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viralemergence / virion

The Global Virome in One Network
https://viralemergence.github.io/virion
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HostClass 'actinopterygii' versus 'actinopteri' #37

Closed maxfarrell closed 3 years ago

maxfarrell commented 3 years ago

There is one instance of a species with HostClass actinopterygii:


require(vroom)
require(dplyr)

virion <- vroom("Virion/Virion.csv.gz")
table(virion$HostClass)

hosttax <- virion %>% select(HostClass, HostOrder, HostFamily, HostGenus, Host) %>% 
hosttax[hosttax$Host=="labroides dimidiatus",] # this is the actinopterygii case
cjcarlson commented 3 years ago

hoo boy. Brings me no pleasure to tell you this, but this is a CLOVERT bug, probably inherited from the class-matching issue Rory and I talked about with NCBITaxonomy.jl handling host class poorly in this specific case. The way that I know this is that there's five records with this species - two from GenBank, one GLOBI, and one from EID2 both work right; but Shaw is wrong.

@rorygibb, do you inherit some of the old taxonomy? I thought we were going to Fully Gut That

rorygibb commented 3 years ago

As per my other comment - there are two spellings of this species in different source databases, one of which gives an automated hit to NCBI, one not. The actinopterygii was an inconsistency between manually resolved higher tax and the automated hit - all fixed now.

Updated version on clovert_dev repo now, so fixes can propagate into VIRION