mpurushothamrao/codon-optimiser-by-codon-bias

It is simple codon optimiser by using codon bias and usage

Codon-Optimiser-by-codon-bias

It is simple codon optimiser by using codon bias and codon usage

Use requiremnts.txt file for required packages To create codon bias dict:

frequencer.py [-h] [-ref REFERENCE] [-out OUTPUT]

to create codon bias dictionary from reference nucleotide itself

optional arguments: -h, --help show this help message and exit

-ref REFERENCE, --reference REFERENCE reference file in nucleotide fasta

-out OUTPUT, --output OUTPUT output file in dict.py

Output of this should be used in case for different expression system in initiator.py and whenever codon_freq is used.

Usage: main.py [-h] [-in INPUTNUCL] [-ip INPUTPROT] [-on OUTPUTNUCL] [-op OUTPUTPROT] [-ref REFERENCE] [-repeat REPEAT]

to optimise codon either from protein or nucleotide itself

optional arguments: -h, --help show this help message and exit

-in INPUTNUCL, --inputnucl INPUTNUCL input file in nucleotide fasta

-ip INPUTPROT, --inputprot INPUTPROT input file in protein fasta

-on OUTPUTNUCL, --outputnucl OUTPUTNUCL output file in nucleotide fasta

-op OUTPUTPROT, --outputprot OUTPUTPROT output file in protein fasta

-ref REFERENCE, --reference REFERENCE reference file in nucleotide fasta

-repeat REPEAT, --repeat REPEAT to access repeat

example: python main.py -in references.fasta -on ref_70.fasta -ref references.fasta -repeat True

Reference file is from http://genomes.urv.cat/HEG-DB/ which is highly expressed gene repository