gene_family_evolution: Скилл анализа эволюции генов

--- name: gene_family_evolution description: "Gene Family Evolution Analysis - Analyze gene family evolution: CAFE gene tree, homology, Ensembl gene tree, and taxonomy. Use this skill for molecular evolution tasks involving get cafe genetree member symbol get homology symbol get genetree member symbol get taxonomy classification. Combines 4 tools from 1 SCP server(s)." --- # Gene Family Evolution Analysis **Discipline**: Molecular Evolution | **Tools Used**: 4 | **Servers**: 1 ## Description Analyze gene family evolution: CAFE gene tree, homology, Ensembl gene tree, and taxonomy. ## Tools Used - **`get_cafe_genetree_member_symbol`** from `ensembl-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl` - **`get_homology_symbol`** from `ensembl-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl` - **`get_genetree_member_symbol`** from `ensembl-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl` - **`get_taxonomy_classification`** from `ensembl-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl` ## Workflow 1. Get CAFE gene family evolution tree 2. Find homologs across species 3. Get full gene tree 4. Get taxonomic classification ## Test Case ### Input ```json { "gene": "TP53", "species": "homo_sapiens" } ``` ### Expected Steps 1. Get CAFE gene family evolution tree 2. Find homologs across species 3. Get full gene tree 4. Get taxonomic classification ## Usage Example > **Note:** Replace `sk-b04409a1-b32b-4511-9aeb-22980abdc05c` with your own SCP Hub API Key. You can obtain one from the [SCP Platform](https://scphub.intern-ai.org.cn). ```python import asyncio import json from contextlib import AsyncExitStack from mcp import ClientSession from mcp.client.streamable_http import streamablehttp_client from mcp.client.sse import sse_client SERVERS = { "ensembl-server": "https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl" } async def connect(url, stack): transport = streamablehttp_client(url=url, headers={"SCP-HUB-API-KEY": "sk-b04409a1-b32b-4511-9aeb-22980abdc05c"}) read, write, _ = await stack.enter_async_context(transport) ctx = ClientSession(read, write) session = await stack.enter_async_context(ctx) await session.initialize() return session def parse(result): try: if hasattr(result, 'content') and result.content: c = result.content[0] if hasattr(c, 'text'): try: return json.loads(c.text) except: return c.text return str(result) except: return str(result) async def main(): async with AsyncExitStack() as stack: # Connect to required servers sessions = {} sessions["ensembl-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl", stack) # Execute workflow steps # Step 1: Get CAFE gene family evolution tree result_1 = await sessions["ensembl-server"].call_tool("get_cafe_genetree_member_symbol", arguments={}) data_1 = parse(result_1) print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}") # Step 2: Find homologs across species result_2 = await sessions["ensembl-server"].call_tool("get_homology_symbol", arguments={}) data_2 = parse(result_2) print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}") # Step 3: Get full gene tree result_3 = await sessions["ensembl-server"].call_tool("get_genetree_member_symbol", arguments={}) data_3 = parse(result_3) print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}") # Step 4: Get taxonomic classification result_4 = await sessions["ensembl-server"].call_tool("get_taxonomy_classification", arguments={}) data_4 = parse(result_4) print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}") # Cleanup print("Workflow complete!") if __name__ == "__main__": asyncio.run(main()) ```