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ucsc_genome_exploration

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UCSC Genome Browser Exploration - Explore genome via UCSC: list genomes, list tracks, get sequence, get track data, and cytoband info. Use this skill for genomics tasks involving list genomes list tracks get sequence get track data get cytoband. Combines 5 tools from 1 SCP server(s).

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UCSC Genome Browser Exploration

Discipline: Genomics | Tools Used: 5 | Servers: 1

Description

Explore genome via UCSC: list genomes, list tracks, get sequence, get track data, and cytoband info.

Tools Used

  • list_genomes from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC
  • list_tracks from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC
  • get_sequence from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC
  • get_track_data from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC
  • get_cytoband from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC

Workflow

  1. List available genomes
  2. List tracks for hg38
  3. Get DNA sequence for BRCA1 region
  4. Get track data
  5. Get cytoband info

Test Case

Input

{
    "genome": "hg38",
    "chrom": "chr17",
    "start": 43044295,
    "end": 43125370
}

Expected Steps

  1. List available genomes
  2. List tracks for hg38
  3. Get DNA sequence for BRCA1 region
  4. Get track data
  5. Get cytoband 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 = {
    "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)

async def main():
    async with AsyncExitStack() as stack:
        # Connect to required servers
        sessions = {}
        sessions["ucsc-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC", stack)

        # Execute workflow steps
        # Step 1: List available genomes
        result_1 = await sessions["ucsc-server"].call_tool("list_genomes", arguments={})
        data_1 = parse(result_1)
        print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

        # Step 2: List tracks for hg38
        result_2 = await sessions["ucsc-server"].call_tool("list_tracks", arguments={})
        data_2 = parse(result_2)
        print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

        # Step 3: Get DNA sequence for BRCA1 region
        result_3 = await sessions["ucsc-server"].call_tool("get_sequence", arguments={})
        data_3 = parse(result_3)
        print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

        # Step 4: Get track data
        result_4 = await sessions["ucsc-server"].call_tool("get_track_data", arguments={})
        data_4 = parse(result_4)
        print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}")

        # Step 5: Get cytoband info
        result_5 = await sessions["ucsc-server"].call_tool("get_cytoband", arguments={})
        data_5 = parse(result_5)
        print(f"Step 5 result: {json.dumps(data_5, indent=2, ensure_ascii=False)[:500]}")

        # Cleanup
        print("Workflow complete!")

if __name__ == "__main__":
    asyncio.run(main())