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| """Run the historical construction snapshot after strict input checks.""" |
| import argparse |
| import hashlib |
| import os |
| import shutil |
| import subprocess |
| import sys |
| from pathlib import Path |
|
|
| import yaml |
|
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| ROOT = Path(__file__).resolve().parents[1] |
| EXPECTED = { |
| "prosite_dat": "00f9598c5ddcef7b9d414cd24b968ad8a746e6b808e8fa525787f0e739f2e9c7", |
| "prosite_doc": "677dfd65f3818b7ebfc729d25abc40c633e72bb408a40eba39a3a770db3dfec1", |
| } |
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|
| def main(): |
| parser = argparse.ArgumentParser(description=__doc__) |
| parser.add_argument("--config", type=Path, default=ROOT / "construction/configs/reference.yaml") |
| args = parser.parse_args() |
| with args.config.open() as handle: |
| config = yaml.safe_load(handle) |
| for key, expected in EXPECTED.items(): |
| path = Path(config["input"][key]) |
| digest = hashlib.sha256(path.read_bytes()).hexdigest() |
| if digest != expected: |
| raise ValueError(f"{path}: wrong PROSITE input (SHA-256 {digest})") |
| if config.get("prosite_release") != "2021_04": |
| raise ValueError("configuration must pin PROSITE release 2021_04") |
| reference = Path(config["input"]["reference_motifbench_cases"]) |
| if not reference.is_file(): |
| raise FileNotFoundError(f"missing historical MotifBench reference cases: {reference}") |
| analysis = config["structure_analysis"] |
| if not analysis.get("use_foldseek") or not analysis.get("foldseek_conservation"): |
| raise ValueError("the historical configuration requires Foldseek conservation") |
| foldseek = shutil.which("foldseek") |
| if not foldseek: |
| foldseek = next((p for p in analysis.get("foldseek_candidates", []) |
| if Path(p).is_file() and os.access(p, os.X_OK)), None) |
| if not foldseek: |
| raise FileNotFoundError("Foldseek executable not found") |
| result = subprocess.run([foldseek, "version"], check=True, capture_output=True, text=True) |
| print(f"Foldseek version: {result.stdout.strip() or result.stderr.strip()}") |
| output = Path(config["output_root"]) |
| if output.exists(): |
| raise FileExistsError(f"refusing to reuse existing output directory: {output}") |
| sys.path.insert(0, str(ROOT / "construction")) |
| from motifbench_prosite.cli import main as run_pipeline |
| run_pipeline(["--config", str(args.config)]) |
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|
| if __name__ == "__main__": |
| main() |
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|
