bio-tAI

This is a Python implementation of the popular tAI metric, originally implemented by mariodosreis/tai. It should be more extensible though perhaps not faster.

If there are codons that are composed of non-ATGCU 'bases', they will be silently ignored from analysis.

There will be small differences in the calculation compared to the original codonR program (O(1e-3)).

These may be the result of a mis-coding in the original data table used in the codonR code, which assigns 1 tRNA to TGA (a stop codon), which wouldn't be right. Based on the known tRNAs in E. coli, TGA may have been unknowingly swapped with TGT keeping it together with the other stop codons in the coding table.

Author:

Copyright (C) 2016 Shyam Saladi - Caltech

Installation

• Clone repo

git clone [email protected]:smsaladi/tAI.git

• Install with pip

cd tAI
pip install .

• If you've already installed the package and want to reinstall, try

pip install . -I

All dependencies should be checked for and, if necessary, installed automatically by pip.

License

The bio-tAI is licensed under the GNU General Public License Version 2.

Making releases

1. Reconcile package requirements in requirements.txt with those listed at install_requires, setup_requires, and test_requires in setup.py.

2. Confirm build passes all tests

3. Update the version number and download_url in setup.py

4. Tag a release on GitHub with the new version number