While snp_frequencies and hap_frequencies each have their own file while cnv_frequencies is stuck in anopheles.py. It would probably make more sense to give it its own file as well.

On the other hand, plot_frequencies_heatmap is in snp_frq.py when it is used to plot all kinds of frequencies heat maps. It could probably be moved to util.py (if there are parasite functions that want to use a similar function) or anopheles.py.