def getCallSetId(self, sampleName):
"""
Returns the callSetId for the specified sampleName in this
VariantSet.
"""
compoundId = datamodel.CallSetCompoundId(
self.getCompoundId(), sampleName)
return str(compoundId)
def testCallSet(self):
name = "sampleName"
variantSet = self.getVariantSet()
dataset = variantSet.getParentContainer()
cid = datamodel.CallSetCompoundId(variantSet.getCompoundId(), name)
self.assertRaises(ValueError, datamodel.CallSetCompoundId,
variantSet.getCompoundId())
self.assertEqual(cid.dataset, dataset.getLocalId())
self.assertEqual(cid.variant_set, variantSet.getLocalId())
self.assertEqual(cid.name, name)
self.assertEqual(cid.dataset_id, dataset.getId())
self.assertEqual(cid.variant_set_id, variantSet.getId())
def _verifyVariantsCallSetIds(self, searchsampleIds):
"""
leaving searchSampleIds will get all samples.
"""
gaCallSetVariants = []
for referenceName in self._referenceNames:
end = datamodel.PysamDatamodelMixin.vcfMax
gaSearchIds = [
str(
datamodel.CallSetCompoundId(self._gaObject.getCompoundId(),
sampleId))
for sampleId in searchsampleIds
]
gaVariants = list(
self._gaObject.getVariants(referenceName, 0, end, gaSearchIds))
self._verifyGaVariantsSample(gaVariants, searchsampleIds)
gaCallSetVariants += gaVariants
localVariants = filter(lambda v: v.CHROM == referenceName,
self._variantRecords)
self._verifyVariantsEqual(gaVariants, localVariants)
self.assertEqual(len(gaCallSetVariants), len(self._variantRecords))