taxonbridge (version 1.0.5)

download_ncbi: Download the NCBI taxonomy

Description

Download the NCBI taxonomy

Usage

download_ncbi(taxonkitpath = NA)

Arguments

taxonkitpath

A string containing the full path to where Taxonkit is installed (optional).

Value

A character vector containing paths to the relevant downloaded and unzipped NCBI data dump files, or if the taxonkitpath parameter was set, the path to All.lineages.tsv.

Details

This method downloads a NCBI taxonomy archive file to a temporary directory, extracts four files (nodes.dmp, names.dmp, merged.dmp and deleted.dmp) from the downloaded archive file, and then removes the archive file. If the path to a Taxonkit installation is supplied, Taxonkit is called and the location of the four files is passed to Taxonkit as an argument. Output is saved in the same temporary folder in a file called All.lineages.tsv.

Examples

# NOT RUN {
download_ncbi()
# }
# NOT RUN {
download_ncbi(taxonkitpath = "/home/usr/bin/taxonkit")
# }