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grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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Updated needed to posted XML? #71

Closed grimbough closed 1 year ago

grimbough commented 1 year ago

The examples shown in this Biostars post (https://www.biostars.org/p/9538506/) suggest that there may be a requirement for an additional key/value pair in the XML generated for requests.

I should look into whether this is really necessary.

grimbough commented 1 year ago

This was a false alarm. Turns out it the original problem was caused by using host = "https://ensembl.org" without any subdomain. This is addressed in https://github.com/grimbough/biomaRt/commit/ab5fb0aa92fdf58fbee96ff8f04e00f1dea72058

The followup investigation of the XML was a mixup using single and double quotations when submitting the query using wget.