getGenome {biomartr} not working for viruses?
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peter.durr • 0
@peterdurr-15932
Last seen 19 months ago
Australia

Hi everyone

I am trying to retrieve various reference genomes of viruses held in Genbank, or more specifically NCBI's RefSeq database.

I am exploring the new package biomartr 0.7.0 - which does just this - i.e. retrieves reference genomes

whilst this seems to work well for most taxons - it is not performing for viruses

here is code in which I compared a bacterial pathogen (Mycobacterium tuberculosis) with a virus (rabies virus)

is.genome.available(organism = "Mycobacterium tuberculosis", db = "refseq")

is.genome.available(organism = "Rabies lyssavirus", db = "refseq")

both of these came back with the response "TRUE"
 

However, when I try fetching these two reference sequences using the following code:

Mtb.genome.refseq <- getGenome(db = "refseq", organism = "Mycobacterium tuberculosis",  path   = file.path("_ncbi_downloads","genomes"))

RABV.genome.refseq <- getGenome(db = "refseq", organism = "Rabies lyssavirus", path   = file.path("_ncbi_downloads","genomes"))

The M. tunberculosis fetch is successful, but the rabies virus fetch fails with the following message:

----------> No reference genome or representative genome was found for 'Rabies lyssavirus'. Thus, download for this species has been omitted. Have you tried to specify 'reference = FALSE' ?

adding the argument reference = FALSE does not solve the problem.

Thanks

PS. I am running the program in RStudio 1.1.447, R 3.5.0, Windows 10.

 

Genbank biomartr Genomic sequences • 1.3k views
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@martin-morgan-1513
Last seen 29 days ago
United States

biomartr is a CRAN package, so you should ask on it's support site.

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Thanks Martin

I had just assumed that biomatr was a Bioconductor package - apologies

I have moved my question to the developers github Issues site

Regards

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Entering edit mode
peter.durr • 0
@peterdurr-15932
Last seen 19 months ago
Australia

As Martin Morgan correctly pointed out, biomartr is a CRAN pacakge

I have moved my question to the developer's github Issues site

 

 

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