Merge pull request #509 from jamesmartini/develop_entropy506

Develop entropy506

src/cogent3/core/profile.py

@@ -277,10 +277,19 @@ def __init__(self, data, motifs, row_indices=None):
         axis = 0 if self.array.ndim == 1 else 1
         validate_freqs_array(self.array, axis=axis)
 
-    def entropy(self):
-        """Shannon entropy per position using log2"""
+    def entropy_terms(self):
+        """Returns
+           -------
+           entropies : array
+                Has same dimension as self.array with
+                safe log operation applied.
+        """
         entropies = safe_p_log_p(self.array)
-        return entropies.sum(axis=1)
+        return self.template.wrap(entropies)
+
+    def entropy(self):
+        """Shannon entropy per position using safe log2"""
+        return self.entropy_terms().row_sum()
 
     def information(self):
         """returns information as -max_entropy - entropy"""

tests/test_core/test_profile.py

@@ -247,6 +247,14 @@ def test_construct_fails(self):
         with self.assertRaises(ValueError):
             got = MotifFreqsArray(data, "AB")
 
+    def test_entropy_terms(self):
+        """Checks entropy_terms works correctly"""
+        data = [[0.25, 0.25, 0.25, 0.25], [0.5, 0.5, 0, 0]]
+        got = MotifFreqsArray(array(data), "ABCD")
+        entropy_terms = got.entropy_terms()
+        expect = [[0.5, 0.5, 0.5, 0.5], [0.5, 0.5, 0, 0]]
+        assert_allclose(entropy_terms.array, expect)
+
     def test_entropy(self):
         """calculates entripies correctly"""
         data = [[0.25, 0.25, 0.25, 0.25], [0.5, 0.5, 0, 0]]