# Python Codon Adaptation Index

An implementation of Sharp and Li’s 1987 formulation of the codon adaption index.

## Installation

This module is available from PyPI and can be downloaded with the following command:

    $ pip install CAI

To install the latest development version:

    $ pip install git+https://github.com/Benjamin-Lee/CodonAdaptationIndex.git

## Quickstart

Finding the CAI of a sequence is easy:

    >>> from CAI import CAI
    >>> CAI("ATG...", reference=["ATGTTT...", "ATGCGC...",...])
    0.24948128951724224

Similarly, from the command line:

    $ CAI -s sequence.fasta -r reference_sequences.fasta
    0.24948128951724224

Determining which sequences to use as the reference set is left to the user, though the HEG-DB is a great resource of highly expressed genes.

## Contributing and Getting Support

If you encounter any issues using CAI, feel free to create an issue.

To contribute to the project, please create a pull request. For more information on how to do so, please look at GitHub’s documentation on pull requests.

## Citation

Lee, B. D. (2018). Python Implementation of Codon Adaptation Index. Journal of Open Source Software, 3 (30), 905. https://doi.org/10.21105/joss.00905

    @article{Lee2018,
      doi = {10.21105/joss.00905},
      url = {https://doi.org/10.21105/joss.00905},
      year  = {2018},
      month = {oct},
      publisher = {The Open Journal},
      volume = {3},
      number = {30},
      pages = {905},
      author = {Benjamin D. Lee},
      title = {Python Implementation of Codon Adaptation Index},
      journal = {Journal of Open Source Software}

## Contact

I’m available for contact at benjamin_lee@college.harvard.edu.

## Reference

Sharp, P. M., & Li, W. H. (1987). The codon adaptation index–a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research, 15(3), 1281–1295.

## Table of Contents

- Usage
  - Basic Usage
  - Advanced Usage
  - Other Genetic Codes
- API Reference
- CLI Reference
- License

## Indices and tables

- Index

- Module Index

- Search Page