Generate and work with GA4GH phenopackets

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  • License: MIT License (MIT License Copyright (c) 2023, The Monarch Initiative Permission is hereby granted, free of charg...)
  • Author: Peter Robinson
  • Tags Global Alliance for Genomics and Health , GA4GH Phenopacket Schema , Human Phenotype Ontology , GA4GH , HPO
  • Requires: Python >=3.5
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Project description

pyphetools

Python Phenopacket Tools

This package currently is designed to test how to use the Python version of the phenopackets package together with pandas to create phenopackets from typical supplemental tables.

Development goals include making builder code similar to the Java package to create valid phenopackets and to perform JSON Schema-based validation.

Setup

For initial development, we will use notebooks mainly. Do the following to get set up. Note that now we are using phenopackets version 2.0.2. openpyxl is needed to read Excel files.

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
pip install jupyter
python -m ipykernel install --name "venv" --display-name "venv"
cd notebooks
jupyter-notebook

We have installed the package in the Python Package Index (pypi) at pyphentools.

Updating package in PyPI

Make sure the build and twine packages are installed.

python3 -m pip install --upgrade build
python3 -m pip install --upgrade twine

Update the version number in the pyproject.toml file Build and install

python3 -m build
python3 -m twine upload dist/*

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