Access to fungi.ensembl.org

[grimbough]

Found on Twitter:

I want the biomaRt package to work with ensemblfungi not only with ensemblecuddlyanimals. I do not want to have to learn perl just to get the gene sequences of the fungal homologs of these proteins without copying and pasting. #fungi #bioinformaticsproblems

— Edward Wallace (@ewjwallace) 18 April 2018

Not clear if this is a request for documentation/examples or that it doesn't work.

[grimbough]

Looks like the mart registry (https://fungi.ensembl.org/biomart/martservice?type=registry) specifies using port 80, but fungi.ensembl.org may only be accessible over https via port 443.

listMarts() just times out eventually with unhelpful errors - same for useMart().

Seems unlikely since the rest of Ensembl is accessible via port 80. Maybe it's intermittent?

[grimbough]

Load the package, and check we have version at least 2.36.1

library(biomaRt)
packageVersion('biomaRt')

[1] ‘2.36.1’

List the available marts:

listMarts(host = "https://fungi.ensembl.org", port = 443)

           biomart                     version
1       fungi_mart      Ensembl Fungi Genes 39
2 fungi_variations Ensembl Fungi Variations 39

Show the first few datasets:

ensembl_fungi <- useMart(host="https://fungi.ensembl.org", 
                         biomart="fungi_mart", 
                         port = 443)
head(listDatasets(ensembl_fungi))

                  dataset                                        description        version
1       aclavatus_eg_gene       Aspergillus clavatus NRRL 1 genes (ASM271v1)       ASM271v1
2         aflavus_eg_gene Aspergillus flavus NRRL3357 genes (JCVI-afl1-v2.0) JCVI-afl1-v2.0
3      afumigatus_eg_gene       Aspergillus fumigatus Af293 genes (ASM265v1)       ASM265v1
4 afumigatusa1163_eg_gene     Aspergillus fumigatus A1163 genes (ASM15014v1)     ASM15014v1
5       agossypii_eg_gene                  Ashbya gossypii genes (ASM9102v1)      ASM9102v1
6       anidulans_eg_gene     Aspergillus nidulans FGSC A4 genes (ASM1142v1)      ASM1142v1