read_nodes_dmp: Read and write the nodes.dmp

In larssnip/microclass: Tools for taxonomic classification of prokaryotes

Read and write the nodes.dmp

Description

Reads and writes the file nodes.dmp of the NCBI Taxonomy

Usage

read_nodes_dmp(filename)
write_nodes_dmp(names.dmp, filename)

Arguments

filename	name of file to be read or written to.
nodes.dmp	a nodes.dmp table (see details below).

Details

The file pair names.dmp and nodes.dmp describe a taxonomy tree. The read_nodes_dmp reads a file formatted as the nodes.dmp file from the NCBI Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy/). This is represented as a tibble in R.

The write_nodes_dmp will write a table with the proper columns (see below) to a file, adding the separators of the NCBI format.

The nodes.dmp table downloaded from NCBI will contain many columns, but only the first 3 of them are relevant for parsing the taxonomy tree. Only these first three columns are read and used by these functions, additional columns are ignored.

Value

The read_nodes_dmp returns a tibble with the columns: tax_id (integers), parent_tax_id (integers) and rank (text).

Author(s)

Lars Snipen.

See Also

read_nodes_dmp.

larssnip/microclass documentation built on Nov. 1, 2023, 2:39 p.m.