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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](https://academic.oup.com/genetics/article/215/2/359/5930450).

# 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

![Workflow](doc/workflow.png)

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](https://www.gnu.org/licenses/gpl.html), either version 3 of the License, or (at your option) any later version.