def verifyGenotypeConversion(self, vcfGenotype, vcfPhaseset, callGenotype,
callPhaseset):
"""
Verifies that the convertGenotype function properly converts the vcf
genotype and phaseset values into the desired call genotype and
phaseset values.
"""
self.assertEqual((callGenotype, callPhaseset),
variants.convertVCFGenotype(vcfGenotype, vcfPhaseset))
def verifyGenotypeConversion(
self, vcfGenotype, vcfPhaseset, callGenotype, callPhaseset):
"""
Verifies that the convertGenotype function properly converts the vcf
genotype and phaseset values into the desired call genotype and
phaseset values.
"""
self.assertEqual(
(callGenotype, callPhaseset),
variants.convertVCFGenotype(vcfGenotype, vcfPhaseset))
def _verifyVariantCallEqual(self, gaCall, pyvcfCall):
genotype, phaseset = variants.convertVCFGenotype(
pyvcfCall.data.GT, pyvcfCall.phased)
# callSetId information is not available in pyvcf.model._Call
self.assertEqual(gaCall.callSetName, pyvcfCall.sample)
self.assertEqual(gaCall.genotype, genotype)
phaseset = None
if pyvcfCall.phased:
phaseset = "*"
self.assertEqual(gaCall.phaseset, phaseset)
if len(gaCall.genotypeLikelihood) > 0:
self._compareTwoListFloats(
gaCall.genotypeLikelihood, pyvcfCall.data.GL)
else:
self.assertNotIn("GL", pyvcfCall.data)
for key, value in gaCall.info.items():
if key != "GT" and key != "GL":
if isinstance(value[0], (list, tuple)):
self._compareTwoListFloats(value[0], getattr(
pyvcfCall.data, key))
elif isinstance(value[0], float):
self._compareTwoFloats(value[0], getattr(
pyvcfCall.data, key))
def _verifyVariantCallEqual(self, gaCall, pyvcfCall):
genotype, phaseset = variants.convertVCFGenotype(
pyvcfCall.data.GT, pyvcfCall.phased)
# callSetId information is not available in pyvcf.model._Call
self.assertEqual(gaCall.callSetName, pyvcfCall.sample)
self.assertEqual(gaCall.genotype, genotype)
phaseset = None
if pyvcfCall.phased:
phaseset = "*"
self.assertEqual(gaCall.phaseset, phaseset)
if len(gaCall.genotypeLikelihood) > 0:
self._compareTwoListFloats(gaCall.genotypeLikelihood,
pyvcfCall.data.GL)
else:
self.assertNotIn("GL", pyvcfCall.data)
for key, value in gaCall.info.items():
if key != "GT" and key != "GL":
if isinstance(value[0], (list, tuple)):
self._compareTwoListFloats(value[0],
getattr(pyvcfCall.data, key))
elif isinstance(value[0], float):
self._compareTwoFloats(value[0],
getattr(pyvcfCall.data, key))