def testFullCoverageCounts(self):
"""
The coverageCounts method must return the correct result when the title
is fully covered by its reads.
"""
hsp1 = HSP(7, subjectStart=0, subjectEnd=5)
hsp2 = HSP(8, subjectStart=5, subjectEnd=10)
titleAlignments = TitleAlignments('subject title', 10)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
c = Counter([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
self.assertEqual(c, titleAlignments.coverageCounts())
def testFullCoverageCounts(self):
"""
The coverageCounts method must return the correct result when the title
is fully covered by its reads.
"""
hsp1 = HSP(7, subjectStart=0, subjectEnd=5)
hsp2 = HSP(8, subjectStart=5, subjectEnd=10)
titleAlignments = TitleAlignments('subject title', 10)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
c = Counter([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
self.assertEqual(c, titleAlignments.coverageCounts())
def testCoverageCountsOverlap(self):
"""
The coverageCounts method must return the correct results when the
title is partially covered by its reads that overlap.
"""
hsp1 = HSP(7, subjectStart=1, subjectEnd=2)
hsp2 = HSP(15, subjectStart=3, subjectEnd=6)
hsp3 = HSP(21, subjectStart=5, subjectEnd=6)
titleAlignments = TitleAlignments('subject title', 10)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
read = Read('id2', 'AAA')
titleAlignment = TitleAlignment(read, [hsp3])
titleAlignments.addAlignment(titleAlignment)
c = Counter([1, 3, 4, 5, 5])
self.assertEqual(c, titleAlignments.coverageCounts())
def testCoverageCountsOverlap(self):
"""
The coverageCounts method must return the correct results when the
title is partially covered by its reads that overlap.
"""
hsp1 = HSP(7, subjectStart=1, subjectEnd=2)
hsp2 = HSP(15, subjectStart=3, subjectEnd=6)
hsp3 = HSP(21, subjectStart=5, subjectEnd=6)
titleAlignments = TitleAlignments('subject title', 10)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
read = Read('id2', 'AAA')
titleAlignment = TitleAlignment(read, [hsp3])
titleAlignments.addAlignment(titleAlignment)
c = Counter([1, 3, 4, 5, 5])
self.assertEqual(c, titleAlignments.coverageCounts())
