chromosome-analysis

name	chromosome_analysis
description	Chromosome Structure Analysis - Analyze chromosome: NCBI summary, UCSC cytoband, genome sequence, and Ensembl assembly info. Use this skill for cytogenetics tasks involving get chromosome summary get cytoband get chromosome sequence get info assembly. Combines 4 tools from 3 SCP server(s).

Chromosome Structure Analysis

Discipline: Cytogenetics | Tools Used: 4 | Servers: 3

Description

Analyze chromosome: NCBI summary, UCSC cytoband, genome sequence, and Ensembl assembly info.

Tools Used

• get_chromosome_summary from ncbi-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI
• get_cytoband from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC
• get_chromosome_sequence from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC
• get_info_assembly from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl

Workflow

1. Get chromosome summary from NCBI
2. Get cytoband info from UCSC
3. Get chromosome sequence
4. Get Ensembl assembly info

Test Case

Input

{
    "taxon": "human",
    "chromosome": "chr21",
    "genome": "hg38",
    "species": "homo_sapiens"
}

Expected Steps

1. Get chromosome summary from NCBI
2. Get cytoband info from UCSC
3. Get chromosome sequence
4. Get Ensembl assembly 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 = {
    "ncbi-server": "https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI",
    "ucsc-server": "https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC",
    "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)
    :  (result)

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