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Enforce pVACvector pathfinder preconditions #1380

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Enforce pVACvector pathfinder preconditions #1380

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6d36294
Fix pvacvector no-edge path scoring crash.
maksimf Mar 18, 2026
2e8c77b
Enforce pvacvector pathfinder preconditions.
maksimf Mar 18, 2026
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4 changes: 4 additions & 0 deletions pvactools/tools/pvacvector/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -257,6 +257,10 @@ def create_distance_matrix(Paths):
return distance_matrix

def find_optimal_path(graph, distance_matrix, seq_dict, base_output_dir, junctions_file, args):
(valid, error) = check_graph_valid(graph, seq_dict)
if not valid:
raise Exception("Invalid graph passed to find_optimal_path: {}".format(error))

init_state = sorted(graph.nodes())
if not os.environ.get('TEST_FLAG') or os.environ.get('TEST_FLAG') == '0':
random.shuffle(init_state)
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23 changes: 23 additions & 0 deletions tests/test_pvacvector.py
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Expand Up @@ -464,6 +464,29 @@ def test_pvacvector_remove_peptides(self):

output_dir.cleanup()

def test_find_optimal_path_raises_on_invalid_graph(self):
with tempfile.TemporaryDirectory() as output_dir:
seq_dict = {"MT.TEST.1": "SYFPEITHI"}
graph = run.initialize_graph(seq_dict.keys())
distance_matrix = run.create_distance_matrix(graph)
junctions_file = run.write_junctions_file(graph, output_dir)
args = argparse.Namespace(
spacers=["None"],
sample_name="single_peptide_no_edges",
)

with self.assertRaises(Exception) as context:
run.find_optimal_path(
graph,
distance_matrix,
seq_dict,
output_dir,
junctions_file,
args,
)

self.assertIn("Invalid graph passed to find_optimal_path", str(context.exception))

def test_prevent_clipping_best_peptide(self):
output_dir = tempfile.TemporaryDirectory()
input_file = os.path.join(self.test_data_dir, 'Test.vector.prevent_clipping_best_peptide.input.fa')
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