bttoxin-pipeline/bttoxin/__init__.py at 1c0e8f90a5f5d6802ec11ec53a3d564a11e617ce - bttoxin-pipeline - Gitea: Git with a cup of tea

lingyuzeng/bttoxin-pipeline

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hotwa 5883e13c56 feat(shotter): 实现 Shotter v1 活性评估与单 FNA 流程，新增 API/CLI/绘图与报告

- 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

2025-12-01 10:11:26 +08:00

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 from __future__ import annotations
 __all__ = [
     "BtToxinRunner",
     "ShotterAPI",
     "PlotAPI",
     "BtSingleFnaPipeline",
 ]
 __version__ = "0.1.0"