pyhegp is a Python library and CLI utility implementing homomorphic encryption of genotypes and phenotypes as described in Private Genomes and Public SNPs: Homomorphic Encryption of Genotypes and Phenotypes for Shared Quantitative Genetics.

Install development version

In a new directory, create a python virtual environment and activate it.

mkdir pyhegp
cd pyhegp
python3 -m venv .venv
source .venv/bin/activate

Install the development version of pyhegp into the virtual environment.

pip install git+https://github.com/encryption4genetics/pyhegp

How to use

Data owners generate summary statistics for their data.

pyhegp summary genotype.csv -o summary.txt

They share this with the data broker who pools it to compute the summary statistics of the complete dataset.

pyhegp pool -o complete-summary.txt summary1.txt summary2.txt ...

The data broker shares these summary statistics with the data owners. The data owners standardize their data using these summary statistics, and encrypt their data using a random key.

pyhegp encrypt -s complete-summary.txt -o encrypted-genotype.csv genotype.csv

Finally, the data owners share the encrypted data with the broker who concatenates it and shares it with all parties.

pyhegp cat -o complete-encrypted-genotype.csv encrypted-genotype1.csv encrypted-genotype2.csv ...

Note that all data sharing is carried out-of-band and is outside the scope of pyhegp.

Run tests

Run the test suite using

python3 -m pytest

License

pyhegp is free software released under the terms of the GNU General Public License, either version 3 of the License, or (at your option) any later version.