cross-species-genomics

name	cross_species_genomics
description	Cross-Species Comparative Genomics - Compare genomes across species: Ensembl compara, alignment, gene trees, and NCBI taxonomy. Use this skill for comparative genomics tasks involving get info compara species sets get alignment region get genetree member symbol get taxonomy. Combines 4 tools from 2 SCP server(s).

Cross-Species Comparative Genomics

Discipline: Comparative Genomics | Tools Used: 4 | Servers: 2

Description

Compare genomes across species: Ensembl compara, alignment, gene trees, and NCBI taxonomy.

Tools Used

• get_info_compara_species_sets from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
• get_alignment_region 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 from ncbi-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI

Workflow

1. Get compara species sets
2. Get genomic alignment
3. Get gene tree
4. Get taxonomy info

Test Case

Input

{
    "gene": "BRCA1",
    "species": "homo_sapiens",
    "region": "17:43044295-43125370"
}

Expected Steps

1. Get compara species sets
2. Get genomic alignment
3. Get gene tree
4. Get taxonomy info

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.

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",
    "ncbi-server": "https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI"
}

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)

  ():
      AsyncExitStack()  stack:
        
        sessions = {}
        sessions[] =  connect(, stack)
        sessions[] =  connect(, stack)

        
        
        result_1 =  sessions[].call_tool(, arguments={})
        data_1 = parse(result_1)
        ()

        
        result_2 =  sessions[].call_tool(, arguments={})
        data_2 = parse(result_2)
        ()

        
        result_3 =  sessions[].call_tool(, arguments={})
        data_3 = parse(result_3)
        ()

        
        result_4 =  sessions[].call_tool(, arguments={})
        data_4 = parse(result_4)
        ()

        
        ()

 __name__ == :
    asyncio.run(main())