| download_ncbi {taxonbridge} | R Documentation |
Download the NCBI taxonomy
Description
Download the NCBI taxonomy
Usage
download_ncbi(taxonkitpath = NA)
Arguments
taxonkitpath |
A string containing the full path to where |
Details
This method downloads a NCBI taxonomy archive file to a temporary directory,
extracts four files (nodes.dmp, names.dmp, merged.dmp and delnodes.dmp)
from the downloaded archive file, and then removes the archive file. Further parsing of
these four files must be carried out with Taxonkit (https://bioinf.shenwei.me/taxonkit/download/),
either automatically or manually. 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 for automatic parsing.
Taxonkit output is saved in the same temporary folder in a file called All.lineages.tsv.gz.
If the path to Taxonkit is not supplied, parsing should be carried out manually using the command:
taxonkit list --data-dir=path/to/downloaded/files --ids 1 | taxonkit lineage --show-lineage-taxids --show-lineage-ranks --show-rank --show-name --data-dir=path/to/downloaded/files | taxonkit reformat --taxid-field 1 --data-dir=path/to/downloaded/files -o All.lineages.tsv.gz
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.gz.
Examples
## Not run: download_ncbi()
## Not run: download_ncbi(taxonkitpath = "/home/usr/bin/taxonkit")