def test_utilities_massSpectrumBuilder_rtwindow(self):
"""
Test the RT window filter
"""
with self.subTest(msg='All-inclusive window'):
filteredData = massSpectrumBuilder(self.msData,
correlationThreshold=0.95,
rtWindow=1000,
simulatedSpecra=False)
expectedFeatureMetadata = pandas.DataFrame(
[[
3.13, 5, '100 - 10 - 1', '3.13_220.1419n',
'M+H, M+Na, M+K, 2M+Na', 219.1419,
'3.12_127.1212m/z; 5.32_89.9812m/z'
],
[
3.12, 5, '100 - 20', '3.12_170.2233m/z', numpy.nan,
170.2233, ''
],
[
0.56, 5, '90 - 100 - 50', '0.56_214.1245n',
'M+H, M+Na, M+K, 2M+Na', 213.1245, ''
]],
columns=[
'Retention Time', 'Peak Width', 'Isotope Distribution',
'Feature Name', 'Adducts', 'm/z', 'Correlated Features'
])
expectedFeatureMetadata['Exclusion Details'] = None
expectedFeatureMetadata['User Excluded'] = False
expectedFeatureMetadata[[
'rsdFilter', 'varianceRatioFilter',
'correlationToDilutionFilter', 'blankFilter',
'artifactualFilter'
]] = pandas.DataFrame([[True, True, True, True, True]],
index=expectedFeatureMetadata.index)
expectedFeatureMetadata[['rsdSP', 'rsdSS/rsdSP', 'correlationToDilution', 'blankValue']] \
= pandas.DataFrame([[numpy.nan, numpy.nan, numpy.nan, numpy.nan]],
index=expectedFeatureMetadata.index)
pandas.util.testing.assert_frame_equal(
filteredData.featureMetadata.sort_index(axis=1),
expectedFeatureMetadata.sort_index(axis=1))
with self.subTest(msg='Restrictive window'):
filteredData = massSpectrumBuilder(self.msData,
correlationThreshold=0.95,
rtWindow=0.1,
simulatedSpecra=False)
expectedFeatureMetadata = copy.copy(self.msData.featureMetadata)
expectedFeatureMetadata['Correlated Features'] = ''
pandas.util.testing.assert_frame_equal(
filteredData.featureMetadata.sort_index(axis=1),
expectedFeatureMetadata.sort_index(axis=1))
def test_utilities_massSpectrumBuilder_correlationThreshold(self):
"""
Test corr cutoff
"""
filteredData = massSpectrumBuilder(self.msData,
correlationThreshold=0.5,
rtWindow=20,
simulatedSpecra=False)
expectedFeatureMetadata = pandas.DataFrame(
[[
3.13, 5, '100 - 10 - 1', '3.13_220.1419n',
'M+H, M+Na, M+K, 2M+Na', 219.1419,
'3.12_127.1212m/z; 3.12_170.2233m/z'
], [5.32, 5, '100', '5.32_89.9812m/z', numpy.nan, 89.9812, ''],
[
0.56, 5, '90 - 100 - 50', '0.56_214.1245n',
'M+H, M+Na, M+K, 2M+Na', 213.1245, ''
]],
columns=[
'Retention Time', 'Peak Width', 'Isotope Distribution',
'Feature Name', 'Adducts', 'm/z', 'Correlated Features'
])
pandas.util.testing.assert_frame_equal(filteredData.featureMetadata,
expectedFeatureMetadata)
def test_utilities_massSpectrumBuilder(self):
"""
Test defaults
"""
filteredData = massSpectrumBuilder(self.msData,
correlationThreshold=0.95,
rtWindow=20,
simulatedSpecra=True)
expectedFeatureMetadata = pandas.DataFrame(
[[
3.13, 5, '100 - 10 - 1', '3.13_220.1419n',
'M+H, M+Na, M+K, 2M+Na', 219.1419, '3.12_127.1212m/z',
[(127.1212, 100.0), (128.124555, 10.0), (129.12791, 1.0),
(221.14917599999998, 100.0), (222.15253099999998, 10.0),
(223.15588599999998, 1.0), (243.131118, 100.0),
