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| author | Arun Isaac | 2025-11-13 02:20:27 +0000 |
|---|---|---|
| committer | Arun Isaac | 2025-11-13 02:20:27 +0000 |
| commit | 530652ab438a977c500df896d30b163c511dfc4a (patch) | |
| tree | 0234f74c1508409eb37db311081021b7a9beb6e2 | |
| parent | fc0e13275d5d96cc6dd0974582d888156b91734f (diff) | |
| download | pyhegp-530652ab438a977c500df896d30b163c511dfc4a.tar.gz pyhegp-530652ab438a977c500df896d30b163c511dfc4a.tar.lz pyhegp-530652ab438a977c500df896d30b163c511dfc4a.zip | |
Parameterize query when checking for the QTL.
This will allow generalization to JWAS later.
| -rw-r--r-- | .guix/hsmice-test.scm | 3 | ||||
| -rw-r--r-- | 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. |