def writeSpecialSubSepc(self, File, binlen=0.1, arealen=50, flag = 'num', stype='dual'):
## write all subspectrum into file
file_name = "data/" + File
fname = File.split('.')[0]
parser = SpectrumParser()
specs = parser.readSpectrum(file_name)
subparser = SubSpectrumGenerator()
subspecs = subparser.generateSpecialSubSpectra(specs, binlen, arealen, flag, stype)
if flag == 'num':
filename = "SubSpectrumData/"+ fname +"_"+stype
elif flag == 'intensity':
filename = "SubSpectrumData/"+ fname +"_"+stype+"_intensity"
with open(filename,'w') as data:
for subspec in subspecs:
seq = ''
for acid in subspec.getAnnotation().getAcids():
seq = seq + acid.getResidue()
data.write('[Title='+ subspec.getTitle() + '###'\
+'SEQ=' +seq+ '###'\
+'POSITION='+ str(subspec.getPosition())+ '###'\
+'LENGTH='+str(len(subspec.getAnnotation().getAcids()))+'###'\
+'LeftAA='+subspec.getLA()+'###'\
+'RightAA='+subspec.getRA()+'###'\
+'BIN_LENGTH='+str(subspec.getBinLength())+'###'\
+'BIN_RANGE='+str(subspec.getBinArea())+'###'\
+'NTermBIN='+str(subspec.getNtermBins())+'###'\
+'CTermBIN='+str(subspec.getCtermBins())+']'+'\n')
data.close() # close file
def t6_action(self):
print "t6_action"
if (not hasattr(self, 't6_filename')):
print "please choose file"
return
peppro = PeptideProcessor()
if (not hasattr(self, 'orginalpois')):
filename = self.t6_filename + "_IonPostion"
if not os.path.exists(filename):
print "please operate Test3 Frist"
return
self.orginalpois = peppro.generateIonPoitionFile(filename)
print self.orginalpois
subprocessor = SubSpectrumProcessor()
subparser = SubSpectrumGenerator()
subspects = list(subparser.generateSubSpecfile(self.t6_filename))
ionpbptables = subprocessor.generateIonPepbondpoiTable(
subspects, self.orginalpois, self.splitflag.get())
# ionpbpchiValues = subprocessor.ChiSquared_TypeandPepbondPoi(subspects,self.orginalpois,self.splitflag.get())
subprocessor.paintionpbpTable(ionpbptables)
# subprocessor.paintChiValues(ionpbpchiValues)
# print pepLendf
print self.t6_filename
print self.splitflag.get()
def writeNoiseSubSepc(self,
File,
num=3,
binlen=0.1,
arealen=50,
flag='num'):
file_name = "data/" + File
fname = File.split('.')[0]
parser = SpectrumParser()
specs = parser.readSpectrum(file_name)
noisesubparser = SubSpectrumGenerator()
noisesubspecs = noisesubparser.generateNoiseSubSpectra(
specs, num, binlen, arealen, flag)
if flag == 'num':
filename = "SubSpectrumData/" + fname + "_Noise"
elif flag == 'intensity':
filename = "SubSpectrumData/" + fname + "_Noise_intensity"
# allbins = np.zeros(int(arealen*2/binlen))
with open(filename, 'w') as data:
# add total value
for noisesubspec in noisesubspecs:
data.write('[Title='+ noisesubspec.getTitle() + '###'\
+'PositionMZ='+ str(noisesubspec.getPositionmz())+ '###'\
+'ParentMass='+ str(noisesubspec.getAnnotation().getParentMass())+ '###'\
+'NTermBIN='+str(noisesubspec.getNtermBins())+'###'\
+'CTermBIN='+str(noisesubspec.getCtermBins())+']'+'\n')
# allbins += np.array(subspec.getBins())
# data.write('[allbins='+str(allbins)+']'+'\n')
data.close()
def t6_action(self):
print "t6_action"
if(not hasattr(self,'t6_filename')):
print "please choose file"
return
peppro = PeptideProcessor()
if(not hasattr(self,'orginalpois')):
filename = self.t6_filename+"_IonPostion"
if not os.path.exists(filename):
print "please operate Test3 Frist"
