Metadata-Version: 1.2
Name: CAI
Version: 1.0.3
Summary: Python implementation of codon adaptation index
Home-page: https://github.com/Benjamin-Lee/CodonAdaptationIndex
Author: Benjamin Lee
Author-email: benjamin_lee@college.harvard.edu
License: MIT
Description: Python Codon Adaptation Index
        =============================
        |DOI| |Docs| |Travis| |CodeFactor| |PyPI|
        
        An implementation of `Sharp and Li's 1987
        formulation <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC340524/pdf/nar00247-0410.pdf>`_
        of the `codon adaption index
        <https://en.wikipedia.org/wiki/Codon_Adaptation_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:
        
        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 <http://genomes.urv.cat/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
        <https://github.com/Benjamin-Lee/CodonAdaptationIndex/issues>`_.
        
        To contribute to the project, please `create a pull request
        <https://github.com/Benjamin-Lee/CodonAdaptationIndex/pulls>`_. For more
        information on how to do so, please look at GitHub's `documentation on pull
        requests <https://help.github.com/articles/about-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
        <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 <mailto: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.
        
        .. |DOI| image:: http://joss.theoj.org/papers/8adf6bd9fd6391d5343d15ea0b6b6525/status.svg
        	:target: http://joss.theoj.org/papers/8adf6bd9fd6391d5343d15ea0b6b6525
        
        .. |Docs| image:: https://readthedocs.org/projects/cai/badge/?version=latest
        	:target: https://cai.readthedocs.io/en/latest/?badge=latest
        	:alt: Documentation Status
        
        .. |Travis| image:: https://travis-ci.org/Benjamin-Lee/CodonAdaptationIndex.svg?branch=master
        	:target: https://travis-ci.org/Benjamin-Lee/CodonAdaptationIndex
        
        .. |CodeFactor| image:: https://www.codefactor.io/repository/github/benjamin-lee/codonadaptationindex/badge/master
        	:target: https://www.codefactor.io/repository/github/benjamin-lee/codonadaptationindex/overview/master
        
        .. |PyPI| image:: https://img.shields.io/pypi/v/CAI.svg
        	:target: https://pypi.org/project/CAI/
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python
Requires-Python: >=3.4
