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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
Python >= 3.9 Optionally some taxonomy definiton files usch as the Taxdump definition files from the NCBI server.
Install from pip or conda :
python3 -m pip install taxidTools
conda install -c conda-forge taxidtoolsClone or copy the github repository to your project for the developement version.
Check our homepage !
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!
This project is licensed under a BSD 3-Clauses License, see the LICENSE file for details.
For questions, problems, suggestions or requests, feel free to contact:
Grégoire Denay, Chemisches- und Veterinär-Untersuchungsamt Rhein-Ruhr-Wupper