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-rw-r--r--tests/unit/computations/test_rqtl.py82
1 files changed, 41 insertions, 41 deletions
diff --git a/tests/unit/computations/test_rqtl.py b/tests/unit/computations/test_rqtl.py
index b16f136..3bf8f81 100644
--- a/tests/unit/computations/test_rqtl.py
+++ b/tests/unit/computations/test_rqtl.py
@@ -1,41 +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"
- )
- })
+"""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": (
+ "Rscript rqtl-wrapper "
+ "--g genofile --p phenofile "
+ "--model normal --method hk "
+ "--nperm 1000 --scale Mb "
+ "--control rs123456 "
+ "--addcovar --interval"
+ )
+ })