def searchReads(
self, readGroupIds, referenceId=None, start=None, end=None):
"""
Returns an iterator over the Reads fulfilling the specified
conditions from the specified ReadGroupIds.
:param str readGroupIds: The IDs of the
:class:`ga4gh.protocol.ReadGroup` of interest.
:param str referenceId: The name of the
:class:`ga4gh.protocol.Reference` we wish to return reads
mapped to.
:param int start: The start position (0-based) of this query. If a
reference is specified, this defaults to 0. 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: The end position (0-based, exclusive) of this query.
If a reference is specified, this defaults to the reference's
length.
:return: An iterator over the
:class:`ga4gh.protocol.ReadAlignment` objects defined by
the query parameters.
:rtype: iter
"""
request = protocol.SearchReadsRequest()
request.readGroupIds = readGroupIds
request.referenceId = referenceId
request.start = start
request.end = end
request.pageSize = self._pageSize
return self._runSearchRequest(
request, "reads", protocol.SearchReadsResponse)
def sendReadsSearch(self, readGroupIds=None):
if readGroupIds is None:
readGroupIds = [self.readGroupId]
request = protocol.SearchReadsRequest()
request.readGroupIds = readGroupIds
request.referenceId = self.referenceId
return self.sendPostRequest('/reads/search', request)
def testReads(self):
# search read group sets
path = utils.applyVersion('/readgroupsets/search')
request = protocol.SearchReadGroupSetsRequest()
request.datasetId = 'simulatedDataset1'
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(response.status_code, 200)
responseData = protocol.SearchReadGroupSetsResponse.fromJsonString(
response.data)
readGroupSets = responseData.readGroupSets
self.assertEqual(len(readGroupSets), 1)
# search reads
path = utils.applyVersion('/reads/search')
request = protocol.SearchReadsRequest()
readGroupId = readGroupSets[0].readGroups[0].id
request.readGroupIds = [readGroupId]
request.referenceId = "chr1"
response = self.sendJsonPostRequest(path, request.toJsonString())
self.assertEqual(response.status_code, 200)
responseData = protocol.SearchReadsResponse.fromJsonString(
response.data)
alignments = responseData.alignments
self.assertEqual(len(alignments), self.numAlignmentsPerReadGroup)
for alignment in alignments:
self.assertEqual(alignment.readGroupId, readGroupId)
def sendReadsSearch(self, readGroupIds=None):
if readGroupIds is None:
readGroupIds = ['simulatedDataset1:aReadGroupSet:one']
request = protocol.SearchReadsRequest()
request.readGroupIds = readGroupIds
request.referenceId = "chr1"
return self.sendPostRequest('/reads/search', request)
def searchReads(self,
readGroupIds,
referenceId=None,
start=None,
end=None):
"""
Returns an iterator over the Reads fulfilling the specified
conditions from the specified ReadGroupIds.
:param str readGroupIds: The IDs of the
:class:`ga4gh.protocol.ReadGroup` of interest.
:param str referenceId: The name of the
:class:`ga4gh.protocol.Reference` we wish to return reads
mapped to.
:param int start: TODO
:param int end: TODO
:return: An iterator over the
:class:`ga4gh.protocol.ReadAlignment` objects defined by
the query parameters.
