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

Project description

https://travis-ci.org/Edinburgh-Genome-Foundry/codon-usage-tables.svg?branch=master

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 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.

Usage

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 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

More biology software

https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png

This library is part of the EGF Codons synthetic biology software suite for DNA design, manufacturing and validation.

Project details


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