Zbik is an early-stage release of the project I did for python classes. The initial idea was to create a terminal-based program for sequence alignment by solving Rosalind's challenge. Some bugs may appear. However, during the test, it did not show any errors.
The script requires at least Python 3.10 to work. Regarding external libraries it only requires NumPy (one of the ideas was not to use biopython in the script).
I prepared a file you can use to have a quick overview of the code.
$ python run_demo.py
run_demo.py uses files from subdirectories. I recommend cd to
a directory with the file and running it from there. In case, you run it from
some IDE, make sure about the correct cwd. I didn't have an opportunity to test it on an other OS than Linux. It should work the same way on other POSIX-compliant OS, but I am not sure if the way of path coding used in the script is compatible with Windows (i.e. ./sequences/)
I didn't manage to implement sequences alignment before the deadline, but I created a framework with an implementation that can solve four problems from Rosalind and has the potential for further development.
TO-DO LIST:
- Add remaining functionality to make Zbik a fully functional CLI tool
- Add distance matrices functionality
- Code refraction