def testConvertLocationHgvsC(self):
loc = protocol.AlleleLocation()
loc.start = 430
loc.referenceSequence = "T"
loc.alternateSequence = "A"
hgvsC = "NM_001005484.1:c.431T>A"
testLoc = self._variantAnnotationSet.convertLocationHgvsC(hgvsC)
self.assertEqual(testLoc, loc)
def testConvertLocationHgvsP(self):
loc = protocol.AlleleLocation()
loc.start = 143
loc.alternateSequence = "Asn"
loc.referenceSequence = "Ile"
hgvsP = "NM_001005484.1:p.Ile144Asn"
testLoc = self._variantAnnotationSet.convertLocationHgvsP(hgvsP)
self.assertEqual(testLoc, loc)
def _createGaAlleleLocation(self):
"""
Convenience method to set the common fields in a AlleleLocation
object.
"""
ret = protocol.AlleleLocation()
ret.created = self._creationTime
ret.updated = self._updatedTime
return ret
def testAddLocations(self):
effect = protocol.TranscriptEffect()
effect.hgvsAnnotation = protocol.HGVSAnnotation()
effect.hgvsAnnotation.protein = "NM_001005484.1:p.Ile144Asn"
effect.hgvsAnnotation.transcript = "NM_001005484.1:c.431T>A"
effect.proteinLocation = protocol.AlleleLocation()
effect.cDNALocation = protocol.AlleleLocation()
effect.CDSLocation = protocol.AlleleLocation()
effect.proteinLocation.alternateSequence = "Asn"
effect.proteinLocation.referenceSequence = "Ile"
effect.proteinLocation.start = 143
effect.CDSLocation.alternateSequence = "A"
effect.CDSLocation.referenceSequence = "T"
effect.CDSLocation.start = 430
effect.cDNALocation.start = 430
protPos = "144/305"
cdnaPos = "431/918"
testEffect = self._variantAnnotationSet.addLocations(
effect, protPos, cdnaPos)
self.assertEqual(testEffect, effect)
def testConvertLocation(self):
loc = protocol.AlleleLocation()
loc.start = 150
pos = "151/305"
testLoc = self._variantAnnotationSet.convertLocation(pos)
self.assertEqual(testLoc, loc)