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giae-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Atunrase Ayo
+
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+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+SOFTWARE.

giae-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: giae
+Version: 0.2.0
+Summary: Genome Interpretation & Annotation Engine - An Explainable, Evidence-Centric Framework for Genomic Interpretation
+Project-URL: Homepage, https://github.com/Ayo-Cyber/GIAE
+Project-URL: Documentation, https://github.com/Ayo-Cyber/GIAE#readme
+Project-URL: Repository, https://github.com/Ayo-Cyber/GIAE.git
+Project-URL: Issues, https://github.com/Ayo-Cyber/GIAE/issues
+Author: GIAE Contributors
+License-Expression: MIT
+License-File: LICENSE
+Keywords: annotation,bioinformatics,biopython,explainable-ai,genomics,interpretation
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: >=3.9
+Requires-Dist: biopython>=1.83
+Requires-Dist: click>=8.1.0
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: rich>=13.0.0
+Provides-Extra: ai
+Requires-Dist: fair-esm>=2.0.0; extra == 'ai'
+Requires-Dist: torch>=2.0.0; extra == 'ai'
+Provides-Extra: dev
+Requires-Dist: mypy>=1.8.0; extra == 'dev'
+Requires-Dist: pytest-cov>=4.1.0; extra == 'dev'
+Requires-Dist: pytest>=8.0.0; extra == 'dev'
+Requires-Dist: ruff>=0.2.0; extra == 'dev'
+Provides-Extra: hmmer
+Requires-Dist: pyhmmer>=0.10.0; extra == 'hmmer'
+Description-Content-Type: text/markdown
+
+# GIAE — Genome Interpretation & Annotation Engine
+
+> **Explainability-first genome annotation. Every prediction shows its reasoning.**
+
+[![Python](https://img.shields.io/badge/python-3.10%2B-blue)](https://python.org)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+[![Version](https://img.shields.io/badge/version-0.2.0-green)](pyproject.toml)
+
+Most genome annotation tools are overconfident. PROKKA, Bakta, and RAST assign a label, hide the evidence, and give you no way to know how certain the prediction is. GIAE takes the opposite approach: every gene interpretation includes the full evidence stack, confidence score, uncertainty sources, and a ranked list of competing hypotheses.
+
+---
+
+## What Makes GIAE Different
+
+| Feature | PROKKA / Bakta / RAST | GIAE |
+|---|---|---|
+| Output | Label only | Label + evidence chain + confidence score |
+| Uncertainty | Hidden | Explicit, calibrated per gene |
+| Conflicting evidence | Silently resolved | Flagged and reported |
+| Unknown genes | "hypothetical protein" | Ranked as research priorities |
+| Reasoning | Opaque | Full reasoning chain in every report |
+
+---
+
+## 4-Layer Evidence Pipeline
+
+```
+Genome (.gb / .fasta)
+       │
+       ▼
+┌──────────────────────────────────────────────┐
+│  1. PROSITE Motif Scan         weight: 0.80  │  1,298 curated patterns (bundled)
+│  2. EBI HMMER / Pfam Domains   weight: 0.90  │  Pfam via EBI web API (online)
+│  3. UniProt API Lookup         weight: 1.00  │  Swiss-Prot reviewed entries (online)
+│  4. Conflict Detection                        │  flags when sources disagree
+└──────────────────────────────────────────────┘
+       │
+       ▼
+  Interpretation + Confidence Score + Novel Gene Report
+```
+
+Confidence is computed from evidence convergence — when PROSITE, Pfam, and UniProt all agree, confidence is HIGH. When they disagree, the conflict is surfaced explicitly rather than silently resolved.
+
+---
+
+## Installation
+
+Install from source (recommended while in active development):
+
+```bash
+git clone https://github.com/Ayo-Cyber/GIAE.git
+cd GIAE
+pip install -e ".[dev]"
+```
+
+Or via pip:
+
+```bash
+pip install giae
+```
+
+**Requirements:** Python 3.10+, BioPython, Click, Rich. No local databases required for the base pipeline — PROSITE (1,298 patterns) is bundled.
