def sendVariantsSearch(self):
response = self.sendVariantSetsSearch()
variantSets = protocol.fromJson(
response.data, protocol.SearchVariantSetsResponse).variant_sets
request = protocol.SearchVariantsRequest()
request.variant_set_id = variantSets[0].id
request.reference_name = "1"
request.start = 0
request.end = 1
return self.sendPostRequest('/variants/search', request)
def sendVariantsSearch(self):
response = self.sendVariantSetsSearch()
variantSets = self.deserialize(
response, protocol.SearchVariantSetsResponse).variant_sets
request = protocol.SearchVariantsRequest()
request.variant_set_ids.append(variantSets[0].id)
request.reference_name = "1"
request.start = 0
request.end = 1
return self.sendPostRequest('/variants/search', request)
def _heavyQuery(variantSetId, callSetIds):
"""
Very heavy query: calls for the specified list of callSetIds
on chromosome 2 (11 pages, 90 seconds to fetch the entire thing
on a high-end desktop machine)
"""
request = protocol.SearchVariantsRequest()
request.reference_name = '2'
request.variant_set_id = variantSetId
for callSetId in callSetIds:
request.call_set_ids.add(callSetId)
request.page_size = 100
request.end = 100000
return request
def testSearchVariants(self):
request = protocol.SearchVariantsRequest()
request.reference_name = self.referenceName
request.start = self.start
request.end = self.end
request.variant_set_id = self.variantSetId
request.call_set_ids.extend(self.callSetIds)
request.page_size = self.pageSize
self.httpClient.search_variants(self.variantSetId,
start=self.start,
end=self.end,
reference_name=self.referenceName,
call_set_ids=self.callSetIds)
self.httpClient._run_search_request.assert_called_once_with(
request, "variants", protocol.SearchVariantsResponse)
def search_variants(self,
variant_set_id,
start=None,
end=None,
reference_name=None,
call_set_ids=None):
"""
Returns an iterator over the Variants fulfilling the specified
conditions from the specified VariantSet.
:param str variant_set_id: The ID of the
:class:`ga4gh.protocol.VariantSet` 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.
:param list call_set_ids: Only return variant calls which belong to
call sets with these IDs. If an empty array, returns variants
without any call objects. If null, returns all variant calls.
:return: An iterator over the :class:`ga4gh.protocol.Variant` objects
defined by the query parameters.
:rtype: iter
"""
request = protocol.SearchVariantsRequest()
request.reference_name = pb.string(reference_name)
request.start = pb.int(start)
request.end = pb.int(end)
request.variant_set_id = variant_set_id
request.call_set_ids.extend(pb.string(call_set_ids))
request.page_size = pb.int(self._page_size)
return self._run_search_request(request, "variants",
protocol.SearchVariantsResponse)