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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,127 @@ | ||
| import os | ||
| import tempfile | ||
| import numpy as np | ||
|
|
||
| from absl import logging | ||
| from absl.testing import absltest | ||
|
|
||
| # Import the class to test. Adjust the module path as needed. | ||
| from alphapulldown.objects import MonomericObject | ||
|
|
||
| # Dummy implementations for the functions used by make_mmseq_features. | ||
| def fake_build_monomer_feature(sequence, msa, template_features): | ||
| # Return a dummy dictionary that will be later updated. | ||
| return {"dummy_feature": 42, | ||
| "template_confidence_scores": None, | ||
| "template_release_date": None} | ||
|
|
||
| # Dummy msa_pairing.MSA_FEATURES list. | ||
| class FakeMSAPairing: | ||
| MSA_FEATURES = ["dummy_feature"] | ||
|
|
||
| # Save originals to restore later. | ||
| _original_build_monomer_feature = None | ||
| _original_get_msa_and_templates = None | ||
| _original_unserialize_msa = None | ||
|
|
||
| def fake_get_msa_and_templates(jobname, query_sequences, a3m_lines, result_dir, | ||
| msa_mode, use_templates, custom_template_path, | ||
| pair_mode, host_url, user_agent): | ||
| # Return fake tuple values. | ||
| fake_unpaired = ["FAKE_UNPAIRED"] | ||
| fake_paired = ["FAKE_PAIRED"] | ||
| fake_unique = ["FAKE_UNIQUE"] | ||
| fake_card = ["FAKE_CARDINALITY"] | ||
| fake_template = ["FAKE_TEMPLATE"] | ||
| return (fake_unpaired, fake_paired, fake_unique, fake_card, fake_template) | ||
|
|
||
| def fake_unserialize_msa(a3m_lines, sequence): | ||
| # Return fake tuple values based solely on the precomputed file. | ||
| fake_unpaired = ["PRECOMPUTED_UNPAIRED"] | ||
| fake_paired = ["PRECOMPUTED_PAIRED"] | ||
| fake_unique = ["PRECOMPUTED_UNIQUE"] | ||
| fake_card = ["PRECOMPUTED_CARDINALITY"] | ||
| fake_template = ["PRECOMPUTED_TEMPLATE"] | ||
| return (fake_unpaired, fake_paired, fake_unique, fake_card, fake_template) | ||
|
|
||
| class MmseqFeaturesTest(absltest.TestCase): | ||
|
|
||
| def setUp(self): | ||
| super(MmseqFeaturesTest, self).setUp() | ||
| # Create a dummy MonomericObject with a known description and sequence. | ||
| self.monomer = MonomericObject("dummy", "ACDE") | ||
| # Create a temporary output directory. | ||
| self.temp_dir = tempfile.TemporaryDirectory() | ||
| self.output_dir = self.temp_dir.name | ||
|
|
||
| # Monkey-patch the functions used inside make_mmseq_features. | ||
| import alphapulldown.objects as objects_mod | ||
| self._original_build_monomer_feature = objects_mod.build_monomer_feature | ||
| self._original_get_msa_and_templates = objects_mod.get_msa_and_templates | ||
| self._original_unserialize_msa = objects_mod.unserialize_msa | ||
|
|
||
| objects_mod.build_monomer_feature = fake_build_monomer_feature | ||
| objects_mod.get_msa_and_templates = fake_get_msa_and_templates | ||
| objects_mod.unserialize_msa = fake_unserialize_msa | ||
|
|
||
| # Override msa_pairing.MSA_FEATURES in the module where make_mmseq_features uses it. | ||
| objects_mod.msa_pairing.MSA_FEATURES = FakeMSAPairing.MSA_FEATURES | ||
|
|
||
| def tearDown(self): | ||
| # Restore originals. | ||
| import alphapulldown.objects as objects_mod | ||
| objects_mod.build_monomer_feature = self._original_build_monomer_feature | ||
| objects_mod.get_msa_and_templates = self._original_get_msa_and_templates | ||
| objects_mod.unserialize_msa = self._original_unserialize_msa | ||
| self.temp_dir.cleanup() | ||
| super(MmseqFeaturesTest, self).tearDown() | ||
|
|
||
| def test_use_precomputed_msa(self): | ||
| """Test that if a precomputed MSA exists and use_precomputed_msa is True, | ||
| the branch using unserialize_msa is taken.""" | ||
| # Create a dummy precomputed a3m file. | ||
| a3m_path = os.path.join(self.output_dir, self.monomer.description + ".a3m") | ||
| precomputed_content = ">dummy\nPRECOMPUTED_CONTENT\n" | ||
| with open(a3m_path, "w") as f: | ||
| f.write(precomputed_content) | ||
|
|
||
| # Call the method with use_precomputed_msa=True. | ||
| self.monomer.make_mmseq_features( | ||
| DEFAULT_API_SERVER="http://fake.api", | ||
| output_dir=self.output_dir, | ||
| use_precomputed_msa=True | ||
| ) | ||
| # Our fake_unserialize_msa returns fake values that we check: | ||
| self.assertEqual(self.monomer.feature_dict["dummy_feature"], 42) | ||
| # Check that template_confidence_scores and template_release_date got set: | ||
| self.assertTrue(isinstance(self.monomer.feature_dict["template_confidence_scores"], np.ndarray)) | ||
| self.assertEqual(self.monomer.feature_dict["template_release_date"], ['none']) | ||
|
|
||
| def test_api_generation(self): | ||
| """Test that if no precomputed MSA exists (or use_precomputed_msa is False), | ||
| the API branch is taken and a new a3m file is created.""" | ||
| a3m_path = os.path.join(self.output_dir, self.monomer.description + ".a3m") | ||
| # Ensure the file does not exist. | ||
| if os.path.exists(a3m_path): | ||
| os.remove(a3m_path) | ||
| # Call the method with use_precomputed_msa=False. | ||
| self.monomer.make_mmseq_features( | ||
| DEFAULT_API_SERVER="http://fake.api", | ||
| output_dir=self.output_dir, | ||
| use_precomputed_msa=False | ||
| ) | ||
| # The fake_get_msa_and_templates returns known fake values. | ||
| self.assertEqual(self.monomer.feature_dict["dummy_feature"], 42) | ||
| # The a3m file should now exist. | ||
| self.assertTrue(os.path.isfile(a3m_path)) | ||
| # Check that the file contains our dummy content from fake_get_msa_and_templates branch. | ||
| with open(a3m_path) as f: | ||
| msa_content = f.read() | ||
| self.assertIn("FAKE_UNPAIRED", msa_content) | ||
| # Check that default template values were added. | ||
| self.assertTrue(isinstance(self.monomer.feature_dict["template_confidence_scores"], np.ndarray)) | ||
| self.assertEqual(self.monomer.feature_dict["template_release_date"], ['none']) | ||
|
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||
|
|
||
| if __name__ == '__main__': | ||
| absltest.main() |