def test__getBeadsVolume_1stage(self, mock_loadIndividualSettings):
self.prep_createBeadsVolSettings(1)
param = 'Initial sample volume'
self.prep_settingsFile(param, [100, 29, 50, 0, 0, -1, -1, -1, -1, -1, -1, -1])
s = ponec.settings(self.mock_csv_path)
s.cutoffs = s.returnProtocolParameter('Number of cutoffs')
s.initial_sample_vol_list = s._returnSampleParameterList('Initial sample volume')
v = s._getBeadsVolume(0, 1)
self.assertEqual(v, 15)
v = s._getBeadsVolume(1, 1)
self.assertEqual(v, 31)
v = s._getBeadsVolume(2, 1)
self.assertEqual(v, 22)
# Rewriting the settings file.
# Now the function should calculate volume from the initial volume and fraction
param = 'Beads volume'
self.prep_settingsFile(param, [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1])
s = ponec.settings(self.mock_csv_path)
s.cutoffs = s.returnProtocolParameter('Number of cutoffs')
s.initial_sample_vol_list = s._returnSampleParameterList('Initial sample volume')
v = s._getBeadsVolume(0, 1)
self.assertEqual(v, 100)
v = s._getBeadsVolume(1, 1)
self.assertEqual(v, 29*0.9)
v = s._getBeadsVolume(2, 1)
self.assertEqual(v, 50*1.5)
# Rewriting the settings file.
# Now the function should calculate volume from the DNA cutoff value
param = 'Fraction'
self.prep_settingsFile(param, [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1])
s = ponec.settings(self.mock_csv_path)
s.cutoffs = s.returnProtocolParameter('Number of cutoffs')
s.initial_sample_vol_list = s._returnSampleParameterList('Initial sample volume')
a,b,c = bl.getBeadsVolumeCoef()
expected_dna_cutoff = 150
f_expected = a + b / expected_dna_cutoff + c / expected_dna_cutoff ** 2
v_expected = 100 * f_expected
v = s._getBeadsVolume(0, 1)
self.assertEqual(v, v_expected)
expected_dna_cutoff = 300
f_expected = a + b / expected_dna_cutoff + c / expected_dna_cutoff ** 2
v_expected = 29 * f_expected
v = s._getBeadsVolume(1, 1)
self.assertEqual(v, v_expected)
expected_dna_cutoff = 100
f_expected = a + b / expected_dna_cutoff + c / expected_dna_cutoff ** 2
v_expected = 50 * f_expected
v = s._getBeadsVolume(2, 1)
self.assertEqual(v, v_expected)
def test__getBeadsVolumeCoef(self):
a, b, c = bl.getBeadsVolumeCoef()
# Coefficients are not None
self.assertIsNotNone(a)
self.assertIsNotNone(b)
self.assertIsNotNone(c)
# Coefficients are of the right type
self.assertIsInstance(a, float)
self.assertIsInstance(b, float)
self.assertIsInstance(c, float)
def test_calcBeadVolFractionFromDNACutoff(self, mock_loadIndividualSettings):
param = 'Initial sample volume'
self.prep_settingsFile(param, [100, 29, 50, 0, 0, -1, -1, -1, -1, -1, -1, -1])
s = ponec.settings(self.mock_csv_path)
s.cutoffs = s.returnProtocolParameter('Number of cutoffs')
s.initial_sample_vol_list = s._returnSampleParameterList('Initial sample volume')
f = s._calcBeadVolFractionFromDNACutoff(1000)
a,b,c = bl.getBeadsVolumeCoef()
f_expected = a + b / 1000 + c / 1000 ** 2
self.assertEqual(f, f_expected)
f = s._calcBeadVolFractionFromDNACutoff(160)
a,b,c = bl.getBeadsVolumeCoef()
f_expected = a + b / 160 + c / 160 ** 2
self.assertEqual(f, f_expected)
def test_getBeadsVolUsingDNACutoff(self, mock_loadIndividualSettings):
self.prep_createBeadsVolSettings(1)
param = 'Initial sample volume'
self.prep_settingsFile(param, [100, 29, 50, 0, 0, -1, -1, -1, -1, -1, -1, -1])
s = ponec.settings(self.mock_csv_path)
s.cutoffs = s.returnProtocolParameter('Number of cutoffs')
s.initial_sample_vol_list = s._returnSampleParameterList('Initial sample volume')
a,b,c = bl.getBeadsVolumeCoef()
f_expected = a + b / 150 + c / 150 ** 2
v = s._getBeadsVolUsingDNACutoff(0, 1)
self.assertEqual(v, f_expected*100)
self.assertFalse(v == 0)
f_expected = a + b / 300 + c / 300 ** 2
v = s._getBeadsVolUsingDNACutoff(1, 1)
self.assertEqual(v, f_expected*29)
f_expected = a + b / 100 + c / 100 ** 2
v = s._getBeadsVolUsingDNACutoff(2, 1)
self.assertEqual(v, f_expected*50)
self.delTempSettingsFile()
del s
self.prep_createBeadsVolSettings(2)
param = 'Initial sample volume'
self.prep_settingsFile(param, [100, 29, 50, 0, 0, -1, -1, -1, -1, -1, -1, -1])
