genome-mcp

Instructions

Implementation Reference

• src/genome_mcp/core/tools.py:584-693 (handler)

  The primary MCP tool handler function for 'kegg_pathway_enrichment', registered via @mcp.tool() decorator. Implements validation, KEGG query execution via QueryExecutor, result processing, and error handling.
  @mcp.tool() async def kegg_pathway_enrichment( gene_list: list[str], organism: str = "hsa", pvalue_threshold: float = 0.05, min_gene_count: int = 2, ) -> KEGGResult: """ KEGG通路富集分析工具 - MVP版本 分析基因列表在KEGG通路中的富集情况，识别显著相关的生物学通路 Args: gene_list: 基因列表（如 ["TP53", "BRCA1", "BRCA2"]） organism: 生物体代码（默认 "hsa" 人类） pvalue_threshold: p值显著性阈值（默认 0.05） min_gene_count: 通路中最小基因数量（默认 2） Returns: 通路富集分析结果，包含： - 显著富集的通路列表 - p值和FDR校正后的统计显著性 - 富集倍数和基因数量信息 - 分析参数和元数据 Examples: # 分析癌症相关基因的通路富集 kegg_pathway_enrichment(["TP53", "BRCA1", "BRCA2", "EGFR"]) # 分析小鼠基因的通路富集 kegg_pathway_enrichment(["Trp53", "Brca1"], organism="mmu") # 使用更严格的显著性阈值 kegg_pathway_enrichment(["TP53", "BRCA1"], pvalue_threshold=0.01) """ try: # 验证KEGG分析参数 ( validated_gene_list, validated_organism, validated_pvalue_threshold, validated_min_gene_count, ) = validate_kegg_params( gene_list=gene_list, organism=organism, pvalue_threshold=pvalue_threshold, min_gene_count=min_gene_count, ) # 使用QueryParser解析为通路富集查询 parsed = QueryParser.parse( validated_gene_list, query_type="pathway_enrichment" ) # 更新参数 parsed.params.update( { "gene_list": validated_gene_list, "organism": validated_organism, "pvalue_threshold": validated_pvalue_threshold, "min_gene_count": validated_min_gene_count, } ) # 执行查询 result = await _query_executor.execute(parsed) # 格式化结果 if "result" in result: enrichment_data = result["result"] # 添加查询信息 enrichment_data["query_info"] = { "gene_list": validated_gene_list, "analysis_date": "2025-10-24", "organism": validated_organism, "method": "KEGG Pathway Enrichment", "parameters": { "pvalue_threshold": validated_pvalue_threshold, "min_gene_count": validated_min_gene_count, }, } return enrichment_data elif "error" in result: return { "error": result["error"], "query_genes": gene_list, "organism": organism, "suggestions": [ "检查基因ID格式是否正确", "确认生物体代码是否支持", "验证网络连接是否正常", ], } else: return { "error": "Unknown error occurred during pathway enrichment analysis", "query_genes": gene_list, "organism": organism, } except ValidationError as e: return format_simple_error( e, query=str(gene_list), operation="kegg_pathway_enrichment" ) except Exception as e: return format_simple_error( e, query=str(gene_list), operation="kegg_pathway_enrichment" )
• src/genome_mcp/core/validation.py:125-181 (schema)

  Input schema validation function specifically for kegg_pathway_enrichment parameters, ensuring valid gene lists, organism codes, p-value thresholds, and gene counts.
  def validate_kegg_params( gene_list: list, organism: str = "hsa", pvalue_threshold: float = 0.05, min_gene_count: int = 2, ) -> tuple[list, str, float, int]: """ 验证KEGG通路分析参数 Args: gene_list: 基因列表 organism: 生物体代码 pvalue_threshold: p值阈值 min_gene_count: 最小基因数量 Returns: 验证后的参数元组 Raises: ValidationError: 基因列表验证失败 """ if not gene_list or not isinstance(gene_list, list): raise ValidationError("Gene list must be a non-empty list") # 过滤有效的基因符号 valid_genes = [] for gene in gene_list: if isinstance(gene, str) and gene.strip(): valid_genes.append(gene.strip()) if not valid_genes: raise ValidationError("No valid gene symbols found in the list") # 验证organism valid_organisms = {"hsa", "mmu", "rno", "dre", "cel", "scf"} if organism not in valid_organisms: organism = "hsa" # 验证pvalue_threshold try: pvalue_threshold = float(pvalue_threshold) if pvalue_threshold <= 0 or pvalue_threshold >= 1: pvalue_threshold = 0.05 except (ValueError, TypeError): pvalue_threshold = 0.05 # 验证min_gene_count try: min_gene_count = int(min_gene_count) if min_gene_count < 1: min_gene_count = 1 elif min_gene_count > 10: min_gene_count = 10 except (ValueError, TypeError): min_gene_count = 2 return valid_genes, organism, pvalue_threshold, min_gene_count
• src/genome_mcp/core/types.py:95-102 (schema)

  Type definition for the KEGG pathway enrichment result structure returned by the tool.
  class KEGGResult(TypedDict): """KEGG通路富集分析结果类型""" query_genes: list[str] enriched_pathways: list[dict[str, Any]] analysis_metadata: dict[str, Any] query_info: dict[str, Any]