Loading deepchem/metrics/tests/test_genomics.py +8 −2 Original line number Diff line number Diff line Loading @@ -21,6 +21,7 @@ class TestGenomicMetrics(unittest.TestCase): """ def test_get_motif_scores(self): """Check that motif_scores have correct shape.""" # Encode motif motif_name = "TAL1_known4" sequences = np.array(["ACGTA", "GATAG", "CGCGC"]) Loading @@ -28,13 +29,18 @@ class TestGenomicMetrics(unittest.TestCase): # sequences now has shape (3, 4, 5, 1) self.assertEqual(sequences.shape, (3, 4, 5, 1)) get_motif_scores(sequences, [motif_name]) motif_scores = get_motif_scores(sequences, [motif_name]) self.assertEqual(motif_scores.shape, (3, 1, 5)) def test_get_pssm_scores(self): """Test get_pssm_scores returns correct shape.""" motif_name = "TAL1_known4" sequences = np.array(["ACGTA", "GATAG", "CGCGC"]) sequences = dc.utils.save.seq_one_hot_encode(sequences, letters=LETTERS) # sequences now has shape (3, 4, 5, 1) self.assertEqual(sequences.shape, (3, 4, 5, 1)) pssm = np.array([[1,0,0,0],[0,1,0,0],[0,0,1,0],[0,0,0,1]]) get_pssm_scores(sequences, [motif_name]) pssm_scores = get_pssm_scores(sequences, pssm) self.assertEqual(pssm_scores.shape, (3, 5)) Loading
deepchem/metrics/tests/test_genomics.py +8 −2 Original line number Diff line number Diff line Loading @@ -21,6 +21,7 @@ class TestGenomicMetrics(unittest.TestCase): """ def test_get_motif_scores(self): """Check that motif_scores have correct shape.""" # Encode motif motif_name = "TAL1_known4" sequences = np.array(["ACGTA", "GATAG", "CGCGC"]) Loading @@ -28,13 +29,18 @@ class TestGenomicMetrics(unittest.TestCase): # sequences now has shape (3, 4, 5, 1) self.assertEqual(sequences.shape, (3, 4, 5, 1)) get_motif_scores(sequences, [motif_name]) motif_scores = get_motif_scores(sequences, [motif_name]) self.assertEqual(motif_scores.shape, (3, 1, 5)) def test_get_pssm_scores(self): """Test get_pssm_scores returns correct shape.""" motif_name = "TAL1_known4" sequences = np.array(["ACGTA", "GATAG", "CGCGC"]) sequences = dc.utils.save.seq_one_hot_encode(sequences, letters=LETTERS) # sequences now has shape (3, 4, 5, 1) self.assertEqual(sequences.shape, (3, 4, 5, 1)) pssm = np.array([[1,0,0,0],[0,1,0,0],[0,0,1,0],[0,0,0,1]]) get_pssm_scores(sequences, [motif_name]) pssm_scores = get_pssm_scores(sequences, pssm) self.assertEqual(pssm_scores.shape, (3, 5))