s = ponec.settings(self.mock_csv_path)
s.cutoffs = s.returnProtocolParameter('Number of cutoffs')
s.initial_sample_vol_list = s._returnSampleParameterList('Initial sample volume')
f_expected = a + b / 900 + c / 900 ** 2
v = s._getBeadsVolUsingDNACutoff(0, 1)
self.assertEqual(v, f_expected*100)
f_expected = a + b / 800 + c / 800 ** 2
v = s._getBeadsVolUsingDNACutoff(1, 1)
self.assertEqual(v, f_expected*29)
f_expected = a + b / 700 + c / 700 ** 2
v = s._getBeadsVolUsingDNACutoff(2, 1)
self.assertEqual(v, f_expected*50)
def test__getBeadsVolume_2stage(self, mock_loadIndividualSettings):
self.prep_createBeadsVolSettings(2)
param = 'Initial sample volume'
self.prep_settingsFile(param, [100, 29, 50, 0, 0, -1, -1, -1, -1, -1, -1, -1])
s = ponec.settings(self.mock_csv_path)
s.cutoffs = s.returnProtocolParameter('Number of cutoffs')
s.initial_sample_vol_list = s._returnSampleParameterList('Initial sample volume')
v = s._getBeadsVolume(0, 1)
self.assertEqual(v, 30)
v = s._getBeadsVolume(1, 1)
self.assertEqual(v, 20)
v = s._getBeadsVolume(2, 1)
self.assertEqual(v, 25)
v = s._getBeadsVolume(0, 2)
self.assertEqual(v, 15)
v = s._getBeadsVolume(1, 2)
self.assertEqual(v, 31)
v = s._getBeadsVolume(2, 2)
self.assertEqual(v, 22)
# Rewriting the settings file.
# Now the function should calculate volume from the initial volume and fraction
param = 'Beads volume'
self.prep_settingsFile(param, [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1])
param = 'Beads volume upper cutoff'
self.prep_settingsFile(param, [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1])
s = ponec.settings(self.mock_csv_path)
s.cutoffs = s.returnProtocolParameter('Number of cutoffs')
s.initial_sample_vol_list = s._returnSampleParameterList('Initial sample volume')
v = s._getBeadsVolume(0, 1)
self.assertEqual(v, 100*0.5)
v = s._getBeadsVolume(1, 1)
self.assertEqual(v, 29*0.6)
v = s._getBeadsVolume(2, 1)
self.assertEqual(v, 50*0.55)
v = s._getBeadsVolume(0, 2)
self.assertEqual(v, 100*(1.0-0.5))
v = s._getBeadsVolume(1, 2)
self.assertEqual(v, 29*(0.9-0.6))
v = s._getBeadsVolume(2, 2)
self.assertEqual(v, 50*(1.5-0.55))
# Rewriting the settings file.
# Now the function should calculate volume from the initial volume and DNA cutoff
param = 'Fraction'
self.prep_settingsFile(param, [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1])
param = 'Fraction upper cutoff'
self.prep_settingsFile(param, [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1])
s = ponec.settings(self.mock_csv_path)
s.cutoffs = s.returnProtocolParameter('Number of cutoffs')
s.initial_sample_vol_list = s._returnSampleParameterList('Initial sample volume')
a,b,c = bl.getBeadsVolumeCoef()
expected_dna_cutoff = 900
f_expected = a + b / expected_dna_cutoff + c / expected_dna_cutoff ** 2
v_expected = 100 * f_expected
v = s._getBeadsVolume(0, 1)
self.assertEqual(v, v_expected)
exp_dna_cutoff_2 = 150
f_expected_2 = a + b / exp_dna_cutoff_2 + c / exp_dna_cutoff_2 ** 2
v_expected_2 = 100 * (f_expected_2 - f_expected)
v = s._getBeadsVolume(0, 2)
self.assertEqual(v, v_expected_2)
expected_dna_cutoff = 800
f_expected = a + b / expected_dna_cutoff + c / expected_dna_cutoff ** 2
v_expected = 29 * f_expected
v = s._getBeadsVolume(1, 1)
self.assertEqual(v, v_expected)
exp_dna_cutoff_2 = 300
f_expected_2 = a + b / exp_dna_cutoff_2 + c / exp_dna_cutoff_2 ** 2
v_expected_2 = 29 * (f_expected_2 - f_expected)
v = s._getBeadsVolume(1, 2)
self.assertEqual(v, v_expected_2)
expected_dna_cutoff = 700
f_expected = a + b / expected_dna_cutoff + c / expected_dna_cutoff ** 2
v_expected = 50 * f_expected
v = s._getBeadsVolume(2, 1)
self.assertEqual(v, v_expected)
exp_dna_cutoff_2 = 100
f_expected_2 = a + b / exp_dna_cutoff_2 + c / exp_dna_cutoff_2 ** 2
v_expected_2 = 50 * (f_expected_2 - f_expected)
v = s._getBeadsVolume(2, 2)
self.assertEqual(v, v_expected_2)
def _calcBeadVolFractionFromDNACutoff(self, dna_size_cutoff):
# Getting polynome coefficients
a, b, c = bl.getBeadsVolumeCoef()
# Calculating volume multiplier (fraction)
frac = a + b / dna_size_cutoff + c / dna_size_cutoff**2
return frac