a5cb891d0e
chore: clean up obsolete test data files
...
- Remove ncbi_dataset download files
- Remove outdated test documentation
2026-01-08 16:59:42 +08:00
8d11216481
docs: update README and add pixi-based tests
...
- 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
2026-01-08 16:59:17 +08:00
ae4c6351d9
feat: migrate from Docker to pixi for BtToxin_Digger execution
...
- Add pixi.toml with digger and pipeline environments
- Implement PixiRunner class replacing DockerContainerManager
- Add run_digger_stage.py for standalone digger execution
- Update run_single_fna_pipeline.py to use PixiRunner
- Remove docker dependency from pyproject.toml
- Delete docker_client.py (no longer needed)
BREAKING CHANGE: Docker is no longer required. Use 'pixi install' instead.
2026-01-08 16:58:45 +08:00
1c0e8f90a5
feat: 支持绑定外部 bt_toxin 数据库 (2025-11-04 更新)
...
- docker_client.py: run_bttoxin_digger() 新增 bttoxin_db_dir 参数，支持挂载外部数据库
- run_single_fna_pipeline.py: 新增 --bttoxin_db_dir 参数，自动检测 external_dbs/bt_toxin
- README.md: 添加 bttoxin_db 更新说明和 Docker 绑定文档
- external_dbs/bt_toxin: 添加 2025-11-04 版本数据库文件
测试验证: HAN055 样本毒素命名版本号变化 (Cry2Aa9→22, Cry2Ab35→41, Cry1Ia40→42, Vip3Aa7→79)
2026-01-04 14:37:49 +08:00
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
3fc41a2924
docs: add mathematical formulation and algorithmic principles for BtToxin_Shotter toxicity prediction
2025-12-01 09:43:35 +08:00
6b923ae567
add test data
2025-12-01 09:41:39 +08:00
b80939f0ca
add math description
2025-11-22 10:09:35 +08:00
06c5cb7448
compare data
2025-11-21 20:29:03 +08:00
82cfb13e50
add usage markdown file
2025-11-21 20:23:15 +08:00
50a901c167
修改测试案例
2025-10-13 22:10:36 +08:00
675bce4b5a
运行时候 docker 内的路径与权限问题解决方案
2025-10-13 22:08:22 +08:00
0b904cd69b
add uv use
2025-10-13 21:08:44 +08:00
d71163df00
first add
2025-10-13 21:05:00 +08:00
c7744836e9
Initial commit: BtToxin Pipeline project structure
2025-10-13 19:22:56 +08:00
