Bioinformatics with Python Cookbook - Second Edition

Getting ready

simuPOP programming may appear difficult, but it will make sense if you understand its event-oriented model. As you might expect, there is a meta-population composed of individuals with a predefined genomic structure. Starting with an initial population that you prepare, a set of initial operators is applied. Then, every time a generation ticks, a set of pre-operators are applied, followed by a mating step that generates the new population for the next cycle. This is followed by a final set of post-operators that are applied again. This cycle (pre-operations, mating, and post-operations) repeats for as many generations as you desire.

The most important part of getting ready is preparing yourself for this model; we will go through ...