(244.13447299999999, 10.0), (245.13782799999998, 1.0),
(259.105058, 100.0), (260.108413, 10.0), (261.111768, 1.0),
(463.273018, 100.0), (464.276373, 10.0), (465.279728, 1.0)]
],
[
3.12, 5, '100 - 20', '3.12_170.2233m/z', numpy.nan, 170.2233,
'', [(170.2233, 100.0), (171.226655, 20.0)]
],
[
5.32, 5, '100', '5.32_89.9812m/z', numpy.nan, 89.9812, '',
[(89.9812, 100)]
],
[
0.56, 5, '90 - 100 - 50', '0.56_214.1245n',
'M+H, M+Na, M+K, 2M+Na', 213.1245, '',
[(215.131776, 90.0), (216.135131, 100.0), (217.138486, 50.0),
(237.113718, 90.0), (238.117073, 100.0), (239.120428, 50.0),
(253.087658, 90.0), (254.091013, 100.0), (255.094368, 50.0),
(451.238218, 90.0), (452.241573, 100.0), (453.244928, 50.0)]
]],
columns=[
'Retention Time', 'Peak Width', 'Isotope Distribution',
'Feature Name', 'Adducts', 'm/z', 'Correlated Features',
'Mass Spectrum'
])
expectedFeatureMetadata['Exclusion Details'] = None
expectedFeatureMetadata['User Excluded'] = False
expectedFeatureMetadata[[
'rsdFilter', 'varianceRatioFilter', 'correlationToDilutionFilter',
'blankFilter', 'artifactualFilter'
]] = pandas.DataFrame([[True, True, True, True, True]],
index=expectedFeatureMetadata.index)
expectedFeatureMetadata[['rsdSP', 'rsdSS/rsdSP', 'correlationToDilution', 'blankValue']] \
= pandas.DataFrame([[numpy.nan, numpy.nan, numpy.nan, numpy.nan]], index=expectedFeatureMetadata.index)
pandas.util.testing.assert_frame_equal(
filteredData.featureMetadata.sort_index(axis=1),
expectedFeatureMetadata.sort_index(axis=1))
def test_utilities_massSpectrumBuilder_rtwindow(self):
"""
Test the RT window filter
"""
with self.subTest(msg='All-inclusive window'):
filteredData = massSpectrumBuilder(self.msData,
correlationThreshold=0.95,
rtWindow=1000,
simulatedSpecra=False)
expectedFeatureMetadata = pandas.DataFrame(
[[
3.13, 5, '100 - 10 - 1', '3.13_220.1419n',
'M+H, M+Na, M+K, 2M+Na', 219.1419,
'3.12_127.1212m/z; 5.32_89.9812m/z'
],
[
3.12, 5, '100 - 20', '3.12_170.2233m/z', numpy.nan,
170.2233, ''
],
[
0.56, 5, '90 - 100 - 50', '0.56_214.1245n',
'M+H, M+Na, M+K, 2M+Na', 213.1245, ''
]],
columns=[
'Retention Time', 'Peak Width', 'Isotope Distribution',
'Feature Name', 'Adducts', 'm/z', 'Correlated Features'
])
pandas.util.testing.assert_frame_equal(
filteredData.featureMetadata, expectedFeatureMetadata)
with self.subTest(msg='Restrictive window'):
filteredData = massSpectrumBuilder(self.msData,
correlationThreshold=0.95,
rtWindow=0.1,
simulatedSpecra=False)
expectedFeatureMetadata = copy.copy(self.msData.featureMetadata)
expectedFeatureMetadata['Correlated Features'] = ''
pandas.util.testing.assert_frame_equal(
filteredData.featureMetadata, expectedFeatureMetadata)
def test_utilities_massSpectrumBuilder_log(self):
"""
Test log attribute
"""
filteredData = massSpectrumBuilder(self.msData,
correlationThreshold=0.8,
rtWindow=50,
simulatedSpecra=False)
self.assertEqual(
filteredData.Attributes['Log'][-1][1],
"Redundant features removed with rtWindow of: %f seconds and correlationThreshold of: %f."
% (50, 0.8))