python-codon-tables 0.1.6

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

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

It is also possible to download new tables directly with download_codons_table(taxid=316407).

All the tables are from kazusa.or.jp and here is the original paper to cite:

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 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:

pip install python_codon_tables

Manual:

(sudo) python setup.py install

Usage

import python_codon_tables as pct

# PRINT THE LIST OF NAMES OF ALL AVAILABLE TABLES
print ('Available tables:', pct.available_codon_tables)

# LOAD ONE TABLE BY NAME
table = pct.get_codons_table("b_subtilis_1423")
print (table['T']['ACA'])  # returns 0.4
print (table['*']['UAA'])  # returns 0.61

# LOAD ALL TABLES AT ONCE
codons_tables = pct.get_all_available_codons_tables()
print (codons_tables['c_elegans_6239']['L']['CUA'])  # returns 0.09

# GET A TABLE DIRECTLY FROM THE INTERNET
table = pct.download_codons_table(taxid=316407)
print (table['*']['UGA'])  # returns 0.29