CSV to Family Phenopacket converter

This is a demo of how to use the Python phenopackets library to write a custom converter to extract Family Phenopackets from CSV files.

Running

To run the demo, you will either need to have the minimum python version and dependencies, as listed in the pyproject.toml installed on your system, use a virtual environment, or best of all use uv. uv can be installed from https://docs.astral.sh/uv/. To run using uv from the project root:

uv run csv_to_phenopackets.py families.csv output

Validation

Validating the output file requires the phenopacket-tools-cli(https://github.com/phenopackets/phenopacket-tools/releases/latest) to be installed. This will require java 17+ to be installed on your system (brew install java on MacOS, or download from https://adoptium.net/en-GB/temurin/releases or https://www.oracle.com/java/technologies/downloads/).

wget https://github.com/phenopackets/phenopacket-tools/releases/download/v1.0.0-RC3/phenopacket-tools-cli-1.0.0-RC3-distribution.zip
unzip phenopacket-tools-cli-1.0.0-RC3-distribution.zip
rm phenopacket-tools-cli-1.0.0-RC3-distribution.zip

To validate the output files, run:

java -jar phenopacket-tools-cli-1.0.0-RC3/phenopacket-tools-cli-1.0.0-RC3.jar validate output/*.json