olgatsiouri1996/codon_optimize_cds_with_many_taxids_multifasta

Linux GUI app to codon optimize a multi-fasta file with coding sequences with multiple taxonomy ids

codon_optimize_cds_with_many_taxids_multifasta

Linux GUI app to codon optimize a multi-fasta file with coding sequences with multiple taxonomy ids

Depedences

1. linux OS (tested on ubuntu 20.04 LTS)
2. python 3.8.2 or later
3. anaconda or miniconda
4. Gooey conda install -c conda-forge gooey(if you get errors during installation or runtime try installing gtk sudo apt-get install libgtk-3-dev)
5. biopython pip install biopython
6. pandas pip install pandas
7. dnachisel pip install dnachisel

linux desktop app installation

1. open a linux text editor and edit in the python file the shebang line (to find where python is type in the terminal which python3)
2. convert to executable with chmod +x codon_optimize_cds_with_many_taxidS_singlefasta_gui.py
3. open a linux text editor and edit the PATHs in the .desktop file
4. move the file to /usr/share/applications
5. reboot your machine

Output

The output multi fasta file will have fasta records with fasta headers:

1. the fasta headers of the input sequences
2. the name or taxonomy id of the organism to codon optimize for(as suffix)