hotwa
5883e13c56
- 新增 scripts/bttoxin_shoter.py：从 BPPRC 正样本 CSV 构建 name/亚家族/家族特异性索引， 解析 BtToxin_Digger All_Toxins.txt，计算 per-hit 权重并以 noisy-OR 合成菌株×目标目/物种分数， 输出 TSV/JSON；含 HMM 加成与配对毒素规则（Vip1/Vip2，Vpa/Vpb），other/unknown 桶。 - 新增端到端工具链： - scripts/run_single_fna_pipeline.py：Digger → Shotter → Plot → 打包 - scripts/plot_shotter.py：绘制热图并生成论文式/摘要式报告 - scripts/bttoxin_api.py 与 bttoxin/api.py：纯 Python API；bttoxin/cli.py 暴露 bttoxin-run - pyproject.toml：项目打包与 CLI 入口 - docs(README): 增加输入文件格式与结果解读，补充单目录写入方案 - chore(gitignore): 忽略 runs/ 与 tests/output - ci: 移除 .woodpecker/test.yml
51 lines
2.1 KiB
Python
51 lines
2.1 KiB
Python
#!/usr/bin/env python3
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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("--image", type=str, default="quay.io/biocontainers/bttoxin_digger:1.0.10--hdfd78af_0")
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ap.add_argument("--platform", type=str, default="linux/amd64")
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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(image=args.image, platform=args.platform, 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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)
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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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