"""Microbiome analysis module for NuroMind"""

from typing import Dict, List, Any


def load_16s(filepath: str) -> Dict[str, Any]:
    """Load 16S rRNA sequencing data (placeholder)"""
    return {
        "type": "16s",
        "filepath": filepath,
        "otu_table": None,
        "taxonomy": None
    }


def diversity_analysis(microbiome_data: Dict[str, Any]) -> Dict[str, float]:
    """Calculate diversity metrics (placeholder)"""
    return {
        "alpha_diversity": {
            "shannon": 2.5,
            "simpson": 0.8,
            "observed_species": 150
        },
        "beta_diversity": {
            "bray_curtis": None,
            "unifrac": None
        }
    }


class DysbiosisDetector:
    """Detect microbial dysbiosis patterns"""
    
    def __init__(self, reference_dataset: Optional[str] = None):
        self.reference = reference_dataset
    
    def detect(self, microbiome_data: Dict[str, Any]) -> Dict[str, Any]:
        """Detect dysbiosis patterns (placeholder)"""
        return {
            "dysbiosis_score": 0.0,
            "altered_taxa": [],
            "recommendations": []
        }


__all__ = ["load_16s", "diversity_analysis", "DysbiosisDetector"]
