def _makeSimulatedAssociation(self, _id=None, phenotype_id=None):
fpa = protocol.FeaturePhenotypeAssociation()
fpa.phenotype_association_set_id = self._parentContainer.getId()
fpa.id = "fpa-{}".format(_id)
fpa.feature_ids.extend(["feature-{}".format(_id)])
fpa.evidence.extend([protocol.Evidence()])
_phenotype_id = "phenotype-{}".format(_id)
if phenotype_id:
_phenotype_id = phenotype_id
fpa.phenotype.MergeFrom(protocol.PhenotypeInstance(id=_phenotype_id))
fpa.description = "description-{}".format(_id)
fpa.environmental_contexts.extend(
[protocol.EnvironmentalContext(id="context-{}".format(_id))])
return fpa
def _toGA4GH(self, association, featureSets=[]):
"""
given an association dict,
return a protocol.FeaturePhenotypeAssociation
"""
# The association dict has the keys: environment, environment
# label, evidence, feature label, phenotype and sources. Each
# key's value is a dict with the RDF predicates as keys and
# subject as values
# 1) map a GA4GH FeaturePhenotypeAssociation
# from the association dict passed to us
feature = association['feature']
fpa = protocol.FeaturePhenotypeAssociation()
fpa.id = association['id']
feature_id = feature['id']
for feature_set in featureSets:
if self.getLocalId() in feature_set.getLocalId():
feature_id = feature_set.getCompoundIdForFeatureId(feature_id)
fpa.feature_ids.extend([feature_id])
msg = 'Association: genotype:[{}] phenotype:[{}] environment:[{}] ' \
'evidence:[{}] publications:[{}]'
fpa.description = msg.format(
association['feature_label'], association['phenotype_label'],
association['environment_label'],
self._getIdentifier(association['evidence']),
association['sources'])
# 2) map a GA4GH Evidence
# from the association's phenotype & evidence
evidence = protocol.Evidence()
phenotype = association['phenotype']
term = protocol.OntologyTerm()
term.term = association['evidence_type']
term.term_id = phenotype['id']
evidence.evidence_type.MergeFrom(term)
evidence.description = self._getIdentifier(association['evidence'])
# 3) Store publications from the list of sources
for source in association['sources'].split("|"):
evidence.info['publications'].values.add().string_value = source
fpa.evidence.extend([evidence])
# 4) map environment (drug) to environmentalContext
environmentalContext = protocol.EnvironmentalContext()
environment = association['environment']
environmentalContext.id = environment['id']
environmentalContext.description = association['environment_label']
term = protocol.OntologyTerm()
term.term = environment['id']
term.term_id = 'http://purl.obolibrary.org/obo/RO_0002606'
environmentalContext.environment_type.MergeFrom(term)
fpa.environmental_contexts.extend([environmentalContext])
# 5) map the phenotype
phenotypeInstance = protocol.PhenotypeInstance()
term = protocol.OntologyTerm()
term.term = phenotype[TYPE]
term.term_id = phenotype['id']
phenotypeInstance.type.MergeFrom(term)
phenotypeInstance.description = phenotype[LABEL]
phenotypeInstance.id = phenotype['id']
fpa.phenotype.MergeFrom(phenotypeInstance)
fpa.phenotype_association_set_id = self.getId()
return fpa