def testHighestFrequencyUnambiguous(self):
"""
If one unambiguous code passed to FloatBaseCounts is most frequent, the
highestFrequency method must give the expected result.
"""
counts = FloatBaseCounts('AAACCTGG')
self.assertEqual(0.375, counts.highestFrequency())
def testOneUnambiguousOneAmbiguousVariable(self):
"""
If one unambiguous code and one incompatible ambiguous code are passed
to FloatBaseCounts, they must be considered confirm variable.
"""
counts = FloatBaseCounts('AS')
self.assertTrue(counts.variable(confirm=True))
def testMostFrequentWithTwoAmbiguousStr(self):
"""
If two overlapping ambiguous codes are passed to FloatBaseCounts, the
mostFrequent method must give the expected result.
"""
counts = FloatBaseCounts('MR')
self.assertEqual({'A'}, counts.mostFrequent())
def testMostFrequentUnambiguous(self):
"""
If one unambiguous code passed to FloatBaseCounts is most frequent, the
mostFrequent method must give the expected result.
"""
counts = FloatBaseCounts('AAACCTGG')
self.assertEqual({'A'}, counts.mostFrequent())
def testEquallyFrequent(self):
"""
If two codes are passed to FloatBaseCounts in equal numbers, the
mostFrequent method must give the expected result.
"""
counts = FloatBaseCounts('AAACCCTGG')
self.assertEqual(set('AC'), counts.mostFrequent())
def testHighestFrequencyWithTwoAmbiguousStr(self):
"""
If two overlapping ambiguous codes are passed to FloatBaseCounts, the
highestFrequency method must give the expected result.
"""
counts = FloatBaseCounts('MR')
self.assertEqual(0.5, counts.highestFrequency())
def testTwoIdenticalUnambiguoussVariable(self):
"""
If an unambiguous code is passed to FloatBaseCounts twice, they must be
considered non-variable.
"""
counts = FloatBaseCounts('AA')
self.assertFalse(counts.variable())
def testTwoDifferentUnambiguoussVariable(self):
"""
If two different unambiguous codes are passed to FloatBaseCounts,
they must be considered variable.
"""
counts = FloatBaseCounts('AT')
self.assertTrue(counts.variable())
def testOneGapVariableConfirm(self):
"""
If one gap and one unambiguous code are passed to FloatBaseCounts,
they must be considered variable if confirm is True.
"""
counts = FloatBaseCounts('A-')
self.assertTrue(counts.variable(confirm=True))
def testEqualFrequency(self):
"""
If two codes are passed to FloatBaseCounts in equal numbers, the
highestFrequency method must give the expected result.
"""
counts = FloatBaseCounts('AAAACCCTGG')
self.assertEqual(0.4, counts.highestFrequency())
def testOneUnambiguousOneAmbiguousVariableUnconfirm(self):
"""
If one unambiguous code and one compatible ambiguous code are passed
to FloatBaseCounts, they must be considered variable if confirm
is False.
"""
counts = FloatBaseCounts('AM')
self.assertTrue(counts.variable(confirm=False))
def testOneUnambiguousOneAmbiguousNonVariable(self):
"""
If one unambiguous code and one compatible ambiguous code are passed
to FloatBaseCounts, they must not be considered confirm variable
if confirm is True.
"""
counts = FloatBaseCounts('AM')
self.assertFalse(counts.variable(confirm=True))
def testTwoAmbiguousVariableConfirmTrue(self):
"""
If two compatible but different ambiguous codes are passed to
FloatBaseCounts, they must not be considered variable if
confirm is True.
"""
counts = FloatBaseCounts('MR')
self.assertFalse(counts.variable(confirm=True))
def testOneAmbiguousHomogeneousM(self):
"""
If one ambiguous code (M = A, C) is passed to FloatBaseCounts, it must
be considered homogeneous correctly, depending on the passed level.
"""
counts = FloatBaseCounts('M')
self.assertFalse(counts.homogeneous(1.0))
self.assertFalse(counts.homogeneous(0.75))
self.assertTrue(counts.homogeneous(0.0))
def testTwoIdenticalUnambiguoussHomogeneous(self):
"""
If an unambiguous code is passed to FloatBaseCounts twice, they must be
considered homogeneous correctly, depending on the passed level.
"""
counts = FloatBaseCounts('AA')
self.assertTrue(counts.homogeneous(1.0))
self.assertTrue(counts.homogeneous(0.75))
self.assertTrue(counts.homogeneous(0.0))
def testTwoDifferentUnambiguoussHomogeneous(self):
"""
If two different unambiguous codes are passed to FloatBaseCounts,
they must be considered homogeneous correctly, depending on the passed
level.
"""
counts = FloatBaseCounts('AG')
self.assertFalse(counts.homogeneous(1.0))
self.assertTrue(counts.homogeneous(0.5))
self.assertTrue(counts.homogeneous(0.2))
def testTwoAmbiguousStr(self):
"""
If two compatible but different ambiguous codes are passed to
FloatBaseCounts, they must be converted into a string correctly.
"""
counts = FloatBaseCounts('MR')
self.assertEqual('A:1.00 C:0.50 G:0.50 (0.500)', str(counts))
def testLength3Ambiguous(self):
"""
If overlapping ambiguous codes are passed to FloatBaseCounts, the
length must give the expected result.
"""
counts = FloatBaseCounts('MRC')
self.assertEqual(3, len(counts))
def testLength4Unambiguous(self):
"""
If all unambiguous bases are given to FloatBaseCounts, its length
must be 4.
"""
counts = FloatBaseCounts('AAAACCCTGG')
self.assertEqual(4, len(counts))
def testMixedCase(self):
"""
If two 2-way ambiguous codes are passed to FloatBaseCounts in mixed
case, they must be converted into a string correctly.
"""
counts = FloatBaseCounts('mM')
self.assertEqual('A:1 C:1 (0.500)', str(counts))
def testTwoAmbiguousStrWithIntegerTotals(self):
"""
If two 2-way ambiguous codes are passed to
FloatBaseCounts, they must be converted into a string correctly
(i.e., with integer counts).
"""
counts = FloatBaseCounts('MMA')
self.assertEqual('A:2 C:1 (0.667)', str(counts))