compare_alleles
Analyze effects of multiple genetic mutations at a specific genomic position to understand variant impacts and hotspot variations.
Instructions
Compare different alleles at the same position.
Useful for understanding effects of different mutations at a hotspot position.
Example: "Compare T>C vs T>G vs T>A at chr19:44908684"
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| chromosome | Yes | ||
| position | Yes | ||
| ref | Yes | ||
| alts | Yes |
Implementation Reference
- scripts/alphagenome_bridge.py:417-450 (handler)Core handler function implementing the compare_alleles tool logic: compares multiple alternate alleles at the same genomic position by calling predict_variant_effect for each and compiling results.def compare_alleles(client, params: Dict[str, Any]) -> Dict[str, Any]: """ Compare different alleles at the same position. """ chromosome = params.get('chromosome') position = params.get('position') ref = params.get('ref') alts = params.get('alts', []) results = {} for alt in alts: try: var_params = { 'chromosome': chromosome, 'position': position, 'ref': ref, 'alt': alt } result = predict_variant_effect(client, var_params) results[f"{ref}>{alt}"] = { 'impact_level': result['interpretation']['impact_level'], 'expression_fc': result['predictions'].get('rna_seq', {}).get('fold_change', 0), 'clinical_sig': result['interpretation']['clinical_significance'] } except Exception as e: print(f"Warning: Failed for allele {alt}: {e}", file=sys.stderr) results[f"{ref}>{alt}"] = {'error': str(e)} return { 'position': f"{chromosome}:{position}", 'reference': ref, 'allele_comparisons': results }
- src/index.ts:191-196 (handler)MCP server tool handler for 'compare_alleles': dispatches to AlphaGenomeClient.compareAlleles and formats response.case 'compare_alleles': { const result = await getClient().compareAlleles(args); return { content: [{ type: 'text', text: JSON.stringify(result, null, 2) }], }; }
- src/tools.ts:368-389 (schema)Tool schema definition including name, description, and input validation schema for compare_alleles.export const COMPARE_ALLELES_TOOL: Tool = { name: 'compare_alleles', description: `Compare different alleles at the same position. Useful for understanding effects of different mutations at a hotspot position. Example: "Compare T>C vs T>G vs T>A at chr19:44908684"`, inputSchema: { type: 'object', properties: { chromosome: { type: 'string', pattern: '^chr([1-9]|1[0-9]|2[0-2]|X|Y)$' }, position: { type: 'number', minimum: 1 }, ref: { type: 'string', pattern: '^[ATGCatgc]+$' }, alts: { type: 'array', items: { type: 'string', pattern: '^[ATGCatgc]+$' }, minItems: 2, }, }, required: ['chromosome', 'position', 'ref', 'alts'], }, };
- src/tools.ts:709-730 (registration)Registration of compare_alleles tool in the ALL_TOOLS array, used by MCP server for tool listing.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, ];
- src/alphagenome-client.ts:328-335 (helper)Client method that bridges to Python by calling the alphagenome_bridge.py with 'compare_alleles' action.async compareAlleles(params: any): Promise<any> { try { return await this.callPythonBridge('compare_alleles', params); } catch (error) { if (error instanceof ApiError) throw error; throw new ApiError(`Allele comparison failed: ${error}`, 500); } }