Merge pull request #20 from genenetwork/feature/biweight-correlation

add biweight r script and tests

2 files changed, 25 insertions, 2 deletions

diff --git a/tests/unit/computations/test_biweight.py b/tests/unit/computations/test_biweight.py
new file mode 100644
index 0000000..ad404f1
--- /dev/null
+++ b/tests/unit/computations/test_biweight.py
@@ -0,0 +1,21 @@
+"""test for biweight script"""
+from unittest import TestCase
+from unittest import mock
+
+from gn3.computations.biweight import calculate_biweight_corr
+
+
+class TestBiweight(TestCase):
+    """test class for biweight"""
+
+    @mock.patch("gn3.computations.biweight.subprocess.check_output")
+    def test_calculate_biweight_corr(self, mock_check_output):
+        """test for calculate_biweight_corr func"""
+        mock_check_output.return_value = "0.1 0.5"
+        results = calculate_biweight_corr(command="Rscript",
+                                          path_to_script="./r_script.R",
+                                          trait_vals=[
+                                              1.2, 1.1, 1.9],
+                                          target_vals=[1.9, 0.4, 1.1])
+
+        self.assertEqual(results, (0.1, 0.5))
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index 5746adf..b1bc6ef 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -98,12 +98,14 @@ class TestCorrelation(TestCase):
 
         self.assertEqual(results, expected_results)
 
-    def test_bicor(self):
+    @mock.patch("gn3.computations.correlations.calculate_biweight_corr")
+    def test_bicor(self, mock_biweight):
         """Test for doing biweight mid correlation """
+        mock_biweight.return_value = (1.0, 0.0)
 
         results = do_bicor(x_val=[1, 2, 3], y_val=[4, 5, 6])
 
-        self.assertEqual(results, (0.0, 0.0)
+        self.assertEqual(results, (1.0, 0.0)
                          )
 
     @mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value")