diff docker/alphafold/run_alphafold_test.py @ 1:6c92e000d684 draft

"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docker/alphafold/run_alphafold_test.py	Tue Mar 01 02:53:05 2022 +0000
@@ -0,0 +1,101 @@
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Tests for run_alphafold."""
+
+import os
+
+from absl.testing import absltest
+from absl.testing import parameterized
+import run_alphafold
+import mock
+import numpy as np
+# Internal import (7716).
+
+
+class RunAlphafoldTest(parameterized.TestCase):
+
+  @parameterized.named_parameters(
+      ('relax', True),
+      ('no_relax', False),
+  )
+  def test_end_to_end(self, do_relax):
+
+    data_pipeline_mock = mock.Mock()
+    model_runner_mock = mock.Mock()
+    amber_relaxer_mock = mock.Mock()
+
+    data_pipeline_mock.process.return_value = {}
+    model_runner_mock.process_features.return_value = {
+        'aatype': np.zeros((12, 10), dtype=np.int32),
+        'residue_index': np.tile(np.arange(10, dtype=np.int32)[None], (12, 1)),
+    }
+    model_runner_mock.predict.return_value = {
+        'structure_module': {
+            'final_atom_positions': np.zeros((10, 37, 3)),
+            'final_atom_mask': np.ones((10, 37)),
+        },
+        'predicted_lddt': {
+            'logits': np.ones((10, 50)),
+        },
+        'plddt': np.ones(10) * 42,
+        'ranking_confidence': 90,
+        'ptm': np.array(0.),
+        'aligned_confidence_probs': np.zeros((10, 10, 50)),
+        'predicted_aligned_error': np.zeros((10, 10)),
+        'max_predicted_aligned_error': np.array(0.),
+    }
+    model_runner_mock.multimer_mode = False
+    amber_relaxer_mock.process.return_value = ('RELAXED', None, None)
+
+    fasta_path = os.path.join(absltest.get_default_test_tmpdir(),
+                              'target.fasta')
+    with open(fasta_path, 'wt') as f:
+      f.write('>A\nAAAAAAAAAAAAA')
+    fasta_name = 'test'
+
+    out_dir = absltest.get_default_test_tmpdir()
+
+    run_alphafold.predict_structure(
+        fasta_path=fasta_path,
+        fasta_name=fasta_name,
+        output_dir_base=out_dir,
+        data_pipeline=data_pipeline_mock,
+        model_runners={'model1': model_runner_mock},
+        amber_relaxer=amber_relaxer_mock if do_relax else None,
+        benchmark=False,
+        random_seed=0)
+
+    base_output_files = os.listdir(out_dir)
+    self.assertIn('target.fasta', base_output_files)
+    self.assertIn('test', base_output_files)
+
+    target_output_files = os.listdir(os.path.join(out_dir, 'test'))
+    expected_files = [
+        'features.pkl', 'msas', 'ranked_0.pdb', 'ranking_debug.json',
+        'result_model1.pkl', 'timings.json', 'unrelaxed_model1.pdb',
+    ]
+    if do_relax:
+      expected_files.append('relaxed_model1.pdb')
+    self.assertCountEqual(expected_files, target_output_files)
+
+    # Check that pLDDT is set in the B-factor column.
+    with open(os.path.join(out_dir, 'test', 'unrelaxed_model1.pdb')) as f:
+      for line in f:
+        if line.startswith('ATOM'):
+          self.assertEqual(line[61:66], '42.00')
+
+
+if __name__ == '__main__':
+  absltest.main()