# Simple Vibe Prompt — Module 5: ORF Finder & Promoter Classifier

## Part 1 — ORF Finder
Read `data/genome1.fasta` as a raw DNA sequence (no header).
Find all ORFs in all 6 reading frames (3 forward, 3 reverse complement): start at ATG, end at TAA/TAG/TGA, keep only ORFs ≥ 100 bp.
Save results to `outputs/module5_orfs_genome1_simple.csv` and print a summary.

## Part 2 — Promoter Classifier
Load `data/all_promoter_sequences.csv` (positive class) and `data/all_incorrect_ORFs.csv` (negative class). Use up to 500 sequences from each.
Encode each sequence as tri-nucleotide (k=3) frequency features.
Use sklearn's MLPClassifier on a 70/30 split. Print accuracy and confusion matrix.
Save to `outputs/module5_gpann_confusion_simple.csv` and `outputs/module5_gpann_metrics_simple.json`.
