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)