def test_parse(self):
for rcv in RCVS:
output_nt = rcv + '.nt'
input_xml = rcv + '.xml.gz'
reference_ttl = TTL_PATH + rcv + '.ttl'
with self.subTest(rcv=rcv):
mock_args = [
"test_clinvar.py", "--inputdir", XML_PATH, "--filename",
input_xml, "--mapfile", MAP_FILE, "--destination", NT_PATH,
"--output", output_nt
]
patch('sys.argv', mock_args).start()
clinvar_parse()
query_graph = RDFGraph()
query_graph.bind_all_namespaces()
query_graph.parse(NT_PATH + output_nt, format='nt')
with open(reference_ttl, 'r') as ref_fh:
ref_graph = "\n".join(ref_fh.readlines())
# debug
LOG.debug(
"Reference graph: %s",
query_graph.serialize(format="turtle").decode("utf-8"))
# Convert output from ClinVar parse to dot then png
dot_file_path = DOT_PATH + rcv + ".dot"
with open(dot_file_path, 'w') as dot_file:
rdf2dot(query_graph, dot_file)
self.assertTrue(
TestUtils.test_graph_equality(ref_graph, query_graph))
class EvidenceTestCase(unittest.TestCase):
def setUp(self):
"""
Because _process_evidence_view uses
self.rawdir to find the evidence file,
the defaults are overriden here to
point to our test file
Note the file name must match what is in
that method - evidence_view
"""
self.test_util = TestUtils()
self.mgi = MGI('rdf_graph', True)
self.mgi.rawdir = os.path.join(os.path.dirname(__file__),
'resources/mgi')
self.mgi.idhash['annot']['6901981'] = ':association'
def tearDown(self):
self.mgi = None
return
def test_sex_specificity_model(self):
self.mgi.graph = RDFGraph(True) # Reset graph
self.mgi._process_evidence_view(limit=None)
logger.debug("Reference graph: %s",
self.mgi.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
:association RO:0002558 ECO:0000006 ;
dc:source J:74619 ;
:has_sex_specificity PATO:0000384 .
J:74619 a IAO:0000310 .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.mgi.graph))
class TestMyChemParser(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.source = MyChem('rdf_graph', True)
# Replaces source.fetch()
data_fh = open(TESTDATA, 'r')
self.test_data = json.load(data_fh)
data_fh.close()
self.source.drugbank_targets.append(self.test_data[0])
self.source.drugcentral_interactors.append(self.test_data[0])
def tearDown(self):
self.source = None
def test_parse(self):
self.source.graph = RDFGraph(True) # Reset graph
self.assertTrue(len(list(self.source.graph)) == 0)
self.source.parse()
triples = """
UNII:46U771ERWK RO:0002606 SNOMED:386761002 ;
rdfs:subClassOf CHEBI:23367 .
SNOMED:386761002 rdfs:label "Local anesthesia" ;
rdfs:subClassOf DOID:4 .
"""
# dbg
logger.debug(
"Reference graph: %s",
self.source.graph.serialize(format="turtle").decode("utf-8"))
self.assertTrue(
self.test_util.test_graph_equality(triples, self.source.graph))
def test_parse(self):
"""
Runs WormBase.parse() and outputs dot file for each allele
This is less of a unit test and more for viewing the
output of an entire run on a single allele,
dot files can be converted to images using
scripts/dot-to-svg.sh
"""
for variant in VARIANTS:
with self.subTest(variant_id=variant):
self.tearDownAndSetUp()
self.gwascatalog.rawdir = RAW_PATH + '/' + variant
self.gwascatalog.parse()
dot_file_path = DOT_PATH + variant + ".dot"
with open(dot_file_path, 'w') as dot_file:
rdf2dot(self.gwascatalog.graph, dot_file)
# debug
LOG.debug(
"Reference graph: %s",
self.gwascatalog.graph.serialize(
format="turtle").decode("utf-8"))
reference_ttl = TTL_PATH + variant + '.ttl'
self.assertTrue(
TestUtils.test_graph_equality(reference_ttl,
self.gwascatalog.graph))
class SGDTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.test_set_1 = {'Allele': 'atp6-L183R (L183R)',
'Chemical': 'glycerol',
'Condition': 'elevated temperature (35 deg C)|nonfermentable carbon source',
'Details': 'similar results obtained with atp6-L247R, and atp6-W136R, all '
'corresponding to human NARP syndrome mutants',
'Experiment Type': 'classical genetics',
'Feature Name': 'Q0085',
'Feature Type': 'ORF',
'Gene Name': 'ATP6',
'Mutant Type': 'reduction of function',
'Phenotype': 'respiratory growth: decreased rate',
'Reference': 'PMID: 21715656|SGD_REF: S000145858',
'Reporter': ' ',
'SGDID': 'S000007268',
'Strain Background': 'Other'}
return
def tearDown(self):
return
def testSGDParser(self):
sgd = SGD('rdf_graph', True)
sgd.graph = RDFGraph(True)
record = self.test_set_1
sgd.make_association(record)
description = sgd._make_description(record)
triples = """
:MONARCH_95158d413dd73476 a OBAN:association ;
OBO:RO_0002558 OBO:APO_0000020 ;
dc:description "{0}";
dc:source PMID:21715656 ;
OBAN:association_has_object MONARCH:OBO_APO_0000309OBO_APO_0000245 ;
OBAN:association_has_predicate OBO:RO_0002200 ;
OBAN:association_has_subject SGD:S000007268 .
SGD:S000007268 rdfs:label "ATP6" ;
RO:0002200 MONARCH:OBO_APO_0000309OBO_APO_0000245 .
APO:0000020 rdfs:label "classical genetics" .
PMID:21715656 a OBO:IAO_0000311 ;
owl:sameAs SGD_REF:S000145858 .
MONARCH:OBO_APO_0000309OBO_APO_0000245 rdfs:label "respiratory growth:decreased rate" ;
rdfs:subClassOf UPHENO:0001001 .
""".format(description)
# test exact contents of graph
self.assertTrue(self.test_util.test_graph_equality(
triples, sgd.graph))
class RGDTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.test_set_1 = {'aspect': 'N',
'date': '2006-10-26',
'evidence': {'has_supporting_reference': ['RGD:1581841', 'PMID:12799311'],
'type': 'IED',
'with_support_from': []},
'negated': False,
'object': {'id': 'MP:0003340', 'taxon': 'NCBITaxon:10116'},
'provided_by': 'RGD',
'qualifiers': [],
'relation': {'id': None},
'source_line': 'RGD\t2535\tEdnra\t\tMP:0003340\tRGD:1581841|PMID:12799311\t'
'IED\t\tN\tendothelin receptor type A\t\tgene\ttaxon:10116\t'
'20061026\tRGD\t\t\n',
'subject': {'fullname': 'endothelin receptor type A',
'id': 'RGD:2535',
'label': 'Ednra',
'synonyms': [],
'taxon': {'id': 'NCBITaxon:10116'},
'type': 'gene'},
'subject_extensions': [{'filler': '\n', 'property': 'isoform'}]}
return
def tearDown(self):
return
def testRGDParser(self):
rgd = RGD('rdf_graph', True)
rgd.graph = RDFGraph(True)
self.assertTrue(len(list(rgd.graph)) == 0)
rgd.make_association(record=self.test_set_1)
triples = """
:MONARCH_b4650e8c3d865f11a1a5 a OBAN:association ;
RO:0002558 ECO:0005611 ;
dc:source RGDRef:1581841 ;
OBAN:association_has_object OBO:MP_0003340 ;
OBAN:association_has_predicate OBO:RO_0002200 ;
OBAN:association_has_subject RGD:2535 ;
pav:createdOn "2006-10-26" .
RGD:2535 OBO:RO_0002200 MP:0003340 .
RGDRef:1581841 a IAO:0000311 ;
owl:sameAs PMID:12799311 .
"""
# dbg
logger.debug("Reference graph: %s",
rgd.graph.serialize(format="turtle")
.decode("utf-8")
)
self.assertTrue(self.test_util.test_graph_equality(
triples, rgd.graph))
class SGDTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.test_set_1 = {
'Allele': 'atp6-L183R (L183R)',
'Chemical': 'glycerol',
'Condition': 'elevated temperature (35 deg C)|nonfermentable carbon source',
'Details': 'similar results obtained with atp6-L247R, and atp6-W136R, all '
'corresponding to human NARP syndrome mutants',
'Experiment Type': 'classical genetics',
'Feature Name': 'Q0085',
'Feature Type': 'ORF',
'Gene Name': 'ATP6',
'Mutant Type': 'reduction of function',
'Phenotype': 'respiratory growth: decreased rate',
'Reference': 'PMID: 21715656|SGD_REF: S000145858',
'Reporter': ' ',
'SGDID': 'S000007268',
'Strain Background': 'Other'}
return
def tearDown(self):
return
def testSGDParser(self):
sgd = SGD('rdf_graph', True)
sgd.graph = RDFGraph(True)
record = self.test_set_1
sgd.make_association(record)
description = sgd._make_description(record)
triples = """
:MONARCH_ba748c98c0f167739128 a OBAN:association ;
OBO:RO_0002558 OBO:APO_0000020 ;
dc:description "{0}";
dc:source PMID:21715656 ;
OBAN:association_has_object MONARCH:APO_0000309APO_0000245 ;
OBAN:association_has_predicate OBO:RO_0002200 ;
OBAN:association_has_subject SGD:S000007268 .
SGD:S000007268 rdfs:label "ATP6" ;
RO:0002200 MONARCH:APO_0000309APO_0000245 .
APO:0000020 rdfs:label "classical genetics" .
PMID:21715656 a OBO:IAO_0000311 ;
owl:sameAs SGD_REF:S000145858 .
MONARCH:APO_0000309APO_0000245 rdfs:label "respiratory growth:decreased rate" ;
rdfs:subClassOf UPHENO:0001001 .
