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test_assocmodel.py
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test_assocmodel.py
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from ontobio.ontol_factory import OntologyFactory
from ontobio.assocmodel import AssociationSet
import logging
import random
QUALITY = 'PATO:0000001'
PLOIDY = 'PATO:0001374'
EUPLOID = 'PATO:0001393'
SHAPE = 'PATO:0000052'
Y_SHAPED = 'PATO:0001201'
def test_assoc_query():
"""
reconstitution test
"""
print("Making ont factory")
factory = OntologyFactory()
# default method is sparql
print("Creating ont")
ont = factory.create('pato')
print("Creating assoc set")
aset = AssociationSet(ontology=ont,
association_map={
'a': [],
'b': [EUPLOID],
'c': [Y_SHAPED],
'd': [EUPLOID, Y_SHAPED],
})
rs = aset.query([],[])
assert len(rs) == 4
rs = aset.query([EUPLOID],[])
assert len(rs) == 2
assert 'b' in rs
assert 'd' in rs
rs = aset.query([EUPLOID, Y_SHAPED],[])
assert len(rs) == 1
assert 'd' in rs
rs = aset.query([PLOIDY, SHAPE],[])
assert len(rs) == 1
assert 'd' in rs
rs = aset.query([],[PLOIDY, SHAPE])
assert len(rs) == 1
assert 'a' in rs
rs = aset.query([PLOIDY], [SHAPE])
assert len(rs) == 1
assert 'b' in rs
rs = aset.query([EUPLOID], [Y_SHAPED])
assert len(rs) == 1
assert 'b' in rs
rs = aset.query([EUPLOID], [PLOIDY])
assert len(rs) == 0
rs = aset.query([PLOIDY], [EUPLOID])
assert len(rs) == 0
rs = aset.query([QUALITY], [PLOIDY])
assert len(rs) == 1
assert 'c' in rs
rs = aset.query([SHAPE], [QUALITY])
assert len(rs) == 0
rs = aset.query([QUALITY], [QUALITY])
assert len(rs) == 0
for s1 in aset.subjects:
for s2 in aset.subjects:
sim = aset.jaccard_similarity(s1,s2)
print("{} vs {} = {}".format(s1,s2,sim))
if s1 == 'a' or s2 == 'a':
assert sim == 0.0
elif s1 == s2:
assert sim == 1.0
else:
assert sim == aset.jaccard_similarity(s2,s1)
terms1 = [QUALITY,PLOIDY,SHAPE]
terms2 = [QUALITY,EUPLOID,Y_SHAPED]
ilist = aset.query_intersections(terms1, terms2)
print(str(ilist))
def test_enrichment():
"""
enrichment
"""
factory = OntologyFactory()
ont = factory.create('pato')
# gene set 'a' is biased to ploidy
termprobs = [(QUALITY,0.8,0.8),
(PLOIDY,0.8,0.2),
(EUPLOID,0.7,0.01),
(SHAPE,0.2,0.75),
(Y_SHAPED,0.01,0.5)
]
amap = {}
geneset_a = []
geneset_b = []
for x in range(1,100):
for y in ['a','b']:
dts = []
for (t,p1,p2) in termprobs:
if y=='a':
p = p1
else:
p = p2
if random.random() < p:
dts.append(t)
g = y + str(x)
if y == 'a':
geneset_a.append(g)
else:
geneset_b.append(g)
amap[g] = dts
logging.info(str(amap))
aset = AssociationSet(ontology=ont,
association_map=amap)
logging.info(str(aset))
print(str(geneset_a))
results = aset.enrichment_test(geneset_a, labels=True)
print(str(results))
print("EXPECTED: {} {}".format(PLOIDY, EUPLOID))
results = aset.enrichment_test(geneset_b, labels=True)
print(str(results))
print("EXPECTED: {} {}".format(SHAPE, Y_SHAPED))
logging.basicConfig(level=logging.DEBUG)
test_enrichment()