BioMCP

Instructions

Implementation Reference

• src/biomcp/individual_tools.py:587-622 (handler)

  MCP tool registration and handler function for 'variant_getter'. Defines input schema via Annotated parameters and docstring. Delegates to internal _variant_details function.
  @mcp_app.tool() @track_performance("biomcp.variant_getter") async def variant_getter( variant_id: Annotated[ str, Field( description="Variant ID (HGVS, rsID, or MyVariant ID like 'chr7:g.140753336A>T')" ), ], include_external: Annotated[ bool, Field( description="Include external annotations (TCGA, 1000 Genomes, functional predictions)" ), ] = True, ) -> str: """Fetch comprehensive details for a specific genetic variant. Retrieves all available information for a variant including: - Gene location and consequences - Population frequencies across databases - Clinical significance from ClinVar - Functional predictions - External annotations (TCGA cancer data, conservation scores) Accepts various ID formats: - HGVS: NM_004333.4:c.1799T>A - rsID: rs113488022 - MyVariant ID: chr7:g.140753336A>T """ return await _variant_details( call_benefit="Fetch comprehensive variant annotations for interpretation", variant_id=variant_id, include_external=include_external, )
• src/biomcp/variants/getter.py:145-182 (helper)

  Internal helper function _variant_details called by the variant_getter tool handler. Defines additional parameters and calls the core get_variant function.
  async def _variant_details( call_benefit: Annotated[ str, "Define and summarize why this function is being called and the intended benefit", ], variant_id: str, include_external: Annotated[ bool, "Include annotations from external sources (TCGA, 1000 Genomes, cBioPortal)", ] = True, assembly: Annotated[ str, "Genome assembly (hg19 or hg38). Default: hg19", ] = DEFAULT_ASSEMBLY, ) -> str: """ Retrieves detailed information for a *single* genetic variant. Parameters: - call_benefit: Define and summarize why this function is being called and the intended benefit - variant_id: A variant identifier ("chr7:g.140453136A>T") - include_external: Include annotations from TCGA, 1000 Genomes, cBioPortal, and Mastermind - assembly: Genome assembly (hg19 or hg38). Default: hg19 Process: Queries the MyVariant.info GET endpoint, optionally fetching additional annotations from external databases Output: A Markdown formatted string containing comprehensive variant annotations (genomic context, frequencies, predictions, clinical data, external annotations). Returns error if invalid. Note: Use the variant_searcher to find the variant id first. """ return await get_variant( variant_id, output_json=False, include_external=include_external, assembly=assembly, )
• src/biomcp/variants/getter.py:42-143 (helper)

  Core implementation get_variant function that queries MyVariant.info API, processes response, adds links/filters/external annotations/OncoKB, and renders to markdown or JSON.
  async def get_variant( # noqa: C901 variant_id: str, output_json: bool = False, include_external: bool = False, assembly: str = DEFAULT_ASSEMBLY, ) -> str: """ Get variant details from MyVariant.info using the variant identifier. The identifier can be a full HGVS-style string (e.g. "chr7:g.140453136A>T") or an rsID (e.g. "rs113488022"). The API response is expected to include a "hits" array; this function extracts the first hit. Args: variant_id: Variant identifier (HGVS or rsID) output_json: Return JSON format if True, else Markdown include_external: Include external annotations (TCGA, 1000 Genomes, cBioPortal) assembly: Genome assembly (hg19 or hg38), defaults to hg19 Returns: Formatted variant data as JSON or Markdown string If output_json is True, the result is returned as a formatted JSON string; otherwise, it is rendered as Markdown. """ response, error = await http_client.request_api( url=f"{MYVARIANT_GET_URL}/{variant_id}", request={"fields": "all", "assembly": assembly}, method="GET", domain="myvariant", ) # Handle errors gracefully with user-friendly messages if error: data_to_return = _format_error_response(error, variant_id) # Skip all processing for error responses if output_json: return json.dumps(data_to_return, indent=2) else: return render.to_markdown(data_to_return) data_to_return = ensure_list(response) # Inject database links into the variant data data_to_return = inject_links(data_to_return) data_to_return = filter_variants(data_to_return) # Collect OncoKB annotations separately for markdown appendage oncokb_annotations: list[str] = [] # Add external annotations if requested if include_external and data_to_return: logger.info( f"Adding external annotations for {len(data_to_return)} variants" ) aggregator = ExternalVariantAggregator() for _i, variant_data in enumerate(data_to_return): logger.info( f"Processing variant {_i}: keys={list(variant_data.keys())}" ) # Get enhanced annotations enhanced = await aggregator.get_enhanced_annotations( variant_id, include_tcga=True, include_1000g=True, include_cbioportal=True, variant_data=variant_data, ) # Add formatted annotations to the variant data formatted = format_enhanced_annotations(enhanced) logger.info( f"Formatted external annotations: {formatted['external_annotations'].keys()}" ) variant_data.update(formatted["external_annotations"]) # Get formatted OncoKB annotation separately gene_aa = aggregator._extract_gene_aa_change(variant_data) # Handle case where method might be mocked as async in tests if inspect.iscoroutine(gene_aa) or inspect.isawaitable(gene_aa): gene_aa = await gene_aa if gene_aa: parts = gene_aa.split(" ", 1) if len(parts) == 2: gene, variant = parts oncokb_formatted = await get_oncokb_annotation_for_variant( gene, variant ) if oncokb_formatted: oncokb_annotations.append(oncokb_formatted) if output_json: return json.dumps(data_to_return, indent=2) else: # Render base markdown and append OncoKB annotations base_markdown = render.to_markdown(data_to_return) if oncokb_annotations: # Append OncoKB annotations as separate markdown sections return base_markdown + "\n" + "\n".join(oncokb_annotations) return base_markdown
• src/biomcp/individual_tools.py:31-31 (registration)

  Import of the _variant_details helper function used by the variant_getter tool.
  from biomcp.variants.getter import _variant_details