Bioinformatics with Python Cookbook - Second Edition

Getting ready

Python can be run on top of different environments. For instance, you can use Python inside the Java Virtual Machine (JVM) (via Jython) or with .NET (with IronPython). However, here, we are concerned not only with Python, but also with the complete software ecology around it; therefore, we will use the standard (CPython) implementation, since the JVM and .NET versions exist mostly to interact with the native libraries of these platforms. A potentially viable alternative would be to use the PyPy implementation of Python (not to be confused with Python Package Index (PyPI).

Save for noted exceptions, we will be using Python 3 only. If you were starting with Python and bioinformatics, any operating system will work, but here, we ...