return
self.orginalpois = peppro.generateIonPoitionFile(filename)
print self.orginalpois
subprocessor = SubSpectrumProcessor()
subparser = SubSpectrumGenerator()
subspects = list(subparser.generateSubSpecfile(self.t6_filename))
ionpbptables = subprocessor.generateIonPepbondpoiTable(subspects,self.orginalpois,self.splitflag.get())
# ionpbpchiValues = subprocessor.ChiSquared_TypeandPepbondPoi(subspects,self.orginalpois,self.splitflag.get())
subprocessor.paintionpbpTable(ionpbptables)
# subprocessor.paintChiValues(ionpbpchiValues)
# print pepLendf
print self.t6_filename
print self.splitflag.get()
def t4_action(self):
print "t4_action"
if (not hasattr(self, 't4_filename')
and not hasattr(self, 't4_noifilename')):
print "please choose file"
return
peppro = PeptideProcessor()
if (not hasattr(self, 'orginalpois')):
filename = self.t4_filename + "_IonPostion"
if not os.path.exists(filename):
print "please operate Test3 Frist"
return
self.orginalpois = peppro.generateIonPoitionFile(filename)
subparser = SubSpectrumGenerator()
subspects = list(subparser.generateSubSpecfile(self.t4_filename))
subprocessor = SubSpectrumProcessor()
ionapChiValues = subprocessor.ChiSquared_TypeandAminoPairs(
subspects, self.orginalpois)
fileName = self.t4_filename + "_typeAPChi"
fw.writeFile_cp(fileName, ionapChiValues)
print self.t4_filename
print self.t4_noifilename
def t9_action(self):
print "t9_action"
if(not hasattr(self,'t9_filename')):
print "please choose file"
return
ionLearner = IonGroupLearner()
if(not hasattr(self,'spectMaxInt')):
print self.t9_orginfilename.split("_")[-2]
filename = "SubSpectrumData/"+self.t9_orginfilename.split("_")[0]+"_SpectMaxInt"
print filename
if not os.path.exists(filename):
print "please operate spectMaxInt Frist"
return
self.spectMaxInt = ionLearner.generateMaxIntentityFile(filename)
if(not hasattr(self,'orginalpois')):
filename = "SubSpectrumData/"+self.t9_orginfilename.split("_")[0]+"_IonPostion"
if not os.path.exists(filename):
print "please operate Test3 Frist"
return
self.orginalpois = ionLearner.generateIonPoitionFile(filename)
subparser = SubSpectrumGenerator()
if(self.t9_orginfilename.split("_")[-2]=='Noise'):
subspects = subparser.generateNoiSubfile(self.t9_filename,'intensity')
else:
subspects = subparser.generateSubSpecfile(self.t9_filename,'intensity')
ionLists = ionLearner.generateIonGroup_Int(subspects, self.orginalpois, self.spectMaxInt)
file_name = "SubSpectrumData/"+self.t9_orginfilename+"_iongroup"
fw.writeIonGroups(ionLists, file_name)
print file_name
def writeSubSepc(self, File, binlen=0.1, arealen=50, flag='num'):
## write all subspectrum into file
file_name = "data/" + File
fname = File.split('.')[0]
parser = SpectrumParser()
specs = parser.readSpectrum(file_name)
subparser = SubSpectrumGenerator()
subspecs = subparser.generateSubSpectra(specs, binlen, arealen, flag)
if flag == 'num':
filename = "SubSpectrumData/" + fname
elif flag == 'intensity':
filename = "SubSpectrumData/" + fname + "_intensity"
with open(filename, 'w') as data:
for subspec in subspecs:
seq = ''
for acid in subspec.getAnnotation().getAcids():
seq = seq + acid.getResidue()
data.write('[Title='+ subspec.getTitle() + '###'\
+'SEQ=' +seq+ '###'\
+'POSITION='+ str(subspec.getPosition())+ '###'\
+'LENGTH='+str(len(subspec.getAnnotation().getAcids()))+'###'\
