Metadata-Version: 1.0
Name: python-codon-tables
Version: 0.1.3.2
Summary: Codon Usage Tables for Python, from kazusa.or.jp
Home-page: https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables
Author: Zulko
Author-email: UNKNOWN
License: MIT
Description-Content-Type: UNKNOWN
Description: Python Codon Tables
        ===================
        
        .. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/codon-usage-tables.svg?branch=master
            :target: https://travis-ci.org/Edinburgh-Genome-Foundry/codon-usage-tables
        
        Provides codon usage tables as dictionnaries, for Python 3+
        
        Supported organisms include: B. subtilis, C. elegans, D. melanogaster, E. coli, G. gallus, H. sapiens,  M. musculus, M. musculus domesticus, S. cerevisiae.
        
        These tables are from `kazusa.or.jp <http://www.kazusa.or.jp/codon/readme_codon.html>`_ and here is the original paper to cite:
        
        .. code::
        
            Codon usage tabulated from the international DNA sequence databases:
            status for the year 2000.
            Nakamura, Y., Gojobori, T. and Ikemura, T. (2000) Nucl. Acids Res. 28, 292.
        
        
        Contribute
        ----------
        
        This project was started at the Edinburgh Genome Foundry by Zulko and is released on `Github <https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables>`_ under a Public Domain licence (and no warranty whatsoever, please cross-check the codon usage with other sources if you are not sure). Feel free to add other tables if you think of more commonly used species.
        
        Installation
        ------------
        
        via pip:
        
        .. code:: bash
        
            pip install python_codon_tables
        
        Manual:
        
        .. code:: bash
        
            (sudo) python setup.py install
        
        Usage
        -----
        
        .. code:: python
        
            import python_codon_tables as pct
        
            # PRINT THE LIST OF NAMES OF ALL AVAILABLE TABLES
            print ('Available tables:', pct.available_tables)
        
            # LOAD ONE TABLE BY NAME
            table = pct.get_table("b_subtilis_1423")
            print (table['T']['ACA'])  # returns 0.4
            print (table['*']['UAA'])  # returns 0.61
        
            # LOAD ALL TABLES AT ONCE
            codon_tables = pct.get_all_tables()
            print (codon_tables['c_elegans_6239']['L']['CUA'])  # returns 0.09
        
Keywords: DNA codon usage
Platform: UNKNOWN
