Generate and work with GA4GH phenopackets

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for ielis from gravatar.com ielis Avatar for pnrobinson from gravatar.com pnrobinson

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • 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
Classifiers
Report project as malware

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

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page