def testResidueCountsOneReadTwoHSPsNotOverlapping(self):
"""
The residueCounts method must return the correct result when just one
read with two HSPs is aligned to a title and the HSPs do not overlap
one another.
HSP1: ACGT
HSP2: CGTT
"""
read = Read('id', 'ACGT')
hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=0,
readEndInSubject=4, subjectStart=0, subjectEnd=4,
readMatchedSequence='ACGT', subjectMatchedSequence='ACGT')
hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
readEndInSubject=14, subjectStart=10, subjectEnd=14,
readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
0: {'A': 1},
1: {'C': 1},
2: {'G': 1},
3: {'T': 1},
10: {'C': 1},
11: {'G': 1},
12: {'T': 1},
13: {'T': 1},
},
titleAlignments.residueCounts())
def testResidueCountsCaseConvertUpperIsDefault(self):
"""
The residueCounts method must convert to uppercase by default.
HSP1: AcgT
HSP2: CGTT
"""
read = Read('id', 'ACGT')
hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
readEndInSubject=14, subjectStart=10, subjectEnd=14,
readMatchedSequence='AcgT', subjectMatchedSequence='ACGT')
hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=11,
readEndInSubject=15, subjectStart=11, subjectEnd=15,
readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
10: {'A': 1},
11: {'C': 2},
12: {'G': 2},
13: {'T': 2},
14: {'T': 1},
},
titleAlignments.residueCounts())
def testResidueCountsTwoReadsTwoHSPsLeftOverhang(self):
"""
The residueCounts method must return the correct result when two
reads, each with one HSP are aligned to a title and the leftmost HSP
is aligned before the left edge of the subject (i.e, will include
negative subject offsets).
Subject: GTT
HSP1: ACGT
HSP2: CGTT
"""
read1 = Read('id', 'ACGT')
hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=-2,
readEndInSubject=2, subjectStart=0, subjectEnd=2,
readMatchedSequence='GT', subjectMatchedSequence='GT')
read2 = Read('id', 'CGTT')
hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=-1,
readEndInSubject=3, subjectStart=0, subjectEnd=3,
readMatchedSequence='GTT', subjectMatchedSequence='GTT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read1, [hsp1])
titleAlignments.addAlignment(titleAlignment)
titleAlignment = TitleAlignment(read2, [hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
-2: {'A': 1},
-1: {'C': 2},
0: {'G': 2},
1: {'T': 2},
2: {'T': 1},
},
titleAlignments.residueCounts())
def testResidueCountsOneReadTwoHSPsNotAtStartOfSubject(self):
"""
The residueCounts method must return the correct result when just one
read with two HSPs is aligned to a title and the leftmost HSP is not
aligned with the left edge of the subject.
HSP1: ACGT
HSP2: CGTT
"""
read = Read('id', 'ACGT')
hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
readEndInSubject=14, subjectStart=10, subjectEnd=14,
readMatchedSequence='ACGT', subjectMatchedSequence='ACGT')
hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=11,
readEndInSubject=15, subjectStart=11, subjectEnd=15,
readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
10: {'A': 1},
11: {'C': 2},
12: {'G': 2},
13: {'T': 2},
14: {'T': 1},
},
titleAlignments.residueCounts())
def testResidueCountsCaseConvertLower(self):
"""
The residueCounts method must return the correct result when asked to
convert residues to lower case.
HSP1: AcgT
HSP2: CGTT
"""
read = Read('id', 'ACGT')
hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
readEndInSubject=14, subjectStart=10, subjectEnd=14,
readMatchedSequence='AcgT', subjectMatchedSequence='ACGT')
hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=11,
readEndInSubject=15, subjectStart=11, subjectEnd=15,
readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
10: {'a': 1},
11: {'c': 2},
12: {'g': 2},
13: {'t': 2},
14: {'t': 1},
},
titleAlignments.residueCounts(convertCaseTo='lower'))
def testResidueCountsOneReadTwoHSPsNotOverlapping(self):
"""
The residueCounts method must return the correct result when just one
read with two HSPs is aligned to a title and the HSPs do not overlap
one another.
HSP1: ACGT
HSP2: CGTT
"""
read = Read('id', 'ACGT')
hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=0,
readEndInSubject=4, subjectStart=0, subjectEnd=4,
readMatchedSequence='ACGT', subjectMatchedSequence='ACGT')
hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
readEndInSubject=14, subjectStart=10, subjectEnd=14,
readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
0: {'A': 1},
1: {'C': 1},
2: {'G': 1},
3: {'T': 1},
10: {'C': 1},
11: {'G': 1},
12: {'T': 1},
13: {'T': 1},
},
titleAlignments.residueCounts())
def testResidueCountsOneReadOneHSPPartialMatch(self):
"""
The residueCounts method must return the correct result when just one
read with one HSP is aligned to a title and only part of the read
matched the subject (all the read bases are still counted and
returned).