""".format(description)
# test exact contents of graph
self.assertTrue(self.test_util.test_graph_equality(triples, sgd.graph))
class CTDTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.source = CTD('rdf_graph', True)
self.source.graph = RDFGraph(True)
self.test_row = [
'Nicotine',
'D009538',
'',
'TOBACCO ADDICTION, SUSCEPTIBILITY TO',
'OMIM:188890',
'therapeutic',
'',
'',
'',
'12345|56789'
]
return
def tearDown(self):
self.source = None
return
def test_therapeutic_relationship(self):
# test that graph is empty
self.assertTrue(len(list(self.source.graph)) == 0)
self.source._process_interactions(self.test_row)
triples = """
:MONARCH_b6c289df47cb72653f79 a OBAN:association ;
RO:0002558 ECO:0000033 ;
dcterms:source PMID:12345, PMID:56789 ;
OBAN:association_has_object OMIM:188890 ;
OBAN:association_has_predicate RO:0002606 ;
OBAN:association_has_subject MESH:D009538 .
MESH:D009538 a owl:Class ;
rdfs:label "Nicotine" ;
biolink:category biolink:ChemicalSubstance ;
RO:0002606 OMIM:188890 .
PMID:12345 a IAO:0000013 .
PMID:56789 a IAO:0000013 .
OMIM:188890 a owl:Class ;
biolink:category biolink:DiseaseOrPhenotypicFeature .
"""
# test exact contents of graph
self.assertTrue(self.test_util.test_graph_equality(
triples, self.source.graph))
class CTDTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.source = CTD('rdf_graph', True)
self.source.graph = RDFGraph(True)
self.test_row = [
'Nicotine',
'D009538',
'',
'TOBACCO ADDICTION, SUSCEPTIBILITY TO',
'OMIM:188890',
'therapeutic',
'',
'',
'',
'12345|56789'
]
return
def tearDown(self):
self.source = None
return
def test_therapeutic_relationship(self):
# test that graph is empty
self.assertTrue(len(list(self.source.graph)) == 0)
self.source._process_interactions(self.test_row)
triples = """
:MONARCH_b6c289df47cb72653f79 a OBAN:association ;
RO:0002558 ECO:0000033 ;
dc:source PMID:12345, PMID:56789 ;
OBAN:association_has_object OMIM:188890 ;
OBAN:association_has_predicate RO:0002606 ;
OBAN:association_has_subject MESH:D009538 .
MESH:D009538 a owl:Class ;
rdfs:label "Nicotine" ;
RO:0002606 OMIM:188890 .
PMID:12345 a IAO:0000013 .
PMID:56789 a IAO:0000013 .
OMIM:188890 a owl:Class .
"""
# test exact contents of graph
self.assertTrue(self.test_util.test_graph_equality(
triples, self.source.graph))
class ReactomeTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.test_set_1 = \
('ENSBTAP00000013354',
'R-BTA-3000480',
'http://www.reactome.org/PathwayBrowser/#/R-BTA-3000480',
'Scavenging by Class A Receptors',
'IEA',
'Bos taurus')
self.gaf_eco = {"IEA": "ECO:0000501"}
return
def tearDown(self):
return
def testEnsemblReactomeParser(self):
'''
'''
reactome = Reactome('rdf_graph', True)
reactome.graph = RDFGraph(True)
self.assertTrue(len(list(reactome.graph)) == 0)
# reactome.parse_gaf_eco('gaf-eco-mapping')
(gene, pathway_id, pathway_iri, pathway_label, go_ecode,
species_name) = self.test_set_1
reactome._add_component_pathway_association('ENSEMBL:' + gene,
'REACT:' + pathway_id,
pathway_label,
self.gaf_eco[go_ecode])
triples = """
ENSEMBL:ENSBTAP00000013354 RO:0002331 REACT:R-BTA-3000480 .
:MONARCH_b582c188b7ec20016206 a OBAN:association ;
OBO:RO_0002558 ECO:0000501 ;
OBAN:association_has_object REACT:R-BTA-3000480 ;
OBAN:association_has_predicate RO:0002331 ;
OBAN:association_has_subject ENSEMBL:ENSBTAP00000013354 .
REACT:R-BTA-3000480 a owl:Class ;
rdfs:label "Scavenging by Class A Receptors" ;
rdfs:subClassOf GO:0009987,
PW:0000001 .
"""
self.assertTrue(
self.test_util.test_graph_equality(triples, reactome.graph))
def test_gene_xref(self):
"""
test FlyBase._process_gene_xref()
"""
for allele in ALLELES:
with self.subTest(allele_id=allele):
self.tearDownAndSetUp()
self.flybase.rawdir = RAW_PATH + '/' + allele
self.flybase._process_gene_xref(limit=None)
LOG.debug(
"Reference graph: %s",
self.flybase.graph.serialize(format="turtle").decode("utf-8"))
reference_ttl = TTL_PATH + allele + '/' + 'gene_xref.ttl'
self.assertTrue(TestUtils.test_graph_equality(
reference_ttl, self.flybase.graph))
class ReactomeTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.test_set_1 = \
('ENSBTAP00000013354', 'R-BTA-3000480',
'http://www.reactome.org/PathwayBrowser/#/R-BTA-3000480',
'Scavenging by Class A Receptors', 'IEA', 'Bos taurus')
return
def tearDown(self):
return
def testEnsemblReactomeParser(self):
reactome = Reactome('rdf_graph', True)
reactome.graph = RDFGraph(True)
self.assertTrue(len(list(reactome.graph)) == 0)
eco_map = Reactome.get_eco_map(Reactome.map_files['eco_map'])
(gene, pathway_id, pathway_iri, pathway_label,
go_ecode, species_name) = self.test_set_1
reactome._add_component_pathway_association(
eco_map, gene, 'ENSEMBL', pathway_id,
'REACT', pathway_label, go_ecode)
triples = """
ENSEMBL:ENSBTAP00000013354 RO:0002331 REACT:R-BTA-3000480 .
:MONARCH_b582c188b7ec20016206 a OBAN:association ;
OBO:RO_0002558 ECO:0000501 ;
OBAN:association_has_object REACT:R-BTA-3000480 ;
OBAN:association_has_predicate RO:0002331 ;
OBAN:association_has_subject ENSEMBL:ENSBTAP00000013354 .
REACT:R-BTA-3000480 a owl:Class ;
rdfs:label "Scavenging by Class A Receptors" ;
rdfs:subClassOf GO:0009987,
PW:0000001 .
"""
self.assertTrue(self.test_util.test_graph_equality(
triples, reactome.graph))
class TestMyChemParser(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.source = MyChem('rdf_graph', True)
# Replaces source.fetch()
data_fh = open(TESTDATA, 'r')
self.test_data = json.load(data_fh)
data_fh.close()
self.source.drugbank_targets.append(self.test_data[0])
self.source.drugcentral_interactors.append(self.test_data[0])
def tearDown(self):
self.source = None
def test_parse(self):
self.source.graph = RDFGraph(True) # Reset graph
self.assertTrue(len(list(self.source.graph)) == 0)
self.source.parse()
triples = """
UNII:46U771ERWK RO:0002606 SNOMED:386761002 ;
rdfs:subClassOf CHEBI:23367 .
SNOMED:386761002 rdfs:label "Local anesthesia" ;
rdfs:subClassOf DOID:4 .
"""
# dbg
logger.debug("Reference graph: %s",
self.source.graph.serialize(format="turtle")
.decode("utf-8")
)
self.assertTrue(self.test_util.test_graph_equality(
triples, self.source.graph))
class EvidenceTestCase(unittest.TestCase):
def setUp(self):
"""
Because _process_evidence_view uses
self.rawdir to find the evidence file,
the defaults are overriden here to
point to our test file
Note the file name must match what is in
that method - evidence_view
"""
self.test_util = TestUtils()
self.mgi = MGI('rdf_graph', True)
self.mgi.rawdir = os.path.join(
os.path.dirname(__file__), 'resources/mgi')
self.mgi.idhash['annot']['6901981'] = ':association'
def tearDown(self):
self.mgi = None
return
def test_sex_specificity_model(self):
self.mgi.graph = RDFGraph(True) # Reset graph
self.mgi._process_evidence_view(limit=None)
logger.debug(
"Reference graph: %s",
self.mgi.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
:association RO:0002558 ECO:0000006 ;
dc:source J:74619 ;
:has_sex_specificity PATO:0000384 .
J:74619 a IAO:0000310 .
"""
self.assertTrue(self.test_util.test_graph_equality(
expected_triples, self.mgi.graph))
class StringTestFakeData(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
# Test set with two proteins from same species
self.test_set_1 = \
[['9606.ENSP00000000233', '9606.ENSP00000003084',
0, 0, 0, 0, 300, 0, 150, 800]]
# Test set with deprecated protein id
self.test_set_2 = \
[['9606.ENSP00000000233', '9606.ENSP00000006101',
0, 0, 0, 0, 300, 0, 150, 800]]
self.columns = [
'protein1', 'protein2', 'neighborhood', 'fusion', 'cooccurence',
'coexpression', 'experimental', 'database', 'textmining',
'combined_score'
]
ensembl = Ensembl('rdf_graph', True)
self.protein_list = ensembl.fetch_protein_gene_map(9606)
return
def tearDown(self):
return
def testFakeDataSet1(self):
string_db = StringDB('rdf_graph', True)
string_db.graph = RDFGraph(True)
self.assertEqual(len(string_db.graph), 0)
ensembl = Ensembl('rdf_graph', True)
prot_map = ensembl.fetch_protein_gene_map(9606)
for key in prot_map.keys():
prot_map[key] = "ENSEMBL:{}".format(prot_map[key])
print("Finished fetching ENSP IDs, fetched {} proteins".format(
len(prot_map.keys())))
dataframe = pd.DataFrame(data=self.test_set_1, columns=self.columns)
string_db._process_protein_links(dataframe, prot_map, 9606)
triples = """
ENSEMBL:ENSG00000001626 RO:0002434 ENSEMBL:ENSG00000004059 .
"""
self.assertTrue(
self.test_util.test_graph_equality(triples, string_db.graph))
def testFakeDataSet2(self):
"""
Dataset contains a deprecated protein ID
that we expect if filtered out by ensembl biomart
We test that this returns an empty graph
:return:
"""
string_db = StringDB('rdf_graph', True)
string_db.graph = RDFGraph()
self.assertEqual(len(string_db.graph), 0)
dataframe = pd.DataFrame(data=self.test_set_2, columns=self.columns)
string_db._process_protein_links(dataframe, self.protein_list, 9606)
self.assertEqual(len(string_db.graph), 0)
class GeneVariantDiseaseTest(unittest.TestCase):
def setUp(self):
"""
"""
self.test_util = TestUtils()
self.orphanet = Orphanet('rdf_graph', True)
self.orphanet.rawdir = os.path.join(os.path.dirname(__file__),
'resources/orphanet')
def tearDown(self):
self.orphanet = None
return
def test_germline_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:ba2ac5d2153c70e2bb98 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0004013 ;
OBAN:association_has_subject HGNC:30497 .
