hotwa
8d11216481
- Add property-based tests for PixiRunner - Add HAN055.fna test data file - Update README with pixi installation and usage guide - Update .gitignore for pixi and test artifacts - Update CLI to remove Docker-related arguments
64 lines
2.5 KiB
Python
64 lines
2.5 KiB
Python
#!/usr/bin/env python3
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"""Bttoxin single-FNA pipeline CLI (pixi-based).
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This CLI uses pixi environments for execution:
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- digger environment: BtToxin_Digger with bioconda dependencies
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- pipeline environment: Python analysis with pandas/matplotlib/seaborn
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Example:
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python -m bttoxin.cli --fna tests/test_data/HAN055.fna --lang zh
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# With custom database
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python -m bttoxin.cli --fna tests/test_data/HAN055.fna --bttoxin_db_dir /path/to/bt_toxin
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"""
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from __future__ import annotations
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import argparse
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from pathlib import Path
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from .api import BtSingleFnaPipeline
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def main() -> int:
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ap = argparse.ArgumentParser(description="Bttoxin single-FNA pipeline (Digger → Shotter → Plot → Bundle)")
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ap.add_argument("--fna", type=Path, required=True, help="Path to a single .fna file")
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ap.add_argument("--toxicity_csv", type=Path, default=Path("Data/toxicity-data.csv"))
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ap.add_argument("--base_workdir", type=Path, default=None, help="Base working dir (default: runs/bttoxin under repo root)")
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ap.add_argument("--bttoxin_db_dir", type=Path, default=None,
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help="外部 bt_toxin 数据库目录路径（默认自动检测 external_dbs/bt_toxin）")
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ap.add_argument("--min_identity", type=float, default=0.0)
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ap.add_argument("--min_coverage", type=float, default=0.0)
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ap.add_argument("--disallow_unknown_families", action="store_true", default=False)
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ap.add_argument("--require_index_hit", action="store_true", default=False)
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ap.add_argument("--lang", type=str, choices=["zh", "en"], default="zh")
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ap.add_argument("--threads", type=int, default=4)
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args = ap.parse_args()
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pipe = BtSingleFnaPipeline(base_workdir=args.base_workdir)
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res = pipe.run(
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fna=args.fna,
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toxicity_csv=args.toxicity_csv,
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min_identity=args.min_identity,
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min_coverage=args.min_coverage,
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allow_unknown_families=not args.disallow_unknown_families,
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require_index_hit=args.require_index_hit,
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lang=args.lang,
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threads=args.threads,
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bttoxin_db_dir=args.bttoxin_db_dir,
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)
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if not res.get("ok"):
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print(f"[bttoxin-run] FAILED at stage={res.get('stage')}")
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return 1
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print("[bttoxin-run] ✓ Done")
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print(f" run_root: {res['run_root']}")
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print(f" digger: {res['digger_dir']}")
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print(f" shotter: {res['shotter_dir']}")
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print(f" bundle: {res['bundle']}")
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print(f" strain: {res.get('strain','')}")
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return 0
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if __name__ == "__main__":
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raise SystemExit(main())
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