96 lines
3.1 KiB
Markdown
96 lines
3.1 KiB
Markdown
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# AGENTS.md - bbav5 基因家族分析执行系统
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## 项目定位
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**执行型 Agent** - 运行基因家族分析流程，调用 run_*.py 脚本
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## 分析阶段速查
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### 核心阶段 (13个)
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| 阶段 | 脚本 | 功能 | 环境 |
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|------|------|------|------|
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| identify | run_identify.py | 基因鉴定 | test4py311 |
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| phylogeny | run_phylogeny.py | 系统发育树 | test4py311 |
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| motif | run_motif.py | MEME motif | test4py311 |
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| domain | run_domain.py | Pfam结构域 | test4py311 |
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| structure | run_structure.py | 基因结构 | test4py311 |
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| promoter | run_promoter.py | 启动子分析 | test4py311 |
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| synteny | run_synteny.py | 种内共线性 | test4py311 |
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| interspecies_synteny | run_interspecies_synteny.py | 种间共线性 | test4py311 |
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| karyotype | run_karyotype.py | 核型图 | test4py311 |
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| combo | run_combo.py | 组合图 | test4py311 |
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| ppi | run_ppi.py | 蛋白互作 | test4py311 |
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| expression | run_expression.py | 表达分析 | **rnaR** |
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| pep | run_pep.py | PEP分析 | test4py311 |
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### RNA-seq 流水线 (5个)
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| 阶段 | 脚本 | 功能 | 环境 |
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|------|------|------|------|
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| rnaseq_qc | run_rnaseq_qc.py | 质控 | **rnaseq** |
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| rnaseq_align | run_rnaseq_align.py | 比对 | **rnaseq** |
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| rnaseq_quant | run_rnaseq_quant.py | 定量 | **rnaseq** |
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| rnaseq_de | run_rnaseq_de.py | 差异表达 | **rnaseq** |
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| rnaseq_enrich | run_rnaseq_enrich_v2.py | 富集分析 | **rnaseq** |
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### 辅助阶段 (9个，无契约)
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genome_prepare_v2, kaks_v2, ortholog, cis_element_http, fetch_expression, tree_plot, ppi_v2, ppi_v2_with_repro, summary
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## 执行流程
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1. **识别意图** → 确定目标阶段
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2. **检查输入** → 验证契约文件存在 (input/ 或 final/)
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3. **执行脚本** → `python apps/cli/run_*.py` 或调用 Skills
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4. **验证输出** → 检查 final/ 目录产物 + Manifest
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5. **报告结果** → artifacts 列表 + metrics 摘要
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## Conda 环境 [关键]
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| 环境名 | 用途 | 激活命令 |
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|--------|------|----------|
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| test4py311 | 标准分析 | `conda activate test4py311` |
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| rnaseq | RNA-seq流程 | `conda activate rnaseq` |
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| rnaR | 表达绘图 | `conda activate rnaR` |
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**注意**: expression阶段用rnaR，其他绘图用test4py311
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## 关键目录
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| 目录 | 内容 |
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|------|------|
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| `apps/cli/` | 27个 run_*.py 脚本 |
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| `gfa_core/schemas/stages/` | 18个契约文件 *_contract_v1.md |
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| `skills/` | 技能封装 |
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| `scripts/` | R绘图脚本 |
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## Manifest 结构
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```json
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{
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"manifest_version": "1.0",
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"stage": "identify",
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"status": "success",
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"prefix": "Ft.SPL",
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"artifacts": { "key": {"path": "final/...", "type": "fasta"} },
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"metrics": { ... }
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}
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```
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## 工作原则
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- **契约优先**: 有契约的阶段执行前检查输入，执行后验证输出
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- **Manifest记录**: 每次执行生成完整 Manifest
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- **可复现性**: reproducibility_v2.py 确保分析可追溯
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- **错误诊断**: 失败时读错误日志，给具体修复建议
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## 常用命令
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```bash
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# 运行鉴定阶段
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python apps/cli/run_identify.py --prefix Ft.SPL --workspace ~/test_workspace
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# 启动前端服务
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python apps/web/vue3/main.py
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```
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