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 __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 testToProtocolElement(self):
datasetId = 'ds1'
dataset = datasets.SimulatedDataset(datasetId, 1, 2, 3, 4, 5)
dataset.setInfo({"test": "test"})
gaDataset = dataset.toProtocolElement()
self.assertIsNotNone(gaDataset.info)
self.assertEqual(gaDataset.info['test'].values[0].string_value, "test")
self.assertEqual(dataset.getId(), gaDataset.id)
def testToProtocolElement(self):
datasetId = 'ds1'
dataset = datasets.SimulatedDataset(datasetId, 1, 2, 3, 4, 5)
gaDataset = dataset.toProtocolElement()
self.assertEqual(dataset.getId(), gaDataset.id)
