This script 0-fold 2-fold and 4-fold codon degeneracy sites from a genome. It requires a genome fasta file and a gff file.
Python3
Download the python script
python3 degeneracy myannotation.gff3 mygenome.fastas
The output are three files: deglist_0fold_sorted.bed deglist_2fold_sorted.bed deglist_4fold_sorted.bed
The position in the bed file conforms to bed file standard (0 based in the 2nd column, 1 based in the 3rd column), and it is the position of the mutable nucleotide not the codon start. The Name column of the bed file includes the following field: type, transcript ID, codon position in the CDS (0 based), codon position in the chromosome (0 based), mutation postion offset from codon start, codon
- Qi Sun - Initial work
This project is licensed under the MIT License - see the LICENSE.md file for details