Metadata-Version: 2.1
Name: CodonTransformer
Version: 1.2.1
Summary: The ultimate tool for codon optimization, transforming protein sequences into optimized DNA sequences specific for your target organisms.
Home-page: https://github.com/adibvafa/CodonTransformer
Author: Adibvafa Fallahpour
Author-email: Adibvafa.fallahpour@mail.utoronto.ca
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython <2.0,>=1.83
Requires-Dist: ipywidgets <9.0,>=7.0.0
Requires-Dist: numpy <2.0,>=1.26.4
Requires-Dist: onnxruntime <2.0,>=1.17.3
Requires-Dist: pandas <3.0,>=2.2.2
Requires-Dist: python-codon-tables <1.0,>=0.1.12
Requires-Dist: pytorch-lightning <3.0,>=2.2.1
Requires-Dist: scipy <2.0,>=1.13.1
Requires-Dist: setuptools <69.0,>=68.2.2
Requires-Dist: torch <3.0,>=2.2.2
Requires-Dist: tqdm <5.0,>=4.66.2
Requires-Dist: transformers <5.0,>=4.40.0

CodonTransformer is ultimate tool for codon optimization, transforming protein sequences into optimized DNA sequences specific for your target organisms. Whether you are a researcher or a practitioner in genetic engineering, CodonTransformer provides a comprehensive suite of features to facilitate your work.

### Key Features

- **CodonData**: Simplifies the process of gathering, preprocessing, and representing data, ensuring you have the clean and well-structured data needed for your research.
- **CodonEvaluation**: Offers robust scripts to evaluate various metrics for codon optimized sequences, helping you assess the quality and effectiveness of your optimizations.
- **CodonPrediction**: Enables easy tokenization, loading, and utilization of CodonTransformer for making predictions. It includes various approaches such as High Frequency Choice (HFC), Background Frequency Choice (BFC), random selection, and ICOR.
- **CodonUtils**: Provides essential utility functions and constants that streamline your workflow and improve efficiency.
- **CodonJupyter**: Comes with tools for creating demo notebooks, allowing you to quickly set up and demonstrate the capabilities of CodonTransformer in an interactive environment.

### Why Choose CodonTransformer?

CodonTransformer is built to make codon optimization accessible and efficient. By leveraging advanced algorithms and a user-friendly interface, it reduces the complexity of genetic sequence optimization, saving you time and effort.
