factorforge-cds 3.0.0__tar.gz

factorforge_cds-3.0.0/LICENSE

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factorforge_cds-3.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: factorforge-cds
+Version: 3.0.0
+Summary: FactorForge — open-source constraint-based CDS design engine by Eijex.
+Author-email: Eijex <eijex.lab@gmail.com>
+License:                                  Apache License
+                                   Version 2.0, January 2004
+                                http://www.apache.org/licenses/
+        
+           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+        
+           1. Definitions.
+        
+              "License" shall mean the terms and conditions for use, reproduction,
+              and distribution as defined by Sections 1 through 9 of this document.
+        
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+        
+              "Legal Entity" shall mean the union of the acting entity and all
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+              direction or management of such entity, whether by contract or
+              otherwise, or (ii) ownership of fifty percent (50%) or more of the
+              outstanding shares, or (iii) beneficial ownership of such entity.
+        
+              "You" (or "Your") shall mean an individual or Legal Entity
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+              on behalf of whom a Contribution has been received by Licensor and
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+           2. Grant of Copyright License. Subject to the terms and conditions of
+              this License, each Contributor hereby grants to You a perpetual,
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+              as of the date such litigation is filed.
+        
+           4. Redistribution. You may reproduce and distribute copies of the
+              Work or Derivative Works thereof in any medium, with or without
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+              meet the following conditions:
+        
+              (a) You must give any other recipients of the Work or
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+        
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+        
+           5. Submission of Contributions. Unless You explicitly state otherwise,
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+              the terms of any separate license agreement you may have executed
+              with Licensor regarding such Contributions.
+        
+           6. Trademarks. This License does not grant permission to use the trade
+              names, trademarks, service marks, or product names of the Licensor,
+              except as required for reasonable and customary use in describing the
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+        
+           7. Disclaimer of Warranty. Unless required by applicable law or
+              agreed to in writing, Licensor provides the Work (and each
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+              appropriateness of using or redistributing the Work and assume any
+              risks associated with Your exercise of permissions under this License.
+        
+           8. Limitation of Liability. In no event and under no legal theory,
+              whether in tort (including negligence), contract, or otherwise,
+              unless required by applicable law (such as deliberate and grossly
+              negligent acts) or agreed to in writing, shall any Contributor be
+              liable to You for damages, including any direct, indirect, special,
+              incidental, or consequential damages of any character arising as a
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+              work stoppage, computer failure or malfunction, or any and all
+              other commercial damages or losses), even if such Contributor
+              has been advised of the possibility of such damages.
+        
+           9. Accepting Warranty or Additional Liability. While redistributing
+              the Work or Derivative Works thereof, You may choose to offer,
+              and charge a fee for, acceptance of support, warranty, indemnity,
+              or other liability obligations and/or rights consistent with this
+              License. However, in accepting such obligations, You may act only
+              on Your own behalf and on Your sole responsibility, not on behalf
+              of any other Contributor, and only if You agree to indemnify,
+              defend, and hold each Contributor harmless for any liability
+              incurred by, or claims asserted against, such Contributor by reason
+              of your accepting any such warranty or additional liability.
+        
+           END OF TERMS AND CONDITIONS
+        
+           APPENDIX: How to apply the Apache License to your work.
+        
+              To apply the Apache License to your work, attach the following
+              boilerplate notice, with the fields enclosed by brackets "[]"
+              replaced with your own identifying information. (Don't include
+              the brackets!)  The text should be enclosed in the appropriate
+              comment syntax for the file format. We also recommend that a
+              file or class name and description of purpose be included on the
+              same "printed page" as the copyright notice for easier
+              identification within third-party archives.
+        
+           Copyright [yyyy] [name of copyright owner]
+        
+           Licensed under the Apache License, Version 2.0 (the "License");
+           you may not use this file except in compliance with the License.
+           You may obtain a copy of the License at
+        
+               http://www.apache.org/licenses/LICENSE-2.0
+        
+           Unless required by applicable law or agreed to in writing, software
+           distributed under the License is distributed on an "AS IS" BASIS,
+           WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+           See the License for the specific language governing permissions and
+           limitations under the License.
