Fix BLAST results protein to taxonomic accession assignment

[chasemc]

Currently the documentation instructs and the code downloads prot.accession2taxid.gz which doesn't have all of the nr accessions.
Proteins that aren't found in prot.accession2taxid.gz are assigned to root which results in contigs becoming unclassified.
Currently this is ameliorated by using prot.accession2taxid.FULL.gz instead of prot.accession2taxid.gz, as shown below. But the code needs to be changed to handle missing accessions. Per our meeting today these should probably be assigned to None and then should be dropped before handing over to LCA.

Assignment to root that needs to be changed:

Autometa/autometa/taxonomy/ncbi.py

Lines 453 to 457 in baf61c0

	# If we still have missing taxids, we will set the sseqid value to the root taxid
	# fill missing taxids with root_taxid
	sseqid_to_taxid_df["cleaned_taxid"] = sseqid_to_taxid_df.merged_taxid.fillna(
	root_taxid
	)

[evanroyrees]

This could be handled in multiple areas. Either specifically when parsing taxids for NCBI or at the LCA step. Any preference?

Autometa/autometa/taxonomy/lca.py

Lines 365 to 399 in baf61c0

	for qseqid, qseqid_taxids in taxids.items():
	# This will convert any deprecated taxids to their current taxids before reduction to LCA.
	# NOTE: we only want to retrieve the set of unique taxids (not a list) for LCA query
	lca_taxid = False
	num_taxids = len(qseqid_taxids)
	while not lca_taxid:
	# Reduce all qseqid taxids to LCA
	if num_taxids >= 2:
	try:
	lca_taxid = functools.reduce(
	lambda taxid1, taxid2: self.lca(node1=taxid1, node2=taxid2),
	qseqid_taxids,
	)
	except ValueError as err:
	logger.warn(
	f"Missing taxids during LCA retrieval. Setting {qseqid} ({len(qseqid_taxids):,} ORF taxids) to root taxid."
	)
	lca_taxid = root_taxid
	missing_taxids.append(
	{
	"qseqid": qseqid,
	"taxids": ",".join(
	[str(taxid) for taxid in qseqid_taxids]
	),
	}
	)
	# If only one taxid was recovered... This is our LCA
	elif num_taxids == 1:
	lca_taxid = qseqid_taxids.pop()
	else:
	# Exception handling where input for qseqid contains no taxids e.g. num_taxids == 0:
	lca_taxid = root_taxid
	lca_taxids.update({qseqid: lca_taxid})
	missing_df = pd.DataFrame(missing_taxids)
	return lca_taxids, missing_df

# discard root taxid from set of query's taxids before #L370
qseqid_taxids.discard(root_taxid)
# or something like this?
from autometa.taxonomy.database import TaxonomyDatabase
qseqid_taxids.discard(TaxonomyDatabase.UNCLASSIFIED_TAXID)

Autometa/autometa/taxonomy/lca.py

Line 370 in baf61c0

while not lca_taxid: