def testToDict(self):
"""
The toDict method must return the expected dictionary.
"""
lsp = LSP(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)
self.assertEqual(
{
'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',
}, lsp.toDict())
def testToDict(self):
"""
The toDict method must return the expected dictionary.
"""
lsp = LSP(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)
self.assertEqual(
{
'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',
},
lsp.toDict())
def testOneAlignment(self):
"""
When one alignment is present that alignment must be returned by
bestAlignment.
"""
alignment = Alignment(44, 'Seq 1')
alignment.addHsp(LSP(10))
alignment.addHsp(LSP(9))
alignments = [alignment]
readAlignments = ReadAlignments(Read('id0', 'aaa'), alignments)
best = bestAlignment(readAlignments)
self.assertEqual('Seq 1', best.subjectTitle)
self.assertEqual(44, best.subjectLength)
def testExpectedAttributes(self):
"""
An LSP must have the expected attributes.
"""
lsp = LSP(7,
readStart=1,
readEnd=2,
readStartInSubject=3,
readEndInSubject=4,
subjectStart=5,
subjectEnd=6,
readMatchedSequence='aaa',
subjectMatchedSequence='ccc',
readFrame=8,
subjectFrame=9)
self.assertEqual(1, lsp.readStart)
self.assertEqual(2, lsp.readEnd)
self.assertEqual(3, lsp.readStartInSubject)
self.assertEqual(4, lsp.readEndInSubject)
self.assertEqual(5, lsp.subjectStart)
self.assertEqual(6, lsp.subjectEnd)
self.assertEqual('aaa', lsp.readMatchedSequence)
self.assertEqual('ccc', lsp.subjectMatchedSequence)
self.assertEqual(7, lsp.score.score)
self.assertEqual(8, lsp.readFrame)
self.assertEqual(9, lsp.subjectFrame)
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 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 testThreeAlignments(self):
"""
When three alignments are present, the one with the lowest first HSP
must be returned by bestAlignment.
"""
alignment1 = Alignment(33, 'Seq 1')
alignment1.addHsp(LSP(10))
alignment1.addHsp(LSP(9))
alignment2 = Alignment(44, 'Seq 2')
alignment2.addHsp(LSP(3))
alignment2.addHsp(LSP(2))
alignment3 = Alignment(55, 'Seq 3')
alignment3.addHsp(LSP(20))
alignment3.addHsp(LSP(19))
alignments = [alignment1, alignment2, alignment3]
readAlignments = ReadAlignments(Read('id0', 'aaa'), alignments)
best = bestAlignment(readAlignments)
self.assertEqual('Seq 2', best.subjectTitle)
self.assertEqual(44, best.subjectLength)
def testBetterThanFalse(self):
"""
Two LSP scores must compare properly with betterThan if the passed
score is better than the score of the LSP.
"""
self.assertFalse(LSP(7).betterThan(5))
def testBetterThanTrue(self):
"""
Two LSP scores must compare properly with betterThan if the passed
score is worse than the score of the LSP.
"""
self.assertTrue(LSP(5).betterThan(7))
def testLt(self):
"""
Two LSPs must compare properly with <
"""
self.assertTrue(LSP(8) < LSP(7))
def testEqual(self):
"""
Two LSPs must compare properly with ==
"""
self.assertEqual(LSP(7), LSP(7))