+        
+Project-URL: Homepage, https://factorforge.vercel.app
+Project-URL: Repository, https://github.com/eijex/factorforge
+Project-URL: Issues, https://github.com/eijex/factorforge/issues
+Keywords: codon optimization,CDS design,synthetic biology,bioinformatics,Nicotiana benthamiana,constraint optimization,dynamic programming
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: biopython>=1.81
+Requires-Dist: requests>=2.31
+Provides-Extra: ml
+Requires-Dist: torch>=2.0; extra == "ml"
+Requires-Dist: transformers>=4.35; extra == "ml"
+Requires-Dist: fair-esm>=2.0; extra == "ml"
+Requires-Dist: pyyaml>=6.0; extra == "ml"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: ruff>=0.1; extra == "dev"
+Dynamic: license-file
+
+# FactorForge
+
+**Open-source constraint-based CDS design engine for *Nicotiana benthamiana* expression workflows.**
+
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](LICENSE)
+[![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
+[![Version](https://img.shields.io/badge/version-3.0.0-green.svg)](https://github.com/eijex/factorforge/releases)
+[![Web App](https://img.shields.io/badge/web-factorforge.vercel.app-brightgreen.svg)](https://factorforge.vercel.app)
+
+FactorForge optimizes protein sequences into *N. benthamiana*-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs.
+
+---
+
+## Quick Start
+
+```bash
+pip install factorforge-cds
+factorforge optimize my_protein.fasta -o output.fasta
+```
+
+Or with Python:
+
+```python
+from factorforge.engines.v2.pipeline import OptimizationPipeline
+
+pipeline = OptimizationPipeline(profile="balanced")
+result = pipeline.run("MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEG...")
+print(result.sequence)   # optimized CDS
+print(result.metadata)   # CAI, GC%, scan results, domestication edits
+```
+
+---
+
+## Access Options
+
+| Method | Description | Link |
+|--------|-------------|------|
+| **Web App** | No installation, demo & light use | [factorforge.vercel.app](https://factorforge.vercel.app) |
+| **CLI / Python** | Local use, batch processing, data privacy | `pip install factorforge` |
+| **Notebooks** | Training & experimentation on Colab / Kaggle | See [notebooks/](notebooks/) |
+
+---
+
+## How It Works
+
+FactorForge runs a deterministic constraint-based pipeline in four stages:
+
+```
+Protein sequence (FASTA or plain text)
+        │
+        ▼
+1. Reverse Translation
+   Selects synonymous codons to maximize CAI
+   against the N. benthamiana codon usage table
+        │
+        ▼
+2. Rule Scan
+   Detects PolyA signals, homopolymers,
+   repeat sequences, forbidden restriction sites
+        │
+        ▼
+3. Domestication
+   Removes Golden Gate / MoClo-incompatible
+   BsaI / BsmBI recognition sites via silent edits
+        │
+        ▼
+4. Output
+   Optimized CDS — FASTA or GenBank
+   with full metrics and scan report
+```
+
+### Optimization Profiles
+
+| Profile | Description |
+|---------|-------------|
+| `balanced` | CAI + GC balance (default) |
+| `high_cai` | Maximum codon adaptation |
+| `gc_target` | Target GC 42.5% for N. benthamiana |
+| `viral_delivery` | Adjusted for viral vector delivery |
+
+---
+
+## Performance
+
+Benchmarked on *N. benthamiana* codon usage table (v2 engine, 3,876 sequences):
+
+| Metric | Value | Target |
+|--------|-------|--------|
+| CAI (mean) | 0.80 | ≥ 0.75 |
+| GC% (mean) | 42.54% | 40–55% |
+| GC% (range) | 40.36–53.81% | 40–55% |
+| AA identity | 100% | 100% |
+| Validator pass rate | 100% | 100% |
+
+---
+
+## Supported Hosts
+
+| Host | Status |
+|------|--------|
+| *Nicotiana benthamiana* | ✅ Supported |
+| *Wolffia globosa* | 🔶 Codon table available, coming soon |
+| Other plant hosts | 📋 Planned |
+
+---
+
+## Installation
+
+**Requirements:** Python 3.10+
+
+```bash
+pip install factorforge-cds
+```
+
+For ML features (ESM2 + BART decoder, experimental):
+
+```bash
+pip install "factorforge-cds[ml]"
+```
+
+For development:
+
+```bash
+git clone https://github.com/eijex/factorforge.git
+cd factorforge
+pip install -e ".[dev]"
+```
+
+---
+
+## CLI Reference
+
+```bash