ENSEMBL:ENSG00000166813 a owl:Class .
HGNC:30497 a owl:Class ;
RO:0004013 ORPHA:938475 ;
oboInOwl:hasExactSynonym "KAS1" ;
owl:equivalentClass ENSEMBL:ENSG00000166813,
ORPHA:268061 .
ORPHA:268061 a owl:Class .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
ENSEMBL:ENSG00000166813 biolink:category biolink:Gene .
ECO:0000322 biolink:category biolink:EvidenceType .
HGNC:30497 biolink:category biolink:Genotype .
HGNC:30497 biolink:category biolink:Gene .
ORPHA:268061 biolink:category biolink:Gene .
ORPHA:938475 biolink:category biolink:Disease .
MONARCH:ba2ac5d2153c70e2bb98 biolink:category biolink:Association .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
return
def test_germline_lof_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline-lof.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:b9ad1b0c562ad4db3f1e a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0004012 ;
OBAN:association_has_subject ORPHA:268061 .
ORPHA:268061 RO:0004012 ORPHA:938475 ;
oboInOwl:hasExactSynonym "KAS1" .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
ECO:0000322 biolink:category biolink:EvidenceType .
ORPHA:268061 biolink:category biolink:Gene .
ORPHA:268061 biolink:category biolink:Genotype .
ORPHA:938475 biolink:category biolink:Disease .
MONARCH:b9ad1b0c562ad4db3f1e biolink:category biolink:Association .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
return
def test_gene_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-variant.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:bdbeb077e365ddedda20 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0004015 ;
OBAN:association_has_subject ORPHA:268061 .
ORPHA:268061 RO:0004015 ORPHA:938475 ;
oboInOwl:hasExactSynonym "KAS1" .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
ECO:0000322 biolink:category biolink:EvidenceType .
ORPHA:268061 biolink:category biolink:Gene .
ORPHA:268061 biolink:category biolink:Genotype .
ORPHA:938475 biolink:category biolink:Disease .
MONARCH:bdbeb077e365ddedda20 biolink:category biolink:Association .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
return
def test_unmapped_disease_assoc_type(self):
"""
Test that a gene disease type that we have
not mapped in translationtable/orphanet.yaml
raises a ValueError
"""
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-mapping.xml'
self.assertRaises(
KeyError, lambda: self.orphanet._process_diseasegene(limit=None))
return
class GeneVariantDiseaseTest(unittest.TestCase):
def setUp(self):
"""
"""
self.test_util = TestUtils()
self.orphanet = Orphanet('rdf_graph', True)
# Override so tests don't break when we update terms
# Note there is no such file ./resources/test_terms.yaml
# self.globaltt = self.orphanet.open_and_parse_yaml(
# os.path.join(os.path.dirname(__file__), './resources/test_terms.yaml'))
self.orphanet.rawdir = os.path.join(
os.path.dirname(__file__), 'resources/orphanet')
def tearDown(self):
self.orphanet = None
return
def test_germline_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8")
)
expected_triples = """
MONARCH:b40e89f44906ccededb6 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0003303 ;
OBAN:association_has_subject <https://monarchinitiative.org/.well-known/genid/bc50c3aece4f4f161d4d> .
ENSEMBL:ENSG00000166813 a owl:Class .
HGNC:30497 a owl:Class .
HGNC:30497 a owl:Class ;
rdfs:label "KS1" ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf OBO:SO_0001217 ;
owl:equivalentClass ENSEMBL:ENSG00000166813,
ORPHA:268061 .
<https://monarchinitiative.org/.well-known/genid/bc50c3aece4f4f161d4d> a GENO:0000002 ;
rdfs:label "germline variant of KS1" ;
GENO:0000418 HGNC:30497;
RO:0003303 ORPHA:938475 ;
:MONARCH_anonymous true ;
:has_cell_origin GENO:0000900 .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(self.test_util.test_graph_equality(
expected_triples, self.orphanet.graph))
return
def test_germline_lof_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline-lof.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.warning(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8")
)
expected_triples = """
MONARCH:b40e89f44906ccededb6 OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0003303 ;
OBAN:association_has_subject <https://monarchinitiative.org/.well-known/genid/ba0884fb61004110> .
HGNC:30497 a owl:Class ;
rdfs:label "KS1" ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf SO:0001217 .
<https://monarchinitiative.org/.well-known/genid/ba0884fb61004110> a GENO:0000002 ;
rdfs:label "germline loss of function variant of KS1" ;
GENO:0000418 HGNC:30497 ;
RO:0003303 ORPHA:938475 ;
:MONARCH_anonymous true ;
:has_cell_origin GENO:0000900 ;
:has_functional_consequence SO:0002054 .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples, self.orphanet.graph))
return
def test_gene_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-variant.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle") .decode("utf-8")
)
expected_triples = """
MONARCH:bd8eebdc522f33aca860 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0003304 ;
OBAN:association_has_subject HGNC:30497 .
HGNC:30497 a owl:Class ;
rdfs:label "KS1" ;
RO:0003304 ORPHA:938475 ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf SO:0001217 .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(self.test_util.test_graph_equality(
expected_triples, self.orphanet.graph))
return
def test_unmapped_disease_assoc_type(self):
"""
Test that a gene disease type that we have
not mapped in translationtable/orphanet.yaml
raises a ValueError
"""
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-mapping.xml'
self.assertRaises(
ValueError, lambda: self.orphanet._process_diseasegene(limit=None))
return
class EvidenceProvenanceTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.assoc_curie = 'MONARCH:test_association'
self.eco_id = 'ECO:0000015'
self.test_set_1 = (
'MGI:1920145', 'Setd5', 'WTSI', 'MEFW', 'male',
'heterozygote', 'MGI:4432631', 'Setd5<tm1a(EUCOMM)Wtsi>',
'targeted mutation 1a, Wellcome Trust Sanger Institute',
'MGI:2159965', 'C57BL/6N', 'MGP',
'Wellcome Trust Sanger Institute Mouse Genetics Project',
'MGP Select Pipeline', 'MGP_001', 'MGP_XRY_001', 'X-ray',
'IMPC_XRY_008_001', 'Number of ribs right', 'MP:0005390',
'skeleton phenotype', 'MP:0000480', 'increased rib number',
'1.637023E-010', '', '8.885439E-007',
'Wilcoxon rank sum test with continuity correction', 'IMPC')
# Generate test curies, these are otherwise generated
# within _add_evidence() and _add_study_provenance()
# these blank nodes are hardcoded as NOT Skolemized ...
self.study_curie = "_:study"
self.evidence_curie = "_:evidence"
# IRIs for testing sparql output
curie_dict = curie_map.get()
curie_util = CurieUtil(curie_dict)
self.assoc_iri = URIRef(curie_util.get_uri(self.assoc_curie))
return
def test_evidence_model(self):
"""
Functional test for _add_evidence()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True) # Reset graph
# Test graph is empty
self.assertTrue(len(list(impc.graph)) == 0)
impc_map = impc.open_and_parse_yaml(impc.map_files['impc_map'])
(p_value, percentage_change, effect_size) = self.test_set_1[23:26]
impc._add_evidence(self.assoc_curie, self.eco_id, impc_map, p_value,
percentage_change, effect_size, self.study_curie)
triples = """
:MONARCH_test_association SEPIO:0000007 <https://monarchinitiative.org/.well-known/genid/b097a98087df7a99> .
<https://monarchinitiative.org/.well-known/genid/b097a98087df7a99> a ECO:0000015 ;
SEPIO:0000084 <https://monarchinitiative.org/.well-known/genid/b89ee584330837c9>,
<https://monarchinitiative.org/.well-known/genid/bc0eeccdea27a1d8> ;
SEPIO:0000085 <https://monarchinitiative.org/.well-known/genid/study> .
<https://monarchinitiative.org/.well-known/genid/bc0eeccdea27a1d8> a OBI:0000175 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 1.637023e-10 .
<https://monarchinitiative.org/.well-known/genid/b89ee584330837c9> a STATO:0000085 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 "8.885439E-007" .
"""
self.assertTrue(self.test_util.test_graph_equality(
triples, impc.graph))
def test_provenance_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
impc_map = impc.open_and_parse_yaml(impc.map_files['impc_map'])
impress_map = json.loads(
impc.fetch_from_url(
impc.map_files['impress_map']).read().decode('utf-8'))
(phenotyping_center, colony) = self.test_set_1[2:4]
(project_fullname, pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name, parameter_stable_id,
parameter_name) = self.test_set_1[12:19]
(statistical_method, resource_name) = self.test_set_1[26:28]
impc._add_study_provenance(
impc_map, impress_map, phenotyping_center, colony,
project_fullname, pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name,
parameter_stable_id, parameter_name,
statistical_method, resource_name)
triples = """
<https://monarchinitiative.org/.well-known/genid/bbdd05a8ca155dda> a OBI:0000471 ;
BFO:0000051 OBO:STATO_0000076,
<https://www.mousephenotype.org/impress/protocol/175/15> ;
BFO:0000050 IMPRESS-procedure:15 ,
<http://www.sanger.ac.uk/science/data/mouse-genomes-project> ;
SEPIO:0000114 <https://www.mousephenotype.org/impress/parameterontologies/1867/91> ;
SEPIO:0000017 <http://www.sanger.ac.uk/> .
<https://monarchinitiative.org/.well-known/genid/bc0b26361b8687b5> a owl:NamedIndividual ;
rdfs:label "MEFW" .
<http://www.sanger.ac.uk/> a foaf:organization ;
rdfs:label "WTSI" .
<http://www.sanger.ac.uk/science/data/mouse-genomes-project> a VIVO:Project ;
rdfs:label "Wellcome Trust Sanger Institute Mouse Genetics Project" .
