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 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 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 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 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 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 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 testSummary(self):
"""
The summary method must return the correct result.
"""
titleAlignments = TitleAlignments('subject title', 10)
titleAlignments.addAlignment(
TitleAlignment(Read('id1', 'ACGT'), [
HSP(30, subjectStart=0, subjectEnd=2),
]))
titleAlignments.addAlignment(
TitleAlignment(Read('id2', 'ACGT'), [
HSP(55, subjectStart=2, subjectEnd=4),
HSP(40, subjectStart=8, subjectEnd=9),
]))
self.assertEqual(
{
'bestScore': 55,
'coverage': 0.5,
'hspCount': 3,
'medianScore': 40,
'readCount': 2,
'subjectLength': 10,
'subjectTitle': 'subject title',
},
titleAlignments.summary())
def testSummary(self):
"""
The summary method must return the correct result.
"""
titleAlignments = TitleAlignments('subject title', 10)
titleAlignments.addAlignment(
TitleAlignment(Read('id1', 'ACGT'), [
HSP(30, subjectStart=0, subjectEnd=2),
]))
titleAlignments.addAlignment(
TitleAlignment(Read('id2', 'ACGT'), [
HSP(55, subjectStart=2, subjectEnd=4),
HSP(40, subjectStart=8, subjectEnd=9),
]))
self.assertEqual(
{
'bestScore': 55,
'coverage': 0.5,
'hspCount': 3,
'medianScore': 40,
'readCount': 2,
'subjectLength': 10,
'subjectTitle': 'subject title',
},
titleAlignments.summary())
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 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 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 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 testAddAlignment(self):
"""
It must be possible to add an alignment to an instance of
TitleAlignments.
"""
titleAlignments = TitleAlignments('subject title', 55)
read = Read('id', 'AAA')
titleAlignment = TitleAlignment(read, [])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(read, titleAlignments[0].read)
self.assertEqual([], titleAlignments[0].hsps)
def testAddAlignment(self):
"""
It must be possible to add an alignment to an instance of
TitleAlignments.
"""
titleAlignments = TitleAlignments('subject title', 55)
read = Read('id', 'AAA')
titleAlignment = TitleAlignment(read, [])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(read, titleAlignments[0].read)
self.assertEqual([], titleAlignments[0].hsps)
def testMedianScoreWithNoHsps(self):
"""
The medianScore function must raise ValueError if there are no HSPs.
"""
titleAlignments = TitleAlignments('subject title', 55)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [])
titleAlignments.addAlignment(titleAlignment)
error = '^arg is an empty sequence$'
six.assertRaisesRegex(self, ValueError, error,
titleAlignments.medianScore)
def testMedianScoreWithNoHsps(self):
"""
The medianScore function must raise ValueError if there are no HSPs.
"""
titleAlignments = TitleAlignments('subject title', 55)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [])
titleAlignments.addAlignment(titleAlignment)
error = '^arg is an empty sequence$'
six.assertRaisesRegex(self, ValueError, error,
titleAlignments.medianScore)
def testMedianScoreOfTwo(self):
"""
The medianScore function must return the median score for the HSPs in
all the alignments matching a title when given 2 scores.
"""
hsp1 = HSP(7)
hsp2 = HSP(15)
titleAlignments = TitleAlignments('subject title', 55)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(11, titleAlignments.medianScore())
def testMedianScoreOfTwo(self):
"""
The medianScore function must return the median score for the HSPs in
all the alignments matching a title when given 2 scores.
"""
hsp1 = HSP(7)
hsp2 = HSP(15)
titleAlignments = TitleAlignments('subject title', 55)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(11, titleAlignments.medianScore())
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 makeTitleAlignments(self, *readIds):
"""
Create a TitleAlignments instance containing reads with the
ids given by C{ids}.
param readIds: A C{list} of integer ids for reads.
@return: A C{TitleAlignments} instance with reads with the given ids.
