From 6c2c31f83786472b3f9cccd5c3cb2f70ceec4a63 Mon Sep 17 00:00:00 2001 From: Alexander_Kabui Date: Fri, 7 Feb 2025 14:24:01 +0300 Subject: refactor: Add rqtl2 default method and update unittests. --- tests/unit/test_rqtl2.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'tests') diff --git a/tests/unit/test_rqtl2.py b/tests/unit/test_rqtl2.py index f7830db..ddce91b 100644 --- a/tests/unit/test_rqtl2.py +++ b/tests/unit/test_rqtl2.py @@ -73,7 +73,7 @@ def test_compose_rqtl2_cmd(): input_file = "/tmp/575732e-691e-49e5-8d82-30c564927c95/input_file.json" output_file = "/tmp/575732e-691e-49e5-8d82-30c564927c95/output_file.json" directory = "/tmp/575732e-691e-49e5-8d82-30c564927c95" - expected_results = f"Rscript /rqtl2_wrapper.R --input_file {input_file} --directory {directory} --output_file {output_file} --nperm 12 --threshold 0.05 --cores 1" + expected_results = f"Rscript /rqtl2_wrapper.R --input_file {input_file} --directory {directory} --output_file {output_file} --nperm 12 --method LMM --threshold 0.05 --cores 1" # test for using default configs assert compose_rqtl2_cmd(rqtl_path="/rqtl2_wrapper.R", @@ -82,12 +82,13 @@ def test_compose_rqtl2_cmd(): workspace_dir=directory, data={ "nperm": 12, - "threshold": 0.05 + "threshold": 0.05, + "method" : "LMM" }, config={}) == expected_results - # test for default permutation and threshold and custom configs - expected_results = f"/bin/rscript /rqtl2_wrapper.R --input_file {input_file} --directory {directory} --output_file {output_file} --nperm 0 --threshold 1 --cores 12" + # test for default permutation, method and threshold and custom configs + expected_results = f"/bin/rscript /rqtl2_wrapper.R --input_file {input_file} --directory {directory} --output_file {output_file} --nperm 0 --method HK --threshold 1 --cores 12" assert (compose_rqtl2_cmd(rqtl_path="/rqtl2_wrapper.R", input_file=input_file, output_file=output_file, -- cgit 1.4.1