retrieve_NCBI_taxonomy: Retrieve NCBI taxonomy file from public database

In franciscolobo/TaxonSampling: Hierarchical Taxonomic Sampling for Maximized Diversity at All Levels

Description

This script downloads the full NCBI taxonomy from <ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz> and extracts it to the folder in 'target.dir'.

Usage

retrieve_NCBI_taxonomy(
  target.dir,
  method = "auto",
  unzip = getOption("unzip"),
  url = "https://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.zip",
  timeout = 600,
  ...
)

Arguments

target.dir	path to the folder where the files will be saved ( accepts relative and absolute paths)
method	Method to be used for downloading files. Current download methods are "internal", "wininet" (Windows only) "libcurl", "wget" and "curl", and there is a value "auto": see _Details_ and _Note_ in the documentation of utils::download.file().
unzip	The unzip method to be used. See the documentation of utils::unzip() for details.
url	URL of the full NCBI taxonomy file.
timeout	maximum time allowed for the download
...	additional attributes (currently ignored)

Value

No return value, called for side effects (see Description).

Examples

## Not run: 
  TaxonSampling::retrieve_NCBI_taxonomy(target.dir = "data_files/taxdump")

## End(Not run)

franciscolobo/TaxonSampling documentation built on Dec. 31, 2021, 12:04 a.m.