Huge News!Announcing our $40M Series B led by Abstract Ventures.Learn More
Socket
Sign inDemoInstall
Socket

python-codon-tables

Package Overview
Dependencies
Maintainers
1
Alerts
File Explorer

Advanced tools

Socket logo

Install Socket

Detect and block malicious and high-risk dependencies

Install

python-codon-tables

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

  • 0.1.12
  • PyPI
  • Socket score

Maintainers
1

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.

Keywords

FAQs


Did you know?

Socket

Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.

Install

Related posts

SocketSocket SOC 2 Logo

Product

  • Package Alerts
  • Integrations
  • Docs
  • Pricing
  • FAQ
  • Roadmap
  • Changelog

Packages

npm

Stay in touch

Get open source security insights delivered straight into your inbox.


  • Terms
  • Privacy
  • Security

Made with ⚡️ by Socket Inc