Simple Newick tree validator and formatter
Project description
Newick Tree Validator and Formatter
Simple utility to validate and format Newick trees.
The main use of this utility is to validate constraint trees used with IQtree2.
IQtree2 can throw hard to understand errors when using constraint trees even if the tree is technically a valid Newick tree.
This utility will catch many of those errors and provide a more detailed error message.
Usage
Validation without formatting:
./main.py <tree.nwk>
In place formatting:
./main.py <tree.nwk> --inplace
Outputting formatted tree to a separate file:
./main.py <tree.nwk> --outfile <output.nwk>
Outputting list of terminal nodes into a text file:
./main.py <tree.nwk> --terminals <terminals.txt>
Requirements
- Python
- Typer
- BioPython
Release
This project uses Poetry for dependency management and packaging.
To build a release, run:
poetry build
To publish a release to PyPI, run:
poetry publish
To publish the release to Github, run:
gh release create 0.4.0 dist/*
Project details
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