taxonomy_kit

require(GCModeller); #' toolkit for process ncbi taxonomy tree data imports "taxonomy_kit" from "metagenomics_kit";

toolkit for process ncbi taxonomy tree data

The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.

.NET clr type export
taxonomy: Taxonomy	A simple organism taxonomy model.
taxonomy_node: TaxonomyNode	The tree node calculation model for NcbiTaxonomyTree, a labeled tree node for a specific ncbi taxid.

.NET clr function exports
biom.string	cast taxonomy object to biom style taxonomy string
biom_string.parse	parse the taxonomy string in BIOM style
taxonomy_name	get taxonomy name
unique_taxonomy	make taxonomy object unique
Ncbi.taxonomy_tree	load ncbi taxonomy tree model from the given data files
ranks	cast the ncbi taxonomy tree model to taxonomy ranks data
taxonomy_ranks	get all taxonomy tree nodes of the specific taxonomy ranks
taxonomy.filter
lineage	get taxonomy lineage model from the ncbi taxonomy tree by given taxonomy id
as.taxonomy.tree	build taxonomy tree based on a given collection of taxonomy object.
consensus
read.mothurTree	Parse the result output from mothur command `summary.tax`.
taxonomy_range
LCA
accession2Taxid	Create a stream read to the ncbi accession id mapping to ncbi taxonomy id

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