mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 14:14:24 +08:00
Fix #457
This commit is contained in:
Dima Molodenskiy
1
.github/workflows/github_actions.yml
vendored
1
.github/workflows/github_actions.yml
vendored
@@ -68,6 +68,7 @@ jobs:
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pytest -s test/test_modelcif.py
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pytest -s test/test_features_with_templates.py
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pytest -s test/test_post_prediction.py
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pytest -s test/test_parse_fold.py
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#export PYTHONPATH=$PWD/alphapulldown/analysis_pipeline:$PYTHONPATH
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## Test analysis pipeline
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#conda install -c bioconda biopandas
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@@ -21,7 +21,7 @@ from absl import logging
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logging.set_verbosity(logging.INFO)
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def parse_fold(input, features_directory, protein_delimiter):
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def parse_fold(input_list, features_directory, protein_delimiter):
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"""
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Parses a list of protein fold specifications and returns structured folding jobs.
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@@ -37,50 +37,54 @@ def parse_fold(input, features_directory, protein_delimiter):
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FileNotFoundError: If any required protein features are missing.
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"""
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all_folding_jobs = []
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for i in input:
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formatted_folds, missing_features, unique_features = [], [], []
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missing_features = set() # Initialize as a set to collect unique missing features
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for i in input_list:
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formatted_folds = []
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protein_folds = [x.split(":") for x in i.split(protein_delimiter)]
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for protein_fold in protein_folds:
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name, number, region = None, 1, "all"
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if len(protein_fold) ==1:
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# protein_fold is in this format: [protein_name]
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if len(protein_fold) == 1:
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# Format: [protein_name]
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name = protein_fold[0]
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elif len(protein_fold) > 1:
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name, number= protein_fold[0], protein_fold[1]
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if ("-") in protein_fold[1]:
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# protein_fold is in this format: [protein_name:1-10:14-30:40-100:etc]
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name = protein_fold[0]
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if "-" in protein_fold[1]:
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# Format: [protein_name:1-10:14-30:40-100:etc]
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try:
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number = 1
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region = protein_fold[1:]
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region = [tuple(int(x) for x in r.split("-")) for r in region]
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except Exception as e:
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logging.error(f"Your format: {i} is wrong. The programme will terminate.")
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except Exception:
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logging.error(f"Your format: {i} is wrong. The program will terminate.")
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sys.exit()
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else:
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# protein_fold is in this format: [protein_name:copy_number:1-10:14-30:40-100:etc]
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# Format: [protein_name:copy_number:1-10:14-30:40-100:etc]
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try:
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number = protein_fold[1]
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if len(protein_fold[2:]) > 0:
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number = int(protein_fold[1])
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if len(protein_fold) > 2:
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region = protein_fold[2:]
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region = [tuple(int(x) for x in r.split("-")) for r in region]
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except Exception as e:
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logging.error(f"Your format: {i} is wrong. The programme will terminate.")
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except Exception:
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logging.error(f"Your format: {i} is wrong. The program will terminate.")
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sys.exit()
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number = int(number)
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unique_features.append(name)
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if not any([exists(join(monomer_dir, f"{name}.pkl")) or exists(join(monomer_dir, f"{name}.pkl.xz")) for
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monomer_dir in features_directory]):
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missing_features.append(name)
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# Check for missing features
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if not any(
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exists(join(monomer_dir, f"{name}{ext}"))
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for monomer_dir in features_directory
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for ext in [".pkl", ".pkl.xz"]
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):
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missing_features.add(name) # Use .add() since missing_features is a set
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formatted_folds.extend([{name: region} for _ in range(number)])
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all_folding_jobs.append(formatted_folds)
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missing_features = set(missing_features)
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if len(missing_features):
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raise FileNotFoundError(
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f"{missing_features} not found in {features_directory}"
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)
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if missing_features:
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raise FileNotFoundError(
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f"{sorted(missing_features)} not found in {features_directory}"
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)
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return all_folding_jobs
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def pad_input_features(feature_dict: dict,
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130
test/test_parse_fold.py
Normal file
130
test/test_parse_fold.py
Normal file
@@ -0,0 +1,130 @@
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import logging
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from absl.testing import parameterized
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from unittest import mock
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from alphapulldown.utils.modelling_setup import parse_fold
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"""
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Test parse_fold function with different scenarios
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"""
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class TestParseFold(parameterized.TestCase):
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def setUp(self) -> None:
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super().setUp()
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# Set logging level to INFO
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logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')
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@parameterized.named_parameters(
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{
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'testcase_name': 'single_protein_no_copy',
