def testCoverageNoReads(self):
"""
The coverage method must return zero when a title alignments has no
alignments (and therefore no coverage).
"""
titleAlignments = TitleAlignments('subject title', 100)
self.assertEqual(0.0, titleAlignments.coverage())
def testCoverageNoReads(self):
"""
The coverage method must return zero when a title alignments has no
alignments (and therefore no coverage).
"""
titleAlignments = TitleAlignments('subject title', 100)
self.assertEqual(0.0, titleAlignments.coverage())
def testFullCoverage(self):
"""
The coverage method must return the correct value when the title is
fully covered by its reads.
"""
hsp1 = HSP(7, subjectStart=0, subjectEnd=50)
hsp2 = HSP(8, subjectStart=50, subjectEnd=100)
titleAlignments = TitleAlignments('subject title', 100)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(1.0, titleAlignments.coverage())
def testFullCoverage(self):
"""
The coverage method must return the correct value when the title is
fully covered by its reads.
"""
hsp1 = HSP(7, subjectStart=0, subjectEnd=50)
hsp2 = HSP(8, subjectStart=50, subjectEnd=100)
titleAlignments = TitleAlignments('subject title', 100)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(1.0, titleAlignments.coverage())
def testPartialCoverage(self):
"""
The coverage method must return the correct value when the title is
partially covered by its reads.
"""
hsp1 = HSP(7, subjectStart=10, subjectEnd=20)
hsp2 = HSP(15, subjectStart=30, subjectEnd=40)
hsp3 = HSP(21, subjectStart=50, subjectEnd=60)
titleAlignments = TitleAlignments('subject title', 100)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
read = Read('id2', 'AAA')
titleAlignment = TitleAlignment(read, [hsp3])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(0.3, titleAlignments.coverage())
def testPartialCoverage(self):
"""
The coverage method must return the correct value when the title is
partially covered by its reads.
"""
hsp1 = HSP(7, subjectStart=10, subjectEnd=20)
hsp2 = HSP(15, subjectStart=30, subjectEnd=40)
hsp3 = HSP(21, subjectStart=50, subjectEnd=60)
titleAlignments = TitleAlignments('subject title', 100)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
read = Read('id2', 'AAA')
titleAlignment = TitleAlignment(read, [hsp3])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(0.3, titleAlignments.coverage())
