get_transcripts
Retrieve detailed transcript structures for a specific gene, including exons, introns, and coding sequences, to analyze gene expression and alternative splicing patterns.
Instructions
Get all transcripts for a gene with detailed structure
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| gene_id | Yes | Ensembl gene ID | |
| species | No | Species name (default: homo_sapiens) | |
| canonical_only | No | Return only canonical transcript (default: false) |
Implementation Reference
- src/index.ts:960-994 (handler)The handler function for the 'get_transcripts' tool. Validates input, queries Ensembl REST API for gene with expanded transcripts, filters optionally for canonical transcripts, and returns formatted JSON with gene info and transcripts.
private async handleGetTranscripts(args: any) { if (!isValidTranscriptArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid transcript arguments'); } try { const species = this.getDefaultSpecies(args.species); const response = await this.apiClient.get(`/lookup/id/${args.gene_id}`, { params: { species, expand: 1 }, }); const gene = response.data; let transcripts = gene.Transcript || []; if (args.canonical_only) { transcripts = transcripts.filter((t: any) => t.is_canonical === 1); } return { content: [ { type: 'text', text: JSON.stringify({ gene_id: gene.id, gene_name: gene.display_name, transcript_count: transcripts.length, transcripts: transcripts, }, null, 2), }, ], }; } catch (error) { return this.handleError(error, 'fetching transcripts'); } } - src/index.ts:584-595 (registration)Registration of the 'get_transcripts' tool in the ListToolsRequestSchema handler, providing name, description, and input schema.
name: 'get_transcripts', description: 'Get all transcripts for a gene with detailed structure', inputSchema: { type: 'object', properties: { gene_id: { type: 'string', description: 'Ensembl gene ID' }, species: { type: 'string', description: 'Species name (default: homo_sapiens)' }, canonical_only: { type: 'boolean', description: 'Return only canonical transcript (default: false)' }, }, required: ['gene_id'], }, }, - src/index.ts:838-839 (registration)Routes calls to the 'get_transcripts' tool to its handler function in the CallToolRequestSchema switch statement.
return this.handleGetTranscripts(args); case 'search_genes': - src/index.ts:283-294 (schema)Type guard function for validating input arguments to the 'get_transcripts' tool.
const isValidTranscriptArgs = ( args: any ): args is { gene_id: string; species?: string; canonical_only?: boolean } => { return ( typeof args === 'object' && args !== null && typeof args.gene_id === 'string' && args.gene_id.length > 0 && (args.species === undefined || typeof args.species === 'string') && (args.canonical_only === undefined || typeof args.canonical_only === 'boolean') ); };