def testOneIntervalEndingAfterHitEndCoverage(self):
"""
If there is a single interval that ends after the end of the hit
but doesn't start at zero, coverage should return the correct value.
"""
ri = ReadIntervals(100)
ri.add(50, 150)
self.assertEqual(0.5, ri.coverage())
def testOneIntervalCoveringAllExtendingLeftCoverage(self):
"""
If there is a single interval that spans the whole hit, including
going negative to the left, coverage should return 1.0.
"""
ri = ReadIntervals(100)
ri.add(-10, 100)
self.assertEqual(1.0, ri.coverage())
def testOneIntervalCoveringAllExtendingRightCoverage(self):
"""
If there is a single interval that spans the whole hit, including
going beyond the hit to the right, coverage should return 1.0.
"""
ri = ReadIntervals(100)
ri.add(0, 110)
self.assertEqual(1.0, ri.coverage())
def testOneIntervalEndingAfterHitEndCoverage(self):
"""
If there is a single interval that ends after the end of the hit
but doesn't start at zero, coverage should return the correct value.
"""
ri = ReadIntervals(100)
ri.add(50, 150)
self.assertEqual(0.5, ri.coverage())
def testOneIntervalStartingBeforeZeroCoverage(self):
"""
If there is a single interval that starts before zero but doesn't
cover the whole hit, coverage should return the correct value.
"""
ri = ReadIntervals(100)
ri.add(-50, 50)
self.assertEqual(0.5, ri.coverage())
def testOneIntervalExactCoveringCoverage(self):
"""
If there is a single interval that spans the whole hit exactly,
coverage should return 1.0.
"""
ri = ReadIntervals(100)
ri.add(0, 100)
self.assertEqual(1.0, ri.coverage())
def testOneIntervalStartingBeforeZeroCoverage(self):
"""
If there is a single interval that starts before zero but doesn't
cover the whole hit, coverage should return the correct value.
"""
ri = ReadIntervals(100)
ri.add(-50, 50)
self.assertEqual(0.5, ri.coverage())
def testOneIntervalCoveringAllExtendingRightCoverage(self):
"""
If there is a single interval that spans the whole hit, including
going beyond the hit to the right, coverage should return 1.0.
"""
ri = ReadIntervals(100)
ri.add(0, 110)
self.assertEqual(1.0, ri.coverage())
def testOneIntervalCoveringAllExtendingLeftCoverage(self):
"""
If there is a single interval that spans the whole hit, including
going negative to the left, coverage should return 1.0.
"""
ri = ReadIntervals(100)
ri.add(-10, 100)
self.assertEqual(1.0, ri.coverage())
def testOneIntervalExactCoveringCoverage(self):
"""
If there is a single interval that spans the whole hit exactly,
coverage should return 1.0.
"""
ri = ReadIntervals(100)
ri.add(0, 100)
self.assertEqual(1.0, ri.coverage())
def testOneIntervalCoveringAllExtendingBothCoverage(self):
"""
If there is a single interval that spans the whole hit, including
starting before zero and also going beyond the hit to the right,
coverage should return 1.0
"""
ri = ReadIntervals(100)
ri.add(-10, 110)
self.assertEqual(1.0, ri.coverage())
def testOneIntervalCoveringAllExtendingBothCoverage(self):
"""
If there is a single interval that spans the whole hit, including
starting before zero and also going beyond the hit to the right,
coverage should return 1.0
"""
ri = ReadIntervals(100)
ri.add(-10, 110)
self.assertEqual(1.0, ri.coverage())
def testTwoOverlappingIntervalsInMiddleCoverage(self):
"""
If there are two overlapping intervals in the middle of the hit,
coverage should return the correct value.
"""
ri = ReadIntervals(100)
ri.add(50, 60)
ri.add(55, 70)
self.assertEqual(0.2, ri.coverage())
def testOneIntervalInMiddleCoverage(self):
"""
If there is a single interval in the middle of the hit, coverage
should return the correct value.
