retrieve_NCBI_taxonomy: Retrieve NCBI taxonomy file from public database

Description Usage Arguments Value Examples

View source: R/retrieve_NCBI_taxonomy.R

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

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retrieve_NCBI_taxonomy(
  target.dir,
  keep.all = TRUE,
  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)

keep.all

logical: should all files be kept (default) or only the ones used by _TaxonSampling_ ('nodes.dmp' and 'names.dmp')?

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, in seconds. Increase when under a slow connection.

...

additional attributes (currently ignored)

Value

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

Examples

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

## End(Not run)

fcampelo/TaxonSampling documentation built on Jan. 14, 2022, 9:42 p.m.