def test_patient_phenotype_model(self):
"""
functional test for _parse_patient_phenotypes()
"""
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 = UDP('rdf_graph', True)
udp._parse_patient_phenotypes(mock_file)
sparql_query = """
SELECT ?patient
WHERE {
?patient a foaf:Person ;
rdfs:label "patient_1" ;
OBO:RO_0002200 OBO:DOID_4,
OBO:HP_000001 .
}
"""
sparql_output = udp.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(udp.graph._getNode(":patient_1")), )]
self.assertEqual(results, expected)
def test_variant_model(self):
"""
functional test for _parse_patient_variants()
"""
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 = UDP('rdf_graph', False)
udp._parse_patient_variants(mock_file)
sparql_query = """
SELECT ?patient
WHERE {
?patient OBO:GENO_0000222 [ a OBO:GENO_0000000 ;
rdfs:label "patient_1 genotype" ;
OBO:GENO_0000382 [ a OBO:SO_0001059 ;
rdfs:label "hg19chr1(CLK2):g.155230432G>A" ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:2069> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 ;
owl:sameAs dbSNP:rs11557757 ] ] .
}
"""
sparql_output = udp.graph.query(sparql_query)
results = list(sparql_output)
expected = [(URIRef(udp.graph._getNode(":patient_1")), )]
self.assertEqual(results, expected)
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/b8a5f377fc8c95d4> .
<https://monarchinitiative.org/.well-known/genid/b641e8da0787b45e> 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/b8a5f377fc8c95d4> a GENO:0000000 ;
rdfs:label "patient_1 genotype" ;
GENO:0000382 <https://monarchinitiative.org/.well-known/genid/b641e8da0787b45e> .
"""
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))
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_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_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_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')