A Python Toolkit for Taxonomy
Project description
TaxidTools - A Python Toolkit for Taxonomy
Overview
Provides a set of classes and tools to work with taxonomy data. Although built to work with the NCBI Taxdump files it can also work with other taxonomy definitions. Currently impelemented:
- Easily load the NCBI taxdump files
- Retrieve name, rank, parent or full ancestry from a unique taxonomic identifier
- Test if a node is parent or descendant of an other
- Find last common ancestor or consensus node from a list of ids
- Calculate the distance between two nodes
- List all children of a given node
- Re-root Taxonomy
- Format to given ranks
Requirements
Python >= 3.9 Optionally some taxonomy definiton files usch as the Taxdump definition files from the NCBI server.
Installation
Install from pip or conda :
python3 -m pip install taxidTools
conda install -c conda-forge taxidtools
Clone or copy the github repository to your project for the developement version.
Usage
Check our homepage !
Contributing
I add new functionnalities as I need them, if you think of a cool new thing you would like to see implemented, post an issue or a pull request!
License
This project is licensed under a BSD 3-Clauses License, see the LICENSE file for details.
Author
For questions, problems, suggestions or requests, feel free to contact:
Grégoire Denay, Chemisches- und Veterinär-Untersuchungsamt Rhein-Ruhr-Wupper
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for taxidTools-2.3.0-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | fff324478cfbd5dad92483b482e3f164a6f9894c285266625690c320ef99f442 |
|
MD5 | a0e335b9019f5a58979a7b5489d03475 |
|
BLAKE2b-256 | f4df6bd15da2ee15a4330a9475930dc2bb2c10b0188e79d8ac4723109a0163df |