def testAddTwo(self):
"""
Adding two reads must result in the expected nucleotides and reads
being stored.
"""
read1 = AlignedRead('id1', '---ACCC--')
read1.setSignificantOffsets([3, 4])
read2 = AlignedRead('id2', '---TG--')
read2.setSignificantOffsets([3])
rc = ReadCluster()
rc.add(read1)
rc.add(read2)
self.assertEqual({read1, read2}, rc.reads)
expectedBases3 = OffsetBases()
expectedBases3.incorporateBase('A')
expectedBases3.incorporateBase('T')
expectedBases4 = OffsetBases()
expectedBases4.incorporateBase('C')
self.assertEqual({
3: expectedBases3,
4: expectedBases4
}, rc.nucleotides)
def testAddOne(self):
"""
Adding a read must result in the expected nucleotides and read
being stored.
"""
read = AlignedRead('id', '---ACGT--')
read.setSignificantOffsets([3])
rc = ReadCluster()
rc.add(read)
expectedBases = OffsetBases()
expectedBases.incorporateBase('A')
self.assertEqual({read}, rc.reads)
self.assertEqual({3: expectedBases}, rc.nucleotides)
self.assertEqual(1, len(rc))
def testMultiplicativeDistanceOneHalf(self):
"""
The commonNucleotidesMultiplicativeDistance method must return 0.5
when the ratio of two bases in one cluster is 50:50.
"""
read1 = AlignedRead('id1', '---TCTC-')
read1.setSignificantOffsets([3, 4, 5, 6])
rc1 = ReadCluster()
rc1.add(read1)
read2 = AlignedRead('id2', '---TG--')
read2.setSignificantOffsets([3, 4])
rc2 = ReadCluster()
rc2.add(read2)
self.assertAlmostEqual(
0.5, ReadCluster.commonNucleotidesMultiplicativeDistance(rc1, rc2))
def testMultiplicativeDistanceOne(self):
"""
The commonNucleotidesMultiplicativeDistance method must return 1.0
when two clusters have no offsets in common.
"""
read1 = AlignedRead('id1', '-----TC-')
read1.setSignificantOffsets([5, 6])
rc1 = ReadCluster()
rc1.add(read1)
read2 = AlignedRead('id2', '---TG--')
read2.setSignificantOffsets([3, 4])
rc2 = ReadCluster()
rc2.add(read2)
self.assertAlmostEqual(
1.0, ReadCluster.commonNucleotidesMultiplicativeDistance(rc1, rc2))
def testCommonOffsetsMaxFractionZero(self):
"""
The commonOffsetsMaxFraction method must return 0.0 when two
clusters have no offsets in common.
"""
read1 = AlignedRead('id1', '---TCCCG-')
read1.setSignificantOffsets([5, 6])
rc1 = ReadCluster()
rc1.add(read1)
read2 = AlignedRead('id2', '---TG--A')
read2.setSignificantOffsets([3, 4, 7])
rc2 = ReadCluster()
rc2.add(read2)
self.assertAlmostEqual(0.0,
ReadCluster.commonOffsetsMaxFraction(rc1, rc2))
def testNonZeroDistance(self):
"""
The distance between two clusters must be as expected.
"""
read1 = AlignedRead('id1', '---TCCCG-')
read1.setSignificantOffsets([3, 4, 5, 6, 7])
rc1 = ReadCluster()
rc1.add(read1)
read2 = AlignedRead('id2', '---TG--A')
read2.setSignificantOffsets([3, 4, 7])
rc2 = ReadCluster()
rc2.add(read2)
# Two of the three common offsets do not match.
self.assertAlmostEqual(
2 / 3, ReadCluster.commonNucleotidesAgreementDistance(rc1, rc2))
def testDistanceOne(self):
"""
The distance between two clusters must be zero when the nucleotides
they have at their signifcant offsets do not match.
"""
read1 = AlignedRead('id1', '---ACCCG-')
read1.setSignificantOffsets([3, 4, 5, 6, 7])
rc1 = ReadCluster()
rc1.add(read1)
read2 = AlignedRead('id2', '---TG--A')
read2.setSignificantOffsets([3, 4, 7])
rc2 = ReadCluster()
rc2.add(read2)
self.assertEqual(
1.0, ReadCluster.commonNucleotidesAgreementDistance(rc1, rc2))
def testCommonOffsetsMaxFractionOneHalf(self):
"""
The commonOffsetsMaxFraction method must return 0.5 when half
the offsets of one cluster are in common with the offsets of another
cluster.
