def test_graph_equality(turtlish, graph):
"""
:param turtlish: String of triples in turtle
format without prefix header
:param graph: Graph object to test against
:return: Boolean, True if graphs contain same
set of triples
"""
turtle_graph = RDFGraph()
turtle_graph.bind_all_namespaces()
prefixes = "\n".join([
"@prefix {}: <{}> .".format(n[0], n[1])
for n in turtle_graph.namespace_manager.namespaces()
])
turtle_string = prefixes + turtlish
mock_file = io.StringIO(turtle_string)
turtle_graph.parse(mock_file, format="turtle")
turtle_triples = set(list(turtle_graph))
ref_triples = set(list(graph))
equality = turtle_triples == ref_triples
if not equality:
LOG.warning(
"Triples do not match\n"
"\tLeft hand difference: %s\n"
"\tRight hand difference: %s",
sorted(turtle_triples - ref_triples),
sorted(ref_triples - turtle_triples))
return equality
def test_graph_equality(self, turtlish, graph):
"""
:param turtlish: String of triples in turtle
format without prefix header
:param graph: Graph object to test against
:return: Boolean, True if graphs contain same
set of triples
"""
turtle_graph = RDFGraph()
turtle_graph.bind_all_namespaces()
prefixes = "\n".join(
["@prefix {}: <{}> .".format(n[0], n[1])
for n in turtle_graph.namespace_manager.namespaces()]
)
turtle_string = prefixes + turtlish
mock_file = io.StringIO(turtle_string)
turtle_graph.parse(mock_file, format="turtle")
turtle_triples = set(list(turtle_graph))
ref_triples = set(list(graph))
equality = turtle_triples == ref_triples
if not equality:
logger.warning("Triples do not match\n"
"Left hand difference: {}\n"
"Right hand difference:{}".format(
turtle_triples - ref_triples,
ref_triples - turtle_triples
))
return equality
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))
def test_snp_trait_association(self):
"""
test the _add_variant_trait_association
:return:
"""
efo_ontology = RDFGraph()
logger.info("Loading EFO ontology in separate rdf graph")
efo_ontology.parse(self.source.files['efo']['url'], format='xml')
efo_ontology.bind_all_namespaces()
logger.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)
sparql_query = """
SELECT ?snp
WHERE {{
<https://monarchinitiative.org/MONARCH_b46cdf48950cb00d> a OBAN:association ;
dc:description "{}" ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0003949 ;
OBAN:association_has_predicate OBO:RO_0002326 ;
OBAN:association_has_subject ?snp .
<https://monarchinitiative.org/MONARCH_70a05d8eb1c3d4b0> a OBAN:association ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0006995 ;
OBAN:association_has_predicate OBO:RO_0002326 ;
OBAN:association_has_subject ?snp .
EFO:0003949 a owl:Class ;
rdfs:label "eye color"^^xsd:string ;
rdfs:subClassOf UPHENO:0001001 .
?snp OBO:RO_0002326 EFO:0003949,
EFO:0006995 .
PMID:25918132 a OBO:IAO_0000013 .
}}
""".format(description)
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1491921")), )]
self.assertEqual(results, expected)
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))
def test_snp_trait_association(self):
"""
test the _add_variant_trait_association
:return:
"""
efo_ontology = RDFGraph()
logger.info("Loading EFO ontology in separate rdf graph")
efo_ontology.parse(self.source.files['efo']['url'], format='xml')
efo_ontology.bind_all_namespaces()
logger.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)
sparql_query = """
SELECT ?snp
WHERE {{
<https://monarchinitiative.org/MONARCH_b46cdf48950cb00d> a OBAN:association ;
dc:description "{}" ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0003949 ;
OBAN:association_has_predicate OBO:RO_0002326 ;
OBAN:association_has_subject ?snp .
<https://monarchinitiative.org/MONARCH_70a05d8eb1c3d4b0> a OBAN:association ;
OBO:RO_0002558 OBO:ECO_0000213 ;
dc:source PMID:25918132 ;
OBAN:association_has_object EFO:0006995 ;
OBAN:association_has_predicate OBO:RO_0002326 ;
OBAN:association_has_subject ?snp .
