From b89ecd37fe19fdb31beebabd2796b74f5dc97743 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sat, 6 Sep 2025 18:16:28 +0100 Subject: Add end-to-end tests for hsmice dataset. * Add hsmice dataset wrangling and test scripts. * Add G-expression script to run test. * Depend on the guix-bioinformatics Guix channel for r-genio. --- e2e-tests/hsmice/check-qtl.py | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 e2e-tests/hsmice/check-qtl.py (limited to 'e2e-tests/hsmice/check-qtl.py') diff --git a/e2e-tests/hsmice/check-qtl.py b/e2e-tests/hsmice/check-qtl.py new file mode 100644 index 0000000..feae361 --- /dev/null +++ b/e2e-tests/hsmice/check-qtl.py @@ -0,0 +1,27 @@ +### pyhegp --- Homomorphic encryption of genotypes and phenotypes +### Copyright © 2025 Arun Isaac +### +### This file is part of pyhegp. +### +### pyhegp is free software: you can redistribute it and/or modify it +### under the terms of the GNU General Public License as published by +### the Free Software Foundation, either version 3 of the License, or +### (at your option) any later version. +### +### pyhegp is distributed in the hope that it will be useful, but +### WITHOUT ANY WARRANTY; without even the implied warranty of +### MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +### General Public License for more details. +### +### You should have received a copy of the GNU General Public License +### along with pyhegp. If not, see . + +import sys + +import pandas as pd + +if __name__ == "__main__": + df = pd.read_csv(sys.argv[1], sep="\t") + qtl = df.query("p < 1e-10") + assert (qtl.chromosome == 4).all() + assert ((qtl.position - 137715608).abs() < 2*10**6).all() -- cgit 1.4.1