class CTTVGeneticsEvidenceString(CTTVEvidenceString):
"""
Class for genetics evidence string specifically.
Holds information required for Open Target's evidence strings for genetic information.
"""
with utilities.open_file(
utilities.get_resource_file(__package__,
config.GEN_EV_STRING_JSON),
"rt") as gen_json_file:
base_json = json.load(gen_json_file)
def __init__(self, clinvar_record, clinvar_record_measure, report, trait,
consequence_type):
a_dictionary = copy.deepcopy(self.base_json)
ref_list = list(
set(clinvar_record.trait_refs_list[trait.trait_counter] +
clinvar_record.observed_refs_list +
clinvar_record_measure.refs_list))
ref_list.sort()
super().__init__(a_dictionary, clinvar_record, ref_list,
consequence_type.ensembl_gene_id, report, trait)
variant_type = get_cttv_variant_type(clinvar_record_measure)
self.add_unique_association_field('alleleOrigin', 'germline')
if clinvar_record_measure.rs_id:
self.set_variant(
'http://identifiers.org/dbsnp/' + clinvar_record_measure.rs_id,
variant_type)
self.add_unique_association_field('variant_id',
clinvar_record_measure.rs_id)
elif clinvar_record_measure.nsv_id:
self.set_variant(
'http://identifiers.org/dbsnp/' +
clinvar_record_measure.nsv_id, variant_type)
self.add_unique_association_field('variant_id',
clinvar_record_measure.nsv_id)
else:
self.set_variant(
'http://www.ncbi.nlm.nih.gov/clinvar/' +
clinvar_record.accession, variant_type)
self.add_unique_association_field('variant_id',
clinvar_record.accession)
self.date = clinvar_record.date
self.db_xref_url = 'http://identifiers.org/clinvar.record/' + clinvar_record.accession
self.url = 'http://www.ncbi.nlm.nih.gov/clinvar/' + clinvar_record.accession
self.association = clinvar_record.clinical_significance not in \
('non-pathogenic', 'probable-non-pathogenic', 'likely benign', 'benign')
self.gene_2_var_ev_codes = [
'http://identifiers.org/eco/cttv_mapping_pipeline'
]
most_severe_so_term = consequence_type.so_term
if most_severe_so_term.accession is None:
self.gene_2_var_func_consequence = 'http://targetvalidation.org/sequence/' + \
most_severe_so_term.so_name
else:
self.gene_2_var_func_consequence = 'http://purl.obolibrary.org/obo/' + \
most_severe_so_term.accession.replace(':', '_')
if len(ref_list) > 0:
self.set_var_2_disease_literature(ref_list)
# Arbitrarily select only one reference among all
self.unique_reference = ref_list[0]
if clinvar_record.clinical_significance:
self.clinical_significance = clinvar_record.clinical_significance
@property
def db_xref_url(self):
if self['evidence']['gene2variant']['provenance_type']['database']['dbxref']['url'] \
== self['evidence']['variant2disease']['provenance_type']['database']['dbxref']['url']:
return \
self['evidence']['variant2disease']['provenance_type']['database']['dbxref']['url']
else:
raise Exception("db_xref_url attributes different")
@db_xref_url.setter
def db_xref_url(self, url):
self['evidence']['gene2variant']['provenance_type']['database'][
'dbxref']['url'] = url
self['evidence']['variant2disease']['provenance_type']['database'][
'dbxref']['url'] = url
@property
def url(self):
if self['evidence']['gene2variant']['urls'][0]['url'] \
== self['evidence']['variant2disease']['urls'][0]['url']:
return self['evidence']['gene2variant']['urls'][0]['url']
else:
raise Exception("url attributes different")
@url.setter
def url(self, url):
self['evidence']['gene2variant']['urls'][0]['url'] = url
self['evidence']['variant2disease']['urls'][0]['url'] = url
@property
def gene_2_var_ev_codes(self):
return self['evidence']['gene2variant']['evidence_codes']
@gene_2_var_ev_codes.setter
def gene_2_var_ev_codes(self, gene_2_var_ev_codes):
self['evidence']['gene2variant'][
'evidence_codes'] = gene_2_var_ev_codes
@property
def gene_2_var_func_consequence(self):
return self['evidence']['gene2variant']['functional_consequence']
@gene_2_var_func_consequence.setter
def gene_2_var_func_consequence(self, so_term):
self['evidence']['gene2variant']['functional_consequence'] = so_term
def set_var_2_disease_literature(self, ref_list):
self['evidence']['variant2disease']['provenance_type']['literature'] = \
{'references': [{'lit_id': reference} for reference in ref_list]}
@property
def association(self):
if self['evidence']['gene2variant']['is_associated'] \
== self['evidence']['variant2disease']['is_associated']:
return self['evidence']['gene2variant']['is_associated']
else:
raise Exception("association attributes different")
@association.setter
def association(self, is_associated):
self['evidence']['gene2variant']['is_associated'] = is_associated
self['evidence']['variant2disease']['is_associated'] = is_associated
def _clear_variant(self):
self['variant']['id'] = []
self['variant']['type'] = []
def set_variant(self, var_id, var_type):
self['variant']['id'] = var_id
self['variant']['type'] = var_type
@property
def unique_reference(self):
return self['evidence']['variant2disease'][
'unique_experiment_reference']
@unique_reference.setter
def unique_reference(self, reference):
self['evidence']['variant2disease'][
'unique_experiment_reference'] = reference
@property
def date(self):
if self['evidence']['gene2variant']['date_asserted'] == \
self['evidence']['variant2disease']['date_asserted']:
return self['evidence']['gene2variant']['date_asserted']
else:
raise Exception("date attributes have different values")
@date.setter
def date(self, date_string):
self['evidence']['gene2variant']['date_asserted'] = date_string
self['evidence']['variant2disease']['date_asserted'] = date_string
@property
def clinical_significance(self):
return self['evidence']['variant2disease']['clinical_significance']
@clinical_significance.setter
def clinical_significance(self, clinical_significance):
self['evidence']['variant2disease'][
'clinical_significance'] = clinical_significance
class CTTVSomaticEvidenceString(CTTVEvidenceString):
"""
Class for somatic evidence string specifically.
