Metadata-Version: 1.0
Name: python_codon_tables
Version: 0.1.8
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+.
        
        Tables for the following organisms are provided with the library (any other
        table can be downloaded using a TaxID):
        
        - *B. subtilis*
        - *C. elegans*
        - *D. melanogaster*
        - *E. coli*
        - *G. gallus*
        - *H. sapiens*
        - *M. musculus*
        - *M. musculus domesticus*
        - *S. cerevisiae*
        
        All the 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.
        
        Usage
        -----
        
        .. code:: python
        
            import python_codon_tables as pct
        
            # PRINT THE LIST OF NAMES OF ALL AVAILABLE TABLES
            print ('Available tables:', pct.available_codon_tables_names)
        
            # LOAD ONE TABLE BY NAME
            table = pct.get_codons_table("b_subtilis_1423")
            print (table['T']['ACA'])  # returns 0.4
            print (table['*']['TAA'])  # returns 0.61
        
            # LOAD ONE TABLE BY TAXID (it will get it from the internet if it is not
            # in the builtin tables)
            table = pct.get_codons_table(1423)
            print (table['T']['ACA'])  # returns 0.4
            print (table['*']['TAA'])  # returns 0.61
        
            # LOAD ALL BUIL-IN TABLES AT ONCE
            codons_tables = pct.get_all_available_codons_tables()
            print (codons_tables['c_elegans_6239']['L']['CTA'])  # returns 0.09
        
        - Notice that by default the tables use nucleotide T instead of U. Using
          ``get_codons_table('e_coli', replace_U_by_T=False)`` will leave Us as Us.
        
        - In ``get_codons_table`` you can also provide a "shorthand" notation
        ``b_subtilis``, which will be automatically extended to ``b_subtilis_1423`` as
        it appears so in the built-in table (use this feature at your own risks!)
        
        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
        
Keywords: DNA codon usage
Platform: UNKNOWN
