Ncbi.taxonomy_tree {taxonomy_kit} R Documentation

load ncbi taxonomy tree model from the given data files

Description

Usage

Ncbi.taxonomy_tree(repo);

Arguments

repo

a directory folder path which contains the NCBI taxonomy tree data files: nodes.dmp and names.dmp. [as string]

Details

Builds the following dictionnary from NCBI taxonomy nodes.dmp and names.dmp files 

 { Taxid namedtuple('Node', ['name', 'rank', 'parent', 'children']
     }
+ https://www.biostars.org/p/13452/ + https://pythonhosted.org/ete2/tutorial/tutorial_ncbitaxonomy.html

Authors

metagenomics_kit

Value

this function returns data object of type NcbiTaxonomyTree.

clr value class

Examples

 const tree = Ncbi.taxonomy_tree("/dir/path/to/ncbi_taxdump_archive/");
[Package taxonomy_kit version 1.0.0.0 Index]