Create README.md

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Author: Chris2004m

README.md

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+# peptide-sequence-synthesis
+
+# Peptide Sequence Synthesis
+
+This project provides a robust, reproducible tool for generating large, high-quality reference peptide sets for neoantigen analysis and benchmarking with pVACtools (notably pVACbind).
+
+## Features
+
+- **Three peptide generation modes:**
+  - Random (from 20 amino acids)
+  - Sampled from a user-supplied FASTA file
+  - Generated by a protein language model (ProtGPT2 via HuggingFace Transformers)
+- **FASTA output** compatible with pVACtools
+- **Command-line interface** for batch processing
+- **Simple GUI** (using PySimpleGUI) for non-technical users
+- **Reproducible and documented**: All parameters and code are managed in git
+
+## Requirements
+
+- Python 3.8+
+- [PySimpleGUI](https://pysimplegui.readthedocs.io/)
+- [transformers](https://huggingface.co/docs/transformers/index)
+- [torch](https://pytorch.org/)
+- (Optional) [Biopython](https://biopython.org/) if you want to extend for peptide property analysis
+
+Install dependencies with:
+```bash
+pip install -r requirements.txt
+```
+
+## Usage
+
+### Command Line
+
+```bash
+python generate_control_peptides.py --mode [random|fasta|protGPT2] --length 9 --count 1000000 --output peptides.fasta [--fasta_file input.fasta] [--temperature 1.0] [--top_k 50]
+```
+
+### GUI
+
+```bash
+python peptide_gui.py
+```
+Follow the prompts to select generation mode, parameters, and output file.
+
+## Reproducibility
+
+- All code and results should be managed in a git repository.
+- Document all parameters used for each run.
+- For large-scale runs, consider using a virtual environment and requirements.txt for consistent environments.
+
+## Version Control
+
+1. Initialize git:
+   ```bash
+   git init
+   ```
+2. Add files and commit:
+   ```bash
+   git add .
+   git commit -m "Initial commit: peptide generator and GUI"
+   ```
+3. Create a GitHub repo and push:
+   ```bash
+   git remote add origin https://github.com/yourusername/peptide-sequence-synthesis.git
+   git branch -M main
+   git push -u origin main
+   ```
+
+## License
+
+[MIT License](LICENSE) or as specified by your lab.
+
+## Acknowledgements
+
+- [pVACtools](https://pvactools.readthedocs.io/)
+- [ProtGPT2](https://huggingface.co/nferruz/ProtGPT2)
+- [PySimpleGUI](https://pysimplegui.readthedocs.io/)
+
+---
+
+*For questions or contributions, please open an issue or pull request on GitHub.*