#!/usr/bin/env python3
"""
Oncogenic Godzilla Audit: TP53 Healthy vs Mutated
The ultimate bio-informatic sabotage detector.
"""

import sys
import numpy as np
from pathlib import Path
import logging

# Add parent directory to path
sys.path.insert(0, str(Path(__file__).parent.parent.parent))
sys.path.insert(0, str(Path(__file__).parent.parent.parent / "4-Infrastructure"))
sys.path.insert(0, str(Path(__file__).parent.parent.parent / "0-Core-Formalism"))

from scripts.rgflow_blind_detector import BlindDetector

logging.basicConfig(level=logging.ERROR)

def run_godzilla_audit():
    # 1. TP53 Reference mRNA (Partial/Representative Segment)
    # This is a lawful, high-informativity biological sequence.
    tp53_healthy = ("ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCC"
                    "CTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAG"
                    "AGGCTGCTCCCCGCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAA"
                    "ACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTG"
                    "CCAACTGGCCAAGACCTGCCCCGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACA"
                    "TGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGT"
                    "GTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTA"
                    "CATGTGTAACAGTTCCTGCATGGGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACTCCAGTGGTAATCTACTGGGACGGAACAGCT"
                    "TTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCGCAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGC"
                    "ACTAAGCGAGCACTGCCCAACAACACCAGCTCCTCTCCCCAGCCAAAGAAGAAACCACTGGATGGAGAATATTTCACCCTTCAGATCCGTGGGCGTGAGCG"
                    "CTTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGGAAGGAGCCAGGGGGGAGCAGGGCTCACTCCAGCCACCTGAAGT"
                    "CCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAAACTCATGTTCAAGACAGAAGGGCCTGACTCAGACTGA")
    
    # 2. Inject "Godzilla" Hotspot Mutations
    # R175H (Arg -> His at codon 175)
    # R248W (Arg -> Trp at codon 248)
    # These are devastating informatic collapses in the genome.
    
    tp53_cancer = list(tp53_healthy)
    
    # R175H: Typical CGC -> CAC transition
    loc_175 = 175 * 3
    tp53_cancer[loc_175:loc_175+3] = list("CAC")
    
    # R248W: Typical CGG -> TGG transition
    loc_248 = 248 * 3
    tp53_cancer[loc_248:loc_248+3] = list("TGG")
    
    tp53_cancer = "".join(tp53_cancer)
    
    # 3. RGFlow Differential Audit
    detector = BlindDetector()
    print("--- ONCOGENIC GODZILLA DIFFERENTIAL AUDIT: TP53 ---")
    
    hotspots = [loc_175, loc_248]
    for start in hotspots:
        window_h = tp53_healthy[max(0, start-100) : min(len(tp53_healthy), start+100)]
        window_c = tp53_cancer[max(0, start-100) : min(len(tp53_cancer), start+100)]
        
        state_h = detector.calculate_window_state(window_h)
        state_c = detector.calculate_window_state(window_c)
        
        # Calculate Delta Sigma
        # In cancer, the mutation drops the spectral coherence of the codon block
        delta_sigma = state_h.sigma_q - state_c.sigma_q
        
        print(f"\nLocus {start} (Codon {start//3}):")
        print(f"  Healthy Sigma: {state_h.sigma_q:.6f}")
        print(f"  Cancer Sigma:  {state_c.sigma_q:.6f}")
        
        if state_c.sigma_q < state_h.sigma_q:
            loss = (delta_sigma / state_h.sigma_q) * 100
            print(f"  [!] DETECTED: Informatic Collapse ({loss:.2f}% reduction in scale-stability)")
            print(f"  [+] RECOMMENDATION: Informatic Stripping (Restoration to reference)")
        else:
            print(f"  Match: Scale-stability preserved or neutral.")

    print("\n--- AUDIT COMPLETE ---")

if __name__ == "__main__":
    run_godzilla_audit()