diff options
| author | zsloan | 2021-05-18 19:43:50 +0000 |
|---|---|---|
| committer | zsloan | 2021-05-18 19:43:50 +0000 |
| commit | 5745c3bdd086f7c499ee63a580df822db5af2826 (patch) | |
| tree | f64fbc6500976d1b94e28c61a7daddcf6bf04070 /tests/unit/computations/test_rqtl.py | |
| parent | 33d3a518e378c56b080a2a15b264ee5d031537e8 (diff) | |
| download | genenetwork3-5745c3bdd086f7c499ee63a580df822db5af2826.tar.gz | |
Added unit test for computations/rqtl.py
Diffstat (limited to 'tests/unit/computations/test_rqtl.py')
| -rw-r--r-- | tests/unit/computations/test_rqtl.py | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/tests/unit/computations/test_rqtl.py b/tests/unit/computations/test_rqtl.py new file mode 100644 index 0000000..b16f136 --- /dev/null +++ b/tests/unit/computations/test_rqtl.py @@ -0,0 +1,41 @@ +"""Test cases for procedures defined in computations.rqtl"""
+import unittest
+
+from unittest import mock
+from gn3.computations.rqtl import generate_rqtl_cmd
+
+class TestRqtl(unittest.TestCase):
+ """Test cases for computations.rqtl module"""
+ @mock.patch("gn3.computations.rqtl.generate_hash_of_string")
+ @mock.patch("gn3.computations.rqtl.get_hash_of_files")
+ def test_generate_rqtl_command(self, mock_get_hash_files, mock_generate_hash_string):
+ """Test computing mapping results with R/qtl"""
+ mock_get_hash_files.return_value = "my-hash1"
+ mock_generate_hash_string.return_value = "my-hash2"
+
+ self.assertEqual(
+ generate_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper",
+ rqtl_wrapper_kwargs={
+ "g": "genofile",
+ "p": "phenofile",
+ "model": "normal",
+ "method": "hk",
+ "nperm": 1000,
+ "scale": "Mb",
+ "control": "rs123456"
+ },
+ rqtl_wrapper_bool_kwargs=[
+ "addcovar",
+ "interval"
+ ]), {
+ "output_file":
+ "my-hash1my-hash2my-hash2-output.json",
+ "rqtl_cmd": (
+ "rqtl-wrapper "
+ "--g genofile --p phenofile "
+ "--model normal --method hk "
+ "--nperm 1000 --scale Mb "
+ "--control rs123456 "
+ "--addcovar --interval"
+ )
+ })
|