batch_modality_screen

Screen multiple genomic variants for specific regulatory effects like expression, splicing, TF binding, or chromatin changes. Use for targeted regulatory studies and modality-specific analysis.

Instructions

Screen variants across specific regulatory modalities.

Efficiently tests multiple variants for specific regulatory effects.

Perfect for: targeted regulatory screens, modality-specific studies.

Example: "Screen 20 variants for splicing effects"

Input Schema

TableJSON Schema

Name	Required	Description	Default
`variants`	Yes
`modality`	Yes	Regulatory modality to screen

Implementation Reference

scripts/alphagenome_bridge.py:622-656 (handler)

Core implementation of batch_modality_screen: maps modality to specific output types, processes each variant by calling predict_variant_effect, collects and returns results.

def batch_modality_screen(client, params: Dict[str, Any]) -> Dict[str, Any]:
    """Screen variants across specific modalities."""
    variants_data = params.get('variants', [])
    modality = params.get('modality', 'expression')

    # Map modality names to OutputType enums
    modality_map = {
        'expression': [dna_client.OutputType.RNA_SEQ, dna_client.OutputType.CAGE],
        'splicing': [dna_client.OutputType.SPLICE_SITES],
        'tf_binding': [dna_client.OutputType.CHIP_TF],
        'chromatin': [dna_client.OutputType.DNASE, dna_client.OutputType.ATAC]
    }
    modalities = modality_map.get(modality, [dna_client.OutputType.RNA_SEQ, dna_client.OutputType.SPLICE_SITES])

    results = []
    for v in variants_data:
        # Create a copy with output_types
        variant_params = v.copy()
        variant_params['output_types'] = modalities
        try:
            result = predict_variant_effect(client, variant_params)
            results.append({
                'variant': result['variant'],
                'predictions': result['predictions'],
                'impact': result['interpretation']['impact_level']
            })
        except Exception as e:
            print(f"Warning: Failed: {e}", file=sys.stderr)
            continue

    return {
        'modalities_tested': [modality],  # Return string representation
        'total_variants': len(results),
        'results': results
    }

src/index.ts:258-263 (handler)

MCP server tool handler: invokes AlphaGenomeClient.batchModalityScreen and formats result as MCP content response.

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

src/tools.ts:635-659 (schema)

Input schema defining variants array (with chromosome, position, ref, alt) and modality enum.

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,
    },
    modality: {
      type: 'string',
      enum: ['expression', 'splicing', 'tf_binding', 'chromatin'],
      description: 'Regulatory modality to screen',
    },
  },
  required: ['variants', 'modality'],
},

src/tools.ts:626-660 (registration)

Tool definition and registration: exports BATCH_MODALITY_SCREEN_TOOL with name, description, and schema for MCP tool listing.

export const BATCH_MODALITY_SCREEN_TOOL: Tool = {
  name: 'batch_modality_screen',
  description: `Screen variants across specific regulatory modalities.

Efficiently tests multiple variants for specific regulatory effects.

Perfect for: targeted regulatory screens, modality-specific studies.

Example: "Screen 20 variants for splicing effects"`,
  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,
      },
      modality: {
        type: 'string',
        enum: ['expression', 'splicing', 'tf_binding', 'chromatin'],
        description: 'Regulatory modality to screen',
      },
    },
    required: ['variants', 'modality'],
  },
};

src/alphagenome-client.ts:436-442 (helper)

Bridge method in AlphaGenomeClient: calls Python bridge script with 'batch_modality_screen' action.

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

AlphaGenome MCP Server