diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/computations/test_gemma.py | 20 |
1 files changed, 20 insertions, 0 deletions
diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py index 23707ef..a7884ea 100644 --- a/tests/unit/computations/test_gemma.py +++ b/tests/unit/computations/test_gemma.py @@ -4,6 +4,7 @@ import unittest from unittest import mock from gn3.computations.gemma import generate_hash_of_string from gn3.computations.gemma import generate_pheno_txt_file +from gn3.computations.gemma import generate_gemma_computation_cmd class TestGemma(unittest.TestCase): @@ -29,3 +30,22 @@ class TestGemma(unittest.TestCase): """Test that a string is hashed correctly""" self.assertEqual(generate_hash_of_string("I^iQP&TlSR^z"), "hMVRw8kbEp49rOmoIkhMjA") + + @mock.patch("gn3.computations.gemma.do_paths_exist") + def test_compose_k_computation_cmd(self, mock_pathsp): + """Test that a K computation cmd is constructed properly""" + mock_pathsp.return_value = True + self.assertEqual( + generate_gemma_computation_cmd( + gemma_cmd="gemma-wrapper", + gemma_kwargs={ + "geno_filename": "genofile.txt", + "trait_filename": "test.txt", + "covar_filename": "genofile_snps.txt"}, + output_file="/tmp/gn2/k_output_gUFhGu4rLG7k+CXLPk1OUg.txt", + ), + ("gemma-wrapper --json -- " + "-g genofile.txt -p " + "test.txt -a genofile_snps.txt " + "-gk > /tmp/gn2/" + "k_output_gUFhGu4rLG7k+CXLPk1OUg.txt")) |