Tool:Reverse Translator by Codon Usage (RTCU)

Question

[Eslam Samir]

Reverse Translator by Codon Usage (RTCU)

The program uses the codon usage preference of your choice to reverse translate a protein sequence

Here is the repository: https://github.com/Eslam-Samir-Ragab/RTCU

How to use:

1. You need to install python 2.7 or python 3 on your machine.
2. You need to install Numpy and Biopython
3. You need to install future module by pip command
4. Click “Clone or download” > “Download ZIP” > extract the downloaded file.
5. Open the file “rtcu.py” with (python.exe).
   • Windows
   • U/Linux : use the command chmod u+x rtcu.py
   • Mac : use the command python rtcu.py
6. State your variables and press Enter.

Example

If you want to reverse translate a protein sequence do the following:

1. Copy the file "original_codon_usage.txt" to a new file with your preferred name, for example "mycodons.txt".
2. Modify the codons for each amino acid in your newly copied file based on your organism / preference.
3. Use this file as a guide for the program by applying this command:

python rtcu.py -in (input_file) -out (output_file) -codon_usage mycodons.txt

The full RTCU Cheat sheet and notes are here

[Pierre Lindenbaum]

thanks for sharing. how is it different from, say, EMBOSS Backtranseq http://embossgui.sourceforge.net/demo/manual/backtranseq.html ? advice: your programs should handle stdin and sdout in order to be used in a pipeline ...

[WouterDeCoster]

Hi Eslam Samir,

I would suggest you to have a look at how to make your tools installable using a setup.py file, or even make them available on PyPI/pip for convenient installation.

Cheers,
Wouter