load_taxonomies: Load and merge GBIF and NCBI taxonomic data

In MoultDB/moultdbtools: Create Custom Taxonomies Based on the NCBI Taxonomy and GBIF Backbone Taxonomy

Load and merge GBIF and NCBI taxonomic data

Description

Load and merge GBIF and NCBI taxonomic data

Usage

load_taxonomies(GBIF_path, NCBI_path)

Arguments

GBIF_path	Path to the GBIF backbone taxonomy (compressed or uncompressed).
NCBI_path	Path to the NCBI taxonomy (compressed or uncompressed).

Details

This method merges a GBIF Taxon.tsv file (see download_gbif()) and a Taxonkit (https://bioinf.shenwei.me/taxonkit/download/) output file (see download_ncbi()).

Value

A tibble containing merged GBIF and NCBI taxonomic data.

Examples

## Not run: load_taxonomies("path/to/GBIF/Taxon.tsv","path/to/NCBI-Taxonkit/All.lineages.tsv.gz")
## Not run: load_taxonomies(download_gbif(), download_ncbi(taxonkitpath = "/path/to/taxonkit"))

MoultDB/moultdbtools documentation built on Feb. 2, 2024, 5:21 p.m.