Configure PRODIGY pipeline for WES execution with S3 and Harbor

tests/test_parsers.py

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+from pathlib import Path
+
+import pytest
+from Bio.PDB.MMCIFParser import MMCIFParser
+from Bio.PDB.PDBParser import PDBParser
+from Bio.PDB.Structure import Structure
+
+from prodigy_prot.modules.parsers import get_parser, parse_structure, validate_structure
+
+from . import TEST_DATA
+
+
+@pytest.fixture
+def input_structure_cif():
+    yield Path(TEST_DATA, "2oob.cif")
+
+
+@pytest.fixture
+def input_structure_pdb() -> Path:
+    return Path(TEST_DATA, "2oob.pdb")
+
+
+def test_get_parser_pdb(input_structure_pdb):
+
+    parser = get_parser(input_structure_pdb)
+    assert isinstance(parser, PDBParser)
+
+
+def test_get_parser_cif(input_structure_cif):
+
+    parser = get_parser(input_structure_cif)
+    assert isinstance(parser, MMCIFParser)
+
+
+def test_validate_structure_pdb(input_structure_pdb):
+
+    parser = PDBParser()
+    structure = parser.get_structure("test_structure", input_structure_pdb)
+    assert isinstance(structure, Structure)
+
+    result = validate_structure(structure)
+    assert result == structure.child_list
+
+
+def test_validate_structure_cif(input_structure_cif):
+
+    parser = MMCIFParser()
+    structure = parser.get_structure("test_structure", input_structure_cif)
+    assert isinstance(structure, Structure)
+
+    result = validate_structure(structure)
+    assert result == structure.child_list
+
+
+def test_parse_structure_pdb(input_structure_pdb):
+
+    parser = PDBParser()
+    structure = parser.get_structure(input_structure_pdb.stem, input_structure_pdb)
+    assert isinstance(structure, Structure)
+
+    result, num_chains, num_res = parse_structure(input_structure_pdb)
+
+    assert result == structure.child_list
+    assert num_chains == 2
+    assert num_res == 116
+
+
+def test_parse_structure_cif(input_structure_cif):
+
+    parser = MMCIFParser()
+    structure = parser.get_structure(input_structure_cif.stem, input_structure_cif)
+    assert isinstance(structure, Structure)
+
+    result, num_chains, num_res = parse_structure(input_structure_cif)
+
+    assert result == structure.child_list
+    assert num_chains == 2
+    assert num_res == 116