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 getAlignmentRatios(scanInfoFName, dtaDir, delta, epsilon=0.02):
scanInfo = DataFile.getScanInfo(scanInfoFName)
dtaNames = DataFile.getDTAFNamesInDir(dtaDir)
scansToUse = scanInfo
"""
for i in range(len(scanInfo) - 1):
if (int(scanInfo[i][0]) + 1 == int(scanInfo[i+1][0])):
if (scanInfo[i][1] == scanInfo[i+1][1]):
scansToUse += [scanInfo[i]]
else:
scansToUse += [scanInfo[i]]
"""
ratios = []
goodRatios = []
for i in range(len(scansToUse)):
for j in range(i + 1, len(scansToUse)):
if j == i + 1:
print '%s percent done' % str(float(i) / len(scansToUse))
if np.abs(np.abs(float(scansToUse[i][1]) - float(scansToUse[j][1])) - delta) < epsilon:
dta1 = '244.%(scanF)04i.%(scanF)04i.1.dta' % {'scanF': int(scansToUse[i][0])}
dta2 = '244.%(scanF)04i.%(scanF)04i.1.dta' % {'scanF': int(scansToUse[j][0])}
spec1 = DataFile.getMassIntPairs(dtaDir + dta1)
spec2 = DataFile.getMassIntPairs(dtaDir + dta2)
ratio = SA.getSharedPeaksRatio(float(scansToUse[i][1]), spec1, float(scansToUse[j][1]), spec2, epsilon)
print ratio, scansToUse[i], scansToUse[j]
ratios.extend([(ratio, scansToUse[i], scansToUse[j])])
with open('heavylightpairs.txt', 'w') as fout:
pickle.dump(ratios, fout)
return ratios
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)
