def getPairedAndUnpairedSpectra(dtaDir, dtaList, Nmod, Cmod, ppm=5, cutOff=0.1, verbose=False):
specPairs = []
unpairedSpecs = []
delta = Nmod + Cmod
for i in range(len(dtaList)):
paired = False
precMass1 = DataFile.getPrecMassAndCharge(dtaList[i])[0]
spec1 = DataFile.getMassIntPairs(dtaList[i])
for j in range(i + 1, len(dtaList)):
precMass2 = DataFile.getPrecMassAndCharge(dtaList[j])[0]
epsilon = ppm * 10 ** -6 * max(precMass1, precMass2)
if np.abs(np.abs(precMass1 - precMass2) - delta) < epsilon:
spec2 = DataFile.getMassIntPairs(dtaList[j])
if precMass1 < precMass2:
N, C = SA.getNandCIons(spec1, spec2, Nmod, Cmod, epsilon=epsilon)
ratio = SA.getSharedPeaksRatio(spec1, spec2, N, C)
else:
N, C = SA.getNandCIons(spec2, spec1, Nmod, Cmod, epsilon=epsilon)
ratio = SA.getSharedPeaksRatio(spec2, spec1, N, C)
if ratio > cutOff:
if verbose:
print 'Pair found', dtaList[i], dtaList[j]
paired = True
specs = (dtaList[i], dtaList[j])
lightInd = int(precMass2 < precMass1)
specPairs.extend([(ratio, specs[lightInd], specs[1 - lightInd])])
if not paired:
unpairedSpecs.extend([dtaList[i]])
if verbose:
print 'No pairs for', dtaList[i]
return specPairs, unpairedSpecs
def getAllPairedIonsDict(lightMergedSpec, heavyMergedSpec, lightPrecMass, pairConfig, epSTD=0.01):
NTermTable, CTermTable = SA.getNandCIons(lightMergedSpec, heavyMergedSpec, Nmod=pairConfig['NMod'], Cmod=pairConfig['CMod'], epsilon=2*epSTD)
NCrossTable, CCrossTable = SA.getCrossPairedIons(lightMergedSpec, heavyMergedSpec, lightPrecMass, Nmod=pairConfig['NMod'], Cmod=pairConfig['CMod'], epsilon=2*epSTD)
NTermIonDict = SA.prepIonTableForAddition(NTermTable, ['b', 'b'])
CTermIonDict = SA.prepIonTableForAddition(CTermTable, ['y', 'y'])
NCrossIonDict = SA.prepIonTableForAddition(NCrossTable, ['y', 'b'])
CCrossIonDict = SA.prepIonTableForAddition(CCrossTable, ['b', 'y'])
return SA.addDicts(SA.reverseDict(SA.addDicts(NTermIonDict, CCrossIonDict)), SA.reverseDict(SA.addDicts(NCrossIonDict, CTermIonDict)))
def getSharedPeaksRatio(lightPath, heavyPath, epsilon):
lightPairs = DataFile.getMassIntPairs(lightPath)
heavyPairs = DataFile.getMassIntPairs(heavyPath)
N, C = SA.getNandCIons(lightPairs, heavyPairs, pairConfig['NMod'], pairConfig['CMod'], epsilon=epsilon)
return SA.getSharedPeaksRatio(lightPairs, heavyPairs, N, C)
def getSharedPeaksRatio(lightPath, heavyPath, epsilon):
lightPairs = DataFile.getMassIntPairs(lightPath)
heavyPairs = DataFile.getMassIntPairs(heavyPath)
N, C = SA.getNandCIons(lightPairs, heavyPairs, 17.0265, -16.0187, epsilon=epsilon)
return SA.getSharedPeaksRatio(lightPairs, heavyPairs, N, C)
def getSharedPeaksRatio(lightPairs, heavyPairs, pairConfig, epsilon):
N, C = SA.getNandCIons(lightPairs, heavyPairs, pairConfig['NMod'], pairConfig['CMod'], epsilon=epsilon)
return SA.getSharedPeaksRatio(lightPairs, heavyPairs, N, C)
