ncbi taxonomy

A package to perform operations on a NCBI taxonomy tree

Dependencies

• Get a NCBI Taxononmy tree dump as a taxdump.tar.gz archive
• Unpack it at a TAXDUMP_FOLDER location

Command Line version

Look for taxonomy nodes by names

node --max-old-space-size=4096 build/tests/main.js -i TAXDUMP_FOLDER --named ".*coccus.*"

Look for a single taxonomy node by TaxonID

node --max-old-space-size=4096 build/tests/main.js -i TAXDUMP_FOLDER --key 9606

Look for taxonomy nodes based on parent node TaxonID

node --max-old-space-size=4096 build/tests/main.js -i TAXDUMP_FOLDER -p 9605

Assert if one node is a descendant of another

a and b are, respectively, the putative descendant and parent.

node --max-old-space-size=4096 build/tests/main.js -i data/ncbiTaxonID -a 1301 -b 131567

NPM Package API

import the package

import { parseTree } from 'ncbitaxonomy';

Invoke a Taxonomy tree object

You need to supply a path to TAXDUMP_FOLDER

parseTree(pathDir:string): Promise<Tree>

The tree object exposes the following properties:

Get the list of ascendants of a node

Returns all list of nodes from provided taxonomic node to the taxonomy root:

lineage(node:TaxNode):TaxNode[]

Check if a node is descendant of another

isChildOf(mayChildNode:TaxNode, mayParentNode:TaxNode):Boolean

Search for nodes

Provide string with a regular expression syntax to look for node names matching it. Alternativeley provide a valid taxonID of the node itself or its direct parent

interface searchCrit {
    name? : string,
    id? : string|number,
    directParent? : string|number
}

The find method will return a possible a zero size array.

find(data:searchCrit):TaxNode[]

Iterating over all nodes

The Tree object is iterable through the nodes() method. The iteration order is the insertion order.

for (let curNode:TaxNode of treeObject) {
// all node will sequentially be accessed here
}