codon_optimizer

A simple tool to produce DNA sequences with the most abundant codons in a specific organism. This tool provides a basic implementation of codon optimization, using a reference codon usage database. More advanced tools like DNAChisel and CodonBERT offer more sophisticated and optimized approaches to codon optimization.

The tool uses a reference codon usage database based on human and mouse data. You can find the database at Kazusa Codon Usage Database. The publication can be accessed via PubMed.

Parameters

-h, --help Show this help message and exit.
-input FILENAME Input path to the fasta file containing sequences to optimize (default: local).
-reffreqtab FILENAME Input path to the reference frequency table. The table should be in a specific format (see the reference_seq folder) (default: Homo sapiens).
-output FILENAME Output fasta file with codon optimized sequences (default: local).
-nolog Disable log output (default: False).
--version Show program's version number and exit.

Installation

Clone the repository:

git clone https://github.com/jeromelane/codon_optimizer.git
cd codon_optimizer

Create a virtual environment and install dependencies:

python3 -m venv venv
source venv/bin/activate
pip install -e .

Usage

Most simple execution:
```
codon_optimizer -input myfile.fa 
```
For example, myfile.fa could be /your/absolute/path/to/tests/cases/input_coding_rna.fa.
Disable logging:
```
codon_optimizer -input myfile.fa -nolog
```

Use a specific codon usage table:

codon_optimizer -input myfile.fa -reffreqtab codonusage.txt

Testing

Install pytest:

source venv/bin/activate
pip install pytest

Run tests using pytest:
```
pytest tests
```
This will run the test suite and display the results in the terminal.
Log file creation: During execution, a log file will be created at output/codon_optimizer.log if logging is enabled.

jeromelane/codon_optimizer

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