Holds information required for Open Target's evidence strings for somatic information.
"""
with utilities.open_file(
utilities.get_resource_file(__package__,
config.SOM_EV_STRING_JSON),
"rt") as som_json_file:
base_json = json.load(som_json_file)
def __init__(self, clinvar_record, clinvar_record_measure, report, trait,
consequence_type):
a_dictionary = copy.deepcopy(self.base_json)
ref_list = list(
set(clinvar_record.trait_refs_list[trait.trait_counter] +
clinvar_record.observed_refs_list +
clinvar_record_measure.refs_list))
ref_list.sort()
super().__init__(a_dictionary, clinvar_record, ref_list,
consequence_type.ensembl_gene_id, report, trait)
self.add_unique_association_field('alleleOrigin', 'somatic')
if clinvar_record_measure.rs_id:
self.add_unique_association_field('variant_id',
clinvar_record_measure.rs_id)
elif clinvar_record_measure.nsv_id:
self.add_unique_association_field('variant_id',
clinvar_record_measure.nsv_id)
else:
self.add_unique_association_field('variant_id',
clinvar_record.accession)
self.date = clinvar_record.date
self.db_xref_url = 'http://identifiers.org/clinvar.record/' + clinvar_record.accession
self.url = 'http://www.ncbi.nlm.nih.gov/clinvar/' + clinvar_record.accession
self.association = clinvar_record.clinical_significance not in \
('non-pathogenic', 'probable-non-pathogenic', 'likely benign', 'benign')
self.set_known_mutations(consequence_type.so_term)
if len(ref_list) > 0:
self.evidence_literature = ref_list
if clinvar_record.clinical_significance:
self.clinical_significance = clinvar_record.clinical_significance
@property
def db_xref_url(self):
return self['evidence']['provenance_type']['database']['dbxref']['url']
@db_xref_url.setter
def db_xref_url(self, url):
self['evidence']['provenance_type']['database']['dbxref']['url'] = url
@property
def url(self):
return self['evidence']['urls'][0]['url']
@url.setter
def url(self, url):
self['evidence']['urls'][0]['url'] = url
@property
def evidence_literature(self):
return self['evidence']['provenance_type']['literature']['references']
@evidence_literature.setter
def evidence_literature(self, ref_list):
self['evidence']['provenance_type']['literature'] = \
{'references': [{'lit_id': reference} for reference in ref_list]}
@property
def association(self):
return self['evidence']['is_associated']
@association.setter
def association(self, is_associated):
self['evidence']['is_associated'] = is_associated
@property
def date(self):
return self['evidence']['date_asserted']
@date.setter
def date(self, date_string):
self['evidence']['date_asserted'] = date_string
def _clear_known_mutations(self):
self['evidence']['known_mutations'] = []
def add_known_mutation(self, new_functional_consequence, so_name):
new_known_mutation = \
{'functional_consequence': new_functional_consequence, 'preferred_name': so_name}
self['evidence']['known_mutations'].append(new_known_mutation)
def set_known_mutations(self, so_term):
if so_term.accession:
new_functional_consequence = \
"http://purl.obolibrary.org/obo/" + so_term.accession.replace(':', '_')
else:
new_functional_consequence = \
'http://targetvalidation.org/sequence/' + so_term.so_name
self.add_known_mutation(new_functional_consequence, so_term.so_name)
@property
def clinical_significance(self):
return self['evidence']['clinical_significance']
@clinical_significance.setter
def clinical_significance(self, clinical_significance):
self['evidence']['clinical_significance'] = clinical_significance
def test_get_resource_file_existent(self):
self.assertTrue(
utilities.get_resource_file("eva_cttv_pipeline",
"resources/json_schema"))
def test_get_resource_file_nonexistent(self):
self.assertEqual(
utilities.get_resource_file("not_a_real_package_39146",
"not_a_real_file"), None)
def test_get_resource_file_existent(self):
self.assertTrue(utilities.get_resource_file("eva_cttv_pipeline", "resources/json_schema"))
def test_get_resource_file_nonexistent(self):
self.assertEqual(utilities.get_resource_file("not_a_real_package_39146", "not_a_real_file"),
None)
class CTTVSomaticEvidenceString(CTTVEvidenceString):
"""
Class for somatic evidence string specifically.
