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        "description": "Python Codon Tables\n===================\n\n.. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/codon-usage-tables.svg?branch=master\n    :target: https://travis-ci.org/Edinburgh-Genome-Foundry/codon-usage-tables\n\nProvides codon usage tables as dictionnaries, for Python 3+.\n\nTables for the following organisms are provided with the library (any other\ntable can be downloaded using a TaxID):\n\n- *B. subtilis*\n- *C. elegans*\n- *D. melanogaster*\n- *E. coli*\n- *G. gallus*\n- *H. sapiens*\n- *M. musculus*\n- *M. musculus domesticus*\n- *S. cerevisiae*\n\nAll the tables are from `kazusa.or.jp <http://www.kazusa.or.jp/codon/readme_codon.html>`_\nand here is the original paper to cite:\n\n.. code::\n\n    Codon usage tabulated from the international DNA sequence databases:\n    status for the year 2000.\n    Nakamura, Y., Gojobori, T. and Ikemura, T. (2000) Nucl. Acids Res. 28, 292.\n\nUsage\n-----\n\n.. code:: python\n\n    import python_codon_tables as pct\n\n    # PRINT THE LIST OF NAMES OF ALL AVAILABLE TABLES\n    print ('Available tables:', pct.available_codon_tables_names)\n\n    # LOAD ONE TABLE BY NAME\n    table = pct.get_codons_table(\"b_subtilis_1423\")\n    print (table['T']['ACA'])  # returns 0.4\n    print (table['*']['TAA'])  # returns 0.61\n\n    # LOAD ONE TABLE BY TAXID (it will get it from the internet if it is not\n    # in the builtin tables)\n    table = pct.get_codons_table(1423)\n    print (table['T']['ACA'])  # returns 0.4\n    print (table['*']['TAA'])  # returns 0.61\n\n    # LOAD ALL BUIL-IN TABLES AT ONCE\n    codons_tables = pct.get_all_available_codons_tables()\n    print (codons_tables['c_elegans_6239']['L']['CTA'])  # returns 0.09\n\n- Notice that by default the tables use nucleotide T instead of U. Using\n  ``get_codons_table('e_coli', replace_U_by_T=False)`` will leave Us as Us.\n\n- In ``get_codons_table`` you can also provide a \"shorthand\" notation\n``b_subtilis``, which will be automatically extended to ``b_subtilis_1423`` as\nit appears so in the built-in table (use this feature at your own risks!)\n\nContribute\n----------\n\nThis 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.\n\nInstallation\n------------\n\nvia pip:\n\n.. code:: bash\n\n    pip install python_codon_tables\n\nManual:\n\n.. code:: bash\n\n    (sudo) python setup.py install\n",
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