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A Python tool for querying and extracting detailed SNP and gene information from NCBI, with section parsing and relevance-based summarization.

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genomic-insight-extractor

A Python tool for querying and extracting detailed SNP and gene information from NCBI, with section parsing and relevance-based summarization.

Features

  • Fetch SNP and gene details from NCBI.
  • Parse and extract sections using BeautifulSoup.
  • Use GPT models to identify relevant sections based on queries.
  • Summarize and prune text for efficient output.

Requirements

Ensure you have Python 3.8 or later installed. Install the required dependencies:

pip install -r requirements.txt

Usage

  1. Set up your OpenAI API Key:
    Update your OpenAI API key in the agent.py file or set it as an environment variable.

    os.environ["OPENAI_API_KEY"] = "<YOUR_API_KEY>"
  2. Update the Query:
    Replace the placeholder query with your desired query in the agent.py file:

    query = "<YOUR_QUERY>"
  3. Run the Agent:
    Execute the script to fetch and process data:

    python agent.py
  4. Output:
    The results will be saved to the appropriate directory and displayed in the terminal.

Notes

  • Ensure you have access to the internet for API calls and data fetching.
  • Modify file paths and configurations as needed for your environment.

License

This project is licensed under the MIT License. See the LICENSE file for details.

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A Python tool for querying and extracting detailed SNP and gene information from NCBI, with section parsing and relevance-based summarization.

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