+
+---
+
+## Quick Start
+
+```bash
+# Offline mode: PROSITE patterns only — no network, instant startup
+# Lambda phage (92 genes) completes in ~4 seconds
+giae interpret lambda_phage.gb --no-uniprot --no-interpro
+
+# Full pipeline: adds EBI HMMER + UniProt API calls
+# Lambda phage takes ~6 minutes (network latency dominates)
+giae interpret lambda_phage.gb
+
+# Save Markdown report to file
+giae interpret lambda_phage.gb --output lambda_report.md
+
+# JSON output for downstream processing
+giae interpret lambda_phage.gb --format json --output results.json
+
+# Large genomes: parallel workers reduce wall time significantly
+# T4 phage (288 genes) — use --no-uniprot --no-interpro for offline speed
+giae interpret T4.gb --workers 4 --no-uniprot --no-interpro
+```
+
+> **Runtime guide:** Offline (PROSITE only) runs in seconds for phage-sized genomes. Online mode (full pipeline) adds ~4–5 seconds per gene for API calls — plan for 5–10 minutes per phage, hours for large bacterial genomes. Use `--workers` to parallelise.
+
+---
+
+## Example Output
+
+A well-characterised gene with converging evidence:
+
+```
+Gene: J — Tail fiber protein
+Hypothesis:  Tail fiber / host receptor-binding protein
+Confidence:  HIGH (0.87)
+Category:    structural_protein
+
+Evidence:
+  [0.82] PROSITE PS51123 — Phage tail fiber repeat
+  [0.94] Pfam PF09255   — Phage_tail_fib (e-value: 2.1e-14)
+  [0.90] UniProt P03722 — Tail fiber protein J, Lambda phage (Swiss-Prot reviewed)
+
+Uncertainty sources: none
+Competing hypotheses: none above threshold
+```
+
+A dark-matter gene with zero detectable signal:
+
+```
+Gene: B — hypothetical protein (147 aa)
+Interpretation: NONE
+Novel Gene Category: DARK MATTER
+Priority:  HIGH PRIORITY
+Reason:    No sequence homology, domains, or motifs detected
+
+Suggested experiments:
+  • Recombinant expression and biochemical activity screening
+  • Deletion mutant phenotyping to assess essentiality
+  • Comparative genomics across related strains
+  • Structural characterization by cryo-EM
+```
+
+---
+
+## Confidence Levels
+
+Every prediction carries a numeric score mapped to a named level:
+
+| Level | Score range | Meaning |
+|-------|-------------|---------|
+| `HIGH` | ≥ 0.80 | Multiple evidence types converge; strong homology or domain hit |
+| `MODERATE` | 0.50 – 0.79 | Some convergence; one strong signal or moderate homology |
+| `LOW` | 0.30 – 0.49 | Weak or single-type evidence; treat as a lead, not a conclusion |
+| `SPECULATIVE` | < 0.30 | Minimal signal; flagged for review |
+
+Scores are adjusted for: evidence diversity (+0.10 for ≥2 types), strong homology (+0.05), high-confidence Pfam domain (+0.08), and penalised for: limited evidence (−0.10), hypothetical homologs (−0.15), single-evidence-type motif-only predictions (capped at 0.85), and conflict (×0.80 penalty).
+
+---
+
+## 7-Phage Benchmark
+
+Benchmarked on seven classic bacteriophage genomes (offline pipeline: PROSITE + Pfam):
+
+| Phage | Genome | Genes | Interpreted | Dark Matter |
+|-------|--------|-------|-------------|-------------|
+| Lambda (λ) | 48.5 kb | 92 | 45 (48.9%) | 44 (47.8%) |
+| T7 | 39.9 kb | 56 | 19 (33.9%) | 36 (64.3%) |
+| PhiX174 | 5.4 kb | 11 | 0 (0.0%) | 11 (100%) |
+| Phi29 | 19.3 kb | 30 | 13 (43.3%) | 16 (53.3%) |
+| Mu | 36.7 kb | 56 | 20 (35.7%) | 35 (62.5%) |
+| P22 | 41.7 kb | 69 | 30 (43.5%) | 38 (55.1%) |
+| T4 | 168.9 kb | 288 | 75 (26.0%) | 213 (73.9%) |
+
+**Median characterization rate: 34.5%**
+
+> **Lambda with the full 4-layer online pipeline:** 48.9% — identical to offline. The 44 dark-matter genes remain dark not because databases are small, but because these proteins genuinely have no detectable sequence-based signal. That is the correct answer.
