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)