def __init__(self, randomSeed=0, numCalls=1, variantDensity=0.5,
numVariantSets=1, numReferenceSets=1,
numReferencesPerReferenceSet=1, numAlignments=2):
super(SimulatedBackend, self).__init__()
# Datasets
dataset1 = datasets.SimulatedDataset(
"simulatedDataset1", randomSeed, numCalls,
variantDensity, numVariantSets, numAlignments)
dataset2 = datasets.SimulatedDataset(
"simulatedDataset2", randomSeed, numCalls,
variantDensity, numVariantSets, numAlignments)
self._datasetIdMap[dataset1.getId()] = dataset1
self._datasetIdMap[dataset2.getId()] = dataset2
self._datasetIds = sorted(self._datasetIdMap.keys())
# References
randomGenerator = random.Random()
randomGenerator.seed(randomSeed)
for i in range(numReferenceSets):
referenceSetId = "referenceSet{}".format(i)
referenceSetSeed = randomGenerator.getrandbits(32)
referenceSet = references.SimulatedReferenceSet(
referenceSetId, referenceSetSeed,
numReferencesPerReferenceSet)
self._referenceSetIdMap[referenceSetId] = referenceSet
for reference in referenceSet.getReferences():
referenceId = reference.getId()
self._referenceIdMap[referenceId] = reference
self._referenceSetIds = sorted(self._referenceSetIdMap.keys())
self._referenceIds = sorted(self._referenceIdMap.keys())
def testCreation(self):
dataset = datasets.Dataset('dataset1')
referenceSet = references.SimulatedReferenceSet("srs1")
localId = "variantAnnotationSetId"
simulatedVariantSet = variants.SimulatedVariantSet(
dataset,
referenceSet,
'variantSet1',
randomSeed=self.randomSeed,
numCalls=self.numCalls,
variantDensity=self.variantDensity)
simulatedVariantAnnotationSet = variants.SimulatedVariantAnnotationSet(
simulatedVariantSet, localId, self.randomSeed)
annotations = simulatedVariantAnnotationSet.getVariantAnnotations(
self.referenceName, self.startPosition, self.endPosition)
self.assertEquals(
simulatedVariantSet.toProtocolElement().id,
simulatedVariantAnnotationSet.toProtocolElement().variant_set_id,
"Variant Set ID should match the annotation's variant set ID")
for variant, ann in annotations:
self.assertEquals(
datetime.datetime.strptime(
ann.created,
"%Y-%m-%dT%H:%M:%S.%fZ").strftime("%Y-%m-%dT%H:%M:%S.%fZ"),
ann.created, "Expect time format to be in ISO8601")
self.assertEqual(variant.id, ann.variant_id)
def __init__(
self, randomSeed=0, numDatasets=2,
numVariantSets=1, numCalls=1, variantDensity=0.5,
numReferenceSets=1, numReferencesPerReferenceSet=1,
numReadGroupSets=1, numReadGroupsPerReadGroupSet=1,
numAlignments=2):
super(SimulatedDataRepository, self).__init__()
# References
for i in range(numReferenceSets):
localId = "referenceSet{}".format(i)
seed = randomSeed + i
referenceSet = references.SimulatedReferenceSet(
localId, seed, numReferencesPerReferenceSet)
self.addReferenceSet(referenceSet)
# Datasets
for i in range(numDatasets):
seed = randomSeed + i
localId = "simulatedDataset{}".format(i)
referenceSet = self.getReferenceSetByIndex(i % numReferenceSets)
dataset = datasets.SimulatedDataset(
localId, referenceSet=referenceSet, randomSeed=seed,
numCalls=numCalls, variantDensity=variantDensity,
numVariantSets=numVariantSets,
numReadGroupSets=numReadGroupSets,
numReadGroupsPerReadGroupSet=numReadGroupsPerReadGroupSet,
numAlignments=numAlignments)
self.addDataset(dataset)
def testRunGetRequest(self):
id_ = "anId"
obj = references.SimulatedReferenceSet(id_)
idMap = {id_: obj}
responseStr = self._backend.runGetRequest(idMap, id_)
class_ = protocol.ReferenceSet
response = class_.fromJsonString(responseStr)
self.assertTrue(isinstance(response, class_))
def testCreation(self):
dataset = datasets.AbstractDataset('dataset1')
localId = "readGroupSetId"
referenceSet = references.SimulatedReferenceSet("srs1")
simulatedReadGroupSet = reads.SimulatedReadGroupSet(
dataset, localId, referenceSet)
for readGroup in simulatedReadGroupSet.getReadGroups():
alignments = list(readGroup.getReadAlignments())
self.assertGreater(len(alignments), 0)
def _getSimulatedVariantSet(self):
dataset = datasets.Dataset('dataset1')
referenceSet = references.SimulatedReferenceSet("srs1")
simulatedVariantSet = variants.SimulatedVariantSet(
dataset,
referenceSet,
'variantSet1',
randomSeed=self.randomSeed,
numCalls=self.numCalls,
variantDensity=self.variantDensity)
return simulatedVariantSet
