[FEATURE REQUEST] Annotate which KOfams were added by our bitscore relaxation heuristic

[ivagljiva]

A small project to improve anvi'o, based upon feedback/ideas @FlorianTrigodet and I heard from our colleagues at the QIB in Norwich.

The need

The bitscore heuristic in anvi-run-kegg-kofams adds back hits that are slightly weaker than the standard KEGG-defined bitscore thresholds, but within the database these annotations are indistiguishable from the standard annotations. Might be nice to be able to see which annotations result from the heuristic.

The solution

There are two ways to do this that I can see. The first option is to append something directly to the annotation itself if it came from the heuristic, so that the function definition looks like something dehydrogenase [EC 1.0.15.4] (annotated due to bitscore heuristic). The second option is to add an additional functional annotation source named KOfam_annotated_by_heuristic (or something similar) that would have the same accession as the KOfam and a YES or NO in the function definition.

Another consideration is whether to make this behavior optional via a new flag, like --indicate-KOfams-from-heuristic.

Beneficiaries

People who want to understand where their KO annotations are coming from.