O'Reilly logo

Bioinformatics with Python Cookbook by Tiago Antao

Stay ahead with the world's most comprehensive technology and business learning platform.

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, tutorials, and more.

Start Free Trial

No credit card required

Optimizing code with Cython and Numba

Here, we will have a short introduction on how to optimize code with Cython and Numba. These are competitive approaches; Cython is a superset of Python that allows you to call C functions and specify C types. Numba is a just-in-time compiler that optimizes the Python code.

As an example, we will reuse the distance recipe from the proteomics chapter. We will compute the distance between all atoms in a PDB file.

Getting ready

Cython normally requires specifying your optimized code in a separate .pyx file (Numba is a more declarative solution without this requirement). As IPython provides a magic to hide this, we will use IPython here. However, note that if you are on plain Python, the Cython development will be ...

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, interactive tutorials, and more.

Start Free Trial

No credit card required