Compare genetic distance to geographic distance

[trvrb]

@cassiawag ---

I'd like to measure whether we see a signal of genetically similar viruses being geographically adjacent. A good way to do this would be to take all the viruses with region = Seattle and do pairwise measurements to compare geographic distance between location (census tract) and genetic distance. You can get location from data/metadata_h3n2_ha.tsv. To measure geographic distance you can get lat/longs for each location from config/lat_longs.tsv. To measure genetic distance you can use aligned_h3n2_genome_2y.fasta.

Please write this as a separate Python script in a new folder analyses/. It should take as inputs --metadata, --alignment and --lat-longs and produce a PNG output via Matplotlib.

This can start as a Jupyter nodebook that is turned into a script once it's working.