'Intensity': {0: 0.3624, 1: 0.040349999999999997, 2: 0.59724999999999995}, \
'Formula': {0: 'H4C2O2', 1: 'H4C2O2', 2: 'H4C2O2'}, \
'info2': {0: 'culture_1', 1: 'culture_1', 2: 'culture_1'}, \
'Sample Name': {0: 'sample_1', 1: 'sample_1', 2: 'sample_1'}})
correc_inten_dict = {'sample_1': {(0, 1): np.array([ 0.0619]), (0, 0): np.array([ 0.2456]), \
(3, 0): np.array([ 0.0003]), (3, 1): np.array([ 0.0001]), (2, 1): np.array([ 0.0015]), \
(2, 0): np.array([ 0.0071]), (5, 0): np.array([ 0.]), (5, 1): np.array([ 0.60045]), \
(1, 0): np.array([ 0.06665]), (4, 1): np.array([ 0.]), (1, 1): np.array([ 0.0164]), \
(4, 0): np.array([ 0.])}}
acetic_frag = Fragment('Acetic', 'H4C2O2', label_dict={'C13': 0})
fragments_dict = {
'Acetic_C13_0':
iso.Infopacket(frag=acetic_frag,
data={'sample_1': np.array([0.3624])},
unlabeled=True,
name='Acetic')
}
label_list = [(0, 1), (0, 0), (3, 0), (3, 1), (2, 1), (2, 0), (5, 0), \
(5, 1), (1, 0), (4, 1), (1, 1), (4, 0)]
def test_corr_matrix():
iso_tracer = 'C'
with pytest.raises(KeyError):
c_matrix = algo.corr_matrix(iso_tracer, no_atom_tracer, na_dict)
def test_matrix_multiplication():
correction_matrix = [[0, 1], [2, 3]]
def test_arrange_fragments_by_mass():
assert algo.change_fragment_keys_to_mass(fragment_dict) == {(186.0, 79.0): iso.Infopacket(frag=[parent_frag_input, daughter_frag_input],
data = data_input, unlabeled=False, name='2PG 185/79'),
(185.0, 79.0): iso.Infopacket(frag=[parent_frag_unlabeled, daughter_frag_unlabeled],
data = data_unlabel, unlabeled=True, name='2PG 185/79')}
def algorithms_yale_constants():
data_input = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 1967.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 1446.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 747.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 1926.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 1969.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 661.77
}
data_unlabel = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 62610,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 58640,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 59950,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 62520,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 59690,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 57200
}
corrected_data_input = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': -55.07,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': -456.52,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': -1214.13,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': -94.,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 43.33,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': -1211.27
}
corrected_data_unlabel = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 64676.13,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 60575.12,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 61928.35,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 64583.16,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 61659.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 59087.6
}
unlabeled_fragment = iso.insert_data_to_fragment_mass(
Multiquantkey('2PG 185/79', 'O3P', '2PG 185/79', 'C3H6O7P'),
'C13_185.0_79.0', data_unlabel)
input_fragment = iso.insert_data_to_fragment_mass(
Multiquantkey('2PG 186/79', 'O3P', '2PG 185/79', 'C3H6O7P'),
'C13_186.0_79.0', data_input)
parent_frag_input = input_fragment[('2PG 186/79_186.0',
'2PG 186/79_79.0')][0][0]
daughter_frag_input = input_fragment[('2PG 186/79_186.0',
'2PG 186/79_79.0')][0][1]
parent_frag_unlabeled = unlabeled_fragment[('2PG 185/79_185.0',
'2PG 185/79_79.0')][0][0]
daughter_frag_unlabeled = unlabeled_fragment[('2PG 185/79_185.0',
'2PG 185/79_79.0')][0][1]
fragment_dict = dict(unlabeled_fragment, **input_fragment)
corrected_fragment_dict = {
(186.0, 79.0):
Infopacket(
frag=['C3H6O7P', 'O3P'],
data={
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)':
-73.459999999999994,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)':
-473.81999999999999,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': -1231.96,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': -112.37,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 25.82,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': -1228.3
},
unlabeled=False,
name='2PG 185/79'),
(185.0, 79.0):
Infopacket(frag=['C3H6O7P', 'O3P'],
data={
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)':
64694.910000000003,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)':
60592.709999999999,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)':
