def testGetPairsNoLandmarksNoTrigPoints(self):
"""
If a scanned read has no landmarks or trig points, its getPairs
method should generate no pairs.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
self.assertEqual([], list(read.getPairs()))
def testGetPairsOneLandmark(self):
"""
If a scanned read has one landmark, its getPairs method should generate
no pairs because there is nothing to pair with.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark = Landmark('name', 'symbol', 0, 2)
read.landmarks.append(landmark)
self.assertEqual([], list(read.getPairs()))
def testGetPairsOneLandmarkOneTrigPointLimitZero(self):
"""
If a scanned read has one landmark and one trig point, but getPairs
is given a limit of 0, no pairs should be generated.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark = Landmark('name', 'symbol', 0, 2)
read.landmarks.append(landmark)
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
self.assertEqual([], list(read.getPairs(limitPerLandmark=0)))
def testGetPairsOneLandmarkOneTrigPoint(self):
"""
If a scanned read has one landmark and one trig point, its getPairs
method should generate one pair.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark = Landmark('name', 'symbol', 0, 2)
read.landmarks.append(landmark)
trigPoint = TrigPoint('name', 'symbol', 0)
read.trigPoints.append(trigPoint)
self.assertEqual([(landmark, trigPoint)], list(read.getPairs()))
def testGetPairsOneLandmarkTwoTrigPoints(self):
"""
If a scanned read has one landmark and two trig points, its getPairs
method should generate two pairs.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark = Landmark('name', 'symbol', 0, 2)
read.landmarks.append(landmark)
trigPoint1 = TrigPoint('name', 'symbol', 1)
trigPoint2 = TrigPoint('name', 'symbol', 2)
read.trigPoints.extend([trigPoint1, trigPoint2])
result = list(read.getPairs())
self.assertEqual([(landmark, trigPoint1), (landmark, trigPoint2)],
result)
def testGetPairsTwoLandmarksTwoTrigPointsMinDistanceThree(self):
"""
If a scanned read has two landmarks and two trig points, its getPairs
method should generate one pair if a minimum distance of 3 is
passed and three trig points are too close.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 3)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
result = list(read.getPairs(minDistance=5))
self.assertEqual([(landmark1, trigPoint2)], result)
def testGetPairsTwoLandmarksOneTrigPoint(self):
"""
If a scanned read has two landmarks and one trig point, its getPairs
method should generate four pairs in the correct order of closeness,
not yielding (landmark, landmark) pairs with the second landmark to
the left of the first (i.e., not yielding (landmark2, landmark1)).
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'symbol', 0, 2)
landmark2 = Landmark('name', 'symbol', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint = TrigPoint('name', 'symbol', 4)
read.trigPoints.append(trigPoint)
result = list(read.getPairs())
self.assertEqual(
[(landmark1, landmark2), (landmark1, trigPoint),
(landmark2, trigPoint)],
result)
def testGetPairsTwoLandmarksTwoTrigPointsLimitOne(self):
"""
If a scanned read has two landmarks and two trig points, its getPairs
method should generate two pairs if a limit of 1 nearby feature per
landmark is passed.
Note that even if limitPerLandmark=1 were not specified, the
(landmark2, landmark1) pair would not be produced since landmark2 is
to the right of landmark1.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 4)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
result = list(read.getPairs(limitPerLandmark=1))
self.assertEqual([(landmark1, landmark2), (landmark2, trigPoint1)],
result)
def testGetPairsTwoLandmarksTwoTrigPointsMaxDistanceThree(self):
"""
If a scanned read has two landmarks and two trig points, its getPairs
method should generate three pairs if a maximum distance of 3 is
passed and one trig point is too far away.
Note that the (landmark2, landmark1) pair is not produced since
landmark2 is to the right of landmark1.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 3)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
result = list(read.getPairs(maxDistance=3))
self.assertEqual(
[(landmark1, landmark2), (landmark1, trigPoint1),
(landmark2, trigPoint1)],
result)
def testGetPairsTwoLandmarksTwoTrigPoints(self):
"""
If a scanned read has two landmarks and two trig points, its getPairs
method should generate six pairs, in the correct order of closeness,
not yielding (landmark, landmark) pairs with the second landmark to
the left of the first until all other pairs have been yielded.
Note that the (landmark2, landmark1) pair is not produced since
landmark2 is to the right of landmark1.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'symbol', 0, 2)
landmark2 = Landmark('name', 'symbol', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'symbol', 4)
trigPoint2 = TrigPoint('name', 'symbol', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
result = list(read.getPairs())
self.assertEqual(
[(landmark1, landmark2), (landmark1, trigPoint1),
(landmark1, trigPoint2),
(landmark2, trigPoint1), (landmark2, trigPoint2)],
result)