[translate] GFF files parsed differently if --genes supplied

[jameshadfield]

Current Behaviour

The code behaves differently if feature_names is supplied (via the --genes argument).

augur/augur/utils.py

Lines 165 to 180 in 7cb3848

	if feature_names is not None:
	if "gene" in feat.qualifiers and feat.qualifiers["gene"][0] in feature_names:
	fname = feat.qualifiers["gene"][0]
	elif "gene_name" in feat.qualifiers and feat.qualifiers["gene_name"][0] in feature_names:
	fname = feat.qualifiers["gene_name"][0]
	elif "locus_tag" in feat.qualifiers and feat.qualifiers["locus_tag"][0] in feature_names:
	fname = feat.qualifiers["locus_tag"][0]
	else:
	fname = None
	else:
	if "gene" in feat.qualifiers:
	fname = feat.qualifiers["gene"][0]
	elif "gene_name" in feat.qualifiers:
	fname = feat.qualifiers["gene_name"][0]
	else:
	fname = feat.qualifiers["locus_tag"][0]

Specifically, the existence of one of {locus_tag, gene_name, gene} is required if --genes are not specified. This applies to the source entry as well.

Expected behavior

--genes should only perform filtering of features, not change how they are parsed.