A Github action to codon optimize sequences.
codon-optimize is a Github Action that receives a path for an amino acid fasta file (faa), a codon table with the absolute frequency of each triplet in JSON format, and a path and name of an output file that will be written. This action will use the provided codon table to codon optimize a given sequence.
If you have some feature that you think will make this action better, please feel free to create an issue.
Every argument is required.
| Option | Description | Default |
|---|---|---|
| input-file | A fasta file with all input sequences that will be read | |
| output-file | Path and file name where output fasta file will be written | |
| input-codon-table | A codon table in JSON file format |
This parameter is the path for your amino acid fasta file (faa) to be codon optimized. This parameter doesn't have any value by default.
Default: undefined
This parameter is the path and file name of the codon-optimized sequences that should be written as a fasta file. This parameter doesn't have any value by default.
Default: undefined
This parameter is the path and file name for the codon table. This table will be used to codon optimize a given sequence. This parameter doesn't have any value by default.
Default: undefined
Basic:
- name: codon-optimizer
uses: Open-Science-Global/codon-optimize@v0.2See action.yml for a comprehensive list of all the options.
See Friendzymes Cookbook for further examples and sample data.