TaxidTools - A Python Toolkit for Taxonomy
taxidTools is a Python library to handle Taxonomy definitions.
Highlights
- Load taxonomy defintions for the NCBI's taxdump files
- Prune, filter, and normalize branches
- Save as JSON for later use
- Determine consensus, last common ancestor, or distances
- Retrieve ancestries or list descendants
- Export as Newick trees
Installation
With pip:
pip install taxidtools
With conda:
conda install -c conda-forge taxidtools
With docker:
docker pull gregdenay/taxidtools
Quickstart
With the NCBI's taxdump files installed locally:
>>> import taxidTools
>>> tax = taxidTools.read_taxdump('nodes.dmp', 'rankedlineage.dmp', 'merged.dmp')
>>> tax.getName('9606')
'Homo sapiens'
>>> lineage = tax.getAncestry('9606')
>>> lineage.filter()
>>> [node.name for node in lineage]
['Homo sapiens', 'Homo', 'Hominidae', 'Primates', 'Mammalia', 'Chordata', 'Metazoa']
>>> tax.lca(['9606', '10090']).name
'Euarchontoglires'
>>> tax.distance('9606', '10090')
18
Documentation
Full documentation is hosted on the homepage
Cite us
If you use taxidTools for your reasearch, you can cite it using the DOI at the top of this page.
1 maintainer
Metadata
1 maintainer
Release files for taxidTools 3.2.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| taxidtools-3.2.1.tar.gz | 18.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| taxidtools-3.2.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 35.6 kB
Release files / taxidtools-3.2.1.tar.gz
| Download URL | taxidtools-3.2.1.tar.gz |
|---|---|
| Size | 18.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
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twine/6.1.0 CPython/3.13.7
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Release files / taxidtools-3.2.1-py3-none-any.whl
| Download URL | taxidtools-3.2.1-py3-none-any.whl |
|---|---|
| Size | 16.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.13.7
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