taxtree 1.0.4

Python library for NCBI taxonomy database.

TaxTree: Python library for NCBI taxonomy database

Supported features:

1. download data from NCBI automatically.
2. use SQLite and SQLAlchemy to persist data.
3. retrieve ancestor taxonomy in any rank.

installation

pip install taxtree

usage

initialize database

Just run:

taxtree

1. All data were saved to ~/.taxtree
2. Downloaded taxdmp.zip path: ~/.taxtree/taxdmp.zip
3. Persistent data file path: ~/.taxtree/taxtree.db

search taxonomy

from taxtree import get_scoped_session, Tax

with get_scoped_session() as session:
    tax = session.query(Tax).filter_by(tax_id='9606').first()

get ancestor

from taxtree import get_scoped_session, Tax, KINGDOM, PHYLUM

with get_scoped_session() as session:
    tax = session.query(Tax).filter_by(tax_id='9606').first()
    kingdom_tax = tax.get_ancestor(KINGDOM)
    phylum_tax = tax.get_ancestor(PHYLUM)