def add_test(self):
'''
Test the add funtion on a temporary result class
Args:
key (tuple):
| file_name
| formula
| charge
| label_percentiles
value (tuple):
| spec_id
| rt
| score
| scaling_factor
| peaks
'''
tmp_results = pyqms.Results()
keys = [
('BSA1.mzML', 'C(37)H(59)N(9)O(16)', 2, (('N', '0.000'), )),
]
values = [
(1337, 13.37, 1, 100, [(443.7112649, 100, 1, 443.7112649, 100)]),
]
for key, value in zip(keys, values):
tmp_results.add(key, value)
assert len(tmp_results.index['files']) == 1
assert len(tmp_results.keys()) == 1
return
def setUp(self):
self.results = pyqms.Results(
lookup={
'formula to molecule': {
'C(37)H(59)N(9)O(16)': ['DDSPDLPK'],
'C(43)H(75)N(15)O(17)S(2)':
['CCTESLVNR#Carbamidomethyl:1;Carbamidomethyl:2']
},
'molecule to formula': {
'DDSPDLPK':
'C(37)H(59)N(9)O(16)',
'CCTESLVNR#Carbamidomethyl:1;Carbamidomethyl:2':
'C(43)H(75)N(15)O(17)S(2)'
},
})
keys = [
('BSA1.mzML', 'C(37)H(59)N(9)O(16)', 2, (('N', '0.000'), )),
('BSA1.mzML', 'C(37)H(59)N(9)O(16)', 2, (('N', '0.000'), )),
('BSA2.mzML', 'C(43)H(75)N(15)O(17)S(2)', 3, (('N', '0.010'), )),
]
values = [
# mmz, mi, rel_icmz, ci
(1337, 13.37, 1, 100, [(443.7112649, 100, 1, 443.7112649, 1)]),
(1338, 13.38, 0.9, 100, [(443.7112649, 100, 1, 443.7112649, 1)]),
(1337, 13.37, 1, 10, [(569.7526156, 10, 1, 569.7526156, 1)])
]
for key, value in zip(keys, values):
self.results.add(key, value)
def add_test(self):
"""
Test the add funtion on a temporary result class
Args:
key (tuple):
| file_name
| formula
| charge
| label_percentiles
value (tuple):
| spec_id
| rt
| score
| scaling_factor
| peaks
"""
tmp_results = pyqms.Results()
keys = [("BSA1.mzML", "C(37)H(59)N(9)O(16)", 2, (("N", "0.000"), ))]
values = [(1337, 13.37, 1, 100, [(443.7112649, 100, 1, 443.7112649,
100)])]
for key, value in zip(keys, values):
tmp_results.add(key, value)
assert len(tmp_results.index["files"]) == 1
assert len(tmp_results.keys()) == 1
return
def setUp(self):
self.results = pyqms.Results(
lookup={
"formula to molecule": {
"C(37)H(59)N(9)O(16)": ["DDSPDLPK"],
"C(43)H(75)N(15)O(17)S(2)":
["CCTESLVNR#Carbamidomethyl:1;Carbamidomethyl:2"],
},
"molecule to formula": {
"DDSPDLPK":
"C(37)H(59)N(9)O(16)",
"CCTESLVNR#Carbamidomethyl:1;Carbamidomethyl:2":
"C(43)H(75)N(15)O(17)S(2)",
},
})
keys = [
("BSA1.mzML", "C(37)H(59)N(9)O(16)", 2, (("N", "0.000"), )),
("BSA1.mzML", "C(37)H(59)N(9)O(16)", 2, (("N", "0.000"), )),
("BSA2.mzML", "C(43)H(75)N(15)O(17)S(2)", 3, (("N", "0.010"), )),
]
values = [
# mmz, mi, rel_icmz, ci
(1337, 13.37, 1, 100, [(443.7112649, 100, 1, 443.7112649, 1)]),
(1338, 13.38, 0.9, 100, [(443.7112649, 100, 1, 443.7112649, 1)]),
(1337, 13.37, 1, 10, [(569.7526156, 10, 1, 569.7526156, 1)]),
]
for key, value in zip(keys, values):
self.results.add(key, value)
def group_14N_15N_pairs_test(self):
tmp_metabolic_labeling_class = pyqms.Results(
params={
'PERCENTILE_FORMAT_STRING': '{0:.3f}',
'BUILD_RESULT_INDEX': True
})
keys = [
('run1', 'C(37)H(59)N(9)O(16)', 2, (('N', '0.000'), )),
('run1', 'C(37)H(59)N(9)O(16)', 2, (('N', '0.990'), )),
]
values = [
(1337, 13.37, 1, 100, [(443.7112649, 100, 1, 443.7112649, 1)]),
(1337, 13.37, 0.9, 200, [(452.7112649, 100, 1, 443.7112649, 1)]),
]
for key, value in zip(keys, values):
tmp_metabolic_labeling_class.add(key, value)
all_key_pairs = []
for light_key, heavy_key in tmp_metabolic_labeling_class._group_14N_15N_pairs(
):
all_key_pairs.append((light_key, heavy_key))
print(all_key_pairs)
assert len(all_key_pairs) == 1
# assert sorted(keys) == sorted(all_key_pairs)
return
#!/usr/bin/env python3.4
# encoding: utf-8
import pyqms
import sys
R = pyqms.Results()
R.lookup = {}
R.lookup['molecule fixed label variations'] = {
'ORGINAL_MOLECULE': [
'R0_C1_R0', # you flip !
'R0_C0_R0',
'K0_C1_K0', # you flip !
'K1_C0_K1', # you flip !
'R0_C1_R1', # decoys since mixed states
'R1_C1_R1'
]
}
VARIANTS = {
(('R0', 'R1'), ): [
['R0_C0_R0', 'R1_C0_R1'],
['R0_C1_R0', 'R1_C1_R1'],
],
(('K0', 'K1'), ): [
['K0_C1_K0', 'K1_C1_K1'],
],
(('k0', 'K1'), ): [
['K0_C1_K0', 'K1_C1_K1'],
],
(('R0', 'R1'), ('K0', 'K1')): [