def testTwoValuesString(self):
"""
If two values have been added to a Stats instance, its __str__
method must return the expected result.
"""
s = Stats()
s.append(3)
s.append(4)
self.assertEqual(('Summary:\n'
' Count: 2\n'
' Max: 4\n'
' Mean: 3.5000\n'
' Median: 3.5000\n'
' Min: 3\n'
' SD: 0.5000\n'
' Variance: 0.2500'), str(s))
def testNoValuesString(self):
"""
If no values have been added to a Stats instance, its __str__
method must raise ValueError.
"""
s = Stats()
error = '^No values have been added to Stats instance\.$'
six.assertRaisesRegex(self, ValueError, error, str, s)
def testNoValuesSummary(self):
"""
If no values have been added to a Stats instance, its summary
method must raise ValueError.
"""
s = Stats()
error = '^No values have been added to Stats instance\.$'
six.assertRaisesRegex(self, ValueError, error, s.summary)
def testUnequal(self):
"""
Stats instances that have had the same values added to them, but in
a different order must be considered unequal.
"""
s1 = Stats()
s1.extend([3, 4, 8])
s2 = Stats()
s2.extend([3, 8, 4])
self.assertNotEqual(s1, s2)
def testEqual(self):
"""
Stats instances that have had the same values added to them in
the same order must be considered equal.
"""
s1 = Stats()
s1.extend([3, 4, 8])
s2 = Stats()
s2.extend([3, 4, 8])
self.assertEqual(s1, s2)
def testThreeValues(self):
"""
If three values have been added to a Stats instance, its summary
method must return the expected result.
"""
s = Stats()
s.append(3)
s.append(4)
s.append(8)
result = s.summary()
self.assertAlmostEqual(2.16024689, result['sd'])
self.assertAlmostEqual(4.66666666, result['variance'])
del result['sd']
del result['variance']
self.assertEqual(
{
'count': 3,
'max': 8,
'mean': 5.0,
'median': 4.0,
'min': 3,
'sum': 15,
}, result)
def testOneValue(self):
"""
If one value has been added to a Stats instance, its summary
method must return the expected result.
"""
s = Stats()
s.append(3)
self.assertEqual(
{
'count': 1,
'max': 3,
'mean': 3.0,
'median': 3.0,
'min': 3,
'sd': 0.0,
'sum': 3,
'variance': 0.0,
}, s.summary())
def testTwoValues(self):
"""
If two values have been added to a Stats instance, its summary
method must return the expected result.
"""
s = Stats()
s.append(3)
s.append(4)
self.assertEqual(
{
'count': 2,
'max': 4,
'mean': 3.5,
'median': 3.5,
'min': 3,
'sd': 0.5,
'sum': 7,
'variance': 0.25,
}, s.summary())
def testDescription(self):
"""
If a description string is given to Stats.__init__, it must appear
in the __str__ result.
"""
s = Stats('Arm length')
s.append(3)
s.append(4)
s.append(8)
self.assertEqual(('Arm length:\n'
' Count: 3\n'
' Max: 8\n'
' Mean: 5.0000\n'
' Median: 4.0000\n'
' Min: 3\n'
' SD: 2.1602\n'
' Variance: 4.6667'), str(s))
def testThreeValuesString(self):
"""
If three values have been added to a Stats instance, its __str__
method must return the expected result.
"""
s = Stats()
s.append(3)
s.append(4)
s.append(8)
self.assertEqual(('Summary:\n'
' Count: 3\n'
' Max: 8\n'
' Mean: 5.0000\n'
' Median: 4.0000\n'
' Min: 3\n'
' SD: 2.1602\n'
' Variance: 4.6667'), str(s))
def analyzeAlphaHelices(reads):
"""
Analyze a set of reads that contain alpha helices using
C{analyzeAlphaHelix} and return their overall statistics.
@return: A C{dict} with the following keys, each of which has a C{Stats}
instance as its value:
'length': The alpha helix lengths.
'initial': The C{int} number of amino acids at the start of
alpha helices that occurred before the first-found extremum.
'final': The C{int} number of amino acids at the end of
alpha helices that occurred after the last-found extremum.
'extremaCount': The number of extrema found in each alpha helix.
'consecutivePeaks': A C{list} of C{int} counts of the number of
consecutive peak AAs found for each time the hydropathy graph
of an alpha helix goes through an overall peak. See the
docstring for C{analyzeAlphaHelix} above.
'consecutiveTroughs': A C{list} of C{int} counts of the number of
consecutive trough AAs found for each time the hydropathy graph
of an alpha helix goes through an overall trough. See the
docstring for C{analyzeAlphaHelix} above.
'noExtremaLength': The lengths of the alpha helies that do not
contain any extrema.
"""
length = Stats('Alpha helix length')
initial = Stats('Initial non-peak non-trough AAs')
final = Stats('Final non-peak non-trough AAs')
extremaCount = Stats('Number of extrema')
consecutivePeaks = Stats('Consecutive peaks')
consecutiveTroughs = Stats('Consecutive troughs')
noExtremaLength = Stats('Length of helices with no extrema')
for read in reads:
readLen = len(read)
length.append(readLen)
analysis = analyzeAlphaHelix(read)
if analysis['initial'] is None:
# No extrema were found in the read.
noExtremaLength.append(readLen)
extremaCount.append(0)
else:
initial.append(analysis['initial'])
final.append(analysis['final'])
extremaCount.append(analysis['extremaCount'])
consecutivePeaks.extend(analysis['consecutivePeaks'])
consecutiveTroughs.extend(analysis['consecutiveTroughs'])
return {
'length': length,
'initial': initial,
'final': final,
'extremaCount': extremaCount,
'consecutivePeaks': consecutivePeaks,
'consecutiveTroughs': consecutiveTroughs,
'noExtremaLength': noExtremaLength,
}