EFO:0003949 a owl:Class ;
rdfs:label "eye color"^^xsd:string ;
rdfs:subClassOf UPHENO:0001001 .
?snp OBO:RO_0002326 EFO:0003949,
EFO:0006995 .
PMID:25918132 a OBO:IAO_0000013 .
}}
""".format(description)
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1491921")),)]
self.assertEqual(results, expected)
def test_graph_equality(turtlish, graph):
"""
:param turtlish: file path or string of triples in turtle
format without prefix header
:param graph: Graph object to test against
:return: Boolean, True if graphs contain same
set of triples
"""
turtle_graph = RDFGraph()
turtle_graph.bind_all_namespaces()
prefixes = "\n".join([
"@prefix {}: <{}> .".format(n[0], n[1])
for n in turtle_graph.namespace_manager.namespaces()
])
headless_ttl = ''
try:
if Path(turtlish).exists():
headless_ttl = Path(turtlish).read_text()
else:
raise OSError
except OSError:
if isinstance(turtlish, str):
headless_ttl = turtlish
else:
raise ValueError("turtlish must be filepath or string")
turtle_string = prefixes + headless_ttl
mock_file = io.StringIO(turtle_string)
turtle_graph.parse(mock_file, format="turtle")
TestUtils.remove_ontology_axioms(graph)
turtle_triples = set(list(turtle_graph))
ref_triples = set(list(graph))
equality = turtle_triples == ref_triples
if not equality:
LOG.warning(
"Triples do not match\n"
"\tLeft hand difference: %s\n"
"\tRight hand difference: %s",
sorted(turtle_triples - ref_triples),
sorted(ref_triples - turtle_triples))
return equality
def main():
hpo = RDFGraph()
root = "HP:0000118"
hpo_terms = OrderedDict()
hpo.parse("http://purl.obolibrary.org/obo/hp.owl", format='xml')
hpo.bind_all_namespaces()
hpo.bind("oboInOwl", "http://www.geneontology.org/formats/oboInOwl#")
tree = {}
tree[root] = {}
path = []
hpo_to_tree(root, hpo_terms, hpo, tree, path)
with open('hpo-tree.json', 'w') as outfile:
json.dump(tree, outfile)
with open('hpo-terms.tsv', 'w') as outfile:
for key, value in hpo_terms.items():
outfile.write("{0}\t{1}\t{2}\t{3}\n".format(
key, value['label'], "|".join(value['lay_person']), value['parents']
))
def main():
hpo = RDFGraph()
root = "HP:0000118"
hpo_terms = OrderedDict()
hpo.parse("http://purl.obolibrary.org/obo/hp.owl", format='xml')
hpo.bind_all_namespaces()
hpo.bind("oboInOwl", "http://www.geneontology.org/formats/oboInOwl#")
tree = {}
tree[root] = {}
path = []
hpo_to_tree(root, hpo_terms, hpo, tree, path)
with open('hpo-tree.json', 'w') as outfile:
json.dump(tree, outfile)
with open('hpo-terms.tsv', 'w') as outfile:
for key, value in hpo_terms.items():
outfile.write("{0}\t{1}\t{2}\t{3}\n".format(
key, value['label'], "|".join(value['lay_person']),
value['parents']))
def process_catalog(self, limit=None):
"""
:param limit:
:return:
"""
src_key = 'catalog'
raw = '/'.join((self.rawdir, self.files[src_key]['file']))
LOG.info("Processing Data from %s", raw)
so_ontology = RDFGraph(False, "SO")
LOG.info("Loading SO ontology in separate rdf graph")
so_ontology.parse(self.files['so']['url'], format='xml')
so_ontology.bind_all_namespaces()
LOG.info("Finished loading SO ontology")
