From e23731f6ca3c1965755281a0d78cfc539cb13e3e Mon Sep 17 00:00:00 2001
From: zly <644706215@qq.com>
Date: Sat, 17 Jan 2026 13:13:31 +0800
Subject: [PATCH] Update docs with new directory structure

- Updated AGENTS.md and README.md to reflect:
  - Removal of motia-backend
  - Moving bttoxin_digger_v5_repro to tools/reproduction/
  - Added crispr_cas to structure
---
 AGENTS.md | 3 +++
 README.md | 6 +++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/AGENTS.md b/AGENTS.md
index f73b93d..52153c8 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -162,6 +162,9 @@ bttoxin-pipeline/
 │   └── toxicity-data.csv        # BPPRC specificity data
 ├── external_dbs/                # Optional external database
 │   └── bt_toxin/                # Updated BtToxin database
+├── tools/                       # Utility tools and environments
+│   └── reproduction/            # Reproduction environments
+│       └── bttoxin_digger/      # BtToxin_Digger reproduction env
 ├── tests/                       # Test suite
 │   ├── test_pixi_runner.py      # Property-based tests
 │   └── test_data/               # Test input files (.fna)
diff --git a/README.md b/README.md
index 65ea978..e08d862 100644
--- a/README.md
+++ b/README.md
@@ -370,13 +370,17 @@ bttoxin-pipeline/
 │   └── toxicity-data.csv     # BPPRC specificity data
 ├── external_dbs/             # External databases (optional)
 │   └── bt_toxin/             # Updated BtToxin database
+├── tools/                    # Utility tools and environments
+│   └── reproduction/         # BtToxin_Digger reproduction env
+│       └── bttoxin_digger/
 ├── tests/                    # Test suite
 │   ├── test_pixi_runner.py   # Property-based tests
 │   └── test_data/            # Test input files
 ├── docs/                     # Documentation
 ├── runs/                     # Pipeline outputs (gitignored)
 ├── backend/                  # FastAPI backend (optional web service)
-└── frontend/                 # Vue.js frontend (optional web UI)
+├── frontend/                 # Vue.js frontend (optional web UI)
+└── crispr_cas/               # CRISPR-Cas analysis module
 ```
 
 ## Docker Deployment