augur curate format-host

[joverlee521]

Inspired by @kimandrews 's work in nextstrain/rabies#8

Copying my comment as an official proposal for a new augur curate format-host command

The host rules can be formatted like <group>/<family>/<genus>/<species>\t<new_host_label>
Picking a couple examples from your script:

host_hierarchy	new_host_label
odd-toed ungulates/*/*/*	Other Ungulate
*/Mephitidae/*/*	Skunk
*/Canidae/Vulpes/*	Fox (Vulpes sp.)
*/Procyonidae/Procyon/*	Raccoon
*/*/*/Canis lupus familiaris	Domestic Dog

Then the generalized script would match starting from group down to species.

I don't think Augur would have any default host rules since the useful groupings will vary widely by pathogen.

[kimandrews]

This is great! It's possible that for other pathogens we may also want to use criteria based on higher Linnaean taxonomic categories (e.g. Class or Order). But I also see downsides to adding more/*/* because it can get confusing.

[joverlee521]

Noting that a lot of the host map in avian-flu is for the common name that is included in the SRA/BioSample record. Seems like host only gets converted to the scientific host when pulling the data directly from NCBI Virus/NCBI Datasets.

For example, NCBI Virus shows "Bos taurus" for PQ468542.1:

The linked GenBank record shows "cattle":

The linked BioSample record shows "CATTLE":

The linke SRA record shows "CATTLE":