listGenomes() fails to filter by *subset* with Ensembl Genomes instances

[almeidasilvaf]

Hi, @HajkD

When using the function listGenomes on Ensembl Genomes instances, it returns all genomes in all Ensembl instances, regardless of what users specify in the argument subset.

Below you can find an example for Ensembl Fungi, but it's the same for all other instances. Obviously, there are not 33791 species on Ensembl Fungi.

library(biomartr)
fungi <- listGenomes(db = "ensembl", subset = "EnsemblFungi", skip_bacteria = TRUE)
#> Starting information retrieval for: EnsemblVertebrates
#> Starting information retrieval for: EnsemblPlants
#> Starting information retrieval for: EnsemblFungi
#> Starting information retrieval for: EnsemblMetazoa
#> Starting information retrieval for: EnsemblBacteria
#> Starting information retrieval for: EnsemblProtists

length(fungi)
#> [1] 33791
head(fungi)
#> [1] "leptobrachium_leishanense"  "mus_musculus_pwkphj"       
#> [3] "strigops_habroptila"        "sus_scrofa_hampshire"      
#> [5] "struthio_camelus_australis" "latimeria_chalumnae"

^{Created on 2023-11-10 with reprex v2.0.2}

Session info

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I know that support for Ensembl Genomes was added recently, so it's still in experimental stage, but this is something that could be easily avoided by writing comprehensive unit tests for functions. Maybe that's something to consider for the future.

I also do not understand why {biomartr} has to download data for all Ensembl instances beforehand, even when users specify that they only want one instance. This could also be fixed to improve efficiency.

Best,
Fabricio

[Roleren]

Hello you are right, these are now fixed in my latest pull request #108. Either wait for merge or pull my version.

Let me know if there is anything else :)

[almeidasilvaf]

Hi, @Roleren

Amazing! Thank you very much!

Feel free to close this issue once the PR is merged.

Best,
Fabricio

[HajkD]

Hi @almeidasilvaf,

Many thanks for notifying us about this issue and @Roleren: Thank you so much for addressing it.

I now merged the fix and biomartr should be in better shape now.

Cheers,
Hajk