How to get Go Terms IDs from given a file that contains gene Ensembl IDs with a python script

Question

[jopealfe]

I have a file that contains some gene Ensembl IDs. My goal is to get all the GO Terms associated to those gene Ensembl IDs with a python script.

Anyone knows about the existence of some python package that allows me to reach my goal ? I'm currently aware of package as mygene, godb, etc. However, none of them as the option to get the GO Terms from gene Ensembl IDs. I've used R as well to get this done and worked just fine. However, I really want to do it with a python script and I'm getting a lot of difficulties.

[cpad0112]

copy/pasted and modified from ensembl rest page (for python 3):

import requests, sys

server = "https://rest.ensembl.org"
ext = "/xrefs/id/ENST00000288602?external_db=GO;all_levels=1"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print(repr(decoded))

[jopealfe]

Thanks! That's what I was looking for!

Do you know if there is a limit to input genes ID to query? I've adapt into a loop to perform the code to several ensembl IDs. What I notice so far is that when the number of input IDs is a large one, it gets me the following error message:

HTTPError: 400 Client Error: Bad Request for url: https://rest.ensembl.org/xrefs/id/ENSG00000068793?external_db=GO;all_levels=1

That Ensembl ID is the 21 input. I guess that it only takes 19/20 consecutive inputs, because when I reduce to 19 inputs it works just fine.

[cpad0112]

For more ids, use post instead of get. Examples are here https://rest.ensembl.org/documentation/info/lookup_post

[jopealfe]

For what I briefly read of the last link, that option does not give the GO ids...

I just now understand why that error. It was because some of the input ID's had no result. I've readapted the code and it works perfectly now, thanks!

[cpad0112]

jopealfe You are right. Ontologies and Taxonomy doesn't support post (as of now).

Answer 1

[jared.andrews07]

You can totally do this with MyGene:

import mygene

mg = mygene.MyGeneInfo()

mg.getgene('ENSG00000123374', fields='go')

Returns a whole bunch of GO terms that you can easily parse.