<https://www.mousephenotype.org/impress/parameterontologies/1867/91> a owl:NamedIndividual ;
rdfs:label "Number of ribs right (X-ray)" .
IMPRESS-procedure:15 a owl:NamedIndividual ;
rdfs:label "MGP Select Pipeline" .
<https://www.mousephenotype.org/impress/protocol/175/15> a owl:NamedIndividual ;
rdfs:label "X-ray" .
"""
# dbg
logger.debug("Reference graph: %s",
impc.graph.serialize(format="turtle")
.decode("utf-8")
)
self.assertTrue(self.test_util.test_graph_equality(
triples, impc.graph))
def test_assertion_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
impc_map = impc.open_and_parse_yaml(impc.map_files['impc_map'])
impc._add_assertion_provenance(
self.assoc_curie, self.evidence_curie, impc_map)
triples = """
MONARCH:test_association SEPIO:0000015 <https://monarchinitiative.org/.well-known/genid/bcb2c00a5c2f9c43> .
<https://monarchinitiative.org/.well-known/genid/bcb2c00a5c2f9c43> a SEPIO:0000001 ;
SEPIO:0000018 <http://www.mousephenotype.org/> ;
SEPIO:0000111 <https://monarchinitiative.org/.well-known/genid/evidence> .
<http://www.mousephenotype.org/> a foaf:organization ;
rdfs:label "International Mouse Phenotyping Consortium" .
"""
# dbg
logger.debug("Reference graph: %s",
impc.graph.serialize(format="turtle")
.decode("utf-8")
)
self.assertTrue(self.test_util.test_graph_equality(
triples, impc.graph))
def test_random_data_set(self):
"""
Download dataset using fetch(), then take a row of data and
run through evidence and provenance functions to test the output
Line of data is hardcoded, but theoretically should work on any line
"""
line_to_test = 1129
count = 0
impc = IMPC('rdf_graph', False) # Not Skolem
impress_map = json.loads(
impc.fetch_from_url(
impc.map_files['impress_map']).read().decode('utf-8'))
impc_map = impc.open_and_parse_yaml(impc.map_files['impc_map'])
# fetch file
impc.fetch(True)
file_path = '/'.join((impc.rawdir, impc.files['all']['file']))
with gzip.open(file_path, 'rt') as csvfile:
filereader = csv.reader(csvfile, delimiter=',', quotechar='\"')
for row in filereader:
count += 1
if count == line_to_test:
self.test_set_1 = row
break
# Some DRY violation with the above tests
(phenotyping_center, colony) = row[2:4]
(project_fullname, pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name, parameter_stable_id,
parameter_name) = row[12:19]
(statistical_method, resource_name) = row[26:28]
(p_value, percentage_change, effect_size) = self.test_set_1[23:26]
impc._add_evidence(self.assoc_curie, self.eco_id, impc_map, p_value,
percentage_change, effect_size, self.study_curie)
impc._add_study_provenance(
impc_map, impress_map, phenotyping_center, colony,
project_fullname, pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name,
parameter_stable_id, parameter_name,
statistical_method, resource_name)
# Note that this doesn't test much since we're dealing with
# multiple part_of and has_part links to individuals
# which results in ambiguity = hard to test
sparql_query = """
SELECT *
WHERE {
?assoc SEPIO:0000007 ?evidenceline .
?evidenceline a ECO:0000015 ;
SEPIO:0000085 _:study .
?study a OBI:0000471 ;
SEPIO:0000114 ?param ;
SEPIO:0000017 ?agent .
}
"""
sparql_output = impc.graph.query(sparql_query)
# Test that query passes and returns one row
self.assertEqual(len(list(sparql_output)), 1)
def tearDown(self):
return
class TestGwasHaplotypeModel(unittest.TestCase):
"""
Test the modelling of a SNP to trait association
from sample GWAS catalog data
"""
def setUp(self):
self.test_util = TestUtils()
self.source = GWASCatalog('rdf_graph', True)
self.source.graph = RDFGraph(True)
self.test_data = {
'snp_label': 'rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?',
'chrom_num': '9;9;9;9',
'chrom_pos': '36998996;37002118;37000690;36997420',
'context':
'intron_variant; intron_variant; intron_variant; intron_variant',
'allele_freq': 'NR',
'trait': 'Intelligence',
'trait_uri': 'http://www.ebi.ac.uk/efo/EFO_0004337',
'pvalue': '0.00000004',
'merged': '0',
'snp_id_current': '',
'mapped_gene': 'PAX5; PAX5; PAX5; PAX5',
'snp_gene_nums': '',
'upstream_gene_num': '107986179',
'downstream_gene_num': '107986180',
'init_sample_desc':
'656 European ancestry individuals from ADHD families',
'replicated_sample_desc': 'NA',
'platform': 'Illumina [795637]',
'pubmed': '22449649'
}
def tearDown(self):
self.source = None
def test_snp_model(self):
"""
Test output model of _process_haplotype()
self._process_haplotype(
variant_curie, strongest_snp_risk_allele,
chrom_num, chrom_pos, context,
risk_allele_frequency, mapped_gene, so_ontology)
"""
self.assertTrue(len(list(self.source.graph)) == 0)
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
so_ontology = RDFGraph()
LOG.info("Loading SO ontology in separate rdf graph")
so_ontology.parse(self.source.files['so']['url'], format='xml')
so_ontology.bind_all_namespaces()
LOG.info("Finished loading SO ontology")
self.source._process_haplotype(
variant_curie, self.test_data['snp_label'],
self.test_data['chrom_num'], self.test_data['chrom_pos'],
self.test_data['context'], self.test_data['allele_freq'],
self.test_data['mapped_gene'], so_ontology)
triples = """
:haplotype_bb627b1f64039b0f751a a SO:0001024 ;
rdfs:label "rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?" ;
GENO:0000382 dbSNP:rs1329573,
dbSNP:rs3758171,
dbSNP:rs3824344,
dbSNP:rs7020413 ;
GENO:0000418 HGNC:8619 ;
RO:0002162 NCBITaxon:9606 .
dbSNP:rs1329573 a SO:0000694,
SO:0001627 ;
rdfs:label "rs1329573-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/b3fad5df82cdfb283329> ;
GENO:0000418 HGNC:8619 ;
RO:0002162 NCBITaxon:9606 .
dbSNP:rs3758171 a SO:0000694,
SO:0001627 ;
rdfs:label "rs3758171-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/b25a2da36647bdd71be3> ;
GENO:0000418 HGNC:8619 ;
RO:0002162 NCBITaxon:9606 .
dbSNP:rs3824344 a SO:0000694,
OBO:SO_0001627 ;
rdfs:label "rs3824344-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/b096a3e94e32fe23374a> ;
GENO:0000418 HGNC:8619 ;
RO:0002162 NCBITaxon:9606 .
dbSNP:rs7020413 a SO:0000694,
SO:0001627 ;
rdfs:label "rs7020413-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/bbb252d9b6cd02e9880a> ;
GENO:0000418 HGNC:8619 ;
RO:0002162 NCBITaxon:9606 .
<https://monarchinitiative.org/.well-known/genid/b25a2da36647bdd71be3> a faldo:Region ;
rdfs:label "GRCh38chr9-36997420-36997420-Region";
faldo:begin <https://monarchinitiative.org/.well-known/genid/b21985847fe0774084eb> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/b21985847fe0774084eb> .
<https://monarchinitiative.org/.well-known/genid/b3fad5df82cdfb283329> a faldo:Region ;
rdfs:label "GRCh38chr9-36998996-36998996-Region";
faldo:begin <https://monarchinitiative.org/.well-known/genid/b55051762f8d5a3dbeb5> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/b55051762f8d5a3dbeb5> .
<https://monarchinitiative.org/.well-known/genid/b096a3e94e32fe23374a> a faldo:Region ;
rdfs:label "GRCh38chr9-37000690-37000690-Region";
faldo:begin <https://monarchinitiative.org/.well-known/genid/b5d61dbc7958a979d046> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/b5d61dbc7958a979d046> .
<https://monarchinitiative.org/.well-known/genid/bbb252d9b6cd02e9880a> a faldo:Region ;
rdfs:label "GRCh38chr9-37002118-37002118-Region";
faldo:begin <https://monarchinitiative.org/.well-known/genid/bb870c3d7606a3e0fc3c> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/bb870c3d7606a3e0fc3c> .
<https://monarchinitiative.org/.well-known/genid/b21985847fe0774084eb> a faldo:Position ;
rdfs:label "GRCh38chr9-36997420";
faldo:position 36997420 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/b55051762f8d5a3dbeb5> a faldo:Position ;
rdfs:label "GRCh38chr9-36998996";
faldo:position 36998996 ;
faldo:reference CHR:GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/b5d61dbc7958a979d046> a faldo:Position ;
rdfs:label "GRCh38chr9-37000690";
faldo:position 37000690 ;
faldo:reference CHR:GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/bb870c3d7606a3e0fc3c> a faldo:Position ;
rdfs:label "GRCh38chr9-37002118";
faldo:position 37002118 ;
faldo:reference CHR:GRCh38chr9 .