:rtype: iter
"""
request = protocol.SearchReadsRequest()
request.readGroupIds = readGroupIds
request.referenceId = referenceId
request.start = start
request.end = end
request.pageSize = self._pageSize
return self._runSearchRequest(request, "reads",
protocol.SearchReadsResponse)
def setUp(self):
self.request = protocol.SearchReadsRequest()
self.backend = backend.SimulatedBackend(numAlignments=0)
referenceSet = self.backend.getReferenceSetByIndex(0)
reference = referenceSet.getReferenceByIndex(0)
self.request.referenceId = reference.getId()
self.dataset = self.backend.getDatasets()[0]
self.readGroupSet = self.dataset.getReadGroupSets()[0]
def setUp(self):
self.request = protocol.SearchReadsRequest()
self.request.referenceId = "chr1"
self.backend = backend.SimulatedBackend()
self.datasetId = self.backend.getDatasetIds()[0]
self.dataset = self.backend.getDataset(self.datasetId)
self.readGroupSetLocalId = "aReadGroupSet"
self.readGroupLocalId = "aReadGroup"
self.readGroupSet = reads.AbstractReadGroupSet(
self.dataset, self.readGroupSetLocalId)
def setUp(self):
self.request = protocol.SearchReadsRequest()
self.backend = backend.Backend(
datarepo.SimulatedDataRepository(numAlignments=0))
dataRepo = self.backend.getDataRepository()
referenceSet = dataRepo.getReferenceSetByIndex(0)
reference = referenceSet.getReferenceByIndex(0)
self.request.reference_id = reference.getId()
self.dataset = dataRepo.getDatasets()[0]
self.readGroupSet = self.dataset.getReadGroupSets()[0]
def createSearchReadsRequest(self):
request = protocol.SearchReadsRequest()
if self.usingWorkaroundsFor(client.HttpClient.workaroundGoogle):
# google says referenceId not a valid field
request = self.SearchReadsRequestGoogle()
setCommaSeparatedAttribute(request, self.args, 'readGroupIds')
request.start = self.args.start
request.end = self.args.end
request.referenceId = self.args.referenceId
return request
def testSearchReads(self):
request = protocol.SearchReadsRequest()
request.readGroupIds = self.readGroupIds
request.referenceId = self.referenceId
request.start = self.start
request.end = self.end
request.pageSize = self.pageSize
self.httpClient.searchReads(
self.readGroupIds, referenceId=self.referenceId,
start=self.start, end=self.end)
self.httpClient._runSearchRequest.assert_called_once_with(
request, "reads", protocol.SearchReadsResponse)
def testUnsupportedReadOperations(self):
path = '/reads/search'
dataset = self.dataRepo.getDatasets()[0]
readGroupSet = dataset.getReadGroupSets()[0]
readGroup = readGroupSet.getReadGroups()[0]
reference = readGroupSet.getReferenceSet().getReferences()[0]
# unmapped Reads
request = protocol.SearchReadsRequest()
request.readGroupIds = [readGroup.getId()]
request.referenceId = None
self.verifySearchMethodNotSupported(request, path)
# multiple ReadGroupSets
request.readGroupIds = [readGroup.getId(), "42"]
request.referenceId = reference.getId()
self.verifySearchMethodNotSupported(request, path)
def testOneDatasetRestriction(self):
# no datasetIds attr
request = protocol.SearchReadsRequest()
with self.assertRaises(AssertionError):
self._backend._getDatasetFromRequest(request)
# datasetIds attr
request = protocol.SearchVariantSetsRequest()
with self.assertRaises(exceptions.NotExactlyOneDatasetException):
self._backend._getDatasetFromRequest(request)
datasetId = 'dataset1'
request.datasetIds = [datasetId]
dataset = self._backend._getDatasetFromRequest(request)
self.assertEquals(dataset.getId(), datasetId)
request.datasetIds = ['dataset1', 'dataset2']
with self.assertRaises(exceptions.NotExactlyOneDatasetException):
self._backend._getDatasetFromRequest(request)
def testReads(self):
path = '/reads/search'
for dataset in self.backend.getDatasets():
for readGroupSet in dataset.getReadGroupSets():
referenceSet = readGroupSet.getReferenceSet()
for reference in referenceSet.getReferences():
for readGroup in readGroupSet.getReadGroups():
# search reads
request = protocol.SearchReadsRequest()
request.readGroupIds = [readGroup.getId()]
request.referenceId = reference.getId()
responseData = self.sendSearchRequest(
path, request, protocol.SearchReadsResponse)
alignments = responseData.alignments
self.assertGreater(len(alignments), 0)
for alignment in alignments:
# TODO more tests here: this is very weak.
self.assertEqual(alignment.readGroupId,
readGroup.getId())
def sendReadsSearch(self, readGroupIds=None, referenceId=""):
request = protocol.SearchReadsRequest()
request.read_group_ids.extend(readGroupIds)
request.reference_id = referenceId
return self.sendPostRequest('/reads/search', request)
def setUp(self):
self.request = protocol.SearchReadsRequest()
self.backend = backend.SimulatedBackend()
self.datasetId = self.backend.getDatasetIds()[0]
self.readGroupId = "{}:readGroupId".format(self.datasetId)
def sendReadsSearch(self, readGroupIds=None):
if readGroupIds is None:
readGroupIds = ['aReadGroupSet:one']
request = protocol.SearchReadsRequest()
request.readGroupIds = readGroupIds
return self.sendRequest('/reads/search', request)
