Entering edit mode
6.1 years ago
Eslam Samir
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110
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:
- You need to install python 2.7 or python 3 on your machine.
- You need to install Numpy and Biopython
- You need to install future module by pip command
- Click “Clone or download” > “Download ZIP” > extract the downloaded file.
- 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
- State your variables and press Enter.
Example
If you want to reverse translate a protein sequence do the following:
- Copy the file "original_codon_usage.txt" to a new file with your preferred name, for example "mycodons.txt".
- Modify the codons for each amino acid in your newly copied file based on your organism / preference.
- 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
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 ...
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