61946.339999999997,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)':
64601.919999999998,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)':
61677.68,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)':
59104.760000000002
},
unlabeled=True,
name='2PG 185/79')
}
unlabeled_fragment_dhap = iso.insert_data_to_fragment_mass(
Multiquantkey('DHAP 169/97', 'H2O4P', 'DHAP 169/97', 'C3H6O6P'),
'C13_169.0_97.0', {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 51670,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 52360,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 52540,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 56580,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 52580,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 58990
})
input_fragment_dhap = iso.insert_data_to_fragment_mass(
Multiquantkey('DHAP 170/97', 'H2O4P', 'DHAP 169/97', 'C3H6O6P'),
'C13_170.0_97.0', {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 1292.67,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 901.67,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 1292.67,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 1468.67,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 1511.67,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 1946.67
})
corrected_data_unlabel_dhap = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 53390.610000000001,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 54103.589999999997,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 54289.580000000002,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 58464.110000000001,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 54330.910000000003,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 60954.370000000003
}
corrected_data_input_dhap = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': -399.24000000000001,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': -821.89999999999998,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': -428.20999999999998,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': -382.83999999999997,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': -205.68000000000001,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 25.52
}
parent_frag_input_dhap = input_fragment_dhap[('DHAP 170/97_170.0',
'DHAP 170/97_97.0')][0][0]
daughter_frag_input_dhap = input_fragment_dhap[('DHAP 170/97_170.0',
'DHAP 170/97_97.0')][0][1]
parent_frag_unlabeled_dhap = unlabeled_fragment_dhap[(
'DHAP 169/97_169.0', 'DHAP 169/97_97.0')][0][0]
daughter_frag_unlabeled_dhap = unlabeled_fragment_dhap[(
'DHAP 169/97_169.0', 'DHAP 169/97_97.0')][0][1]
corrected_fragment_dict_dhap = {
(169.0, 97.0):
iso.Infopacket(
frag=[parent_frag_unlabeled_dhap, daughter_frag_unlabeled_dhap],
data=corrected_data_unlabel_dhap,
unlabeled=True,
name='DHAP 169/97'),
(170.0, 97.0):
iso.Infopacket(frag=[parent_frag_input_dhap, daughter_frag_input_dhap],
data=corrected_data_input_dhap,
unlabeled=False,
name='DHAP 169/97')
}
fragment_dict_dhap = dict(unlabeled_fragment_dhap, **input_fragment_dhap)
metabolite_frag_dict = {'dhap': fragment_dict_dhap, '2pg': fragment_dict}
corrected_metabolite_dict = {
'dhap': corrected_fragment_dict_dhap,
'2pg': corrected_fragment_dict
}
return parent_frag_input, daughter_frag_input, \
fragment_dict, data_input, parent_frag_unlabeled, \
daughter_frag_unlabeled, data_unlabel, corrected_fragment_dict, metabolite_frag_dict, corrected_fragment_dict_dhap, corrected_fragment_dict
def algorithms_yale_constants():
data_input = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 1967.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 1446.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 747.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 1926.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 1969.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 661.77
}
data_unlabel = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 62610,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 58640,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 59950,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 62520,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 59690,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 57200
}
corrected_data_input = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': -55.07,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': -456.52,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': -1214.13,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': -94.,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 43.33,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': -1211.27