Holds information required for Open Target's evidence strings for somatic information.
"""
with utilities.open_file(
utilities.get_resource_file(__package__,
config.SOM_EV_STRING_JSON),
"rt") as som_json_file:
base_json = json.load(som_json_file)
def __init__(self, clinvar_record, clinvar_record_measure, report, trait,
consequence_type):
a_dictionary = copy.deepcopy(self.base_json)
ref_list = list(
set(clinvar_record.trait_refs_list[trait.trait_counter] +
clinvar_record.observed_refs_list +
clinvar_record_measure.refs_list))
ref_list.sort()
super().__init__(a_dictionary, clinvar_record, ref_list,
consequence_type.ensembl_gene_id, report, trait)
self.add_unique_association_field('alleleOrigin', 'somatic')
if clinvar_record_measure.rs_id:
self.add_unique_association_field('variant_id',
clinvar_record_measure.rs_id)
elif clinvar_record_measure.nsv_id:
self.add_unique_association_field('variant_id',
clinvar_record_measure.nsv_id)
else:
self.add_unique_association_field('variant_id',
clinvar_record.accession)
self.date = clinvar_record.date
self.last_evaluated_date = clinvar_record.last_evaluated_date
self.db_xref_url = 'http://identifiers.org/clinvar.record/' + clinvar_record.accession
self.url = 'http://www.ncbi.nlm.nih.gov/clinvar/' + clinvar_record.accession
# See https://github.com/opentargets/platform/issues/1139#issuecomment-682592678
self.association = True
self.set_known_mutations(consequence_type.so_term)
if len(ref_list) > 0:
self.evidence_literature = ref_list
if clinvar_record.clinical_significance:
self.clinical_significance = process_clinical_significance(
clinvar_record.clinical_significance)
# Populate star rating and review status
star_rating, review_status = clinvar_record.score
self.clinvar_rating = (star_rating, review_status)
# Populate mode of inheritance (if present)
self.mode_of_inheritance = clinvar_record.mode_of_inheritance
@property
def db_xref_url(self):
return self['evidence']['provenance_type']['database']['dbxref']['url']
@db_xref_url.setter
def db_xref_url(self, url):
self['evidence']['provenance_type']['database']['dbxref']['url'] = url
@property
def url(self):
return self['evidence']['urls'][0]['url']
@url.setter
def url(self, url):
self['evidence']['urls'][0]['url'] = url
@property
def evidence_literature(self):
return self['evidence']['provenance_type']['literature']['references']
@evidence_literature.setter
def evidence_literature(self, ref_list):
self['evidence']['provenance_type']['literature'] = \
{'references': [{'lit_id': reference} for reference in ref_list]}
@property
def association(self):
return self['evidence']['is_associated']
@association.setter
def association(self, is_associated):
self['evidence']['is_associated'] = is_associated
@property
def date(self):
return self['evidence']['date_asserted']
@date.setter
def date(self, date_string):
self['evidence']['date_asserted'] = date_string
@property
def last_evaluated_date(self):
return self['evidence']['last_evaluated_date']
@last_evaluated_date.setter
def last_evaluated_date(self, clinvar_last_evaluated_date):
if clinvar_last_evaluated_date:
self['evidence'][
'last_evaluated_date'] = clinvar_last_evaluated_date
def _clear_known_mutations(self):
self['evidence']['known_mutations'] = []
def add_known_mutation(self, new_functional_consequence, so_name):
new_known_mutation = \
{'functional_consequence': new_functional_consequence, 'preferred_name': so_name}
self['evidence']['known_mutations'].append(new_known_mutation)
def set_known_mutations(self, so_term):
if so_term.accession:
new_functional_consequence = \
"http://purl.obolibrary.org/obo/" + so_term.accession.replace(':', '_')
else:
new_functional_consequence = \
'http://targetvalidation.org/sequence/' + so_term.so_name
self.add_known_mutation(new_functional_consequence, so_term.so_name)
@property
def clinical_significance(self):
return self['evidence']['clinical_significance']
@clinical_significance.setter
def clinical_significance(self, clinical_significance):
self['evidence']['clinical_significance'] = clinical_significance
@property
def clinvar_rating(self):
return self['evidence']['clinvar_rating']
@clinvar_rating.setter
def clinvar_rating(self, clinvar_rating_data):
star_rating, review_status = clinvar_rating_data
self['evidence']['clinvar_rating'] = {
'star_rating': star_rating,
'review_status': review_status,
}
@property
def mode_of_inheritance(self):
return self['evidence'].get('mode_of_inheritance')
@mode_of_inheritance.setter
def mode_of_inheritance(self, mode_of_inheritance):
if mode_of_inheritance:
self['evidence']['mode_of_inheritance'] = mode_of_inheritance