zly
74ca20707c
feat(crispr): implement CRISPR-Cas detection and fusion analysis module
2026-01-14 15:34:45 +08:00
zly
80e7d1ffb6
feat(scripts): add protein file (.faa) support to pipeline\n\n- Add detect_sequence_type() function for automatic file type detection\n- Rename run_single_fna_pipeline() to run_single_file_pipeline()\n- Add backward compatibility alias for existing callers\n- Add --input CLI argument (preferred over --fna)\n- Support .faa protein files alongside .fna/.fa/.fasta genome files\n- Auto-detect sequence type and pass correct suffix to BtToxin_Digger\n- Update documentation with protein file examples\n\nCo-Authored-By: Claude <noreply@anthropic.com>
2026-01-13 23:45:34 +08:00
zly
fe353fc0bc
chore: 初始版本提交 - 简化架构 + 轮询改造
...
- 移除 Motia Streams 实时通信，改用 3 秒轮询
- 简化前端代码，移除冗余组件
- 简化后端架构，准备 FastAPI 重构
- 更新 pixi.toml 环境配置
- 保留 bttoxin_digger_v5_repro 作为参考文档
Co-Authored-By: Claude <noreply@anthropic.com >
2026-01-13 16:50:09 +08:00
ae4c6351d9
feat: migrate from Docker to pixi for BtToxin_Digger execution
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- 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
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- 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
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
