annobee

Annobee

About The Project

annobee is designed to analyze genetic variants to determine their pathogenicity using multiple established criteria. It integrates several functions to set various genetic criteria based on evolutionary conservation, allele frequency, and ACMG/AMP standards. The main functionality is centralized in the main.py.

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Built With

• Python

Getting Started

To get a local copy up and running follow these simple example steps.

Prerequisites

• MongoDB: You can download it from MongoDB Download Center.
• Python: Download Python here.

Requirements

• flask==2.0.1
• numpy==1.23.5
• pandas==1.5.3
• requests==2.25.1
• tqdm==4.65.0

Installation

1. Clone the repo

   git clone https://github.com/variantAnnotation/annobee-sdk.git

2. Follow to directory where you clone the repo:

   cd annobee-sdk

3. Install requirements and dependencies:

   pip install -r requirements.txt

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Usage

Starting the Flask API

To start the Flask API that the SDK communicates with:

python app.py

Command-Line Interface

To use the annobee-sdk, you can execute the CLI tool with various options to evaluate genetic variant criteria.

Example 1: Evaluate Specific Criteria (PS1)

python cli.py 1-14973-A-AG --endpoint http://localhost:5000/api/interpret -ps1

Example 2: Evaluate All Criteria

python cli.py 1-14973-A-AG --endpoint http://localhost:5000/api/interpret -all

Using the Annobee Class in a Python Script

Here's an example script that evaluates multiple variants using the Annobee class:

import json
from cli import Annobee

def evaluate_variant(annobee, variant, criteria):
    variant_info = annobee.get_criteria(variant)
    results = {}
    
    if criteria == 'all':
        results = annobee.get_all(variant_info)
    else:
        for criterion in criteria:
            if criterion == 'PS1':
                results['PS1'] = annobee.get_ps1(variant_info)
            elif criterion == 'PM5':
                results['PM5'] = annobee.get_pm5(variant_info)
            elif criterion == 'BP7':
                results['BP7'] = annobee.get_bp7(variant_info)
            elif criterion == 'PVS1':
                results['PVS1'] = annobee.get_pvs1(variant_info)
            # Add more criteria as needed
            
    return results

if __name__ == '__main__':
    # Set the endpoint
    endpoint = 'http://localhost:5000/api/interpret'
    annobee = Annobee(endpoint=endpoint)

    # List of variants
    variants = [
        '1-14973-A-AG',
        '2-23214-G-T',
        '3-45321-C-A',
        '4-55423-T-G',
        '5-67432-A-C'
    ]

    # Evaluate one criterion for one variant
    print("Evaluating one criterion (PS1) for one variant:")
    result_one_criterion = evaluate_variant(annobee, variants[0], ['PS1'])
    print(json.dumps(result_one_criterion, indent=4))

    # Evaluate three criteria for one variant
    print("\nEvaluating three criteria (PS1, PM5, BP7) for one variant:")
    result_three_criteria = evaluate_variant(annobee, variants[0], ['PS1', 'PM5', 'BP7'])
    print(json.dumps(result_three_criteria, indent=4))

    # Evaluate all criteria for one variant
    print("\nEvaluating all criteria for one variant:")
    result_all_criteria = evaluate_variant(annobee, variants[0], 'all')
    print(json.dumps(result_all_criteria, indent=4))

Running the Test Script

Ensure your Flask API is running and that the cli.py script with the Annobee class is in the same directory or properly installed. Then run the test.py script:

python test.py

This will print the results of evaluating both one criterion, three criteria, and all criteria for the first variant in the list using the specified endpoint. Adjust the criteria and variant list as needed for your specific use case.

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Roadmap

• Adding testing metrics regarding the performance of the platform

Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

License

Distributed under the MIT License. See LICENSE.txt for more information.