}
corrected_data_unlabel = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 64676.13,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 60575.12,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 61928.35,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 64583.16,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 61659.77,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 59087.6
}
unlabeled_fragment = iso.insert_data_to_fragment_mass(
Multiquantkey('2PG 185/79', 'O3P', '2PG 185/79', 'C3H6O7P'),
'C13_185.0_79.0', data_unlabel)
input_fragment = iso.insert_data_to_fragment_mass(
Multiquantkey('2PG 186/79', 'O3P', '2PG 185/79', 'C3H6O7P'),
'C13_186.0_79.0', data_input)
parent_frag_input = input_fragment[('2PG 186/79_186.0',
'2PG 186/79_79.0')][0][0]
daughter_frag_input = input_fragment[('2PG 186/79_186.0',
'2PG 186/79_79.0')][0][1]
parent_frag_unlabeled = unlabeled_fragment[('2PG 185/79_185.0',
'2PG 185/79_79.0')][0][0]
daughter_frag_unlabeled = unlabeled_fragment[('2PG 185/79_185.0',
'2PG 185/79_79.0')][0][1]
fragment_dict = dict(unlabeled_fragment, **input_fragment)
corrected_fragment_dict = {
(186.0, 79.0):
iso.Infopacket(frag=[parent_frag_input, daughter_frag_input],
data=corrected_data_input,
unlabeled=False,
name='2PG 185/79'),
(185.0, 79.0):
iso.Infopacket(frag=[parent_frag_unlabeled, daughter_frag_unlabeled],
data=corrected_data_unlabel,
unlabeled=True,
name='2PG 185/79')
}
unlabeled_fragment_dhap = iso.insert_data_to_fragment_mass(
Multiquantkey('DHAP 169/97', 'H2O4P', 'DHAP 169/97', 'C3H6O6P'),
'C13_169.0_97.0', {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 51670,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 52360,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 52540,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 56580,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 52580,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 58990
})
input_fragment_dhap = iso.insert_data_to_fragment_mass(
Multiquantkey('DHAP 170/97', 'H2O4P', 'DHAP 169/97', 'C3H6O6P'),
'C13_170.0_97.0', {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 1292.67,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 901.67,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 1292.67,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 1468.67,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 1511.67,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 1946.67
})
corrected_data_unlabel_dhap = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': 53375.11,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': 54087.88,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': 54273.82,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': 58447.14,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': 54315.14,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 60936.67
}
corrected_data_input_dhap = {
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 1)': -384.00,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 17)': -806.37,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 33)': -412.71,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 49)': -366.16,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 65)': -190.21,
'TA_SCS-ATP BCH_19May16_1June16.wiff (sample 81)': 42.83
}
parent_frag_input_dhap = input_fragment_dhap[('DHAP 170/97_170.0',
'DHAP 170/97_97.0')][0][0]
daughter_frag_input_dhap = input_fragment_dhap[('DHAP 170/97_170.0',
'DHAP 170/97_97.0')][0][1]
parent_frag_unlabeled_dhap = unlabeled_fragment_dhap[(
'DHAP 169/97_169.0', 'DHAP 169/97_97.0')][0][0]
daughter_frag_unlabeled_dhap = unlabeled_fragment_dhap[(
'DHAP 169/97_169.0', 'DHAP 169/97_97.0')][0][1]
corrected_fragment_dict_dhap = {
(169.0, 97.0):
iso.Infopacket(
frag=[parent_frag_unlabeled_dhap, daughter_frag_unlabeled_dhap],
data=corrected_data_unlabel_dhap,
unlabeled=True,
name='DHAP 169/97'),
(170.0, 97.0):
iso.Infopacket(frag=[parent_frag_input_dhap, daughter_frag_input_dhap],
data=corrected_data_input_dhap,
unlabeled=False,
name='DHAP 169/97')
}
fragment_dict_dhap = dict(unlabeled_fragment_dhap, **input_fragment_dhap)
metabolite_frag_dict = {'dhap': fragment_dict_dhap, '2pg': fragment_dict}
corrected_metabolite_dict = {
'dhap': corrected_fragment_dict_dhap,
'2pg': corrected_fragment_dict
}
return parent_frag_input, daughter_frag_input, \
fragment_dict, data_input, parent_frag_unlabeled, \
daughter_frag_unlabeled, data_unlabel, corrected_fragment_dict, metabolite_frag_dict, corrected_fragment_dict_dhap, corrected_fragment_dict