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test_golr_associations.py
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test_golr_associations.py
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"""
Integration tests for ontobio.golr.golr_associations
"""
from ontobio.golr.golr_associations import search_associations, search_associations_compact,\
select_distinct_subjects, get_objects_for_subject, get_subjects_for_object
HUMAN_SHH = 'HGNC:10848'
HOLOPROSENCEPHALY = 'HP:0001360'
TWIST_ZFIN = 'ZFIN:ZDB-GENE-050417-357'
DVPF = 'GO:0009953'
LSD = 'DOID:9455'
DANIO = 'NCBITaxon:7954'
def test_select_distinct():
"""
Find distinct genes
"""
results = select_distinct_subjects(subject_category='gene',
object_category='phenotype',
subject_taxon='NCBITaxon:9606')
print("DISTINCT SUBJECTS={}".format(results))
assert len(results) > 0
def test_go_assocs():
"""
Test basic association search functionality
"""
payload = search_associations(subject=TWIST_ZFIN,
object_category='function'
)
assocs = payload['associations']
assert len(assocs) > 0
def test_go_assocs_negated():
"""
Test NOT is handled correctly
"""
payload = search_associations(subject='MGI:1332638',
object='GO:0005730',
object_category='function'
)
assocs = payload['associations']
assert len(assocs) > 0
# we expect at least one of these to be negative
neg_assocs = [a for a in assocs if a['negated']]
assert len(neg_assocs) > 0
# we also place NOT as a qualifier
neg_assocs2 = [a for a in assocs if 'not' in a['qualifiers']]
assert len(neg_assocs2) > 0
def test_go_assocs_compact():
assocs = search_associations_compact(subject=TWIST_ZFIN,
object_category='function'
)
assert len(assocs) == 1
a = assocs[0]
assert a['subject'] == TWIST_ZFIN
objs = a['objects']
assert 'GO:0002040' in objs
# test reciprocal query
for obj in objs:
print("TEST FOR {}".format(obj))
rassocs = search_associations_compact(object=obj,
##subject_category='gene', # this is sometimes gene_product, protein.. in GO
object_category='function',
subject_taxon=DANIO,
rows=-1)
for a in rassocs:
print(" QUERY FOR {} -> {}".format(obj,a))
m = [a for a in rassocs if a['subject'] == TWIST_ZFIN]
assert len(m) == 1
def test_pheno_assocs():
payload = search_associations(subject=TWIST_ZFIN,
object_category='phenotype'
)
assocs = payload['associations']
assert len(assocs) > 0
for a in assocs:
print(str(a))
assocs = [a for a in assocs if a['subject']['id'] == TWIST_ZFIN]
assert len(assocs) > 0
def test_pheno_assocs_compact():
assocs = search_associations_compact(subject=TWIST_ZFIN,
rows=1000,
object_category='phenotype'
)
assert len(assocs) == 1
a = assocs[0]
assert a['subject'] == TWIST_ZFIN
assert 'ZP:0007631' in a['objects']
def test_pheno_objects():
results = search_associations(subject=TWIST_ZFIN,
fetch_objects=True,
rows=0,
object_category='phenotype'
)
objs = results['objects']
print(str(objs))
assert len(objs) > 1
assert 'ZP:0007631' in objs
def test_func_objects():
results = search_associations(subject=TWIST_ZFIN,
fetch_objects=True,
rows=0,
object_category='function'
)
objs = results['objects']
print(objs)
assert DVPF in objs
assert len(objs) > 1
def test_pheno_objects_shh_2():
"""
Equivalent to above, using convenience method
"""
objs = get_objects_for_subject(subject=HUMAN_SHH,
object_category='phenotype')
print(objs)
assert HOLOPROSENCEPHALY in objs
assert len(objs) > 50
def test_pheno2gene():
"""
given a phenotype term, find genes
"""
subjs = get_subjects_for_object(object=HOLOPROSENCEPHALY,
subject_category='gene',
subject_taxon='NCBITaxon:9606')
print(subjs)
print(len(subjs))
assert HUMAN_SHH in subjs
assert len(subjs) > 50
def test_disease_assocs():
payload = search_associations(subject=HUMAN_SHH,
object_category='disease'
)
print(str(payload))
assocs = payload['associations']
assert len(assocs) > 0
def test_disease2gene():
payload = search_associations(subject=LSD,
subject_category='disease',
object_category='gene')
assocs = payload['associations']
for a in assocs:
print(str(a))
assert len(assocs) > 0
def test_species_facet():
payload = search_associations(subject_category='gene',
object_category='phenotype',
facet_fields=['subject_taxon', 'subject_taxon_label'],
rows=0)
fcs = payload['facet_counts']
print(str(fcs))
assert 'Homo sapiens' in fcs['subject_taxon_label'].keys()