Download and cache an NCBI genome assembly summary — BascetDownloadNcbiGenomeMetadata • Zorn

Downloads the NCBI assembly_summary.txt metadata file for a RefSeq/GenBank group. By default this caches RefSeq bacteria metadata under file.path(tools::R_user_dir("Zorn", "cache"), "ncbi", "refseq", "bacteria", "assembly_summary.txt"). This is platform-specific and portable across Linux, macOS, and Windows. If the cached file already exists, it is reused unless overwrite = TRUE.

Usage

BascetDownloadNcbiGenomeMetadata(
  db = "refseq",
  group = "bacteria",
  cacheDir = defaultNcbiGenomeCacheDir(),
  overwrite = FALSE,
  dest = NULL
)

Arguments

db: NCBI source database, usually "refseq" or "genbank".
group: NCBI genome group, default "bacteria".
cacheDir: Cache root directory. Defaults to the Zorn cache under the user cache directory.
overwrite: Re-download when the cached file already exists.
dest: Optional explicit output file path. When provided, this path is used instead of file.path(cacheDir, db, group, "assembly_summary.txt").

Value

Path to the cached assembly_summary.txt.