National Pest Management

    ncbitaxonomy
    TypeScript icon, indicating that this package has built-in type declarations

    1.0.6 • Public • Published

    ncbi taxonomy

    A package to perform operations on a NCBI taxonomy tree

    Dependencies

    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
    }
     

    Keywords

    none

    Install

    npm i ncbitaxonomy

    DownloadsWeekly Downloads

    2

    Version

    1.0.6

    License

    ISC

    Unpacked Size

    49.2 kB

    Total Files

    14

    Last publish

    Collaborators

    • glaunay