codon_optimizer

A simple tool to produce DNA sequences with the most abundant codons in a specific organism.

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 should be represented in a specific format (see reference_seq folder) (default: Homo sapiens)
• -output FILENAME Output fasta file with codon optimized sequences (default: local)
• -nolog Detailed output (default: False)
• --version show program's version number and exit

Usage

# Most simple execution
python codon_optimizer.py -input myfile.fa
# disable log
python codon_optimizer.py -input myfile.fa -nolog
# use a specific codon usage table
python codon_optimizer.py -input myfile.fa -reffreqtab codonusage.txt

Egg can be built and installed using following command:

 python setup.py install

Once codon_optimizer installed test can be applied with the following command in the root folder:

 python -m test