semvec/pypi-packages huggingface dataset:
taxoniq-accession-db 0.0.1
taxoniq-accession-db: NCBI nucleotide accession index for taxoniq
License: MIT License

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](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7408187/) and selected data sources that
cross-reference it.

Taxoniq's features include:

- Pre-computed indexes updated monthly from NCBI, [WoL](https://biocore.github.io/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](https://ncbiinsights.ncbi.nlm.nih.gov/2018/02/22/new-taxonomy-files-available-with-lineage-type-and-host-information/),
the related accession2taxid database, the [WoL](https://biocore.github.io/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')]
```