"""
read1 = AlignedRead('id1', '---TCCCG-')
read1.setSignificantOffsets([5, 6])
rc1 = ReadCluster()
rc1.add(read1)
read2 = AlignedRead('id2', '---TG--A')
read2.setSignificantOffsets([3, 4, 6, 7])
rc2 = ReadCluster()
rc2.add(read2)
self.assertAlmostEqual(0.0,
ReadCluster.commonOffsetsMaxFraction(rc1, rc2))
def testMerge(self):
"""
Merging two clusters must result in the expected nucleotides and reads
being stored.
"""
read1 = AlignedRead('id1', '---ACCC--')
read1.setSignificantOffsets([3, 4])
read2 = AlignedRead('id2', '---TG--')
read2.setSignificantOffsets([3])
rc1 = ReadCluster()
rc1.add(read1)
rc1.add(read2)
read3 = AlignedRead('id3', '---GGCC--')
read3.setSignificantOffsets([3, 4, 6])
rc2 = ReadCluster()
rc2.add(read3)
expectedBases3 = OffsetBases()
expectedBases3.incorporateBase('A')
expectedBases3.incorporateBase('T')
expectedBases3.incorporateBase('G')
expectedBases4 = OffsetBases()
expectedBases4.incorporateBase('C')
expectedBases4.incorporateBase('G')
expectedBases6 = OffsetBases()
expectedBases6.incorporateBase('C')
rc1.merge(rc2)
self.assertEqual(
{
3: expectedBases3,
4: expectedBases4,
6: expectedBases6,
}, rc1.nucleotides)
def testMultiplicativeDistanceZero(self):
"""
The commonNucleotidesMultiplicativeDistance method must return 0.0
when two clusters agree completely on nucleotides at their common
offsets.
"""
read1 = AlignedRead('id1', '-----TC-')
read1.setSignificantOffsets([5, 6])
rc1 = ReadCluster()
rc1.add(read1)
read2 = AlignedRead('id2', '-----TC-')
read2.setSignificantOffsets([5, 6])
read3 = AlignedRead('id3', '-----TC-')
read3.setSignificantOffsets([5, 6])
rc2 = ReadCluster()
rc2.add(read2)
rc2.add(read3)
self.assertAlmostEqual(
0.0, ReadCluster.commonNucleotidesMultiplicativeDistance(rc1, rc2))
def testCommonOffsetsMaxFractionOne(self):
"""
The commonOffsetsMaxFraction method must return 1.0 when all of
one of the offsets in one cluster are in the intersection of the
offsets of another cluster.
"""
read1 = AlignedRead('id1', '---TCCCG-')
read1.setSignificantOffsets([3, 4])
read2 = AlignedRead('id2', '---TCCCG-')
read2.setSignificantOffsets([6, 7])
rc1 = ReadCluster()
rc1.add(read1)
rc1.add(read2)
read3 = AlignedRead('id3', '---TG--A')
read3.setSignificantOffsets([3, 4, 7])
rc2 = ReadCluster()
rc2.add(read3)
self.assertAlmostEqual(1.0,
ReadCluster.commonOffsetsMaxFraction(rc1, rc2))
def testDistanceZero(self):
"""
The distance between two clusters must be 0.0 when they match at all
common significant offsets.
"""
read1 = AlignedRead('id1', '---TCCCG-')
read1.setSignificantOffsets([3, 4, 5, 6, 7])
rc1 = ReadCluster()
rc1.add(read1)
read2 = AlignedRead('id2', '---TC--A')
read2.setSignificantOffsets([3, 4, 7])
read3 = AlignedRead('id3', '---TG--G')
read3.setSignificantOffsets([7])
rc2 = ReadCluster()
rc2.add(read2)
rc2.add(read3)
# All three common offsets match.
self.assertEqual(
0.0, ReadCluster.commonNucleotidesAgreementDistance(rc1, rc2))
def testEmpty(self):
"""
An empty instance must have length zero.
"""
self.assertEqual(0, len(ReadCluster()))