def getVariantId(self, gaVariant):
"""
Returns an ID string suitable for the specified GA Variant
object in this variant set.
"""
compoundId = datamodel.VariantCompoundId(
self.getCompoundId(), gaVariant.referenceName, gaVariant.start)
return str(compoundId)
def getVariantId(self, gaVariant):
"""
Produces a variant ID for a variant annotated within this
variant annotation set.
:param gaVariant: protocol.Variant
:return: compoundId String
"""
md5 = self.hashVariant(gaVariant)
compoundId = datamodel.VariantCompoundId(
self._variantSetId, gaVariant.referenceName,
gaVariant.start, md5)
return str(compoundId)
def testGetVariant(self):
variantSet = self._gaObject
for reference_name in self._reference_names:
refnameVariants = self._getPyvcfVariants(reference_name)
for variant in refnameVariants:
# positive test: get the expected variant
md5 = self._hashVariant(variant)
compoundId = datamodel.VariantCompoundId(
variantSet.getCompoundId(), reference_name,
str(variant.start), md5)
gotVariant = variantSet.getVariant(compoundId)
self.assertEqual(str(compoundId), gotVariant.id)
# negative test: change start position to past variant
wrongStart = variant.end
compoundId = datamodel.VariantCompoundId(
variantSet.getCompoundId(), reference_name,
str(wrongStart), md5)
try:
gotVariant = variantSet.getVariant(compoundId)
self.assertNotEqual(variant.start, gotVariant.start)
except exceptions.ObjectNotFoundException:
pass
# negative test: change reference name
compoundId = datamodel.VariantCompoundId(
variantSet.getCompoundId(), "wrong reference name",
str(variant.start), md5)
with self.assertRaises(exceptions.ObjectNotFoundException):
variantSet.getVariant(compoundId)
# negative test: change hash
compoundId = datamodel.VariantCompoundId(
variantSet.getCompoundId(), reference_name,
str(variant.start), "wrong hash")
with self.assertRaises(exceptions.ObjectNotFoundException):
variantSet.getVariant(compoundId)
def testVariant(self):
referenceName = "referenceName"
start = "start"
variantSet = self.getVariantSet()
dataset = variantSet.getParentContainer()
cid = datamodel.VariantCompoundId(variantSet.getCompoundId(),
referenceName, start)
self.assertRaises(ValueError, datamodel.VariantCompoundId,
variantSet.getCompoundId())
self.assertRaises(ValueError, datamodel.VariantCompoundId,
variantSet.getCompoundId(), referenceName)
self.assertEqual(cid.dataset, dataset.getLocalId())
self.assertEqual(cid.variantSet, variantSet.getLocalId())
self.assertEqual(cid.referenceName, referenceName)
self.assertEqual(cid.start, start)
self.assertEqual(cid.datasetId, dataset.getId())
self.assertEqual(cid.variantSetId, variantSet.getId())