"""
# dbg
LOG.debug("Reference graph: %s",
self.source.graph.serialize(format="turtle").decode("utf-8"))
self.assertTrue(
self.test_util.test_graph_equality(triples, self.source.graph))
class TestGwasSNPModel(unittest.TestCase):
"""
Test the modelling of a SNP to trait association
from sample GWAS catalog data
"""
def setUp(self):
self.test_util = TestUtils()
self.source = GWASCatalog('rdf_graph', True)
self.source.graph = RDFGraph(True) # Reset graph
self.source.graph.bind_all_namespaces()
self.test_data = {
'snp_label': 'rs1491921-C',
'chrom_num': '5',
'chrom_pos': '21259029',
'context': 'intergenic_variant',
'allele_freq': '0.013',
'trait': 'Diisocyanate-induced asthma',
'trait_uri': 'http://www.ebi.ac.uk/efo/EFO_0006995, http://www.ebi.ac.uk/efo/EFO_0003949',
'pvalue': '0.0000007',
'merged': '0',
'snp_id_current': '1491921',
'mapped_gene': 'LOC102723561 - GUSBP1',
'snp_gene_nums': '',
'upstream_gene_num': '107986179',
'downstream_gene_num': '107986180',
'init_sample_desc': '74 European ancestry cases, 824 European ancestry controls',
'replicated_sample_desc': 'NA',
'platform': 'Illumina [1556551]',
'pubmed': '25918132'
}
def tearDown(self):
self.source = None
self.efo_ontology = None
def test_snp_type_resolution(self):
"""
Given the label: rs1491921-C
return dbSNP:rs1491921, snp
"""
self.assertTrue(len(list(self.source.graph)) == 0)
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
self.assertEqual(variant_curie, "dbSNP:rs1491921")
self.assertEqual(variant_type, 'snp')
def test_snp_model(self):
"""
Test output model of _add_snp_to_graph()
"""
self.assertTrue(len(list(self.source.graph)) == 0)
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
self.source._add_snp_to_graph(
variant_curie, self.test_data['snp_label'], self.test_data['chrom_num'],
self.test_data['chrom_pos'], self.test_data['context'],
self.test_data['allele_freq'])
triples = """
dbSNP:rs1491921 a OBO:SO_0000694, OBO:SO_0001628 ;
rdfs:label "rs1491921-C" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029-21259029-Region> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 ;
dc:description "0.013 [risk allele frequency]" .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029-21259029-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr5-21259029> a faldo:Position ;
faldo:position 21259029 ;
faldo:reference OBO:CHR_GRCh38chr5 .
"""
# To debug
# print(self.source.graph.serialize(format="turtle").decode("utf-8"))
# self.assertTrue(False)
# dbg
# LOG.debug(
# "Reference graph: %s",
# self.source.graph.serialize(format="turtle").decode("utf-8"))
self.assertTrue(self.test_util.test_graph_equality(triples, self.source.graph))
def test_snp_gene_relation(self):
"""
test the _add_snp_gene_relation function
:return:
"""
self.assertTrue(len(list(self.source.graph)) == 0)
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
self.source._add_snp_gene_relation(
variant_curie, self.test_data['snp_gene_nums'],
self.test_data['upstream_gene_num'],
self.test_data['downstream_gene_num'])
triples = """
dbSNP:rs1491921 OBO:RO_0002528 NCBIGene:107986180 ;
OBO:RO_0002529 NCBIGene:107986179 .
"""
self.assertTrue(self.test_util.test_graph_equality(triples, self.source.graph))
def test_deprecated_snp(self):
"""
test the _add_deprecated_snp
:return:
"""
self.assertTrue(len(list(self.source.graph)) == 0)
# fake data
snp_id_current = '12345'
merged = '1'
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
self.source._add_deprecated_snp(
variant_curie, snp_id_current, merged,
self.test_data['chrom_num'], self.test_data['chrom_pos'])
triples = """
dbSNP:rs1491921 a owl:NamedIndividual ;
OBO:IAO_0100001 dbSNP:rs12345 ;
owl:deprecated true .
dbSNP:rs12345 MONARCH:cliqueLeader true .
"""
self.assertTrue(self.test_util.test_graph_equality(triples, self.source.graph))
def test_snp_trait_association(self):
"""
test the _add_variant_trait_association
:return:
"""
self.assertTrue(len(list(self.source.graph)) == 0)
efo_ontology = RDFGraph()
LOG.info("Loading EFO ontology in separate rdf graph")
efo_ontology.parse(self.source.files['efo']['url'], format='xml')
efo_ontology.bind_all_namespaces()
LOG.info("Finished loading EFO ontology")
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
description = self.source._make_description(
self.test_data['trait'], self.test_data['init_sample_desc'],
self.test_data['replicated_sample_desc'],
self.test_data['platform'], self.test_data['pvalue'])
self.source._add_variant_trait_association(
variant_curie, self.test_data['trait_uri'], efo_ontology,
self.test_data['pubmed'], description)
triples = """
MONARCH:bffc7a930c08cc8fe931 a OBAN:association ;
dc:description "{0}" ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0003949 ;
OBAN:association_has_predicate RO:0003304 ;
OBAN:association_has_subject dbSNP:rs1491921 .
MONARCH:bff9b97458d67ed7f517 a OBAN:association ;
dc:description "{0}" ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0006995 ;
OBAN:association_has_predicate RO:0003304 ;
OBAN:association_has_subject dbSNP:rs1491921 .
EFO:0003949 a owl:Class ;
rdfs:label "eye color"^^xsd:string ;
rdfs:subClassOf UPHENO:0001001 .
dbSNP:rs1491921 RO:0003304 EFO:0003949,
EFO:0006995 .
PMID:25918132 a OBO:IAO_0000013 .
""".format(description)
# dbg
# LOG.debug(
# "Reference graph: %s",
# self.source.graph.serialize(format="turtle").decode("utf-8"))
self.assertTrue(self.test_util.test_graph_equality(triples, self.source.graph))
class TestGwasHaplotypeModel(unittest.TestCase):
"""
Test the modelling of a SNP to trait association
from sample GWAS catalog data
"""
def setUp(self):
self.test_util = TestUtils()
self.source = GWASCatalog('rdf_graph', True)
self.source.graph = RDFGraph(True)
self.test_data = {
'snp_label': 'rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?',
'chrom_num': '9;9;9;9',
'chrom_pos': '36998996;37002118;37000690;36997420',
'context': 'intron_variant; intron_variant; intron_variant; intron_variant',
'allele_freq': 'NR',
'trait': 'Intelligence',
'trait_uri': 'http://www.ebi.ac.uk/efo/EFO_0004337',
'pvalue': '0.00000004',
'merged': '0',
'snp_id_current': '',
'mapped_gene': 'PAX5; PAX5; PAX5; PAX5',
'snp_gene_nums': '',
'upstream_gene_num': '107986179',
'downstream_gene_num': '107986180',
'init_sample_desc': '656 European ancestry individuals from ADHD families',
'replicated_sample_desc': 'NA',
'platform': 'Illumina [795637]',
'pubmed': '22449649'
}
def tearDown(self):
self.source = None
def test_snp_model(self):
"""
Test output model of _process_haplotype()
self._process_haplotype(
variant_curie, strongest_snp_risk_allele,
chrom_num, chrom_pos, context,
risk_allele_frequency, mapped_gene, so_ontology)
"""
self.assertTrue(len(list(self.source.graph)) == 0)
variant_curie, variant_type = self.source._get_curie_and_type_from_id(
self.test_data['snp_label'])
so_ontology = RDFGraph()
LOG.info("Loading SO ontology in separate rdf graph")
so_ontology.parse(self.source.files['so']['url'], format='xml')
so_ontology.bind_all_namespaces()
LOG.info("Finished loading SO ontology")
self.source._process_haplotype(
variant_curie, self.test_data['snp_label'], self.test_data['chrom_num'],
self.test_data['chrom_pos'], self.test_data['context'],
self.test_data['allele_freq'], self.test_data['mapped_gene'], so_ontology)
triples = """
:haplotype_bb627b1f64039b0f751a a OBO:GENO_0000871 ;
rdfs:label "rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?" ;
OBO:GENO_0000382 dbSNP:rs1329573,
dbSNP:rs3758171,
dbSNP:rs3824344,
dbSNP:rs7020413 ;
OBO:SO_0001627 HGNC:8619 ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs1329573 a OBO:SO_0000694,
SO:0001627 ;
rdfs:label "rs1329573-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996-36998996-Region> ;
OBO:SO_0001627 HGNC:8619 ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs3758171 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs3758171-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420-36997420-Region> ;
OBO:SO_0001627 HGNC:8619 ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs3824344 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs3824344-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690-37000690-Region> ;
OBO:SO_0001627 HGNC:8619 ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
dbSNP:rs7020413 a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs7020413-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118-37002118-Region> ;
OBO:SO_0001627 HGNC:8619 ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420-36997420-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996-36998996-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690-37000690-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118-37002118-Region> a faldo:Region ;
faldo:begin <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> ;
faldo:end <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36997420> a faldo:Position ;
faldo:position 36997420 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996> a faldo:Position ;
faldo:position 36998996 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37000690> a faldo:Position ;
faldo:position 37000690 ;
faldo:reference OBO:CHR_GRCh38chr9 .
<https://monarchinitiative.org/.well-known/genid/GRCh38chr9-37002118> a faldo:Position ;
faldo:position 37002118 ;
faldo:reference OBO:CHR_GRCh38chr9 .
"""
# dbg
# LOG.debug(
# "Reference graph: %s",
# self.source.graph.serialize(format="turtle").decode("utf-8"))
# Does not seem to acknowlage these constant triples
self.assertTrue(self.test_util.test_graph_equality(triples, self.source.graph))
class UDPTestCase(unittest.TestCase):
"""
Test UDP parser
"""
def setUp(self):
self.test_util = TestUtils()
return
def tearDown(self):
return
def test_dbsnp_indel_resolution(self):
"""
unit test for _get_rs_id()
Test that we can resolve indels that
have different insertion sequence(s)
for one rsid
15 51766637 374313651 in-del -/A/AA/AAA/AAAA/CAAA/TAAA
"""
udp = UDP('rdf_graph', True)
rs_map = udp._parse_rs_map_file(udp.map_files['dbsnp_map'])
variant_type = 'indel'
variant = {
'build': 'hg19',
'chromosome': 'chr15',
'reference_allele': '-',
'variant_allele': 'AAAA',
'position': '51766637'
}
rsid = udp._get_rs_id(variant, rs_map, variant_type)
self.assertEqual(rsid, '374313651')
def test_dbsnp_snp_mapping(self):
"""
unit test for _get_rs_id()
Test that we can resolve snps in dbsnp
to rsids
"""
udp = UDP('rdf_graph', True)
rs_map = udp._parse_rs_map_file(udp.map_files['dbsnp_map'])
variant_type = 'snp'
variant = {
'build': 'hg19',
'chromosome': 'chr15',
'reference_allele': 'A',
'variant_allele': 'C',
'position': '54624219'
}
rsid = udp._get_rs_id(variant, rs_map, variant_type)
self.assertEqual(rsid, '755532609')
def test_patient_phenotype_model(self):
"""
functional test for _parse_patient_phenotypes()
"""
udp = UDP('rdf_graph', True)
udp.graph = RDFGraph(True)
# test that graph is empty
self.assertTrue(len(list(udp.graph)) == 0)
mock_lines = [
'patient_1\tHP:000001\tyes',
'patient_1\tHP:000002\tno'
]
mock_data = MagicMock()
mock_data.__iter__.return_value = iter(mock_lines)
mock_file = mock_open(mock=mock_data)
udp._parse_patient_phenotypes(mock_file)
triples = """
:patient_1 a foaf:Person ;
rdfs:label "patient_1" ;
RO:0002200 DOID:4,
HP:000001 .
