COG-translator
🧬 ↩️ Easy translation of COG names
Pure Python package for easy translation between COG names, codes and categories.
Notice
The COG database has been updated in September 2020 and thus this repository is now deprecated. It works well for the 2014 version of the COG database. I will try to update it whenever possible.
Installation
pip install COG-translator
or
git clone https://github.com/vinisalazar/COG-translator.git
cd COG-translator
python setup.py install # or even `pip install .`
Usage
import COG
# Simple module functions
COG.name_from_code("COG0001") # returns 'Glutamate-1-semialdehyde aminotransferase'
COG.cat_from_letter("WH") # returns {'W': ('Cellular processes and signaling', 'Extracellular structures'),
# 'H': ('Metabolism', 'Coenzyme transport and metabolism')}
COG.letter_from_code("COG0001") # returns {'H': ('Metabolism', 'Coenzyme transport and metabolism')}
# Also has the COGTranslator and COGFunction classes which hold the translation data
from COG import COGTranslator
cogt = COGTranslator() # By default loads data file into memory
cogt.name_from_code("COG0001") # Faster than module function because data already loaded.
Have fun. All contributions welcome. If you have any problems, feel free to open an issue.
If you use this software, please cite this GitHub repository: Salazar, V. W. (2019). COG-translator: easy translation of COG names. Retrieved from https://github.com/vinisalazar/COG-translator/
COG reference: Galperin, M. Y., Makarova, K. S., Wolf, Y. I., & Koonin, E. V. (2014). Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Research, 43(D1), D261--D269.