+'LeftAA='+subspec.getLA()+'###'\
+'RightAA='+subspec.getRA()+'###'\
+'BIN_LENGTH='+str(subspec.getBinLength())+'###'\
+'BIN_RANGE='+str(subspec.getBinArea())+'###'\
+'NTermBIN='+str(subspec.getNtermBins())+'###'\
+'CTermBIN='+str(subspec.getCtermBins())+']'+'\n')
data.close() # close file
def t3_action(self):
print "t3_action"
if (not hasattr(self, 't3_filename')
and not hasattr(self, 't3_noifilename')):
print "please choose file"
return
subparser = SubSpectrumGenerator()
subspects = list(subparser.generateSubSpecfile(self.t3_filename))
noisubspects = list(subparser.generateNoiSubfile(self.t3_noifilename))
subprocessor = SubSpectrumProcessor()
allNtermbins, allCtermbins, allSubbins, subNum = subprocessor.calculateBins(
subspects)
allNOiNtermbins, allNoiCtermbins, allNoibins, noiNum = subprocessor.calculateBins(
noisubspects)
chiValues = subprocessor.ChiSquared_TypeandBreakPoint(
subNum, noiNum, allSubbins, allNoibins)
poiChiValues, poichiV = subprocessor.sortChiValues(chiValues)
orginalpois = [poiChiValues[i][1] for i in range(len(poiChiValues))
][0:21] # get top 21 chivalues
# store orginalpois
fw.writeIonPoi(orginalpois, self.t3_filename)
# #n-term
if self.pic.get() == 0:
NchiValues = subprocessor.ChiSquared_TypeandBreakPoint(
subNum, noiNum, allNtermbins, allNOiNtermbins)
subprocessor.paintChiValues(NchiValues)
elif self.pic.get() == 1:
#c-term
CchiValues = subprocessor.ChiSquared_TypeandBreakPoint(
subNum, noiNum, allCtermbins, allNoiCtermbins)
subprocessor.paintChiValues(CchiValues)
else:
#all
subprocessor.paintChiValues(chiValues)
print self.pic.get()
print self.t3_filename
print self.t3_noifilename
def t9_action(self):
print "t9_action"
if (not hasattr(self, 't9_filename')):
print "please choose file"
return
ionLearner = IonGroupLearner()
if (not hasattr(self, 'spectMaxInt')):
print self.t9_orginfilename.split("_")[-2]
filename = "SubSpectrumData/" + self.t9_orginfilename.split(
"_")[0] + "_SpectMaxInt"
print filename
if not os.path.exists(filename):
print "please operate spectMaxInt Frist"
return
self.spectMaxInt = ionLearner.generateMaxIntentityFile(filename)
if (not hasattr(self, 'orginalpois')):
filename = "SubSpectrumData/" + self.t9_orginfilename.split(
"_")[0] + "_IonPostion"
if not os.path.exists(filename):
print "please operate Test3 Frist"
return
self.orginalpois = ionLearner.generateIonPoitionFile(filename)
subparser = SubSpectrumGenerator()
if (self.t9_orginfilename.split("_")[-2] == 'Noise'):
subspects = subparser.generateNoiSubfile(self.t9_filename,
'intensity')
else:
subspects = subparser.generateSubSpecfile(self.t9_filename,
'intensity')
ionLists = ionLearner.generateIonGroup_Int(subspects, self.orginalpois,
self.spectMaxInt)
file_name = "SubSpectrumData/" + self.t9_orginfilename + "_iongroup"
fw.writeIonGroups(ionLists, file_name)
print file_name
def t2_action(self):
print "t2_action"
if(not hasattr(self,'t2_filename')):
print "please choose file"
return
subparser = SubSpectrumGenerator()
subspects = list(subparser.generateSubSpecfile(self.t2_filename, self.v.get()))
subprocessor = SubSpectrumProcessor()
allNtermbins,allCtermbins,allSubbins,subNum = subprocessor.calculateBins(subspects)
showpics = []
showpics.append(allNtermbins)
showpics.append(allCtermbins)
showpics.append(allSubbins)
subprocessor.paintSubSpects(showpics[self.pic.get()])
