From 530652ab438a977c500df896d30b163c511dfc4a Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Thu, 13 Nov 2025 02:20:27 +0000
Subject: Parameterize query when checking for the QTL.

This will allow generalization to JWAS later.
---
 .guix/hsmice-test.scm         | 3 ++-
 e2e-tests/hsmice/check-qtl.py | 5 ++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.guix/hsmice-test.scm b/.guix/hsmice-test.scm
index 1982f65..3f6f7c5 100644
--- a/.guix/hsmice-test.scm
+++ b/.guix/hsmice-test.scm
@@ -186,7 +186,8 @@ genome-wide association study} library for R.")
           (for-each (cut invoke
                          "python3"
                          #$(local-file "../e2e-tests/hsmice/check-qtl.py")
-                         <>)
+                         <>
+			 "p < 1e-10")
                     (find-files #$hsmice-r-mixed-model-gwas
                                 "\\-pvalues$"))))))
 
diff --git a/e2e-tests/hsmice/check-qtl.py b/e2e-tests/hsmice/check-qtl.py
index 6e342b1..f7dd739 100644
--- a/e2e-tests/hsmice/check-qtl.py
+++ b/e2e-tests/hsmice/check-qtl.py
@@ -20,9 +20,12 @@ import sys
 
 import pandas as pd
 
+data_file = sys.argv[1]
+query_expression = sys.argv[2]
+
 if __name__ == "__main__":
     df = pd.read_csv(sys.argv[1], sep="\t")
-    qtl = df.query("p < 1e-10")
+    qtl = df.query(query_expression)
     # Assert that the QTL is on chromosome 4.
     assert (qtl.chromosome == 4).all()
     # Assert that the QTL is within 2 Mb of the expected position.
-- 
cgit 1.4.1