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'input': ['protein1'],
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'features_directory': ['dir1'],
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'protein_delimiter': '_',
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'mock_side_effect': {
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'dir1/protein1.pkl': True,
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'dir1/protein1.pkl.xz': False,
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},
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'expected_result': [[{'protein1': 'all'}]],
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},
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{
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'testcase_name': 'single_protein_with_copy_number',
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'input': ['protein1:2'],
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'features_directory': ['dir1'],
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'protein_delimiter': '_',
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'mock_side_effect': {
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'dir1/protein1.pkl': True,
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'dir1/protein1.pkl.xz': False,
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},
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'expected_result': [[{'protein1': 'all'}, {'protein1': 'all'}]],
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},
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{
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'testcase_name': 'single_protein_with_region',
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'input': ['protein1:1-10'],
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'features_directory': ['dir1'],
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'protein_delimiter': '_',
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'mock_side_effect': {
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'dir1/protein1.pkl': True,
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'dir1/protein1.pkl.xz': False,
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},
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'expected_result': [[{'protein1': [(1, 10)]}]],
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},
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{
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'testcase_name': 'single_protein_with_copy_and_regions',
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'input': ['protein1:2:1-10:20-30'],
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'features_directory': ['dir1'],
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'protein_delimiter': '_',
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'mock_side_effect': {
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'dir1/protein1.pkl': True,
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'dir1/protein1.pkl.xz': False,
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},
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'expected_result': [[{'protein1': [(1, 10), (20, 30)]}, {'protein1': [(1, 10), (20, 30)]}]],
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},
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{
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'testcase_name': 'multiple_proteins',
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'input': ['protein1:2_protein2:1-50'],
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'features_directory': ['dir1'],
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'protein_delimiter': '_',
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'mock_side_effect': {
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'dir1/protein1.pkl': True,
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'dir1/protein1.pkl.xz': False,
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'dir1/protein2.pkl': True,
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'dir1/protein2.pkl.xz': False,
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},
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'expected_result': [[{'protein1': 'all'}, {'protein1': 'all'}, {'protein2': [(1, 50)]}]],
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},
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{
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'testcase_name': 'missing_features',
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'input': ['protein1', 'protein2'],
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'features_directory': ['dir1'],
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'protein_delimiter': '_',
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'mock_side_effect': {
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'dir1/protein1.pkl': False,
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'dir1/protein1.pkl.xz': False,
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'dir1/protein2.pkl': False,
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'dir1/protein2.pkl.xz': False,
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},
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'expected_exception': FileNotFoundError,
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'expected_exception_message': "['protein1', 'protein2'] not found in ['dir1']",
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},
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{
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'testcase_name': 'invalid_format',
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'input': ['protein1::1-10'],
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'features_directory': ['dir1'],
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'protein_delimiter': '_',
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'mock_side_effect': {},
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'expected_exception': SystemExit,
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},
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{
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'testcase_name': 'feature_exists_in_multiple_dirs',
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'input': ['protein1'],
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'features_directory': ['dir1', 'dir2'],
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'protein_delimiter': '_',
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'mock_side_effect': {
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'dir1/protein1.pkl': False,
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'dir1/protein1.pkl.xz': False,
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'dir2/protein1.pkl': True,
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'dir2/protein1.pkl.xz': False,
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},
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'expected_result': [[{'protein1': 'all'}]],
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},
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)
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def test_parse_fold(self, input, features_directory, protein_delimiter, mock_side_effect,
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expected_result=None, expected_exception=None, expected_exception_message=None):
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"""Test parse_fold with different input scenarios"""
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with mock.patch('alphapulldown.utils.modelling_setup.exists') as mock_exists, \
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mock.patch('sys.exit') as mock_exit:
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mock_exists.side_effect = lambda path: mock_side_effect.get(path, False)
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# Mock sys.exit to raise SystemExit exception
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mock_exit.side_effect = SystemExit
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logging.info(f"Testing with input: {input}, features_directory: {features_directory}, "
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f"protein_delimiter: '{protein_delimiter}'")
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logging.info(f"Mock side effects: {mock_side_effect}")
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if expected_exception:
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with self.assertRaises(expected_exception) as context:
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result = parse_fold(input, features_directory, protein_delimiter)
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if expected_exception_message:
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self.assertEqual(str(context.exception), expected_exception_message)
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else:
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result = parse_fold(input, features_directory, protein_delimiter)
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logging.info(f"Result: {result}, Expected: {expected_result}")
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self.assertEqual(result, expected_result)
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