+
+> **PhiX174 at 0%** is expected and correct. Its proteins (viral jelly-roll β-barrel capsid, DNA pilot tube) are structurally unique folds with no sequence-recognizable motifs. Structural homology search (Foldseek/AlphaFold) is next on the roadmap.
+
+All 7 GenBank files and benchmark reports are in [`case_studies/`](case_studies/).
+
+---
+
+## Novel Gene Discovery
+
+Every run produces a `Novel Gene Report` — a structured research agenda for genes that couldn't be interpreted:
+
+```
+Novel Gene Discovery
+  Dark Matter:  44  (zero evidence from any source)
+  Weak Signal:  13  (confidence < 35%)
+  Conflicting:   0
+
+Top Research Priorities:
+  1. B    — 147 aa  HIGH PRIORITY  dark_matter
+  2. ea22 — 113 aa  HIGH PRIORITY  dark_matter
+  3. orf  — 98  aa  HIGH PRIORITY  dark_matter
+```
+
+Three novelty categories:
+- **Dark matter** — zero computational evidence from any source
+- **Weak evidence** — some hits, but confidence below threshold (< 35%)
+- **Conflict** — two or more evidence sources contradict each other
+
+Each candidate includes suggested experiments scaled to protein length and category.
+
+---
+
+## Python API
+
+Use GIAE programmatically for batch processing or integration into pipelines:
+
+```python
+from giae.parsers.genbank import parse_genbank
+from giae.engine.interpreter import Interpreter
+
+# Load genome
+genome = parse_genbank("lambda_phage.gb")
+
+# Run offline pipeline (fast, no network)
+interpreter = Interpreter(use_uniprot=False, use_interpro=False)
+summary = interpreter.interpret_genome(genome)
+
+print(f"Interpreted {summary.interpreted_genes}/{summary.total_genes} genes")
+print(f"Dark matter: {summary.novel_gene_report.dark_matter_count}")
+
+# Inspect individual results
+for result in summary.results:
+    if result.interpretation:
+        print(result.interpretation.get_explanation())
+
+# Quick single-sequence interpretation
+interp = interpreter.quick_interpret("MKVLIFFVIALFSSATAAF...", sequence_type="protein")
+print(interp)
+```
+
+---
+
+## CLI Reference
+
+```
+Usage: giae [OPTIONS] COMMAND [ARGS]...
+
+Commands:
+  interpret   Interpret a genome file (.gb or .fasta)
+  db          Database management (download databases, check status)
+```
+
+### `giae interpret`
+
+```
+Options:
+  --output, -o PATH           Write report to file (default: stdout)
+  --format, -f [report|json]  Output format (default: report)
+  --workers, -w INT           Parallel workers, 1–16 (default: 1)
+  --no-uniprot                Skip UniProt API (offline mode)
+  --no-interpro               Skip EBI HMMER domain search (offline mode)
+  --verbose, -v               Show pipeline details
+```
+
+### `giae db`
+
+Manages optional local databases for the plugin layer. The base pipeline (PROSITE) needs no setup — databases here unlock the local HMMER and BLAST plugins.
+
+```bash
+# Check what's installed
+giae db status
+
+# Download PROSITE (latest from ExPASy — updates the bundled copy)
+giae db download prosite
+
+# Download SwissProt for local BLAST (requires BLAST+ installed)
+giae db download swissprot
+
+# Download Pfam for local HMMER (requires HMMER3 installed)
+giae db download pfam
+
+# Force re-download
+giae db download prosite --force
+```
+
+> **Do you need to run `giae db`?** No, for the base pipeline. PROSITE (1,298 patterns) is bundled. `giae db` is only needed if you want local BLAST or HMMER plugins, which bypass the EBI web API with locally-installed tools and larger databases.
