batch_pathogenicity_filter

Instructions

Implementation Reference

• scripts/alphagenome_bridge.py:526-550 (handler)

  Core handler function that processes a batch of variants, assesses pathogenicity for each using assess_pathogenicity helper, filters those above threshold, sorts by score, and returns summary.

  def batch_pathogenicity_filter(client, params: Dict[str, Any]) -> Dict[str, Any]:
      """Filter variants by pathogenicity threshold."""
      variants_data = params.get('variants', [])
      threshold = params.get('threshold', 0.5)
  
      pathogenic_variants = []
      for v in variants_data:
          try:
              result = assess_pathogenicity(client, v)
              if result['pathogenicity_score'] >= threshold:
                  pathogenic_variants.append({
                      'variant': result['variant'],
                      'score': result['pathogenicity_score'],
                      'classification': result['classification']
                  })
          except Exception as e:
              print(f"Warning: Failed for variant: {e}", file=sys.stderr)
              continue
  
      pathogenic_variants.sort(key=lambda x: x['score'], reverse=True)
      return {
          'total_analyzed': len(variants_data),
          'pathogenic_count': len(pathogenic_variants),
          'pathogenic_variants': pathogenic_variants
      }

• src/tools.ts:510-545 (schema)

  Defines the Tool object with name, description, and inputSchema for validating batch variant inputs and threshold.

  export const BATCH_PATHOGENICITY_FILTER_TOOL: Tool = {
    name: 'batch_pathogenicity_filter',
    description: `Filter variants by pathogenicity threshold.
  
  Efficiently identifies pathogenic variants from large lists.
  
  Perfect for: VCF filtering, prioritizing clinical variants.
  
  Example: "Filter 100 variants for pathogenicity > 0.7"`,
    inputSchema: {
      type: 'object',
      properties: {
        variants: {
          type: 'array',
          items: {
            type: 'object',
            properties: {
              chromosome: { type: 'string' },
              position: { type: 'number' },
              ref: { type: 'string' },
              alt: { type: 'string' },
            },
            required: ['chromosome', 'position', 'ref', 'alt'],
          },
          minItems: 1,
        },
        threshold: {
          type: 'number',
          minimum: 0,
          maximum: 1,
          description: 'Pathogenicity threshold (0-1, default: 0.5)',
        },
      },
      required: ['variants'],
    },
  };

• src/index.ts:228-233 (registration)

  Registers the tool in the MCP server request handler switch statement, calling the client method.

  case 'batch_pathogenicity_filter': {
    const result = await getClient().batchPathogenicityFilter(args);
    return {
      content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
    };
  }

• src/alphagenome-client.ts:388-395 (helper)

  Client proxy method that invokes the Python bridge with action 'batch_pathogenicity_filter'.

  async batchPathogenicityFilter(params: any): Promise<any> {
    try {
      return await this.callPythonBridge('batch_pathogenicity_filter', params);
    } catch (error) {
      if (error instanceof ApiError) throw error;
      throw new ApiError(`Batch pathogenicity filter failed: ${error}`, 500);
    }
  }

• src/tools.ts:709-730 (registration)

  Exports the full list of tools including BATCH_PATHOGENICITY_FILTER_TOOL, used by the MCP server for listTools.

  export const ALL_TOOLS: Tool[] = [
    PREDICT_VARIANT_TOOL,
    BATCH_SCORE_TOOL,
    ASSESS_PATHOGENICITY_TOOL,
    PREDICT_TISSUE_SPECIFIC_TOOL,
    COMPARE_VARIANTS_TOOL,
    PREDICT_SPLICE_IMPACT_TOOL,
    PREDICT_EXPRESSION_IMPACT_TOOL,
    ANALYZE_GWAS_LOCUS_TOOL,
    COMPARE_ALLELES_TOOL,
    BATCH_TISSUE_COMPARISON_TOOL,
    PREDICT_TF_BINDING_IMPACT_TOOL,
    PREDICT_CHROMATIN_IMPACT_TOOL,
    COMPARE_PROTECTIVE_RISK_TOOL,
    BATCH_PATHOGENICITY_FILTER_TOOL,
    COMPARE_VARIANTS_SAME_GENE_TOOL,
    PREDICT_ALLELE_SPECIFIC_EFFECTS_TOOL,
    ANNOTATE_REGULATORY_CONTEXT_TOOL,
    BATCH_MODALITY_SCREEN_TOOL,
    GENERATE_VARIANT_REPORT_TOOL,
    EXPLAIN_VARIANT_IMPACT_TOOL,
  ];