"""
titleAlignments = TitleAlignments("subject title", 55)
for readId in readIds:
titleAlignment = TitleAlignment(Read("id" + str(readId), "A"), [])
titleAlignments.addAlignment(titleAlignment)
return titleAlignments
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 makeTitleAlignments(self, *readIds):
"""
Create a TitleAlignments instance containing reads with the
ids given by C{ids}.
param readIds: A C{list} of integer ids for reads.
@return: A C{TitleAlignments} instance with reads with the given ids.
"""
titleAlignments = TitleAlignments('subject title', 55)
for readId in readIds:
titleAlignment = TitleAlignment(Read('id' + str(readId), 'A'), [])
titleAlignments.addAlignment(titleAlignment)
return titleAlignments
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 testReadCount(self):
"""
The readCount function must indicate how many reads matched a title.
"""
hsp1 = HSP(7)
hsp2 = HSP(14)
hsp3 = HSP(21)
titleAlignments = TitleAlignments('subject title', 55)
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(2, titleAlignments.readCount())
def testReadCount(self):
"""
The readCount function must indicate how many reads matched a title.
"""
hsp1 = HSP(7)
hsp2 = HSP(14)
hsp3 = HSP(21)
titleAlignments = TitleAlignments('subject title', 55)
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(2, titleAlignments.readCount())
def testHSPs(self):
"""
The hsps function must produce a list of all HSPs.
"""
hsp1 = HSP(7)
hsp2 = HSP(14)
hsp3 = HSP(21)
titleAlignments = TitleAlignments("subject title", 55)
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([7, 14, 21], [hsp.score.score for hsp in titleAlignments.hsps()])
def testBestHsp(self):
"""
The bestHsp function must return the HSP with the best score for the
HSPs all the alignments matching a title.
"""
hsp1 = LSP(7)
hsp2 = LSP(15)
hsp3 = LSP(21)
titleAlignments = TitleAlignments("subject title", 55)
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(hsp1, titleAlignments.bestHsp())
def testHSPs(self):
"""
The hsps function must produce a list of all HSPs.
"""
hsp1 = HSP(7)
hsp2 = HSP(14)
hsp3 = HSP(21)
titleAlignments = TitleAlignments('subject title', 55)
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([7, 14, 21],
[hsp.score.score for hsp in titleAlignments.hsps()])
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 testBetterThanFalse(self):
"""
The hasScoreBetterThan function must return False if there is no HSP
with a score better than the passed value.
"""
hsp1 = LSP(7)
hsp2 = LSP(15)
hsp3 = LSP(21)
titleAlignments = TitleAlignments("subject title", 55)
read = Read("id1", "AAA")
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
read = Read("id2", "AAA")
titleAlignment = TitleAlignment(read, [hsp3])
titleAlignments.addAlignment(titleAlignment)
self.assertFalse(titleAlignments.hasScoreBetterThan(7))
def testReads(self):
"""
The reads function must return a Reads instance with the reads for
the title.
"""
hsp1 = HSP(7)
hsp2 = HSP(14)
hsp3 = HSP(21)
titleAlignments = TitleAlignments('subject title', 55)
read1 = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read1, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
read2 = Read('id2', 'AAA')
titleAlignment = TitleAlignment(read2, [hsp3])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual([read1, read2], list(titleAlignments.reads()))
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 testHspCount(self):
"""
The hspCount function must indicate how many HSPs were found in
total for all the alignments to a title.
"""
hsp1 = HSP(7)
hsp2 = HSP(14)
hsp3 = HSP(21)
titleAlignments = TitleAlignments('subject title', 55)
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(3, titleAlignments.hspCount())
def testBetterThanTrue(self):
"""
The hasScoreBetterThan function must return True if there is an HSP
with a score better than the passed value.
"""
hsp1 = HSP(7)
hsp2 = HSP(15)
hsp3 = HSP(21)
titleAlignments = TitleAlignments('subject title', 55)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
read = Read('id2', 'AAA')
titleAlignment = TitleAlignment(read, [hsp3])
titleAlignments.addAlignment(titleAlignment)
self.assertTrue(titleAlignments.hasScoreBetterThan(20))
def testBestHspWithNoHsps(self):
"""
The bestHsp function must raise ValueError if there are no HSPs.
