Checking existence of specific genome in getCollection function

[TakahiroYamada]

Hi Hello. I'm Takahiro Yamada and greatly thanks to you for very convenient R package, biomartr.
I tried to get a genome from NCBI GenBank database and faced following error.

> biomartr::getCollection(db = "genbank" , "GCA_900240375.1")
Starting collection retrieval (genome, proteome, cds, gff/gtf, rna, repeat masker, assembly stats) for GCA_900240375.1 ...
|===============================================================================| 100%   54 MB
Unfortunatey, no entry for 'GCA_900240375.1' was found in the 'refseq' database. Please consider specifying 'db = genbank' or 'db = ensembl' or 'db = ensemblgenomes' or 'db = uniprot' to check whether 'GCA_900240375.1' is available in these databases.
 error: No entry was found for organism GCA_900240375.1. Could the name be misspelled?

The species of this genome is registered in NCBI GenBank, and GenBank assembly accession is registered but RefSeq assembly accession is not (please see following URL).
https://www.ncbi.nlm.nih.gov/assembly/GCA_900240375.1

I suppose my error was generated because of the following code in getCollection.R,

getCollection <-
        function(db = "refseq",
                 organism,
                 reference = TRUE,
                 release = NULL,
                 gunzip = FALSE,
                 remove_annotation_outliers = FALSE,
                 path = file.path("_db_downloads","collections")
        ) {
        
        new_name <- stringr::str_replace_all(organism," ","_")
        message("Starting collection retrieval (genome, proteome, cds, gff/gtf, rna, repeat masker, assembly stats) for ", new_name, " ...")
            
        org_exists <- is.genome.available(db = "refseq", organism, details = TRUE) 
...

The above code org_exists <- is.genome.available(db = "refseq", organism, details = TRUE) may be org_exists <- is.genome.available(db = db, organism, details = TRUE) if genome should be checked based on user specified database?

I also confirmed is.genome.available(db = "genbank" , "GCA_900240375.1") generates TRUE.

Thank you!

Takahiro

[HajkD]

Hi Takahiro,

Thank you so much for contacting me and absolutely brilliant that you caught this bug!
Thank you very much!

I already fixed this bug and the function should work accordingly now.

Thank you!

Hajk

[TakahiroYamada]

Great!
Thank you very much for your prompt fixing it!

Takahiro