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Codon Usage Tables for Python, from kazusa.or.jp

Project 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

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