"""
titleAlignments = TitleAlignments('subject title', 55)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [])
titleAlignments.addAlignment(titleAlignment)
read = Read('id2', 'AAA')
titleAlignment = TitleAlignment(read, [])
titleAlignments.addAlignment(titleAlignment)
if _pypy:
error = '^arg is an empty sequence$'
else:
error = '^max\\(\\) arg is an empty sequence$'
six.assertRaisesRegex(self, ValueError, error, titleAlignments.bestHsp)
def testReads(self):
"""
The reads function must return a Reads instance with the reads for
the title.
"""
hsp1 = HSP(7)
hsp2 = HSP(14)
hsp3 = HSP(21)
titleAlignments = TitleAlignments('subject title', 55)
read1 = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read1, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
read2 = Read('id2', 'AAA')
titleAlignment = TitleAlignment(read2, [hsp3])
titleAlignments.addAlignment(titleAlignment)
self.assertEqual([read1, read2], list(titleAlignments.reads()))
def testReadIds(self):
"""
The readIds function must return the set of read ids for the alignments
matching a title.
"""
hsp1 = LSP(7)
hsp2 = LSP(15)
hsp3 = LSP(21)
titleAlignments = TitleAlignments('subject title', 55)
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(set(['id1', 'id2']), titleAlignments.readIds())
def testHspCount(self):
"""
The hspCount function must indicate how many HSPs were found in
total for all the alignments to a title.
"""
hsp1 = HSP(7)
hsp2 = HSP(14)
hsp3 = HSP(21)
titleAlignments = TitleAlignments('subject title', 55)
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(3, titleAlignments.hspCount())
def testWorstHsp(self):
"""
The worstHsp function must return the HSP with the worst score for all
the HSPs for all the alignments matching a title.
"""
hsp1 = HSP(7)
hsp2 = HSP(15)
hsp3 = HSP(21)
titleAlignments = TitleAlignments('subject title', 55)
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(hsp1, titleAlignments.worstHsp())
def testReadIds(self):
"""
The readIds function must return the set of read ids for the alignments
matching a title.
"""
hsp1 = LSP(7)
hsp2 = LSP(15)
hsp3 = LSP(21)
titleAlignments = TitleAlignments('subject title', 55)
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(set(['id1', 'id2']), titleAlignments.readIds())
def testBetterThanTrue(self):
"""
The hasScoreBetterThan function must return True if there is an HSP
with a score better than the passed value.
"""
hsp1 = LSP(7)
hsp2 = LSP(15)
hsp3 = LSP(21)
titleAlignments = TitleAlignments('subject title', 55)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments.addAlignment(titleAlignment)
read = Read('id2', 'AAA')
titleAlignment = TitleAlignment(read, [hsp3])
titleAlignments.addAlignment(titleAlignment)
self.assertTrue(titleAlignments.hasScoreBetterThan(9))
def testMedianScoreOfThree(self):
"""
The medianScore function must return the median score for the HSPs in
all the alignments matching a title when given 3 scores.
"""
hsp1 = HSP(7)
hsp2 = HSP(15)
hsp3 = HSP(21)
titleAlignments = TitleAlignments("subject title", 55)
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(15, titleAlignments.medianScore())
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 testWorstHsp(self):
"""
The worstHsp function must return the HSP with the worst score for all
the HSPs for all the alignments matching a title.
"""
hsp1 = LSP(7)
hsp2 = LSP(15)
hsp3 = LSP(21)
titleAlignments = TitleAlignments('subject title', 55)
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(hsp3, titleAlignments.worstHsp())
def testBestHspWithNoHsps(self):
"""
The bestHsp function must raise ValueError if there are no HSPs.
"""
titleAlignments = TitleAlignments('subject title', 55)
read = Read('id1', 'AAA')
titleAlignment = TitleAlignment(read, [])
titleAlignments.addAlignment(titleAlignment)
read = Read('id2', 'AAA')
titleAlignment = TitleAlignment(read, [])
titleAlignments.addAlignment(titleAlignment)
if _pypy:
error = '^arg is an empty sequence$'
else:
error = '^max\(\) arg is an empty sequence$'
six.assertRaisesRegex(self, ValueError, error, titleAlignments.bestHsp)
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())
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 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())
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)
def testToDict(self):
"""
The toDict method must return the expected result.
