Taxoniq: Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data

Taxoniq is a Python and command-line interface to the NCBI Taxonomy database and selected data sources that cross-reference it.

Taxoniq's features include:

• Pre-computed indexes updated monthly from NCBI, WoL and cross-referenced databases
• Completely offline operation: all indexes are bundled with the package; no network calls are made when querying
• A CLI capable of JSON I/O, batch processing and streaming of inputs for ease of use and pipelining in shell scripts
• A stable, well-documented, type-hinted Python API (Python 3.6 and higher is supported)
• Comprehensive testing and continuous integration
• An intuitive interface with useful defaults
• Compactness, readability, and extensibility

The Taxoniq package bundles an indexed, compressed copy of the NCBI taxonomy database files, the related accession2taxid database, the WoL database, and relevant information from other databases. Accessions which appear in NCBI BLAST nt/nr databases (and by inclusion, RefSeq) are indexed so that given a taxon ID, accession ID, or taxon name, you can quickly retrieve the taxon's rank, lineage, description, citations, representative RefSeq IDs, LCA information, evolutionary distance, and more, as described in the Cookbook section below.

Installation

pip3 install taxoniq

Synopsis

t = taxoniq.Taxon(9606)
assert t.scientific_name == "Homo sapiens"
assert t.common_name == "human"
assert t.ranked_lineage == [taxoniq.Taxon(scientific_name='Homo sapiens'),
                            taxoniq.Taxon(scientific_name='Homo'),
                            taxoniq.Taxon(scientific_name='Hominidae'),
                            taxoniq.Taxon(scientific_name='Primates'),
                            taxoniq.Taxon(scientific_name='Mammalia'),
                            taxoniq.Taxon(scientific_name='Chordata'),
                            taxoniq.Taxon(scientific_name='Metazoa'),
                            taxoniq.Taxon(scientific_name='Eukaryota')]