#!/usr/bin/env python3
"""
Pathogenicity Tool - Mock implementation for testing
"""

import sys
import pandas as pd
from pathlib import Path
from typing import Dict, List, Optional
import click

class PathogenicityTool:
    """Mock pathogenicity prediction tool"""
    
    def __init__(self, model: str = "ensemble", threshold: float = 0.5, verbose: bool = False):
        self.model = model
        self.threshold = threshold
        self.verbose = verbose
    
    def predict_file(self, input_file: str, output_file: str) -> Dict:
        """Mock prediction function"""
        return {
            'variants_analyzed': 5,
            'pathogenic_count': 2
        }

def main():
    """Command line interface for pathogenicity predictor"""
    click.echo("Pathogenicity predictor - Mock implementation")

if __name__ == '__main__':
    main() 