local(url, local_file, NULL, db = "genbank")
    suppressWarnings(summary.file <-
                         tibble::as_tibble(
                             readr::read_delim(
                                 local_file,
                                 comment = "#",
                                 delim = "\t",
                                 quote = "\"",
                                 escape_backslash = FALSE,
                                 col_names = c(
                                     "assembly_accession",
                                     "bioproject",
                                     "biosample",
                                     "wgs_master",
                                     "refseq_category",
                                     "taxid",
                                     "species_taxid",
                                     "organism_name",
                                     "infraspecific_name",
                                     "isolate",
                                     "version_status",
                                     "assembly_level",
                                     "release_type",
                                     "genome_rep",
                                     "seq_rel_date",
                                     "asm_name",
                                     "submitter",
                                     "gbrs_paired_asm",
                                     "paired_asm_comp",
                                     "ftp_path",
                                     "excluded_from_refseq"
                                 ),
                                 col_types = readr::cols(
                                    assembly_accession = readr::col_character(),
                                     bioproject = readr::col_character(),
                                     biosample = readr::col_character(),
                                     wgs_master = readr::col_character(),
                                     refseq_category = readr::col_character(),
                                     taxid = readr::col_integer(),
                                     species_taxid = readr::col_integer(),
                                     organism_name = readr::col_character(),
                                    infraspecific_name = readr::col_character(),
                                     isolate = readr::col_character(),
                                     version_status = readr::col_character(),
                                     assembly_level = readr::col_character(),
                                     release_type = readr::col_character(),
                                     genome_rep = readr::col_character(),
                                     seq_rel_date = readr::col_date(),
                                     asm_name = readr::col_character(),
                                     submitter = readr::col_character(),
                                     gbrs_paired_asm = readr::col_character(),
                                     paired_asm_comp = readr::col_character(),
                                     ftp_path = readr::col_character(),
                                excluded_from_refseq = readr::col_character()
                                 )
                             )
                         ))

    return(summary.file)
}