export_protein_data
Export protein data from UniProt in specialized formats like GFF, GenBank, EMBL, or XML for analysis and integration.
Instructions
Export data in specialized formats (GFF, GenBank, etc.)
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| accession | Yes | UniProt accession number | |
| format | Yes | Export format |
Implementation Reference
- src/index.ts:1821-1850 (handler)The main handler function for the 'export_protein_data' tool. It validates input using isValidProteinInfoArgs, fetches protein data from UniProt API in the specified format (gff, genbank, embl, xml), and returns the data as text content.
private async handleExportProteinData(args: any) { if (!isValidProteinInfoArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid export protein data arguments'); } try { const response = await this.apiClient.get(`/uniprotkb/${args.accession}`, { params: { format: args.format }, }); return { content: [ { type: 'text', text: String(response.data), }, ], }; } catch (error) { return { content: [ { type: 'text', text: `Error exporting protein data: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; } } - src/index.ts:780-781 (registration)Dispatch case in the CallToolRequestSchema handler that routes calls to the export_protein_data tool to its handler function.
case 'export_protein_data': return this.handleExportProteinData(args); - src/index.ts:687-697 (schema)Tool registration and input schema definition in the ListToolsRequestSchema response. Defines the tool name, description, and input schema requiring accession and format.
name: 'export_protein_data', description: 'Export data in specialized formats (GFF, GenBank, etc.)', inputSchema: { type: 'object', properties: { accession: { type: 'string', description: 'UniProt accession number' }, format: { type: 'string', enum: ['gff', 'genbank', 'embl', 'xml'], description: 'Export format' }, }, required: ['accession', 'format'], }, }, - src/index.ts:79-89 (helper)Input validation helper function used by the export_protein_data handler to validate arguments (accession required, format optional with limited enums). Note: enum includes xml but not all export formats; handler relies on API.
const isValidProteinInfoArgs = ( args: any ): args is { accession: string; format?: string } => { return ( typeof args === 'object' && args !== null && typeof args.accession === 'string' && args.accession.length > 0 && (args.format === undefined || ['json', 'tsv', 'fasta', 'xml'].includes(args.format)) ); };