mondo_file = '/'.join((self.rawdir, self.files['mondo']['file']))
with open(mondo_file, 'r') as mondo_fh:
mondo_data = json.load(mondo_fh)
col = self.files[src_key]['columns']
with open(raw, 'r', encoding="iso-8859-1") as csvfile:
reader = csv.reader(csvfile, delimiter='\t')
row = next(reader)
if self.check_fileheader(col, row):
pass
for row in reader:
if len(col) != len(row):
LOG.error('BadRow: %i has %i columns', reader.line_num,
row)
continue
# head -1 gwas-catalog-associations_ontology-annotated.tsv |
# tr '\t' '\n' | sed "s|\(.*\)|# = row[col.index('\1')]|g"
# = row[col.index('DATE ADDED TO CATALOG')]
pubmed_num = row[col.index('PUBMEDID')].strip()
# = row[col.index('FIRST AUTHOR')]
# = row[col.index('DATE')]
# = row[col.index('JOURNAL')]
# = row[col.index('LINK')]
# = row[col.index('STUDY')]
disease_or_trait = row[col.index('DISEASE/TRAIT')].strip()
initial_sample_description = row[col.index(
'INITIAL SAMPLE SIZE')].strip()
replicate_sample_description = row[col.index(
'REPLICATION SAMPLE SIZE')].strip()
# = row[col.index('REGION')]
chrom_num = row[col.index('CHR_ID')].strip()
chrom_pos = row[col.index('CHR_POS')].strip()
# = row[col.index('REPORTED GENE(S)')]
mapped_gene = row[col.index('MAPPED_GENE')].strip()
upstream_gene_num = row[col.index('UPSTREAM_GENE_ID')].strip()
downstream_gene_num = row[col.index(
'DOWNSTREAM_GENE_ID')].strip()
snp_gene_nums = row[col.index('SNP_GENE_IDS')].strip()
# = row[col.index('UPSTREAM_GENE_DISTANCE')]
# = row[col.index('DOWNSTREAM_GENE_DISTANCE')]
strongest_snp_risk_allele = row[col.index(
'STRONGEST SNP-RISK ALLELE')].strip()
# = row[col.index('SNPS')]
merged = row[col.index('MERGED')].strip()
snp_id_current = row[col.index('SNP_ID_CURRENT')].strip()
context = row[col.index('CONTEXT')].strip()
# = row[col.index('INTERGENIC')]
risk_allele_frequency = row[col.index(
'RISK ALLELE FREQUENCY')].strip()
pvalue = row[col.index('P-VALUE')].strip()
# = row[col.index('PVALUE_MLOG')]
# = row[col.index('P-VALUE (TEXT)')]
# = row[col.index('OR or BETA')]
# = row[col.index('95% CI (TEXT)')]
platform_with_snps_passing_qc = row[col.index(
'PLATFORM [SNPS PASSING QC]')].strip()
# = row[col.index('CNV')]
mapped_trait = row[col.index('MAPPED_TRAIT')].strip()
mapped_trait_uri = row[col.index('MAPPED_TRAIT_URI')].strip()
# = row[col.index('STUDY ACCESSION')]
# = row[col.index('GENOTYPING TECHNOLOGY')]
if self.test_mode:
continue
# 06-May-2015 25917933
# Zai CC 20-Nov-2014 J Psychiatr Res http://europepmc.org/abstract/MED/25917933
# A genome-wide association study of suicide severity scores in bipolar disorder.
# Suicide in bipolar disorder
# 959 European ancestry individuals NA
# 10p11.22 10 32704340 C10orf68, CCDC7, ITGB1 CCDC7
# rs7079041-A rs7079041 0 7079041 intron 0 2E-6 5.698970
snp_id_current = snp_id_current.split(' ')[0]
# note: that these will no longer pattern match other instances
variant_curie, variant_type = self._get_curie_and_type_from_id(
strongest_snp_risk_allele)
if strongest_snp_risk_allele == '':
LOG.debug("No strongest SNP risk allele for %s:\n%s",
pubmed_num, str(row))