"""
self.assertTrue(self.test_util.test_graph_equality(
triples, udp.graph))
def test_variant_model(self):
"""
functional test for _parse_patient_variants()
"""
udp = UDP('rdf_graph', True)
udp.graph = RDFGraph(True)
# test that graph is empty
self.assertTrue(len(list(udp.graph)) == 0)
data = ['patient_1',
'family_1',
'1',
'HG19',
'155230432',
'G',
'A',
'Maternal',
'Biallelic',
'Non-synonymous;DOWNSTREAM',
'CLK2',
'',
'',
'',
'',
'',
'',
'',
'Compound heterozygous',
'Heterozygous',
'',
'0.002747253',
'']
test_data = "\t".join(data)
mock_lines = [test_data]
mock_data = MagicMock()
mock_data.__iter__.return_value = iter(mock_lines)
mock_file = mock_open(mock=mock_data)
udp._parse_patient_variants(mock_file)
triples = """
:patient_1 GENO:0000222 <https://monarchinitiative.org/.well-known/genid/ba5f377fc8c95d4a6d7a> .
<https://monarchinitiative.org/.well-known/genid/b41e8da0787b45e24c4f> a SO:0001059 ;
rdfs:label "hg19chr1(CLK2):g.155230432G>A" ;
GENO:0000418 HGNC:2069 ;
RO:0002162 NCBITaxon:9606 ;
owl:sameAs dbSNP:rs11557757 .
<https://monarchinitiative.org/.well-known/genid/ba5f377fc8c95d4a6d7a> a GENO:0000000 ;
rdfs:label "patient_1 genotype" ;
GENO:0000382 <https://monarchinitiative.org/.well-known/genid/b41e8da0787b45e24c4f> .
"""
self.assertTrue(self.test_util.test_graph_equality(triples, udp.graph))
class EvidenceProvenanceTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.assoc_curie = 'MONARCH:test_association'
self.eco_id = 'ECO:0000015'
# Headers:
# 01 marker_accession_id,
# 02 marker_symbol,
# 03 phenotyping_center,
# 04 colony_raw,
# 05 sex,
# 06 zygosity,
# 07 allele_accession_id,
# 08 allele_symbol,
# 09 allele_name,
# 10 strain_accession_id,
# 11 strain_name,
# 12 project_name,
# 13 project_fullname,
# 14 pipeline_name,
# 15 pipeline_stable_id,
# 16 procedure_stable_id,
# 17 procedure_name,
# 18 parameter_stable_id,
# 19 parameter_name,
# 20 top_level_mp_term_id,
# 21 top_level_mp_term_name,
# 22 mp_term_id,
# 23 mp_term_name,
# 24 p_value,
# 25 percentage_change,
# 26 effect_size,
# 27 statistical_method,
# 28 resource_name
self.test_set_1 = (
'MGI:1920145', # 01
'Setd5', # 02
'WTSI', # 03
'MEFW', # 04
'male', # 05
'heterozygote', # 06
'MGI:4432631', # 07
'Setd5<tm1a(EUCOMM)Wtsi>', # 08
'targeted mutation 1a, Wellcome Trust Sanger Institute', # 09
'MGI:2159965', # 10
'C57BL/6N', # 11
'MGP', # 12
'Wellcome Trust Sanger Institute Mouse Genetics Project', # 13
'MGP Select Pipeline', # 14
'MGP_001', # 15
'MGP_XRY_001', # 16
'X-ray', # 17
'IMPC_XRY_008_001', # 18
'Number of ribs right', # 19
'MP:0005390', # 20
'skeleton phenotype', # 21
'MP:0000480', # 22
'increased rib number', # 23
'1.637023E-010', # 24
'', # 25
'8.885439E-007', # 26
'Wilcoxon rank sum test with continuity correction', # 27
'IMPC' # 28
)
# Generate test curies, these are otherwise generated
# within _add_evidence() and _add_study_provenance()
# these blank nodes are hardcoded as NOT Skolemized ...
self.study_curie = "_:study"
self.evidence_curie = "_:evidence"
# IRIs for testing sparql output
curie_dict = curie_map.get()
curie_util = CurieUtil(curie_dict)
self.assoc_iri = URIRef(curie_util.get_uri(self.assoc_curie))
return
def test_evidence_model(self):
"""
Functional test for _add_evidence()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True) # Reset graph
# Test graph is empty
self.assertTrue(len(list(impc.graph)) == 0)
(p_value, percentage_change, effect_size) = self.test_set_1[23:26]
impc._add_evidence(
self.assoc_curie, self.eco_id, p_value, percentage_change, effect_size,
self.study_curie)
triples = """
:MONARCH_test_association SEPIO:0000007 <https://monarchinitiative.org/.well-known/genid/b97a98087df7a99d8a38> .
<https://monarchinitiative.org/.well-known/genid/b97a98087df7a99d8a38> a ECO:0000015 ;
SEPIO:0000084 <https://monarchinitiative.org/.well-known/genid/b41ad2bfd375c9de8888>,
<https://monarchinitiative.org/.well-known/genid/b216606de82749b03956> ;
SEPIO:0000085 <https://monarchinitiative.org/.well-known/genid/study> .
<https://monarchinitiative.org/.well-known/genid/b216606de82749b03956> a OBI:0000175 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 1.637023e-10 .
<https://monarchinitiative.org/.well-known/genid/b41ad2bfd375c9de8888> a STATO:0000085 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 "8.885439E-007" .
"""
self.assertTrue(self.test_util.test_graph_equality(
triples, impc.graph))
def test_provenance_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
(phenotyping_center,
colony) = self.test_set_1[2:4]
(project_name,
project_fullname,
pipeline_name,
pipeline_stable_id,
procedure_stable_id,
procedure_name,
parameter_stable_id,
parameter_name) = self.test_set_1[11:19]
(statistical_method, resource_name) = self.test_set_1[26:28]
impc._add_study_provenance(
phenotyping_center, colony,
project_name,
pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name,
parameter_stable_id, parameter_name,
statistical_method, resource_name)
# dbg
LOG.info(
"Provenance graph as turtle:\n%s\n",
impc.graph.serialize(format="turtle").decode("utf-8")
)
triples = """
<https://monarchinitiative.org/.well-known/genid/b0b26361b8687b5ad9ef> a owl:NamedIndividual ;
rdfs:label "MEFW" .
<https://monarchinitiative.org/.well-known/genid/b6f14f763c8d0629360e> a OBI:0000471 ;
BFO:0000050 <http://www.sanger.ac.uk/science/data/mouse-genomes-project>,
IMPC-pipe:MGP_001 ;
BFO:0000051 STATO:0000076,
IMPC-proc:MGP_XRY_001 ;
SEPIO:0000017 <http://www.sanger.ac.uk/> ;
SEPIO:0000114 <https://www.mousephenotype.org/impress/OntologyInfo?action=list&procID=MGP_XRY_001#IMPC_XRY_008_001> .
<http://www.sanger.ac.uk/> a foaf:organization ;
rdfs:label "WTSI" .
<http://www.sanger.ac.uk/science/data/mouse-genomes-project> a VIVO:Project ;
rdfs:label "MGP" .
<https://www.mousephenotype.org/impress/OntologyInfo?action=list&procID=MGP_XRY_001#IMPC_XRY_008_001> a owl:NamedIndividual ;
rdfs:label "Number of ribs right (X-ray)" .
IMPC-pipe:MGP_001 a owl:NamedIndividual ;
rdfs:label "MGP Select Pipeline" .
IMPC-proc:MGP_XRY_001 a owl:NamedIndividual ;
rdfs:label "X-ray" .
"""
# dbg
LOG.info(
"Reference graph: %s",
impc.graph.serialize(format="turtle").decode("utf-8")
)
self.assertTrue(
self.test_util.test_graph_equality(triples, impc.graph))
def test_assertion_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
impc._add_assertion_provenance(self.assoc_curie, self.evidence_curie)
triples = """
MONARCH:test_association SEPIO:0000015 <https://monarchinitiative.org/.well-known/genid/bf92df374a884963e805> .
<https://monarchinitiative.org/.well-known/genid/bf92df374a884963e805> a SEPIO:0000001 ;
SEPIO:0000018 <https://www.mousephenotype.org/> ;
SEPIO:0000111 <https://monarchinitiative.org/.well-known/genid/evidence> .
<https://www.mousephenotype.org/> a foaf:organization ;
rdfs:label "International Mouse Phenotyping Consortium" .
"""
# dbg
LOG.info(
"Assertion graph:\n %s\n", impc.graph.serialize(
format="turtle").decode("utf-8")
)
self.assertTrue(self.test_util.test_graph_equality(triples, impc.graph))
@unittest.skip("Timeouts on travis")
def test_random_data_set(self):
"""
Download dataset using fetch(), then take a row of data and
run through evidence and provenance functions to test the output
Line of data is hardcoded, but theoretically should work on any line
"""
line_to_test = 1129
count = 0
impc = IMPC('rdf_graph', False) # Not Skolem
self.test_set_N = []
# fetch file
# impc.fetch(True)
file_path = '/'.join((impc.rawdir, impc.files['all']['file']))
with gzip.open(file_path, 'rt') as csvfile:
filereader = csv.reader(csvfile, delimiter=',', quotechar='\"')
for row in filereader:
count += 1
if count < line_to_test:
continue
elif count == line_to_test:
self.test_set_N = row
elif count > line_to_test:
LOG.info("stopped at line:\t%s\n", count)
break
# Some DRY violation with the above tests
(phenotyping_center, colony) = self.test_set_N[2:4]
(project_name,project_fullname, pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name, parameter_stable_id,
parameter_name) = self.test_set_N[11:19]
(statistical_method, resource_name) = self.test_set_N[26:28]
(p_value, percentage_change, effect_size) = self.test_set_N[23:26]
# adding evidence
impc._add_evidence(
self.assoc_curie, self.eco_id, p_value, percentage_change, effect_size,
self.study_curie)
# adding study
impc._add_study_provenance(
phenotyping_center, colony, project_name,
pipeline_name,
pipeline_stable_id,
procedure_stable_id, procedure_name,
parameter_stable_id, parameter_name,
statistical_method, resource_name, line_to_test)
# Note that this doesn't test much since we're dealing with
# multiple part_of and has_part links to individuals
# which results in ambiguity = hard to test
# dbg
LOG.info(
"Row %i graph as ntriples:\n%s\n",
line_to_test, impc.graph.serialize(format="ntriples").decode("utf-8")
)
sparql_query = """
SELECT *
WHERE {
?assoc SEPIO:0000007 ?evidenceline .