+
+---
+
+## Project Structure
+
+```
+GIAE/
+├── src/giae/
+│   ├── analysis/           # Evidence extraction modules
+│   │   ├── motif.py        # PROSITE pattern scanning
+│   │   ├── prosite.py      # PROSITE database parser
+│   │   ├── uniprot.py      # UniProt REST API client
+│   │   ├── interpro.py     # EBI HMMER / InterPro client
+│   │   ├── hmmer.py        # Local HMMER plugin
+│   │   ├── blast_local.py  # Local BLAST plugin
+│   │   └── ai.py           # ESM-2 embedding plugin
+│   ├── cli/
+│   │   ├── main.py         # CLI entrypoint
+│   │   └── db.py           # Database management commands
+│   ├── engine/
+│   │   ├── interpreter.py  # Main orchestrator
+│   │   ├── aggregator.py   # Evidence aggregation & weighting
+│   │   ├── hypothesis.py   # Hypothesis generation
+│   │   ├── confidence.py   # Confidence scoring
+│   │   ├── conflict.py     # Conflict detection
+│   │   ├── novelty.py      # Novel gene discovery & ranking
+│   │   └── plugin.py       # Plugin manager
+│   ├── models/             # Core data models
+│   │   ├── genome.py
+│   │   ├── gene.py
+│   │   ├── protein.py
+│   │   ├── evidence.py
+│   │   └── interpretation.py
+│   ├── output/
+│   │   ├── report.py       # Markdown report generator
+│   │   ├── reasoning.py    # Reasoning chain formatter
+│   │   └── json_export.py  # JSON serialization
+│   └── parsers/            # FASTA / GenBank parsers
+├── tests/                  # pytest test suite
+├── case_studies/           # 7 phage GenBank files + benchmark reports
+├── data/prosite/           # Bundled PROSITE database (1,298 patterns)
+├── pyproject.toml
+└── QUICKSTART.md
+```
+
+---
+
+## Plugin System
+
+GIAE has a plugin architecture for optional heavy-weight evidence sources. Plugins are auto-detected at startup — if the required binary or database path doesn't exist, the plugin is silently skipped. The base pipeline always runs.
+
+| Plugin | Requirement | Evidence Type | Weight |
+|--------|-------------|---------------|--------|
+| `HmmerPlugin` | HMMER3 + `~/.giae/hmmer/pfam.hmm` | `DOMAIN_HIT` | 0.90 |
+| `BlastLocalPlugin` | BLAST+ + `~/.giae/blast/swissprot` | `BLAST_HOMOLOGY` | 1.00 |
+| `EsmPlugin` | PyTorch + ESM-2 model | `SEQUENCE_FEATURE` | 0.50 |
+
+Install plugin dependencies with `giae db download pfam` / `giae db download swissprot`.
+
+---
+
+## Roadmap
+
+- [ ] **Foldseek / AlphaFold structural search** — `STRUCTURAL_HOMOLOGY` evidence (already in codebase); resolves PhiX174-class cases where sequence-based methods fail completely
+- [ ] **EBI BLAST async API** — replace text-based UniProt search with real sequence similarity search
+- [ ] **Interactive HTML reports** — evidence network visualization across all genes
+- [ ] **Database caching** — avoid re-running API calls on identical sequences; essential for large genomes
+- [ ] **Bacterial genome scaling** — currently validated on phages; next target is 4–6 Mb bacterial genomes
+- [ ] **Comparison mode** — diff two genome interpretations side by side
+
+---
+
+## Contributing
+
+Issues, PRs, and genome challenges welcome.
+
+```bash
+# Run tests
+pytest tests/ -v
+
+# Run with coverage
+pytest tests/ --cov=giae --cov-report=term-missing
+```
+
+---
+
+## Citation
+
+If you use GIAE in research, please cite:
+
+```
+GIAE — Genome Interpretation & Annotation Engine (v0.2.0)
+https://github.com/Ayo-Cyber/GIAE
+```
+
+A formal publication is in preparation.
+
+---
+
+## License
+
+MIT — see [LICENSE](LICENSE).
+
+---
+
+*GIAE v0.2.0 — Benchmarked on Lambda, T7, PhiX174, Phi29, Mu, P22, and T4.*