# still consider adding in the EFO terms
# for what the study measured?
continue
if variant_curie is not None and variant_curie[0] == '_' and \
strongest_snp_risk_allele is not None:
self.graph.addTriple(variant_curie,
self.globaltt['label'],
strongest_snp_risk_allele,
object_is_literal=True)
if variant_type == 'snp':
self._add_snp_to_graph(variant_curie,
strongest_snp_risk_allele,
chrom_num, chrom_pos, context,
risk_allele_frequency)
self._add_deprecated_snp(variant_curie, snp_id_current,
merged, chrom_num, chrom_pos)
self._add_snp_gene_relation(variant_curie, snp_gene_nums,
upstream_gene_num,
downstream_gene_num)
elif variant_type == 'haplotype':
self._process_haplotype(variant_curie,
strongest_snp_risk_allele,
chrom_num, chrom_pos, context,
risk_allele_frequency, mapped_gene,
so_ontology)
elif variant_type is None and snp_id_current != '':
LOG.warning("There's a snp id we can't manage: %s",
strongest_snp_risk_allele)
continue
description = self._make_description(
disease_or_trait, initial_sample_description,
replicate_sample_description,
platform_with_snps_passing_qc, pvalue)
self._add_variant_trait_association(variant_curie,
mapped_trait_uri,
mapped_trait, mondo_data,
pubmed_num, description)
if not self.test_mode and (limit is not None
and reader.line_num > limit):
break
# TODO loop through the location hash,
# and make all snps at that location equivalent
for loc in self.id_location_map:
snp_ids = self.id_location_map[loc]
if len(snp_ids) > 1:
LOG.info("%s has >1 snp id: %s", loc, str(snp_ids))
def process_catalog(self, limit=None):
"""
:param limit:
:return:
"""
raw = '/'.join((self.rawdir, self.files['catalog']['file']))
LOG.info("Processing Data from %s", raw)
efo_ontology = RDFGraph(False, "EFO")
LOG.info("Loading EFO ontology in separate rdf graph")
efo_ontology.parse(self.files['efo']['url'], format='xml')
efo_ontology.bind_all_namespaces()
LOG.info("Finished loading EFO ontology")
so_ontology = RDFGraph(False, "SO")
LOG.info("Loading SO ontology in separate rdf graph")
so_ontology.parse(self.files['so']['url'], format='xml')
so_ontology.bind_all_namespaces()
LOG.info("Finished loading SO ontology")
with open(raw, 'r', encoding="iso-8859-1") as csvfile:
filereader = csv.reader(csvfile, delimiter='\t')
header = next(filereader, None) # the header row
header_len = len(header)
LOG.info('header length:\t %i', header_len)
for row in filereader:
if not row:
pass
else:
if header_len != len(row):
LOG.error('BadRow: %i has %i columns', filereader.line_num, row)
(date_added_to_catalog,
pubmed_num,
first_author,
pub_date,
journal,
link,
study_name,
disease_or_trait,
initial_sample_description,
replicate_sample_description,
region,
chrom_num,
chrom_pos,
reported_gene_nums,
mapped_gene,
upstream_gene_num,
downstream_gene_num,
snp_gene_nums,
upstream_gene_distance,
downstream_gene_distance,
strongest_snp_risk_allele,
snps,
merged,
snp_id_current,
context,
intergenic_flag,
risk_allele_frequency,
pvalue,
pvalue_mlog,
pvalue_text,
or_or_beta,
confidence_interval_95,
platform_with_snps_passing_qc,
cnv_flag,
mapped_trait,
mapped_trait_uri,
study_accession,
GENOTYPING_TECHNOLOGY
) = row
if self.test_mode:
continue
# 06-May-2015 25917933
# Zai CC 20-Nov-2014 J Psychiatr Res http://europepmc.org/abstract/MED/25917933
# A genome-wide association study of suicide severity scores in bipolar disorder.
# Suicide in bipolar disorder
# 959 European ancestry individuals NA
# 10p11.22 10 32704340 C10orf68, CCDC7, ITGB1 CCDC7
# rs7079041-A rs7079041 0 7079041 intron 0 2E-6 5.698970
variant_curie, variant_type = self._get_curie_and_type_from_id(
strongest_snp_risk_allele)
if strongest_snp_risk_allele.strip() == '':
LOG.debug(
"No strongest SNP risk allele for %s:\n%s",
pubmed_num, str(row))
# still consider adding in the EFO terms
# for what the study measured?
continue
if variant_type == 'snp':
self._add_snp_to_graph(
variant_curie, strongest_snp_risk_allele, chrom_num,
chrom_pos, context, risk_allele_frequency)
self._add_deprecated_snp(
variant_curie, snp_id_current, merged, chrom_num, chrom_pos)
self._add_snp_gene_relation(
variant_curie, snp_gene_nums, upstream_gene_num,
downstream_gene_num)
elif variant_type == 'haplotype':
self._process_haplotype(
variant_curie, strongest_snp_risk_allele, chrom_num,
chrom_pos, context, risk_allele_frequency, mapped_gene,
so_ontology)
elif variant_type is None:
LOG.warning(
"There's a snp id i can't manage: %s",
strongest_snp_risk_allele)
continue
description = self._make_description(
disease_or_trait, initial_sample_description,
replicate_sample_description,
platform_with_snps_passing_qc, pvalue)
self._add_variant_trait_association(
variant_curie, mapped_trait_uri, efo_ontology,
pubmed_num, description)
if not self.test_mode and (
limit is not None and filereader.line_num > limit):
break
# TODO loop through the location hash,
# and make all snps at that location equivalent
for l in self.id_location_map:
snp_ids = self.id_location_map[l]
if len(snp_ids) > 1:
LOG.info("%s has >1 snp id: %s", l, str(snp_ids))
return
def process_catalog(self, limit=None):
"""
:param limit:
:return:
"""
raw = '/'.join((self.rawdir, self.files['catalog']['file']))
logger.info("Processing Data from %s", raw)
efo_ontology = RDFGraph()
logger.info("Loading EFO ontology in separate rdf graph")
efo_ontology.parse(self.files['efo']['url'], format='xml')
efo_ontology.bind_all_namespaces()
logger.info("Finished loading EFO ontology")
so_ontology = RDFGraph()
logger.info("Loading SO ontology in separate rdf graph")
so_ontology.parse(self.files['so']['url'], format='xml')
so_ontology.bind_all_namespaces()
logger.info("Finished loading SO ontology")
line_counter = 0
with open(raw, 'r', encoding="iso-8859-1") as csvfile:
filereader = csv.reader(csvfile, delimiter='\t')
header = next(filereader, None) # the header row
header_len = len(header)
logger.info('header length:\t %i', header_len)
for row in filereader:
if not row:
pass
else:
line_counter += 1
if header_len != len(row):
logger.error(
'BadRow: %i has %i columns', line_counter, row)
pass
(date_added_to_catalog, pubmed_num, first_author,
pub_date, journal, link, study_name, disease_or_trait,
initial_sample_description, replicate_sample_description,
region, chrom_num, chrom_pos, reported_gene_nums,
mapped_gene, upstream_gene_num, downstream_gene_num,
snp_gene_nums, upstream_gene_distance,
downstream_gene_distance, strongest_snp_risk_allele, snps,
merged, snp_id_current, context, intergenic_flag,
risk_allele_frequency, pvalue, pvalue_mlog, pvalue_text,
or_or_beta, confidence_interval_95,
platform_with_snps_passing_qc, cnv_flag, mapped_trait,
mapped_trait_uri, study_accession) = row
if self.testMode:
