taxidTools 2.3.0

A Python Toolkit for Taxonomy

TaxidTools - A Python Toolkit for Taxonomy

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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

[e-mail]