TaxTree: Python library for NCBI taxonomy database
Supported features:
- download data from NCBI automatically.
- use SQLite and SQLAlchemy to persist data.
- retrieve ancestor taxonomy in any rank.
installation
pip install taxtree
usage
initialize database
Just run:
taxtree
- All data were saved to
~/.taxtree - Downloaded
taxdmp.zippath:~/.taxtree/taxdmp.zip - 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)
1 maintainer
Metadata
1 maintainer
Release files for taxtree 1.0.4
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| taxtree-1.0.4.tar.gz | 4.1 kB | Without provenance | Details |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| taxtree-1.0.4-py2.7.egg | Legacy Egg format | - | - | Details |
| taxtree-1.0.4-py2-none-any.whl | Python 2 | none | any | Details |
Total release size: 11.5 kB
Release files / taxtree-1.0.4.tar.gz
| Download URL | taxtree-1.0.4.tar.gz |
|---|---|
| Size | 4.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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twine/3.4.1 importlib_metadata/3.7.3 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.59.0 CPython/3.7.9
|
Release files / taxtree-1.0.4-py2.7.egg
| Download URL | taxtree-1.0.4-py2.7.egg |
|---|---|
| Size | 3.6 kB |
| Tags | Egg |
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twine/3.4.1 importlib_metadata/3.7.3 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.59.0 CPython/3.7.9
|
Release files / taxtree-1.0.4-py2-none-any.whl
| Download URL | taxtree-1.0.4-py2-none-any.whl |
|---|---|
| Size | 3.7 kB |
| Tags | Python 2 |
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SHA-256 checksum How to use checksums |
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No |
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twine/3.4.1 importlib_metadata/3.7.3 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.59.0 CPython/3.7.9
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Security for taxtree 1.0.4
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