def _migrate_allele_frequencies(additional_numeric_annotations):
# NOTE: This is assuming all values in `additionalNumericVariantAnnotations` are frequencies
frequencies = []
for pop in additional_numeric_annotations:
frequencies.append(
reports_5_0_0.AlleleFrequency(
alternateFrequency=additional_numeric_annotations[pop],
population=pop.split('_')[-1],
study='_'.join(pop.split('_')[:-1])))
return frequencies
def _migrate_reported_variant_cancer(self, old_instance, assembly,
participant_id, sample_ids):
ne_instance = old_instance.reportedVariantCancer
new_instance = self.convert_class(
self.new_model.ReportedVariantCancer,
ne_instance) # :type: reports_5_0_0.ReportedVariant
new_instance.variantCoordinates = self.convert_class(
reports_5_0_0.VariantCoordinates, ne_instance)
new_instance.variantCoordinates.assembly = self._migrate_assembly(
assembly)
if old_instance.reportedVariantCancer.cDnaChange:
new_instance.cdnaChanges = [
old_instance.reportedVariantCancer.cDnaChange
]
if ne_instance.proteinChange:
new_instance.proteinChanges = [ne_instance.proteinChange]
# NOTE: missing fields: genomicChanges
sample_id = sample_ids.get(old_instance.alleleOrigins[0], None)
if not sample_id:
raise MigrationError('Couldn\'t retrieve Sample ID for {}'.format(
old_instance.alleleOrigins[0]))
# builds up the VariantCall object
# NOTE: fields that cannot be filled "phaseSet"
new_instance.variantCalls = [
reports_5_0_0.VariantCall(
depthReference=ne_instance.depthReference,
depthAlternate=ne_instance.depthAlternate,
vaf=ne_instance.vaf,
zygosity=reports_5_0_0.Zygosity.na,
alleleOrigins=old_instance.alleleOrigins,
participantId=participant_id,
sampleId=sample_id)
]
if ne_instance.commonAf is not None:
new_instance.alleleFrequencies = [
reports_5_0_0.AlleleFrequency(
study='genomics_england',
population='ALL',
alternateFrequency=self.convert_string_to_float(
ne_instance.commonAf) / 100)
]
# NOTE: some fields cannot be filled: "fdp50", "recurrentlyReported", "others"
new_instance.variantAttributes = reports_5_0_0.VariantAttributes(
ihp=ne_instance.ihp)
new_instance.alleleOrigins = old_instance.alleleOrigins
new_instance.reportEvents = self.convert_collection(
list(zip(ne_instance.reportEvents, new_instance.reportEvents)),
self._migrate_report_event_cancer)
return new_instance
def migrate_reported_variant_cancer(self, old_instance, assembly, participant_id, sample_id):
"""
NOTE: fields that cannot be filled are "genomicChanges", "references"
:type old_instance: reports_4_0_0.ReportedSomaticVariants
:type assembly: reports_5_0_0.Assembly
:type participant_id: str
:type sample_id: str
:rtype reports_5_0_0.ReportedVariantCancer
:return:
"""
new_instance = self.convert_class(
self.new_model.ReportedVariantCancer,
old_instance.reportedVariantCancer) # :type: reports_5_0_0.ReportedVariant
# builds up the variant coordinates
new_instance.variantCoordinates = reports_5_0_0.VariantCoordinates(
chromosome=old_instance.reportedVariantCancer.chromosome,
position=old_instance.reportedVariantCancer.position,
reference=old_instance.reportedVariantCancer.reference,
alternate=old_instance.reportedVariantCancer.alternate,
assembly=self.migrate_assembly(assembly)
)
# field cDnaChange renamed to cdnaChange
if old_instance.reportedVariantCancer.cDnaChange:
new_instance.cdnaChanges = [old_instance.reportedVariantCancer.cDnaChange]
# field proteinChange changed to a list
if old_instance.reportedVariantCancer.proteinChange:
new_instance.proteinChanges = [old_instance.reportedVariantCancer.proteinChange]
# NOTE: missing fields: genomicChanges
# builds up the VariantCall object
# NOTE: fields that cannot be filled "phaseSet"
new_instance.variantCalls = [reports_5_0_0.VariantCall(
depthReference=old_instance.reportedVariantCancer.depthReference,
depthAlternate=old_instance.reportedVariantCancer.depthAlternate,
vaf=old_instance.reportedVariantCancer.vaf,
zygosity=reports_5_0_0.Zygosity.na,
alleleOrigins=old_instance.alleleOrigins,
participantId=participant_id,
sampleId=sample_id
)]
# builds up an AlleleFrequency object
if old_instance.reportedVariantCancer.commonAf is not None:
new_instance.alleleFrequencies = [reports_5_0_0.AlleleFrequency(
study='genomics_england',
population='ALL',
alternateFrequency=self.convert_string_to_float(old_instance.reportedVariantCancer.commonAf)
)]
# builds up the VariantAttributes
# NOTE: some fields cannot be filled: "fdp50", "recurrentlyReported", "others"
new_instance.variantAttributes = reports_5_0_0.VariantAttributes(
ihp=old_instance.reportedVariantCancer.ihp
)
# list of allele origins is flattened and received as a parameter
new_instance.alleleOrigins = old_instance.alleleOrigins
# migrates cancer report events
new_instance.reportEvents = self.migrate_report_events_cancer(old_instance.reportedVariantCancer.reportEvents)
return self.validate_object(
object_to_validate=new_instance, object_type=self.new_model.ReportedVariantCancer
)