def testCoverageInfoNoReads(self):
"""
When a title has no reads aligned to it, the coverageInfo method
must return an empty result.
"""
titleAlignments = TitleAlignments('subject title', 55)
coverage = titleAlignments.coverageInfo()
self.assertEqual({}, coverage)
def testCoverageInfoNoReads(self):
"""
When a title has no reads aligned to it, the coverageInfo method
must return an empty result.
"""
titleAlignments = TitleAlignments('subject title', 55)
coverage = titleAlignments.coverageInfo()
self.assertEqual({}, coverage)
def testCoverageInfoOneReadWithOneHSP(self):
"""
When a title has one read with one HSP aligned to it, the coverageInfo
method must return just the indices and bases from that read.
"""
titleAlignments = TitleAlignments('subject title', 55)
hsp = HSP(15, subjectStart=3, subjectEnd=6, readMatchedSequence='CGT')
read = Read('id1', 'AAACGT')
titleAlignment = TitleAlignment(read, [hsp])
titleAlignments.addAlignment(titleAlignment)
coverage = titleAlignments.coverageInfo()
self.assertEqual({
3: [(15, 'C')],
4: [(15, 'G')],
5: [(15, 'T')],
}, coverage)
def testCoverageInfoOneReadWithOneHSP(self):
"""
When a title has one read with one HSP aligned to it, the coverageInfo
method must return just the indices and bases from that read.
"""
titleAlignments = TitleAlignments('subject title', 55)
hsp = HSP(15, subjectStart=3, subjectEnd=6, readMatchedSequence='CGT')
read = Read('id1', 'AAACGT')
titleAlignment = TitleAlignment(read, [hsp])
titleAlignments.addAlignment(titleAlignment)
coverage = titleAlignments.coverageInfo()
self.assertEqual(
{
3: [(15, 'C')],
4: [(15, 'G')],
5: [(15, 'T')],
},
coverage)
def testCoverageInfoOneReadWithTwoHSPs(self):
"""
When a title has one read with two HSPs aligned to it, the coverageInfo
method must return the correct indices and bases from that read.
"""
titleAlignments = TitleAlignments('subject title', 55)
hsp1 = HSP(15, subjectStart=1, subjectEnd=4, readMatchedSequence='A-A')
hsp2 = HSP(10, subjectStart=3, subjectEnd=6, readMatchedSequence='CGT')
read = Read('id1', 'AAACGT')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
coverage = titleAlignments.coverageInfo()
self.assertEqual(
{
1: [(15, 'A')],
2: [(15, '-')],
3: [(15, 'A'), (10, 'C')],
4: [(10, 'G')],
5: [(10, 'T')],
}, coverage)
def testCoverageInfoOneReadWithTwoHSPs(self):
"""
When a title has one read with two HSPs aligned to it, the coverageInfo
method must return the correct indices and bases from that read.
"""
titleAlignments = TitleAlignments('subject title', 55)
hsp1 = HSP(15, subjectStart=1, subjectEnd=4, readMatchedSequence='A-A')
hsp2 = HSP(10, subjectStart=3, subjectEnd=6, readMatchedSequence='CGT')
read = Read('id1', 'AAACGT')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
coverage = titleAlignments.coverageInfo()
self.assertEqual(
{
1: [(15, 'A')],
2: [(15, '-')],
3: [(15, 'A'), (10, 'C')],
4: [(10, 'G')],
5: [(10, 'T')],
},
coverage)
def testCoverageInfoTwoReadsWithThreeHSPs(self):
"""
When a title has two reads (one with two HSPs, one with one) aligned
to it, the coverageInfo method must return the correct indices and
bases from the read.
"""
titleAlignments = TitleAlignments('subject title', 55)
# First read.
hsp1 = HSP(15, subjectStart=1, subjectEnd=4, readMatchedSequence='A-A')
hsp2 = HSP(10, subjectStart=3, subjectEnd=6, readMatchedSequence='CGT')
read = Read('id1', 'AAACGT')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
# Second read.
hsp1 = HSP(20,
subjectStart=5,
subjectEnd=10,
readMatchedSequence='CGGTA')
read = Read('id2', 'AAACGTCGGTAAAA')
titleAlignment = TitleAlignment(read, [hsp1])
titleAlignments.addAlignment(titleAlignment)
coverage = titleAlignments.coverageInfo()
self.assertEqual(
{
1: [(15, 'A')],
2: [(15, '-')],
3: [(15, 'A'), (10, 'C')],
4: [(10, 'G')],
5: [(10, 'T'), (20, 'C')],
6: [(20, 'G')],
7: [(20, 'G')],
8: [(20, 'T')],
9: [(20, 'A')],
}, coverage)
def testCoverageInfoTwoReadsWithThreeHSPs(self):
"""
When a title has two reads (one with two HSPs, one with one) aligned
to it, the coverageInfo method must return the correct indices and
bases from the read.
"""
titleAlignments = TitleAlignments('subject title', 55)
# First read.
hsp1 = HSP(15, subjectStart=1, subjectEnd=4, readMatchedSequence='A-A')
hsp2 = HSP(10, subjectStart=3, subjectEnd=6, readMatchedSequence='CGT')
read = Read('id1', 'AAACGT')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
# Second read.
hsp1 = HSP(20, subjectStart=5, subjectEnd=10,
readMatchedSequence='CGGTA')
read = Read('id2', 'AAACGTCGGTAAAA')
titleAlignment = TitleAlignment(read, [hsp1])
titleAlignments.addAlignment(titleAlignment)
coverage = titleAlignments.coverageInfo()
self.assertEqual(
{
1: [(15, 'A')],
2: [(15, '-')],
3: [(15, 'A'), (10, 'C')],
4: [(10, 'G')],
5: [(10, 'T'), (20, 'C')],
6: [(20, 'G')],
7: [(20, 'G')],
8: [(20, 'T')],
9: [(20, 'A')],
},
coverage)
