Variant Pathogenicity Predictor
Integrate REVEL, CADD, PolyPhen and other scores to predict variant pathogenicity.
Usage
CODEBLOCK0
Parameters
- -
--variant: Variant in format chr:pos:ref:alt - INLINECODE1 : VCF file with variants
- INLINECODE2 : Gene symbol
- INLINECODE3 : Prediction scores to use (REVEL,CADD,PolyPhen)
Integrated Scores
- - REVEL (Rare Exome Variant Ensemble Learner)
- CADD (Combined Annotation Dependent Depletion)
- PolyPhen-2 (Polymorphism Phenotyping)
- SIFT (Sorting Intolerant From Tolerant)
- MutationTaster
Output
- - Pathogenicity classification
- ACMG guideline interpretation
- Individual score breakdown
- Confidence assessment
Risk Assessment
| Risk Indicator | Assessment | Level |
|---|
| Code Execution | Python/R scripts executed locally | Medium |
| Network Access |
No external API calls | Low |
| File System Access | Read input files, write output files | Medium |
| Instruction Tampering | Standard prompt guidelines | Low |
| Data Exposure | Output files saved to workspace | Low |
Security Checklist
- - [ ] No hardcoded credentials or API keys
- [ ] No unauthorized file system access (../)
- [ ] Output does not expose sensitive information
- [ ] Prompt injection protections in place
- [ ] Input file paths validated (no ../ traversal)
- [ ] Output directory restricted to workspace
- [ ] Script execution in sandboxed environment
- [ ] Error messages sanitized (no stack traces exposed)
- [ ] Dependencies audited
Prerequisites
No additional Python packages required.
Evaluation Criteria
Success Metrics
- - [ ] Successfully executes main functionality
- [ ] Output meets quality standards
- [ ] Handles edge cases gracefully
- [ ] Performance is acceptable
Test Cases
- 1. Basic Functionality: Standard input → Expected output
- Edge Case: Invalid input → Graceful error handling
- Performance: Large dataset → Acceptable processing time
Lifecycle Status
- - Current Stage: Draft
- Next Review Date: 2026-03-06
- Known Issues: None
- Planned Improvements:
- Performance optimization
- Additional feature support
变异致病性预测器
整合REVEL、CADD、PolyPhen等多种评分，预测变异致病性。
使用方法
bash
python scripts/main.py --variant chr17:43094692:G:A --gene BRCA1
python scripts/main.py --vcf variants.vcf --output report.json
参数说明
- - --variant：格式为chr:pos:ref:alt的变异信息
- --vcf：包含变异信息的VCF文件
- --gene：基因符号
- --scores：使用的预测评分（REVEL、CADD、PolyPhen）
整合评分
- - REVEL（罕见外显子组变异集成学习器）
- CADD（联合注释依赖耗竭）
- PolyPhen-2（多态性表型分析）
- SIFT（从耐受性中筛选不耐受变异）
- MutationTaster
输出结果
- - 致病性分类
- ACMG指南解读
- 各项评分明细
- 可信度评估
风险评估
| 风险指标 | 评估内容 | 等级 |
|---|
| 代码执行 | 本地执行Python/R脚本 | 中 |
| 网络访问 |
无外部API调用 | 低 |
| 文件系统访问 | 读取输入文件，写入输出文件 | 中 |
| 指令篡改 | 标准提示词指南 | 低 |
| 数据泄露 | 输出文件保存至工作区 | 低 |
安全检查清单
- - [ ] 无硬编码凭据或API密钥
- [ ] 无未经授权的文件系统访问（../）
- [ ] 输出不暴露敏感信息
- [ ] 已实施提示注入防护
- [ ] 输入文件路径已验证（无../遍历）
- [ ] 输出目录限制在工作区内
- [ ] 脚本在沙盒环境中执行
- [ ] 错误信息已清理（不暴露堆栈跟踪）
- [ ] 依赖项已审计
前置条件
无需额外Python包。
评估标准
成功指标
- - [ ] 成功执行主要功能
- [ ] 输出符合质量标准
- [ ] 优雅处理边界情况
- [ ] 性能可接受
测试用例
- 1. 基本功能：标准输入 → 预期输出
- 边界情况：无效输入 → 优雅错误处理
- 性能测试：大数据集 → 可接受处理时间
生命周期状态
- - 当前阶段：草案
- 下次评审日期：2026-03-06
- 已知问题：无
- 计划改进：
- 性能优化
- 新增功能支持
