#!/usr/bin/env python
# coding: utf-8

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from ontobio.ontol_factory import OntologyFactory

# Create ontology object, for GO
# Transparently uses remote SPARQL service.
# (May take a few seconds to run first time, Jupyter will show '*'. BE PATIENT, do
# not re-execute cell)
ofactory = OntologyFactory()
ont = ofactory.create('go')


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ont


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from ontobio.io.gafparser import GafParser
from ontobio.assoc_factory import AssociationSetFactory

p = GafParser()
afactory = AssociationSetFactory()

def make_assocs(group):
    url = "http://geneontology.org/gene-associations/gene_association.{}.gz".format(group)
    if group == 'human':
        url = "http://geneontology.org/gene-associations/goa_human.gaf.gz"
    assocs = p.parse(url)
    return afactory.create_from_assocs(assocs, ontology=ont)
    


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asoc_mouse = make_assocs('mgi')


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asoc_mouse.subjects[0:5]


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asoc_mouse.jaccard_similarity('MGI:MGI:1918911', 'MGI:MGI:3698435')


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asoc_mouse.annotations('MGI:MGI:1918911')


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asoc_hsap = make_assocs('human')


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asoc_hsap.subjects[0:5]


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