Merge pull request #507 from GavinHuttley/develop

BUG: MotifCounts.to_freq_array() now handles a 1D array

src/cogent3/core/profile.py

@@ -215,8 +215,12 @@ def _to_freqs(self, pseudocount=0):
         data = self.array
         if pseudocount:
             data = data + pseudocount
-        row_sum = data.sum(axis=1)
-        freqs = data / numpy.vstack(row_sum)
+        axis = None if self.array.ndim == 1 else 1
+        row_sum = data.sum(axis=axis)
+        if axis is not None:
+            freqs = data / numpy.vstack(row_sum)
+        else:
+            freqs = data / row_sum
         return freqs
 
     def to_freq_array(self, pseudocount=0):
@@ -231,9 +235,9 @@ def to_freq_array(self, pseudocount=0):
         a MotifFreqsArray
         """
         freqs = self._to_freqs(pseudocount=pseudocount)
-        return MotifFreqsArray(
-            freqs, self.template.names[1], row_indices=self.template.names[0]
-        )
+        motifs = self.template.names[-1]
+        row_indices = None if self.array.ndim == 1 else self.template.names[0]
+        return MotifFreqsArray(freqs, motifs, row_indices=row_indices)
 
     def to_pssm(self, background=None, pseudocount=0):
         """returns a PSSM array

tests/test_core/test_profile.py

@@ -124,6 +124,14 @@ def test_to_freqs_pseudocount(self):
         expect = adj / vstack(adj.sum(axis=1))
         assert_allclose(got.array, expect)
 
+    def test_to_freqs_1d(self):
+        """produce a freqs array from 1D counts"""
+        data = [43, 48, 114, 95]
+        total = sum(data)
+        a = MotifCountsArray([43, 48, 114, 95], motifs=("T", "C", "A", "G"))
+        f = a.to_freq_array()
+        assert_allclose(f.array, array([v / total for v in data], dtype=float))
+
     def test_to_pssm(self):
         """produces a PSSM array"""
         data = array(