somes notes on the tools I'm using for codon usage and tRNA analysis.
from: https://github.com/mol-evol/gcua?tab=readme-ov-file#codon-usage-analysis
Using GCUA(general codon usage analysis tool) to generate codon frequency/usage table
using the following command first
git clone https://github.com/mol-evol/gcua.git
cd gcua
pip install -r requirements.txt.
check installation with
python gcua.py --version
run the interactive menu system of gcua by
python gcua.py
Load the fasta file first via option, then export metrics, for our purposes, codon usage data and comprehensive metrics may be the most useful, I've done it on our Mimivirus refrence genome first.
there is a bug in the GCUA original script, where the wrong name of export_base_comp() is called instead, navigate to line 5379 in gcua.py and change self._export_base_composition() to self._export_base_comp()
McInerney JO. GCUA: general codon usage analysis. Bioinformatics. 1998;14(4):372-3. doi: 10.1093/bioinformatics/14.4.372. PMID: 9632833.