Allow selection of metadata ID column

[jameshadfield]

A number of augur commands perform linkage between input sequences (FASTA, sometimes VCF) and metadata via a column in the metadata.

The default columns are (only the first found column will be used):

augur/augur/io/metadata.py

Line 18 in 7139595

DEFAULT_ID_COLUMNS = ("strain", "name")

Augur filter has the ability to modify this, but other augur commands do not:

augur/augur/filter/__init__.py

Line 21 in 7139595

input_group.add_argument('--metadata-id-columns', default=DEFAULT_ID_COLUMNS, nargs="+", help="names of possible metadata columns containing identifier information, ordered by priority. Only one ID column will be inferred.")

We should add this ability to all applicable augur commands - export v2, refine, frequencies. There may be others? We don't need to add it to export v1.

This will allow us to simplify workflows such as monkeypox, dengue and RSV which use accession as the sequence identifier.

[victorlin]

@jameshadfield: This will allow us to simplify workflows such as monkeypox, dengue and RSV which use accession as the sequence identifier.

I created PRs for monkeypox and RSV. I don't see any references in dengue, so no PR there.

[jameshadfield]

I created PRs for monkeypox and RSV. I don't see any references in dengue, so no PR there.

Thanks! The dengue work is happening on a branch so I'll let @j23414 update that as desired 😄