Loading deepchem/metrics/genomic_metrics.py +6 −6 Original line number Diff line number Diff line Loading @@ -100,14 +100,13 @@ def in_silico_mutagenesis(model, X): Parameters ---------- model: TensorGraph SequenceDNN? X: array... What shape? Currently only SequenceDNN will work, but other models may be added. X: ndarray Shape (N_sequences, 1, N_letters, sequence_length) Returns ------- #(num_task, N_sequences, 1, N_letters, sequence_length) ISM score array. (num_task, N_sequences, N_letters, sequence_length) ISM score array. (num_task, N_sequences, 1, N_letters, sequence_length) ISM score array. """ mutagenesis_scores = np.empty(X.shape + (model.num_tasks,), dtype=np.float32) wild_type_predictions = model.predict(NumpyDataset(X)) Loading @@ -133,4 +132,5 @@ def in_silico_mutagenesis(model, X): (model.num_tasks,)) mutagenesis_scores[ sequence_index] = wild_type_prediction - mutated_predictions return np.rollaxis(mutagenesis_scores, -1) rolled_scores = np.rollaxis(mutagenesis_scores, -1) return rolled_scores deepchem/metrics/tests/test_genomics.py +1 −5 Original line number Diff line number Diff line Loading @@ -58,8 +58,4 @@ class TestGenomicMetrics(unittest.TestCase): # Call in-silico mutagenesis mutagenesis_scores = in_silico_mutagenesis(model, X) print("mutagenesis_scores.shape") print(mutagenesis_scores.shape) self.assertEqual(mutagenesis_scores.shape, (1, 10, 1, 4, 50)) Loading
deepchem/metrics/genomic_metrics.py +6 −6 Original line number Diff line number Diff line Loading @@ -100,14 +100,13 @@ def in_silico_mutagenesis(model, X): Parameters ---------- model: TensorGraph SequenceDNN? X: array... What shape? Currently only SequenceDNN will work, but other models may be added. X: ndarray Shape (N_sequences, 1, N_letters, sequence_length) Returns ------- #(num_task, N_sequences, 1, N_letters, sequence_length) ISM score array. (num_task, N_sequences, N_letters, sequence_length) ISM score array. (num_task, N_sequences, 1, N_letters, sequence_length) ISM score array. """ mutagenesis_scores = np.empty(X.shape + (model.num_tasks,), dtype=np.float32) wild_type_predictions = model.predict(NumpyDataset(X)) Loading @@ -133,4 +132,5 @@ def in_silico_mutagenesis(model, X): (model.num_tasks,)) mutagenesis_scores[ sequence_index] = wild_type_prediction - mutated_predictions return np.rollaxis(mutagenesis_scores, -1) rolled_scores = np.rollaxis(mutagenesis_scores, -1) return rolled_scores
deepchem/metrics/tests/test_genomics.py +1 −5 Original line number Diff line number Diff line Loading @@ -58,8 +58,4 @@ class TestGenomicMetrics(unittest.TestCase): # Call in-silico mutagenesis mutagenesis_scores = in_silico_mutagenesis(model, X) print("mutagenesis_scores.shape") print(mutagenesis_scores.shape) self.assertEqual(mutagenesis_scores.shape, (1, 10, 1, 4, 50))