continue
# 06-May-2015 25917933 Zai CC 20-Nov-2014 J Psychiatr Res http://europepmc.org/abstract/MED/25917933
# A genome-wide association study of suicide severity scores in bipolar disorder.
# Suicide in bipolar disorder
# 959 European ancestry individuals NA
# 10p11.22 10 32704340 C10orf68, CCDC7, ITGB1 CCDC7
# rs7079041-A rs7079041 0 7079041 intron 0 2E-6 5.698970
variant_curie, variant_type = \
self._get_curie_and_type_from_id(
strongest_snp_risk_allele)
if strongest_snp_risk_allele.strip() == '':
logger.debug(
"No strongest SNP risk allele for %s:\n%s",
pubmed_num, str(row))
# still consider adding in the EFO terms
# for what the study measured?
continue
if variant_type == 'snp':
self._add_snp_to_graph(
variant_curie, strongest_snp_risk_allele,
chrom_num, chrom_pos,
context, risk_allele_frequency)
self._add_deprecated_snp(variant_curie, snp_id_current,
merged, chrom_num, chrom_pos)
self._add_snp_gene_relation(
variant_curie, snp_gene_nums, upstream_gene_num,
downstream_gene_num)
elif variant_type == 'haplotype':
self._process_haplotype(
variant_curie, strongest_snp_risk_allele,
chrom_num, chrom_pos, context,
risk_allele_frequency, mapped_gene, so_ontology)
elif variant_type is None:
logger.warning(
"There's a snp id i can't manage: %s",
strongest_snp_risk_allele)
continue
description = self._make_description(
disease_or_trait, initial_sample_description,
replicate_sample_description,
platform_with_snps_passing_qc, pvalue)
self._add_variant_trait_association(
variant_curie, mapped_trait_uri, efo_ontology,
pubmed_num, description)
if not self.testMode and\
(limit is not None and line_counter > limit):
break
# TODO loop through the location hash,
# and make all snps at that location equivalent
for l in self.id_location_map:
snp_ids = self.id_location_map[l]
if len(snp_ids) > 1:
logger.info("%s has >1 snp id: %s", l, str(snp_ids))
return
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)
"""
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
so_ontology = RDFGraph()
logger.info("Loading SO ontology in separate rdf graph")
so_ontology.parse(self.source.files['so']['url'], format='xml')
so_ontology.bind_all_namespaces()
logger.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)
sparql_query = """
SELECT ?snp
WHERE {
:haplotype_bcb627b1f64039b0 a OBO:GENO_0000871 ;
rdfs:label "rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?" ;
OBO:GENO_0000382 ?snp,
dbSNP:rs3758171,
dbSNP:rs3824344,
dbSNP:rs7020413 ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
?snp a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs1329573-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996-36998996-Region> ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/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:GENO_0000418 <http://identifiers.org/hgnc/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:GENO_0000418 <http://identifiers.org/hgnc/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:GENO_0000418 <http://identifiers.org/hgnc/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 .
}
"""
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1329573")), )]
self.assertEqual(results, expected)
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))
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))
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)
"""
variant_curie, variant_type = \
self.source._get_curie_and_type_from_id(self.test_data['snp_label'])
so_ontology = RDFGraph()
logger.info("Loading SO ontology in separate rdf graph")
so_ontology.parse(self.source.files['so']['url'], format='xml')
so_ontology.bind_all_namespaces()
logger.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)
sparql_query = """
SELECT ?snp
WHERE {
:haplotype_bcb627b1f64039b0 a OBO:GENO_0000871 ;
rdfs:label "rs1329573-?; rs7020413-?; rs3824344-?; rs3758171-?" ;
OBO:GENO_0000382 ?snp,
dbSNP:rs3758171,
dbSNP:rs3824344,
dbSNP:rs7020413 ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/HGNC:8619> ;
OBO:RO_0002162 OBO:NCBITaxon_9606 .
?snp a OBO:SO_0000694,
OBO:SO_0001627 ;
rdfs:label "rs1329573-?" ;
faldo:location <https://monarchinitiative.org/.well-known/genid/GRCh38chr9-36998996-36998996-Region> ;
OBO:GENO_0000418 <http://identifiers.org/hgnc/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:GENO_0000418 <http://identifiers.org/hgnc/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:GENO_0000418 <http://identifiers.org/hgnc/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:GENO_0000418 <http://identifiers.org/hgnc/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 .
}
"""
sparql_output = self.source.graph.query(sparql_query)
# Test that query passes and returns one row
results = list(sparql_output)
expected = [(URIRef(self.source.graph._getNode("dbSNP:rs1329573")),)]
self.assertEqual(results, expected)