print self.v.get()
print self.pic.get()
print self.t2_filename
def writeNoiseSubSepc(self, File, num=3, binlen=0.1, arealen=50, flag = 'num'):
file_name = "data/"+ File
fname = File.split('.')[0]
parser = SpectrumParser()
specs = parser.readSpectrum(file_name)
noisesubparser = SubSpectrumGenerator()
noisesubspecs = noisesubparser.generateNoiseSubSpectra(specs, num, binlen, arealen, flag)
if flag == 'num':
filename = "SubSpectrumData/"+ fname + "_Noise"
elif flag == 'intensity':
filename = "SubSpectrumData/"+ fname + "_Noise_intensity"
# allbins = np.zeros(int(arealen*2/binlen))
with open(filename,'w') as data:
# add total value
for noisesubspec in noisesubspecs:
data.write('[Title='+ noisesubspec.getTitle() + '###'\
+'PositionMZ='+ str(noisesubspec.getPositionmz())+ '###'\
+'ParentMass='+ str(noisesubspec.getAnnotation().getParentMass())+ '###'\
+'NTermBIN='+str(noisesubspec.getNtermBins())+'###'\
+'CTermBIN='+str(noisesubspec.getCtermBins())+']'+'\n')
# allbins += np.array(subspec.getBins())
# data.write('[allbins='+str(allbins)+']'+'\n')
data.close()
def t7_action(self):
print "t7_action"
if(not hasattr(self,'t7_filename')):
print "please choose file"
return
ionLearner = IonGroupLearner()
if(not hasattr(self,'orginalpois')):
filename = self.t7_filename+"_IonPostion"
if not os.path.exists(filename):
print "please operate Test3 Frist"
return
self.orginalpois = ionLearner.generateIonPoitionFile(filename)
subprocessor = SubSpectrumProcessor()
subparser = SubSpectrumGenerator()
subspects = list(subparser.generateSubSpecfile(self.t7_filename))
ionchiValues = subprocessor.ChiSquared_TypeandType(subspects,self.orginalpois)
fileName = self.t7_filename + "_typetypeChi"
fw.writeFile_cp(fileName, ionchiValues)
# subprocessor.paintChiValues(ionchiValues)
print self.t7_filename
def t2_action(self):
print "t2_action"
if (not hasattr(self, 't2_filename')):
print "please choose file"
return
subparser = SubSpectrumGenerator()
subspects = list(
subparser.generateSubSpecfile(self.t2_filename, self.v.get()))
subprocessor = SubSpectrumProcessor()
allNtermbins, allCtermbins, allSubbins, subNum = subprocessor.calculateBins(
subspects)
showpics = []
showpics.append(allNtermbins)
showpics.append(allCtermbins)
showpics.append(allSubbins)
subprocessor.paintSubSpects(showpics[self.pic.get()])
print self.v.get()
print self.pic.get()
print self.t2_filename
def t7_action(self):
print "t7_action"
if (not hasattr(self, 't7_filename')):
print "please choose file"
return
ionLearner = IonGroupLearner()
if (not hasattr(self, 'orginalpois')):
filename = self.t7_filename + "_IonPostion"
if not os.path.exists(filename):
print "please operate Test3 Frist"
return
self.orginalpois = ionLearner.generateIonPoitionFile(filename)
subprocessor = SubSpectrumProcessor()
subparser = SubSpectrumGenerator()
subspects = list(subparser.generateSubSpecfile(self.t7_filename))
ionchiValues = subprocessor.ChiSquared_TypeandType(
subspects, self.orginalpois)
fileName = self.t7_filename + "_typetypeChi"
fw.writeFile_cp(fileName, ionchiValues)
# subprocessor.paintChiValues(ionchiValues)
print self.t7_filename
def t4_action(self):
print "t4_action"
if(not hasattr(self,'t4_filename') and not hasattr(self,'t4_noifilename')):
print "please choose file"
return
peppro = PeptideProcessor()
if(not hasattr(self,'orginalpois')):
