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transcriptome_analysis

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Transcriptome Analysis Pipeline - Analyze transcriptome: Ensembl transcript lookup, sequence retrieval, haplotype analysis, and UCSC track data. Use this skill for transcriptomics tasks involving get lookup id get sequence id get transcript haplotypes get track data. Combines 4 tools from 2 SCP server(s).

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Transcriptome Analysis Pipeline

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

Description

Analyze transcriptome: Ensembl transcript lookup, sequence retrieval, haplotype analysis, and UCSC track data.

Tools Used

  • get_lookup_id from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
  • get_sequence_id from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
  • get_transcript_haplotypes from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
  • get_track_data from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC

Workflow

  1. Look up transcript details
  2. Get transcript sequence
  3. Analyze transcript haplotypes
  4. Get UCSC track data

Test Case

Input

{
    "transcript_id": "ENST00000269305",
    "species": "homo_sapiens",
    "genome": "hg38"
}

Expected Steps

  1. Look up transcript details
  2. Get transcript sequence
  3. Analyze transcript haplotypes
  4. Get UCSC track data

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)

async def main():
    async with AsyncExitStack() as stack:
        # Connect to required servers
        sessions = {}
        sessions["ensembl-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl", stack)
        sessions["ucsc-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC", stack)

        # Execute workflow steps
        # Step 1: Look up transcript details
        result_1 = await sessions["ensembl-server"].call_tool("get_lookup_id", arguments={})
        data_1 = parse(result_1)
        print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

        # Step 2: Get transcript sequence
        result_2 = await sessions["ensembl-server"].call_tool("get_sequence_id", arguments={})
        data_2 = parse(result_2)
        print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

        # Step 3: Analyze transcript haplotypes
        result_3 = await sessions["ensembl-server"].call_tool("get_transcript_haplotypes", arguments={})
        data_3 = parse(result_3)
        print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

        # Step 4: Get UCSC 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]}")

        # Cleanup
        print("Workflow complete!")

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