+# Basic optimization (DP feasibility engine, default)
+factorforge optimize input.fasta -o output.fasta
+
+# Rule-based engine with profile
+factorforge optimize input.fasta -e v2 -p balanced -o output.fasta
+
+# With MoClo construct template, GenBank output
+factorforge optimize input.fasta -e v2 -p balanced \
+  --template standard_expression -o output.gb --format genbank
+
+# Custom GC target range
+factorforge optimize input.fasta --gc-min 40 --gc-max 50 -o output.fasta
+
+# List available engines
+factorforge list-engines
+```
+
+**Key options:**
+
+| Option | Default | Description |
+|--------|---------|-------------|
+| `--engine`, `-e` | `dp` | Engine: `dp` (feasibility) or `v2` (rule-based) |
+| `--profile`, `-p` | `balanced` | Optimization profile |
+| `--objective` | `feasibility_best` | DP objective |
+| `--gc-min` / `--gc-max` | 40 / 55 | GC% target range |
+| `--format` | `fasta` or `genbank` | Output format |
+| `--scan-mode` | `full` | Rule scan: `full` or `fast` |
+
+---
+
+## Output
+
+Each optimized sequence includes:
+
+- **Optimized CDS** — synonymous codon replacements only, AA identity 100%
+- **CAI score** — codon adaptation index for *N. benthamiana*
+- **GC content** — global and first-region
+- **Scan report** — PolyA signals detected/fixed, homopolymers, restriction sites
+- **Domestication report** — BsaI/BsmBI sites removed, edit count
+- **Construct ID** — reproducible hash for tracking
+
+---
+
+## ⚠️ Validation Status
+
+FactorForge predictions are **in-silico only** and have not been experimentally
+validated in wet-lab conditions.
+
+We are actively seeking researchers to test these predictions. If you use
+FactorForge in your experiments, we'd love to hear from you:
+
+- Did the optimized sequence express well?
+- How did CAI / GC% correlate with actual expression levels?
+- Any unexpected results?
+
+**Share your results** → [GitHub Issues](https://github.com/eijex/factorforge/issues)
+or email: eijex.lab@gmail.com
+
+Validated results will be credited in [VALIDATION.md](VALIDATION.md) and future releases.
+
+---
+
+## 🛠️ Developed With
+
+This project was built using the following tools and platforms:
+
+| Tool | Role |
+|------|------|
+| [Claude](https://claude.ai) / [Claude Code](https://claude.ai/code) (Anthropic) | Architecture design, domain analysis, code review |
+| [Codex](https://github.com/openai/codex) (OpenAI) | Code generation and implementation |
+| [Google Colab](https://colab.research.google.com) | ML training (Run 1, Run 2) |
+| [Kaggle](https://www.kaggle.com) | ML training (alpha_run1, alpha_run2) |
+| [ESM2](https://github.com/facebookresearch/esm) (Meta) | Protein language model (encoder) |
+| [PyTorch](https://pytorch.org) | ML framework |
+| [Conda](https://docs.conda.io) / [Miniconda](https://docs.anaconda.com/miniconda/) | Environment management |
+| [Vercel](https://vercel.com) | Web deployment |
+| [GitHub](https://github.com) | Version control and open-source hosting |
+| [HuggingFace](https://huggingface.co) | Model ecosystem |
+| [BioPython](https://biopython.org) | Biological sequence processing |
+
+---
+
+## Citing
+
+If you use FactorForge in your research, please cite:
+
+```
+FactorForge v3.0.0 (2026). Open-source constraint-based CDS design engine.
+Eijex. https://github.com/eijex/factorforge
+```
+
+*A citable publication is in preparation. Until then, please cite the GitHub repository.*
+
+---
+
+## License & Disclaimer
+
+FactorForge source code is licensed under the [Apache License 2.0](LICENSE).
+
+**Disclaimer:** FactorForge is provided for research purposes only. Predictions
+are computational and have not been experimentally validated. The authors make
+no warranties regarding expression outcomes in wet-lab settings. Use at your
+own discretion.
+
+---
+
+## Get in Touch
+
+- **GitHub Issues** — bug reports, feature requests, wet-lab results: [github.com/eijex/factorforge/issues](https://github.com/eijex/factorforge/issues)
+- **Email** — collaborations, feedback, questions: eijex.lab@gmail.com
+- **Web** — [factorforge.vercel.app](https://factorforge.vercel.app)