Introducing the Genepop format

The Genepop format is used in many conservation genetics studies. It's the format of the Genepop application and is the de facto format for many population genetics analysis. If you come from other fields (for example, have a lot of sequencing experience), you may not have heard of it, but this format is widely used (as its citation record proves) and is worth a look. Here, we will convert some datasets from previous recipes to this format and introduce the Genepop parser from Biopython.

Getting ready

You will need to run the previous recipe because its output will be required for this one.

If you are not using Docker, you might not be using some of the code that I produced earlier (mostly to deal with the bread and butter of data conversion). You can find this code at https://github.com/tiagoantao/pygenomics and install it from

pip install pygenomics

Note that at this stage, we will not use the Genepop application (this will change in the next recipe), so...