?evidenceline a ECO:0000015 ;
SEPIO:0000085 _:study .
?study a OBI:0000471 ;
SEPIO:0000114 ?param ;
SEPIO:0000017 ?agent .
}
"""
sparql_output = impc.graph.query(sparql_query)
LOG.info(
"Test that query for row %i passes and returns one row", int(line_to_test))
# print("Sparql Output: %s\n", list(sparql_output) )
# it is an array with one list with five vars in it
self.assertEqual(len(list(sparql_output)), 1)
def tearDown(self):
return
class EvidenceProvenanceTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.assoc_curie = 'MONARCH:test_association'
self.eco_id = 'ECO:0000015'
# Headers:
# 01 marker_accession_id,
# 02 marker_symbol,
# 03 phenotyping_center,
# 04 colony_raw,
# 05 sex,
# 06 zygosity,
# 07 allele_accession_id,
# 08 allele_symbol,
# 09 allele_name,
# 10 strain_accession_id,
# 11 strain_name,
# 12 project_name,
# 13 project_fullname,
# 14 pipeline_name,
# 15 pipeline_stable_id,
# 16 procedure_stable_id,
# 17 procedure_name,
# 18 parameter_stable_id,
# 19 parameter_name,
# 20 top_level_mp_term_id,
# 21 top_level_mp_term_name,
# 22 mp_term_id,
# 23 mp_term_name,
# 24 p_value,
# 25 percentage_change,
# 26 effect_size,
# 27 statistical_method,
# 28 resource_name
self.test_set_1 = (
'MGI:1920145', # 01
'Setd5', # 02
'WTSI', # 03
'MEFW', # 04
'male', # 05
'heterozygote', # 06
'MGI:4432631', # 07
'Setd5<tm1a(EUCOMM)Wtsi>', # 08
'targeted mutation 1a, Wellcome Trust Sanger Institute', # 09
'MGI:2159965', # 10
'C57BL/6N', # 11
'MGP', # 12
'Wellcome Trust Sanger Institute Mouse Genetics Project', # 13
'MGP Select Pipeline', # 14
'MGP_001', # 15
'MGP_XRY_001', # 16
'X-ray', # 17
'IMPC_XRY_008_001', # 18
'Number of ribs right', # 19
'MP:0005390', # 20
'skeleton phenotype', # 21
'MP:0000480', # 22
'increased rib number', # 23
'1.637023E-010', # 24
'', # 25
'8.885439E-007', # 26
'Wilcoxon rank sum test with continuity correction', # 27
'IMPC' # 28
)
# Generate test curies, these are otherwise generated
# within _add_evidence() and _add_study_provenance()
# these blank nodes are hardcoded as NOT Skolemized ...
self.study_curie = "_:study"
self.evidence_curie = "_:evidence"
# IRIs for testing sparql output
curie_dict = curie_map.get()
curie_util = CurieUtil(curie_dict)
self.assoc_iri = URIRef(curie_util.get_uri(self.assoc_curie))
return
def test_evidence_model(self):
"""
Functional test for _add_evidence()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True) # Reset graph
# Test graph is empty
self.assertTrue(len(list(impc.graph)) == 0)
(p_value, percentage_change, effect_size) = self.test_set_1[23:26]
impc._add_evidence(
self.assoc_curie, self.eco_id, p_value, percentage_change, effect_size,
self.study_curie)
triples = """
:MONARCH_test_association SEPIO:0000007 <https://monarchinitiative.org/.well-known/genid/b97a98087df7a99d8a38> .
<https://monarchinitiative.org/.well-known/genid/b97a98087df7a99d8a38> a ECO:0000015 ;
SEPIO:0000084 <https://monarchinitiative.org/.well-known/genid/b41ad2bfd375c9de8888>,
<https://monarchinitiative.org/.well-known/genid/b216606de82749b03956> ;
SEPIO:0000085 <https://monarchinitiative.org/.well-known/genid/study> .
<https://monarchinitiative.org/.well-known/genid/b216606de82749b03956> a OBI:0000175 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 1.637023e-10 .
<https://monarchinitiative.org/.well-known/genid/b41ad2bfd375c9de8888> a STATO:0000085 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 "8.885439E-007" .
"""
self.assertTrue(self.test_util.test_graph_equality(
triples, impc.graph))
def test_provenance_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
(phenotyping_center, colony) = self.test_set_1[2:4]
(project_fullname, pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name, parameter_stable_id,
parameter_name) = self.test_set_1[12:19]
(statistical_method, resource_name) = self.test_set_1[26:28]
impc._add_study_provenance(
phenotyping_center, colony,
project_fullname,
pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name,
parameter_stable_id, parameter_name,
statistical_method, resource_name, 0)
# dbg
logger.info(
"Provenance graph as turtle:\n%s\n",
impc.graph.serialize(format="turtle").decode("utf-8")
)
triples = """
<https://monarchinitiative.org/.well-known/genid/bdd05a8ca155ddaf415e> a OBI:0000471 ;
BFO:0000051 OBO:STATO_0000076,
<https://www.mousephenotype.org/impress/protocol/175/15> ;
BFO:0000050 IMPRESS-procedure:15 ,
<http://www.sanger.ac.uk/science/data/mouse-genomes-project> ;
SEPIO:0000114 <https://www.mousephenotype.org/impress/parameterontologies/1867/91> ;
SEPIO:0000017 <http://www.sanger.ac.uk/> .
<https://monarchinitiative.org/.well-known/genid/b0b26361b8687b5ad9ef> a owl:NamedIndividual ;
rdfs:label "MEFW" .
<http://www.sanger.ac.uk/> a foaf:organization ;
rdfs:label "WTSI" .
<http://www.sanger.ac.uk/science/data/mouse-genomes-project> a VIVO:Project ;
rdfs:label "Wellcome Trust Sanger Institute Mouse Genetics Project" .
<https://www.mousephenotype.org/impress/parameterontologies/1867/91> a owl:NamedIndividual ;
rdfs:label "Number of ribs right (X-ray)" .
IMPRESS-procedure:15 a owl:NamedIndividual ;
rdfs:label "MGP Select Pipeline" .
<https://www.mousephenotype.org/impress/protocol/175/15> a owl:NamedIndividual ;
rdfs:label "X-ray" .
"""
# dbg
logger.debug(
"Reference graph: %s", impc.graph.serialize(format="turtle").decode("utf-8")
)
self.assertTrue(
self.test_util.test_graph_equality(triples, impc.graph))
def test_assertion_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
impc._add_assertion_provenance(self.assoc_curie, self.evidence_curie)
triples = """
MONARCH:test_association SEPIO:0000015 <https://monarchinitiative.org/.well-known/genid/bf92df374a884963e805> .
<https://monarchinitiative.org/.well-known/genid/bf92df374a884963e805> a SEPIO:0000001 ;
SEPIO:0000018 <https://www.mousephenotype.org/> ;
SEPIO:0000111 <https://monarchinitiative.org/.well-known/genid/evidence> .
<https://www.mousephenotype.org/> a foaf:organization ;
rdfs:label "International Mouse Phenotyping Consortium" .
"""
# dbg
logger.info(
"Assertion graph:\n %s\n", impc.graph.serialize(
format="turtle").decode("utf-8")
)
self.assertTrue(self.test_util.test_graph_equality(triples, impc.graph))
def test_random_data_set(self):
"""
Download dataset using fetch(), then take a row of data and
run through evidence and provenance functions to test the output
Line of data is hardcoded, but theoretically should work on any line
"""
line_to_test = 1129
count = 0
impc = IMPC('rdf_graph', False) # Not Skolem
self.test_set_N = []
# fetch file
# impc.fetch(True)
file_path = '/'.join((impc.rawdir, impc.files['all']['file']))
with gzip.open(file_path, 'rt') as csvfile:
filereader = csv.reader(csvfile, delimiter=',', quotechar='\"')
for row in filereader:
count += 1
if count < line_to_test:
continue
elif count == line_to_test:
self.test_set_N = row
elif count > line_to_test:
logger.info("stopped at line:\t%s\n", count)
break
# Some DRY violation with the above tests
(phenotyping_center, colony) = self.test_set_N[2:4]
(project_fullname, pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name, parameter_stable_id,
parameter_name) = self.test_set_N[12:19]
(statistical_method, resource_name) = self.test_set_N[26:28]
(p_value, percentage_change, effect_size) = self.test_set_N[23:26]
# adding evidence
impc._add_evidence(
self.assoc_curie, self.eco_id, p_value, percentage_change, effect_size,
self.study_curie)
# adding study
impc._add_study_provenance(
phenotyping_center, colony, project_fullname,
pipeline_name,
pipeline_stable_id,
procedure_stable_id, procedure_name,
parameter_stable_id, parameter_name,
statistical_method, resource_name, line_to_test)
# Note that this doesn't test much since we're dealing with
# multiple part_of and has_part links to individuals
# which results in ambiguity = hard to test
# dbg
logger.info(
"Row %i graph as ntriples:\n%s\n", line_to_test, impc.graph.serialize(
format="ntriples").decode("utf-8")
)
sparql_query = """
SELECT *
WHERE {
?assoc SEPIO:0000007 ?evidenceline .
?evidenceline a ECO:0000015 ;
SEPIO:0000085 _:study .
?study a OBI:0000471 ;
SEPIO:0000114 ?param ;
SEPIO:0000017 ?agent .
