[new feature] Support more ensembl genome, such as plants and fungi

openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

Apache License 2.0

365 stars 68 forks source link

[new feature] Support more ensembl genome, such as plants and fungi #298

Open y9c opened 6 months ago

y9c commented 6 months ago

https://plants.ensembl.org/index.html

y9c commented 6 months ago

install rice reference genome by:

pyensembl install --species rice

install Arabidopsis reference genome by:

pyensembl install --species cress

y9c commented 5 months ago

Hi @iskandr,

I would like to follow up if there is a plan to support more species.

iskandr commented 4 months ago

I'm open to it!

I closed the PR with rice support (https://github.com/openvax/pyensembl/pull/295) because it touched way too much code (and had some mistakes and merge conflicts). Can we add plants and fungi in a more granular fashion? And, if it requires switching between multiple source servers can we change that code first before adding new species?