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80a72c3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | import os
from pathlib import Path
import subprocess
from test_basic_usage import REPO_ROOT, DATA_DIR, normalise_output
def test_basic_usage(tmp_path):
# setup test data
af_id = "AF-A0A0A9LVA1-F1-model_v4"
example_structure_path = DATA_DIR / f"{af_id}.pdb"
expected_cols = [
['chain_id', 'sequence_md5', 'nres', 'ndom', 'chopping', 'confidence'],
['AF-A0A0A9LVA1-F1-model_v4', 'aed99aecb8126442b8129ea77da917af', '16', '0', 'NULL', '0.932'],
]
expected_output = "\n".join(["\t".join(row) for row in expected_cols])
orig_path = Path.cwd()
script_path = REPO_ROOT / "scripts" / "get_predictions.py"
model_path = REPO_ROOT / "weight" / "model_v1"
results_file = tmp_path / "test_output.tsv"
# make sure we can run this in an isolated directory
results_output = None
try:
os.chdir(str(tmp_path))
cmd_args = ["python", str(script_path), "--structure_file", str(example_structure_path), "-o", str(results_file),
"--model_dir", str(model_path), "--renumber_pdbs",
]
completed_process = subprocess.run(cmd_args, check=True, capture_output=True)
results_output = results_file.read_text().strip()
except subprocess.CalledProcessError as e:
print(f"ERROR: CMD: {e.cmd}")
print(f"ERROR: STDOUT: {e.stdout.decode()}")
print(f"ERROR: STDERR: {e.stderr.decode()}")
raise
finally:
os.chdir(str(orig_path))
# check the process ran successfully
assert completed_process.returncode == 0
# check the output file has the expected content
assert normalise_output(results_output) == normalise_output(expected_output)
# check that the logs warned about stride failing
assert "Stride failed" in completed_process.stderr.decode()
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