search

scverse / genomic-features

Genomic Features in Python from BioConductor's AnnotationHub
https://genomic-features.readthedocs.io
BSD 3-Clause "New" or "Revised" License
18 stars 5 forks source link

Example where we directly connect to the ensembl servers #71

Open ivirshup opened 2 months ago

ivirshup commented 2 months ago

Description of feature

It would be nice to have an example where we directly connect to the ensembl mysql servers to run a query. Especially for the biomart version, much more information should be available.

It may also be important to note that users may need to interact with the servers through ibis to be able to make full use of the extra information.

ivirshup commented 2 months ago

Actually these tables aren't quite the same, so maybe this just needs to go into a gist somewhere. The tables on the service use integers as ids instead of strings. One can connect with:

import ibis

conn = ibis.mysql.connect("ensembldb.ensembl.org", user="anonymous", database="homo_sapiens_core_108_38")

and docs can be found here: https://useast.ensembl.org/info/data/mysql.html

Though the service seems to be down at the moment.