lingyuzeng/bttoxin-pipeline
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feat(crispr): reserve CRISPR-Cas module infrastructure for future implementation\n\n- Add [feature.crispr] environment to pixi.toml (commented, ready to activate)\n- Create comprehensive CRISPR implementation plan document\n- Document 4-phase implementation roadmap:\n * Phase 1: CRISPR detection using CRISPRCasFinder\n * Phase 2: Spacer-toxin gene association analysis\n * Phase 3: Integration with shoter scoring (reserved parameters)\n * Phase 4: Enhanced visualization\n- Define data structures, API contracts, and usage examples\n- Document scientific background and testing strategy\n\nStatus: RESERVED - not yet implemented, all infrastructure prepared for future activation.\n\nCo-Authored-By: Claude <noreply@anthropic.com>

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zly
2026-01-13 23:55:12 +08:00
parent 029e49bf6a
commit 89ed5cfa1a
2 changed files with 343 additions and 3 deletions
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37
pixi.toml
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@@ -44,6 +44,36 @@ python-dotenv = "*"
httpx = "*"
pytest = "*"
# =========================
# CRISPR-Cas 环境：预留用于未来的 CRISPR-Cas 分析
# =========================
# 此环境预留用于 CRISPR-Cas 系统分析模块
# 实现计划：
# 1. 使用 CRISPRCasFinder 或 similar 工具识别 CRISPR arrays
# 2. 提取 spacer 序列并与毒素基因关联分析
# 3. 评估 CRISPR-Cas 系统对宿主防御的影响
#
# 预期依赖（待激活时添加）:
# python = ">=3.9"
# crisprcasfinder = "*" # 或使用 pyCRISPRcas
# biopython = "*"
# pandas = ">=2.0.0"
#
# 使用方式：
# pixi run -e crispr crispr-detect --input genome.fna --output crispr_results.json
# pixi run -e crispr crispr-fusion --toxins all_toxins.txt --crispr crispr_results.json
# =========================
# [feature.crispr.dependencies]
# # 预留依赖，实际实现时取消注释
# python = ">=3.9"
# # crisprcasfinder = "*" # 需要配置安装源
# biopython = "*"
# pandas = ">=2.0.0"
# =========================
# [feature.crispr.tasks]
# crispr-detect = "python crispr_cas/scripts/detect_crispr.py"
# crispr-fusion = "python crispr_cas/scripts/fusion_analysis.py"
# =========================
# 环境定义
# =========================
@@ -52,6 +82,7 @@ digger = ["digger"]
pipeline = ["pipeline"]
frontend = ["frontend"]
webbackend = ["webbackend"]
# crispr = ["crispr"] # 取消注释以激活 CRISPR 环境
# =========================
# pipeline tasks
@@ -59,7 +90,7 @@ webbackend = ["webbackend"]
[feature.pipeline.tasks]
pipeline = "python scripts/run_single_fna_pipeline.py"
digger-only = "python scripts/run_digger_stage.py"
shotter = "python scripts/bttoxin_shoter.py"
shoter = "python scripts/bttoxin_shoter.py"
plot = "python scripts/plot_shotter.py"
# =========================
@@ -76,6 +107,6 @@ fe-lint = { cmd = "pnpm lint", cwd = "frontend" }
# webbackend tasks
# =========================
[feature.webbackend.tasks]
api-dev = "uvicorn web.backend.main:app --reload --host 0.0.0.0 --port 8000"
api-test = "pytest web/backend/ -v"
api-dev = "uvicorn backend.app.main:app --reload --host 0.0.0.0 --port 8000"
api-test = "pytest backend/ -v"
web-start = "bash scripts/start_web.sh"