}
"""
sparql_output = impc.graph.query(sparql_query)
logger.info("Test that query for row %i passes and returns one row", int(line_to_test))
# print("Sparql Output: %s\n", list(sparql_output) )
# it is an array with one list with five vars in it
self.assertEqual(len(list(sparql_output)), 1)
def tearDown(self):
return
class StringTestFakeData(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
# Test set with two proteins from same species
self.test_set_1 = [[
'9606.ENSP00000000233', '9606.ENSP00000003084',
0, 0, 0, 0, 300, 0, 150, 800]]
# Test set with deprecated protein id
self.test_set_2 = [[
'9606.ENSP00000000233', '9606.ENSP00000006101',
0, 0, 0, 0, 300, 0, 150, 800]]
self.columns = [
'protein1', 'protein2', 'neighborhood', 'fusion', 'cooccurence',
'coexpression', 'experimental', 'database', 'textmining', 'combined_score']
ensembl = Ensembl('rdf_graph', True)
self.protein_list = ensembl.fetch_protein_gene_map('9606')
return
def tearDown(self):
return
def testFakeDataSet1(self):
string_db = StringDB('rdf_graph', True)
string_db.graph = RDFGraph(True)
self.assertEqual(len(string_db.graph), 0)
ensembl = Ensembl('rdf_graph', True)
prot_map = ensembl.fetch_protein_gene_map('9606')
for key in prot_map.keys():
for i, gene in enumerate(prot_map[key]):
prot_map[key][i] = "ENSEMBL:{}".format(gene)
print(
"Finished fetching ENSP IDs, fetched {} proteins"
.format(len(prot_map.keys())))
dataframe = pd.DataFrame(data=self.test_set_1, columns=self.columns)
string_db._process_protein_links(dataframe, prot_map, '9606')
# g1 <interacts with> g2
triples = """
ENSEMBL:ENSG00000001626 RO:0002434 ENSEMBL:ENSG00000004059 .
"""
self.assertTrue(self.test_util.test_graph_equality(triples, string_db.graph))
def testFakeDataSet2(self):
"""
Dataset contains a deprecated protein ID
that we expect if filtered out by ensembl biomart
We test that this returns an empty graph
:return:
"""
string_db = StringDB('rdf_graph', True)
string_db.graph = RDFGraph()
self.assertEqual(len(string_db.graph), 0)
dataframe = pd.DataFrame(data=self.test_set_2, columns=self.columns)
string_db._process_protein_links(dataframe, self.protein_list, '9606')
self.assertEqual(len(string_db.graph), 0)
class GeneVariantDiseaseTest(unittest.TestCase):
def setUp(self):
"""
"""
self.test_util = TestUtils()
self.orphanet = Orphanet('rdf_graph', True)
# Override so tests don't break when we update terms
self.globaltt = self.orphanet.open_and_parse_yaml(
os.path.join(os.path.dirname(__file__),
'./resources/test_terms.yaml'))
self.orphanet.rawdir = os.path.join(os.path.dirname(__file__),
'resources/orphanet')
def tearDown(self):
self.orphanet = None
return
def test_germline_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline.xml'
self.orphanet._process_diseasegene(limit=None)
logger.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:b2cd4dfacc21d0e28c39 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object Orphanet:938475 ;
OBAN:association_has_predicate RO:0003303 ;
OBAN:association_has_subject <https://monarchinitiative.org/.well-known/genid/b56f798350412a34> .
ENSEMBL:ENSG00000166813 a owl:Class .
HGNC:30497 a owl:Class .
Orphanet:268061 a owl:Class ;
rdfs:label "KS1" ;
dc:description "kinesin family member 7" ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf OBO:SO_0001217 ;
owl:equivalentClass ENSEMBL:ENSG00000166813,
HGNC:30497 .
<https://monarchinitiative.org/.well-known/genid/b56f798350412a34> a GENO:0000002 ;
rdfs:label "germline variant of KS1" ;
GENO:0000418 Orphanet:268061 ;
RO:0003303 Orphanet:938475 ;
:MONARCH_anonymous true ;
:has_cell_origin GENO:0000900 .
Orphanet:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
def test_germline_lof_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline-lof.xml'
self.orphanet._process_diseasegene(limit=None)
logger.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:b53dada0eb229a75e705 OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object Orphanet:938475 ;
OBAN:association_has_predicate RO:0003303 ;
OBAN:association_has_subject <https://monarchinitiative.org/.well-known/genid/ba0884fb61004110> .
Orphanet:268061 a owl:Class ;
rdfs:label "KS1" ;
dc:description "kinesin family member 7" ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf SO:0001217 .
<https://monarchinitiative.org/.well-known/genid/ba0884fb61004110> a GENO:0000002 ;
rdfs:label "germline loss of function variant of KS1" ;
GENO:0000418 Orphanet:268061 ;
RO:0003303 Orphanet:938475 ;
:MONARCH_anonymous true ;
:has_cell_origin GENO:0000900 ;
:has_functional_consequence SO:0002054 .
Orphanet:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
def test_gene_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-variant.xml'
self.orphanet._process_diseasegene(limit=None)
logger.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:b64684a0ea6ae59fdb09 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object Orphanet:938475 ;
OBAN:association_has_predicate RO:0003304 ;
OBAN:association_has_subject Orphanet:268061 .
Orphanet:268061 a owl:Class ;
rdfs:label "KS1" ;
RO:0003304 Orphanet:938475 ;
dc:description "kinesin family member 7" ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf SO:0001217 .
Orphanet:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
def test_unmapped_disease_assoc_type(self):
"""
Test that a gene disease type that we have
not mapped in translationtable/orphanet.yaml
raises a ValueError
"""
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-mapping.xml'
self.assertRaises(
ValueError, lambda: self.orphanet._process_diseasegene(limit=None))
class RGDTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.test_set_1 = {
'aspect':
'N',
'date':
'2006-10-26',
'evidence': {
'has_supporting_reference': ['RGD:1581841', 'PMID:12799311'],
'type': 'IED',
'with_support_from': []
},
'negated':
False,
'object': {
'id': 'MP:0003340',
'taxon': 'NCBITaxon:10116'
},
'provided_by':
'RGD',
'qualifiers': [],
'relation': {
'id': None
},
'source_line':
'RGD\t2535\tEdnra\t\tMP:0003340\tRGD:1581841|PMID:12799311\t'
'IED\t\tN\tendothelin receptor type A\t\tgene\ttaxon:10116\t'
'20061026\tRGD\t\t\n',
'subject': {
'fullname': 'endothelin receptor type A',
'id': 'RGD:2535',
'label': 'Ednra',
'synonyms': [],
'taxon': {
'id': 'NCBITaxon:10116'
},
'type': 'gene'
},
'subject_extensions': [{
'filler': '\n',
'property': 'isoform'
}]
}
return
def tearDown(self):
return
def testRGDParser(self):
rgd = RGD('rdf_graph', True)
rgd.graph = RDFGraph(True)
self.assertTrue(len(list(rgd.graph)) == 0)
rgd.make_association(record=self.test_set_1)
triples = """
:MONARCH_b4650e8c3d865f11a1a5 a OBAN:association ;
RO:0002558 ECO:0005611 ;
dcterms:source RGDRef:1581841 ;
OBAN:association_has_object OBO:MP_0003340 ;
OBAN:association_has_predicate OBO:RO_0002200 ;
OBAN:association_has_subject RGD:2535 ;
pav:createdOn "2006-10-26" .
RGD:2535 OBO:RO_0002200 MP:0003340 .
RGDRef:1581841 a IAO:0000311 ;
owl:sameAs PMID:12799311 .
"""
# dbg
logger.debug("Reference graph: %s",
rgd.graph.serialize(format="turtle").decode("utf-8"))
self.assertTrue(self.test_util.test_graph_equality(triples, rgd.graph))
class StringTestFakeData(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
# Test set with two proteins from same species
self.test_set_1 = [[
'9606.ENSP00000000233', '9606.ENSP00000003084',
0, 0, 0, 0, 300, 0, 150, 800]]
# Test set with deprecated protein id
self.test_set_2 = [[
'9606.ENSP00000000233', '9606.ENSP00000006101',
0, 0, 0, 0, 300, 0, 150, 800]]
self.columns = [
'protein1', 'protein2', 'neighborhood', 'fusion', 'cooccurence',
'coexpression', 'experimental', 'database', 'textmining', 'combined_score']
ensembl = Ensembl('rdf_graph', True)
self.protein_list = ensembl.fetch_protein_gene_map('9606')
return
def tearDown(self):
return
def testFakeDataSet1(self):
string_db = StringDB('rdf_graph', True)
string_db.graph = RDFGraph(True)
self.assertEqual(len(string_db.graph), 0)
ensembl = Ensembl('rdf_graph', True)
prot_map = ensembl.fetch_protein_gene_map('9606')
[prot_map.update({k: ['ENSEMBL:' + prot_map[k]]}) for k in prot_map.keys()]
print("Finished fetching ENSP IDs, fetched {} proteins".format(len(prot_map)))
# just looking
# for key in prot_map:
# if string_db.graph.curie_regexp.match(prot_map[key]) is None:
# print("INVALID curie for %s from %s", prot_map[key], key)
dataframe = pd.DataFrame(data=self.test_set_1, columns=self.columns)
string_db._process_protein_links(dataframe, prot_map, '9606')
# g1 <interacts with> g2
triples = """
ENSEMBL:ENSG00000001626 RO:0002434 ENSEMBL:ENSG00000004059 .
ENSEMBL:ENSG00000001626 rdf:type SO:0000704 .
ENSEMBL:ENSG00000004059 rdf:type SO:0000704 .
"""
self.assertTrue(self.test_util.test_graph_equality(triples, string_db.graph))
def testFakeDataSet2(self):
"""
Dataset contains a deprecated protein ID
that we expect if filtered out by ensembl biomart
We test that this returns an empty graph
:return:
"""
string_db = StringDB('rdf_graph', True)
string_db.graph = RDFGraph()
self.assertEqual(len(string_db.graph), 0)
dataframe = pd.DataFrame(data=self.test_set_2, columns=self.columns)
string_db._process_protein_links(dataframe, self.protein_list, '9606')
self.assertEqual(len(string_db.graph), 0)
