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jrderuiter / pybiomart

A simple pythonic interface to biomart.
MIT License
53 stars 11 forks source link

Does pybiomart support v0.9 of Biomart? #3

Closed uludag closed 5 years ago

uludag commented 7 years ago

Hi, I was trying to use pybiomart to call genenames.org Biomart service, however I was not able to construct a working pybam BiomartServer object.

from pybiomart import Server
server = Server(host='http://biomart.genenames.org', path="/martservice/results")
server.list_marts()

Is this because pybam is not supporting v0.9 of Biomart?

--mahmut

jrderuiter commented 7 years ago

The library is currently geared towards Biomart 0.8 (I think this is the version that Ensembl is using), which is probably why you are running into problems. I'll get back to you when I've had time to look into it!

uludag commented 7 years ago

Thanks Julian. No urgency on our side, for now I use more generic libraries in two simple Biomart scripts that given Ensembl gene ids return gene names and aliases. I would like to try pybam when it supports Biomart 0.9. --mahmut

jrderuiter commented 5 years ago

Unfortunately I don't have any time to work on this for the time being. If there is more general interest, we can consider re-opening the issue.