"""
ri = ReadIntervals(100)
ri.add(50, 60)
self.assertEqual(0.1, ri.coverage())
def testOneIntervalInMiddleCoverage(self):
"""
If there is a single interval in the middle of the hit, coverage
should return the correct value.
"""
ri = ReadIntervals(100)
ri.add(50, 60)
self.assertEqual(0.1, ri.coverage())
def testTwoOverlappingIntervalsInMiddleCoverage(self):
"""
If there are two overlapping intervals in the middle of the hit,
coverage should return the correct value.
"""
ri = ReadIntervals(100)
ri.add(50, 60)
ri.add(55, 70)
self.assertEqual(0.2, ri.coverage())
def coverage(self):
"""
Get the fraction of this title sequence that is matched by its reads.
@return: The C{float} fraction of the title sequence matched by its
reads.
"""
intervals = ReadIntervals(self.subjectLength)
for hsp in self.hsps():
intervals.add(hsp.subjectStart, hsp.subjectEnd)
return intervals.coverage()
def coverage(self):
"""
Get the fraction of this title sequence that is matched by its reads.
@return: The C{float} fraction of the title sequence matched by its
reads.
"""
intervals = ReadIntervals(self.subjectLength)
for hsp in self.hsps():
intervals.add(hsp.subjectStart, hsp.subjectEnd)
return intervals.coverage()
def testPairOfTwoOverlappingIntervalsCoverage(self):
"""
If there are two sets of two overlapping intervals in the middle of
the hit, coverage should return the correct value.
"""
ri = ReadIntervals(100)
# First overlapping pair, 50-70.
ri.add(50, 60)
ri.add(55, 70)
# First overlapping pair, 80-95.
ri.add(80, 90)
ri.add(85, 95)
self.assertEqual(0.35, ri.coverage())
def testPairOfTwoOverlappingIntervalsCoverage(self):
"""
If there are two sets of two overlapping intervals in the middle of
the hit, coverage should return the correct value.
"""
ri = ReadIntervals(100)
# First overlapping pair, 50-70.
ri.add(50, 60)
ri.add(55, 70)
# First overlapping pair, 80-95.
ri.add(80, 90)
ri.add(85, 95)
self.assertEqual(0.35, ri.coverage())
def testOverlappingIntervalsThatCoverEverythingCoverage(self):
"""
If there are sets of overlapping intervals that cover the whole hit,
coverage should return the correct value.
"""
ri = ReadIntervals(100)
ri.add(-10, 20)
ri.add(15, 40)
ri.add(40, 70)
ri.add(66, 89)
ri.add(77, 93)
ri.add(70, 110)
self.assertEqual(1.0, ri.coverage())
def testOverlappingIntervalsThatCoverEverythingCoverage(self):
"""
If there are sets of overlapping intervals that cover the whole hit,
coverage should return the correct value.
"""
ri = ReadIntervals(100)
ri.add(-10, 20)
ri.add(15, 40)
ri.add(40, 70)
ri.add(66, 89)
ri.add(77, 93)
ri.add(70, 110)
self.assertEqual(1.0, ri.coverage())
def testEmptyCoverageOnZeroLengthSequence(self):
"""
When no intervals are added, coverage should return 0.0
"""
ri = ReadIntervals(0)
self.assertEqual(0.0, ri.coverage())
def testEmptyCoverage(self):
"""
When no intervals are added, coverage should return 0.0
"""
ri = ReadIntervals(100)
self.assertEqual(0.0, ri.coverage())
def testEmptyCoverageOnZeroLengthSequence(self):
"""
When no intervals are added, coverage should return 0.0
"""
ri = ReadIntervals(0)
self.assertEqual(0.0, ri.coverage())
def testEmptyCoverage(self):
"""
When no intervals are added, coverage should return 0.0
"""
ri = ReadIntervals(100)
self.assertEqual(0.0, ri.coverage())