"""
read = Read('the-id', 'AAA')
hsp1 = HSP(0, readStart=1, readEnd=2,
readStartInSubject=3, readEndInSubject=4,
subjectStart=5, subjectEnd=6,
readMatchedSequence='aaa', subjectMatchedSequence='ccc',
readFrame=7, subjectFrame=8, identicalCount=9,
positiveCount=10)
hsp2 = HSP(10, readStart=11, readEnd=12,
readStartInSubject=13, readEndInSubject=14,
subjectStart=15, subjectEnd=16,
readMatchedSequence='ggg', subjectMatchedSequence='ttt',
readFrame=17, subjectFrame=18, identicalCount=19,
positiveCount=20)
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments = TitleAlignments('subject title', 10)
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
'subjectTitle': 'subject title',
'subjectLength': 10,
'titleAlignments': [
{
'hsps': [
{
'score': 0,
'readStart': 1,
'readEnd': 2,
'readStartInSubject': 3,
'readEndInSubject': 4,
'subjectStart': 5,
'subjectEnd': 6,
'readFrame': 7,
'subjectFrame': 8,
'identicalCount': 9,
'positiveCount': 10,
'readMatchedSequence': 'aaa',
'subjectMatchedSequence': 'ccc',
},
{
'score': 10,
'readStart': 11,
'readEnd': 12,
'readStartInSubject': 13,
'readEndInSubject': 14,
'subjectStart': 15,
'subjectEnd': 16,
'readFrame': 17,
'subjectFrame': 18,
'identicalCount': 19,
'positiveCount': 20,
'readMatchedSequence': 'ggg',
'subjectMatchedSequence': 'ttt',
},
],
'read': {
'id': 'the-id',
'quality': None,
'sequence': 'AAA',
},
},
],
},
titleAlignments.toDict())
def testToDict(self):
"""
The toDict method must return the expected result.
"""
read = Read('the-id', 'AAA')
hsp1 = HSP(0,
readStart=1,
readEnd=2,
readStartInSubject=3,
readEndInSubject=4,
subjectStart=5,
subjectEnd=6,
readMatchedSequence='aaa',
subjectMatchedSequence='ccc',
readFrame=7,
subjectFrame=8,
identicalCount=9,
positiveCount=10)
hsp2 = HSP(10,
readStart=11,
readEnd=12,
readStartInSubject=13,
readEndInSubject=14,
subjectStart=15,
subjectEnd=16,
readMatchedSequence='ggg',
subjectMatchedSequence='ttt',
readFrame=17,
subjectFrame=18,
identicalCount=19,
positiveCount=20)
titleAlignment = TitleAlignment(read, [hsp1, hsp2])
titleAlignments = TitleAlignments('subject title', 10)
titleAlignments.addAlignment(titleAlignment)
self.assertEqual(
{
'subjectTitle':
'subject title',
'subjectLength':
10,
'titleAlignments': [
{
'hsps': [
{
'score': 0,
'readStart': 1,
'readEnd': 2,
'readStartInSubject': 3,
'readEndInSubject': 4,
'subjectStart': 5,
'subjectEnd': 6,
'readFrame': 7,
'subjectFrame': 8,
'identicalCount': 9,
'positiveCount': 10,
'readMatchedSequence': 'aaa',
'subjectMatchedSequence': 'ccc',
},
{
'score': 10,
'readStart': 11,
'readEnd': 12,
'readStartInSubject': 13,
'readEndInSubject': 14,
'subjectStart': 15,
'subjectEnd': 16,
'readFrame': 17,
'subjectFrame': 18,
'identicalCount': 19,
'positiveCount': 20,
'readMatchedSequence': 'ggg',
'subjectMatchedSequence': 'ttt',
},
],
'read': {
'id': 'the-id',
'quality': None,
'sequence': 'AAA',
},
},
],
}, titleAlignments.toDict())