"""
read = Read('id', 'ACGT')
hsp = HSP(33,
readStart=0,
readEnd=2,
readStartInSubject=0,
readEndInSubject=4,
subjectStart=0,
subjectEnd=4,
readMatchedSequence='ACGT',
subjectMatchedSequence='ACGT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read, [hsp])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual({
0: {
'A': 1
},
1: {
'C': 1
},
2: {
'G': 1
},
3: {
'T': 1
},
}, titleAlignments.residueCounts())
def testResidueCountsTwoReadsTwoHSPsLeftOverhang(self):
"""
The residueCounts method must return the correct result when two
reads, each with one HSP are aligned to a title and the leftmost HSP
is aligned before the left edge of the subject (i.e, will include
negative subject offsets).
Subject: GTT
HSP1: ACGT
HSP2: CGTT
"""
read1 = Read('id', 'ACGT')
hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=-2,
readEndInSubject=2, subjectStart=0, subjectEnd=2,
readMatchedSequence='GT', subjectMatchedSequence='GT')
read2 = Read('id', 'CGTT')
hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=-1,
readEndInSubject=3, subjectStart=0, subjectEnd=3,
readMatchedSequence='GTT', subjectMatchedSequence='GTT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read1, [hsp1])
titleAlignments.addAlignment(titleAlignment)
titleAlignment = TitleAlignment(read2, [hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
-2: {'A': 1},
-1: {'C': 2},
0: {'G': 2},
1: {'T': 2},
2: {'T': 1},
},
titleAlignments.residueCounts())
def testResidueCountsCaseConvertUpperIsDefault(self):
"""
The residueCounts method must convert to uppercase by default.
HSP1: AcgT
HSP2: CGTT
"""
read = Read('id', 'ACGT')
hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
readEndInSubject=14, subjectStart=10, subjectEnd=14,
readMatchedSequence='AcgT', subjectMatchedSequence='ACGT')
hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=11,
readEndInSubject=15, subjectStart=11, subjectEnd=15,
readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
10: {'A': 1},
11: {'C': 2},
12: {'G': 2},
13: {'T': 2},
14: {'T': 1},
},
titleAlignments.residueCounts())
def testResidueCountsCaseConvertLower(self):
"""
The residueCounts method must return the correct result when asked to
convert residues to lower case.
HSP1: AcgT
HSP2: CGTT
"""
read = Read('id', 'ACGT')
hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
readEndInSubject=14, subjectStart=10, subjectEnd=14,
readMatchedSequence='AcgT', subjectMatchedSequence='ACGT')
hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=11,
readEndInSubject=15, subjectStart=11, subjectEnd=15,
readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
10: {'a': 1},
11: {'c': 2},
12: {'g': 2},
13: {'t': 2},
14: {'t': 1},
},
titleAlignments.residueCounts(convertCaseTo='lower'))
def testResidueCountsOneReadTwoHSPsNotAtStartOfSubject(self):
"""
The residueCounts method must return the correct result when just one
read with two HSPs is aligned to a title and the leftmost HSP is not
aligned with the left edge of the subject.
HSP1: ACGT
HSP2: CGTT
"""
read = Read('id', 'ACGT')
hsp1 = HSP(33, readStart=0, readEnd=4, readStartInSubject=10,
readEndInSubject=14, subjectStart=10, subjectEnd=14,
readMatchedSequence='ACGT', subjectMatchedSequence='ACGT')
hsp2 = HSP(33, readStart=0, readEnd=4, readStartInSubject=11,
readEndInSubject=15, subjectStart=11, subjectEnd=15,
readMatchedSequence='CGTT', subjectMatchedSequence='CGTT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
10: {'A': 1},
11: {'C': 2},
12: {'G': 2},
13: {'T': 2},
14: {'T': 1},
},
titleAlignments.residueCounts())
def testResidueCountsNoReads(self):
"""
When a title has no reads aligned to it, the residueCounts method
must retrun an empty result.
"""
titleAlignments = TitleAlignments('subject title', 55)
counts = titleAlignments.residueCounts()
self.assertEqual(0, len(counts))
def testResidueCountsNoReads(self):
"""
When a title has no reads aligned to it, the residueCounts method
must return an empty result.
"""
titleAlignments = TitleAlignments('subject title', 55)
counts = titleAlignments.residueCounts()
self.assertEqual(0, len(counts))
def testResidueCountsOneReadOneHSP(self):
"""
The residueCounts method must return the correct result when just one
read with one HSP is aligned to a title.
"""
read = Read('id', 'ACGT')
hsp = HSP(33, readStart=0, readEnd=4, readStartInSubject=0,
readEndInSubject=4, subjectStart=0, subjectEnd=4,
readMatchedSequence='ACGT', subjectMatchedSequence='ACGT')
titleAlignments = TitleAlignments('subject title', 55)
titleAlignment = TitleAlignment(read, [hsp])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
0: {'A': 1},
1: {'C': 1},
2: {'G': 1},
3: {'T': 1},
},
titleAlignments.residueCounts())
