def searchVariantAnnotations(self,
variantAnnotationSetId,
referenceName=None,
referenceId=None,
start=None,
end=None,
effects=[]):
"""
Returns an iterator over the Annotations fulfilling the specified
conditions from the specified AnnotationSet.
"""
request = protocol.SearchVariantAnnotationsRequest()
request.variantAnnotationSetId = variantAnnotationSetId
request.referenceName = referenceName
request.referenceId = referenceId
request.start = start
request.end = end
request.effects = effects
for effect in request.effects:
if 'id' not in effect:
raise exceptions.BadRequestException(
"Each ontology term should have an id set")
request.pageSize = self._pageSize
return self._runSearchRequest(
request, "variantannotations",
protocol.SearchVariantAnnotationsResponse)
def readsGenerator(self, request):
"""
Returns a generator over the (read, nextPageToken) pairs defined
by the specified request
"""
if not request.reference_id:
raise exceptions.UnmappedReadsNotSupported()
if len(request.read_group_ids) < 1:
raise exceptions.BadRequestException(
"At least one readGroupId must be specified")
elif len(request.read_group_ids) == 1:
return self._readsGeneratorSingle(request)
else:
return self._readsGeneratorMultiple(request)
def search_variant_annotations(self,
variant_annotation_set_id,
reference_name="",
reference_id="",
start=0,
end=0,
effects=[]):
"""
Returns an iterator over the Variant Annotations fulfilling
the specified conditions from the specified VariantSet.
:param str variant_annotation_set_id: The ID of the
:class:`ga4gh.protocol.VariantAnnotationSet` of interest.
:param int start: Required. The beginning of the window (0-based,
inclusive) for which overlapping variants should be returned.
Genomic positions are non-negative integers less than reference
length. Requests spanning the join of circular genomes are
represented as two requests one on each side of the join
(position 0).
:param int end: Required. The end of the window (0-based, exclusive)
for which overlapping variants should be returned.
:param str reference_name: The name of the
:class:`ga4gh.protocol.Reference` we wish to return variants from.
:return: An iterator over the
:class:`ga4gh.protocol.VariantAnnotation` objects
defined by the query parameters.
:rtype: iter
"""
request = protocol.SearchVariantAnnotationsRequest()
request.variant_annotation_set_id = variant_annotation_set_id
request.reference_name = reference_name
request.reference_id = reference_id
request.start = start
request.end = end
for effect in effects:
request.effects.add().CopyFrom(protocol.OntologyTerm(**effect))
for effect in request.effects:
if not effect.id:
raise exceptions.BadRequestException(
"Each ontology term should have an id set")
request.page_size = pb.int(self._page_size)
return self._run_search_request(
request, "variantannotations",
protocol.SearchVariantAnnotationsResponse)
def rnaQuantificationsGenerator(self, request):
"""
Returns a generator over the (rnaQuantification, nextPageToken) pairs
defined by the specified request.
"""
if len(request.rna_quantification_set_id) < 1:
raise exceptions.BadRequestException(
"Rna Quantification Set Id must be specified")
else:
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(
request.rna_quantification_set_id)
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
rnaQuantSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
return self._topLevelObjectGenerator(
request, rnaQuantSet.getNumRnaQuantifications(),
rnaQuantSet.getRnaQuantificationByIndex)
def _readsGeneratorMultiple(self, request):
compoundId = datamodel.ReadGroupCompoundId.parse(
request.read_group_ids[0])
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id)
referenceSet = readGroupSet.getReferenceSet()
if referenceSet is None:
raise exceptions.ReadGroupSetNotMappedToReferenceSetException(
readGroupSet.getId())
reference = referenceSet.getReference(request.reference_id)
readGroupIds = readGroupSet.getReadGroupIds()
if set(readGroupIds) != set(request.read_group_ids):
raise exceptions.BadRequestException(
"If multiple readGroupIds are specified, "
"they must be all of the readGroupIds in a ReadGroupSet")
intervalIterator = ReadsIntervalIterator(request, readGroupSet,
reference)
return intervalIterator