Error: Unexpected format to the list of available marts.

[sciencepeak]

Hi,

We are using the getGenePositions() that is used in SPATA2 that is used in our project. There is an error possibly related to getGenePositions() not following the latest API of biomaRt.

Error message

Error: Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://dec2016.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
In addition: Warning message:
Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://" 
Called from: .listMarts(host = host, path = path, port = port, includeHosts = TRUE, 
    httr_config = httr_config, archive = archive, ensemblRedirect = ensemblRedirect, 
    warn = FALSE)

My updates of the getGenePositions() function include:

• I fix the broken call to the biomaRt API and use the latest ensembl version. The previous version is 6 years old.

• The parameter list and output of the function is basically unchanged to ensure dependent codes working.

• The gene_names parameter is enhanced so that it can retrieve all the genes without user input.

• The ignoreAlt option's logic is separated and rewritten to work more consistently.

Thanks again for your contribution to the science community.

Best,