Genetic Codes

A pure Python library with no imports for working with the NCBI Genetic Codes

The NCBI Genetic Codes are central to working with alternate genetic codes. This Python tool kit includes a library that exposes the genetic codes so you can query a codon and get its variants or query a code and get its table.

Installation

You can install pygenetic_code with pip.

pip install pygenetic_code
pygenetic_code --version

Conda installation is coming.

Usage

Standalone

You can just print translation tables using the pygenetic_code command. There are currently a couple of options:

• json prints the table in machine readable json format.
• difference prints a .tsv file with the the difference from the standard (translation table 1) code
• maxdifference prints a .tsv file with the difference from the most common amino acid. The main difference is that TGA is more frequently tryptophan than a stop.

Library

In your python application you want to access the translate() function, that has this signature:

amino_acid = translate(codon, translation_table=1, one_letter=False)

The codon is the codon that you want to translate as either an RNA (e.g. AUG) or DNA (e.g. ATG) sequence. The translation_table is your required translation table (see the NCBI website for valid tables), and one_letter is whether to return a three letter amino acid code (e.g. Met or Ter) or a one letter amino acid code (e.g. M or *).

The library provides other ways to access the genetic codes, and those are exemplified in the pytest files in tests/

Citing

Please cite this repository as:

Edwards, Robert A. 2023. pygenetic_code. https://github.com/linsalrob/genetic_codes

A full DOI citation is coming soon.