Purpose: Command-line tool that computes the length normalized codon frequency of each 61 sense codons of a coding sequence (CDS), and returns a comma-separated table.
Relative freq. of codon_i= (frequency of codon_i)/(total number of codons in the CDSj)
How to Use :
- Ensure that python3 (version 3.8 or higher) and pandas v2.0 or higher are installed.
Recommended to install python3 via anaconda https://docs.anaconda.com/anaconda/install/index.html - Download the CodonCount.pyz file in this github repo into your working folder with the input fasta file(s).
- Open a terminal window (bash, gitbash, powershell, etc) in the same working folder.
- To run the programn, tpe the command below in the terminal shell (be sure to replace arguments with the actual name the input and output files):
python3 CodonCount.pyz -CDS example.fasta -out example_output