check_gene
Verify gene presence in single-cell RNA sequencing data before creating visualizations or coloring by genes, ensuring accurate analysis.
Instructions
Check if genes exist in adata.var_names. This tool should be called before gene expression visualizations or color by genes.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| var_names | No | gene names. |
Implementation Reference
- src/scmcp/tool/util.py:80-82 (handler)The core handler function that implements the check_gene tool: returns a dictionary {gene: exists} for each gene in var_names against adata.var_names.
def check_gene(adata, var_names): return {v: v in adata.var_names for v in var_names} - src/scmcp/schema/util.py:45-51 (schema)Pydantic model defining the input schema for check_gene: expects a list of gene names (var_names).
class VarNamesModel(JSONParsingModel): """ListObsModel""" var_names: List[str] = Field( default=None, description="gene names." ) - src/scmcp/tool/util.py:34-38 (registration)MCP Tool object creation for 'check_gene', specifying name, description, and input schema. This tool is later included in util_tools dict used by the server.
check_gene_tool = types.Tool( name="check_gene", description="Check if genes exist in adata.var_names. This tool should be called before gene expression visualizations or color by genes.", inputSchema=VarNamesModel.model_json_schema(), ) - src/scmcp/tool/util.py:98-104 (registration)util_tools dictionary that maps tool names to Tool instances, imported and used in server.py for MCP tool registration.
util_tools = { "mark_var": mark_var_tool, "list_var": list_var_tool, "list_obs": list_obs_tool, "check_gene": check_gene_tool, "merge_adata": merge_adata_tool, }