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

1. Clone the repository:

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

2. Create a virtual environment and install dependencies:

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

Usage

1. Most simple execution:

   codon_optimizer -input myfile.fa 

   For example, myfile.fa could be /your/absolute/path/to/tests/cases/input_coding_rna.fa.

2. Disable logging:

   codon_optimizer -input myfile.fa -nolog

3. Use a specific codon usage table:

   codon_optimizer -input myfile.fa -reffreqtab codonusage.txt

Testing

1. Install pytest:

   source venv/bin/activate
   pip install pytest

2. Run tests using pytest:

   pytest tests

   This will run the test suite and display the results in the terminal.

3. Log file creation: During execution, a log file will be created at output/codon_optimizer.log if logging is enabled.