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 <YOUR_SCP_HUB_API_KEY> with your own SCP Hub API Key. You can obtain one from the SCP Platform.

import asyncio
import json
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, transport_type):
    transport = streamablehttp_client(url=url, headers={"SCP-HUB-API-KEY": "<YOUR_SCP_HUB_API_KEY>"})
    read, write, _ = await transport.__aenter__()
    ctx = ClientSession(read, write)
    session = await ctx.__aenter__()
    await session.initialize()
    return session, ctx, transport

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():
    # Connect to required servers
    sessions = {}
    sessions["ucsc-server"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC", "streamable-http")

    # 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())