allow more ranks for viral taxonomy

[bluegenes]

I'm doing some virus work and running up against an issue with our use of only 7 ranks (superkingdom -->species).

For cowpox genome (GCA_000839185.1; random example):

The taxonomic information listed on NCBI is:

Viruses; Varidnaviria; Bamfordvirae; Nucleocytoviricota; Pokkesviricetes; \
Chitovirales; Poxviridae; Chordopoxvirinae; Orthopoxvirus; Cowpox virus

Using this script, we get the following:

GCA_000839185.1,10243,Viruses,Nucleocytoviricota,Pokkesviricetes, \
Chitovirales,Poxviridae,Orthopoxvirus,Cowpox virus,

(missing realm/clade Varidnaviria, kingdom Bamfordvirae and subfamily Chordopoxvirinae)

at ICTV, Varidnaviria is rank realm while on NCBI, it's rank clade

The full taxonomy, if we include the empty ICTV ranks, is:

GCF_000839185.1,Varidnaviria,,Bamfordvirae,,Nucleocytoviricota,, \
Pokkesviricetes,,Chitovirales,,Poxviridae,Chordopoxvirinae,Orthopoxvirus,,Cowpox virus,

where Varidnaviria is Realm (we would need to add 'Viruses' at the front if we want it)

Might be worth enabling use of all ICTV ranks, which I'm working on for sourmash tax here: sourmash-bio/sourmash#2608.

This doesn't necessarily need to be fixed here, but it seemed a decent spot to file this issue, since this was used to build our last GenBank tax files.

quick fix:

in make-lineage-csv.py, use the following for viruses:

want_taxonomy = ['superkingdom', 'clade', 'subrealm', 'kingdom', 'subkingdom', 'phylum', 'subphylum', 'class', 'subclass', 'order', 'suborder', 'family', 'subfamily', 'genus', 'subgenus', 'species']

superkingdom adds 'Viruses' while clade adds Varidnaviria

This produces the following lineage:

GCA_000839185.1,10243,Viruses,Varidnaviria,,Bamfordvirae,,Nucleocytoviricota,, \
Pokkesviricetes,,Chitovirales,,Poxviridae,Chordopoxvirinae,Orthopoxvirus,,Cowpox virus

I'll make a PR just to have it somewhere.