Handle "unclassified X"

[LLansing]

There are some taxa that are the format unclassified X, such as unclassified Lactobacillus. We need to determine what distinguishes these taxa from the parent taxa (e.g. how are reads classified as unclassified Lactobacillus different from reads classified as the genus Lactobacillus?)

Within our framework, these reads are going unanalyzed because these taxa do not have an assigned rank (such as G for genus), but they do have reads assigned to them.

Proposed solution: drop those taxa and add their reads to the relevant parent taxa

[LLansing]

The solution should be generalized easily, but these are some taxa seen so far

• unclassified Lactobacillus
• unclassified Gilliamella
• unclassified Commensalibacter
• unclassified Bombella
• unclassified Apibacter

Also worth noting, these taxa may have all NA values (in the case that they have no reads assigned to them

[LLansing]

Generalized solution via function _scripts/initial_processing.R$aggregateunclassified()