Python Codon Tables
===================
.. image:: https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/actions/workflows/build.yml/badge.svg
:target: https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/actions/workflows/build.yml
:alt: GitHub CI build status
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
More biology software
-----------------------
.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png
:target: https://edinburgh-genome-foundry.github.io/
This library is part of the `EGF Codons <https://edinburgh-genome-foundry.github.io/>`_ synthetic biology software suite for DNA design, manufacturing and validation.
Raw data
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