search

ropensci / taxizedb

Tools for Working with Taxonomic SQL Databases
Other
30 stars 7 forks source link

"name2taxid" can't handle names with underscores correctly #41

Closed gpli closed 6 years ago

gpli commented 6 years ago 
> taxid2name("1071085")
[1] "haloarchaeon 3A1_DGR"
> taxid2name("1071085") %>% name2taxid
[1] NA
arendsee commented 6 years ago

@gpli Thanks for the report. I think taxizedb is assuming all underscores are a stand-in for spaces, which in the case of haloarchaeon 3A1_DGR is not true. I'll look into it.

sckott commented 6 years ago

@arendsee see also the pr https://github.com/ropensci/taxizedb/pull/42

arendsee commented 6 years ago

@sckott ah, I missed that somehow

arendsee commented 6 years ago

I've added a test and documentation.

Now the info on how names are handled is listed under "NCBI database" in ?name2taxid.