regulatory-region-analysis

name	regulatory_region_analysis
description	Regulatory Region Analysis - Analyze regulatory regions: get overlapping features, binding matrix, sequence, and phenotype associations. Use this skill for epigenomics tasks involving get overlap region get species binding matrix get sequence get phenotype region. Combines 4 tools from 2 SCP server(s).

Regulatory Region Analysis

Discipline: Epigenomics | Tools Used: 4 | Servers: 2

Description

Analyze regulatory regions: get overlapping features, binding matrix, sequence, and phenotype associations.

Tools Used

• get_overlap_region from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
• get_species_binding_matrix from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
• get_sequence from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC
• get_phenotype_region from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl

Workflow

1. Get overlapping regulatory features
2. Get transcription factor binding
3. Retrieve DNA sequence
4. Check phenotype associations

Test Case

Input

{
    "region": "7:140753336-140753436",
    "species": "homo_sapiens",
    "genome": "hg38"
}

Expected Steps

1. Get overlapping regulatory features
2. Get transcription factor binding
3. Retrieve DNA sequence
4. Check phenotype associations

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",
    "ucsc-server": "https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC"
}

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())