filename = self.t4_filename+"_IonPostion"
if not os.path.exists(filename):
print "please operate Test3 Frist"
return
self.orginalpois = peppro.generateIonPoitionFile(filename)
subparser = SubSpectrumGenerator()
subspects = list(subparser.generateSubSpecfile(self.t4_filename))
subprocessor = SubSpectrumProcessor()
ionapChiValues = subprocessor.ChiSquared_TypeandAminoPairs(subspects,self.orginalpois)
fileName = self.t4_filename + "_typeAPChi"
fw.writeFile_cp(fileName, ionapChiValues)
print self.t4_filename
print self.t4_noifilename
def t3_action(self):
print "t3_action"
if(not hasattr(self,'t3_filename') and not hasattr(self,'t3_noifilename')):
print "please choose file"
return
subparser = SubSpectrumGenerator()
subspects = list(subparser.generateSubSpecfile(self.t3_filename))
noisubspects = list(subparser.generateNoiSubfile(self.t3_noifilename))
subprocessor = SubSpectrumProcessor()
allNtermbins,allCtermbins,allSubbins,subNum = subprocessor.calculateBins(subspects)
allNOiNtermbins,allNoiCtermbins,allNoibins,noiNum = subprocessor.calculateBins(noisubspects)
chiValues = subprocessor.ChiSquared_TypeandBreakPoint(subNum,noiNum,allSubbins,allNoibins)
poiChiValues,poichiV = subprocessor.sortChiValues(chiValues)
orginalpois = [poiChiValues[i][1] for i in range(len(poiChiValues))][0:21] # get top 21 chivalues
# store orginalpois
fw.writeIonPoi(orginalpois,self.t3_filename)
# #n-term
if self.pic.get() == 0:
NchiValues = subprocessor.ChiSquared_TypeandBreakPoint(subNum,noiNum,allNtermbins,allNOiNtermbins)
subprocessor.paintChiValues(NchiValues)
elif self.pic.get() == 1:
#c-term
CchiValues = subprocessor.ChiSquared_TypeandBreakPoint(subNum,noiNum,allCtermbins,allNoiCtermbins)
subprocessor.paintChiValues(CchiValues)
else:
#all
subprocessor.paintChiValues(chiValues)
print self.pic.get()
print self.t3_filename
print self.t3_noifilename
# ionLists = iglearner.generateIonGroup_Int(dualsubspects, orginalpois, spectMaxInt)
#
#
# file_name4 = "SubSpectrumData/"+"IonGroups_DualInt"
# wfile = write_file()
## wfile.writeSpectMaxInt(spectMaxInt)
#
## iglearner.paintMaxInt(spectMaxInt)
## wfile.writeIonPoi(orginalpois)
# wfile.writeIonGroups(ionLists, file_name4)
#
## ionLists = iglearner.generateIonGroup(subspects, orginalpois)
###
################################ Test 5#####################################
filename1 = "SubSpectrumData/"+"new_CHPP_LM3_RP3_2_atype_intensity_20160120"
subparser = SubSpectrumGenerator()
atypesubspects = list(subparser.generateSubSpecfile(filename1,'intensity'))
filename2 = "SubSpectrumData/"+"IonPostion"
iglearner = IonGroupLearner()
orginalpois = iglearner.generateIonPoitionFile(filename2) # directly get original pois from file
print orginalpois
# file_name = 'data/new_CHPP_LM3_RP3_2.mgf'
# parser = SpectrumParser()
# specs = list(parser.readSpectrum(file_name)) # orignal datas file
#
# spectMaxInt = iglearner.generateMaxIntentity(specs)
file_name3 = "SubSpectrumData/"+"SpectMaxInt"
spectMaxInt = iglearner.generateMaxIntentityFile(file_name3)
# ionLists = iglearner.generateIonGroup_Int(dualsubspects, orginalpois, spectMaxInt)
#
#
# file_name4 = "SubSpectrumData/"+"IonGroups_DualInt"
# wfile = write_file()
## wfile.writeSpectMaxInt(spectMaxInt)
#
## iglearner.paintMaxInt(spectMaxInt)
## wfile.writeIonPoi(orginalpois)
# wfile.writeIonGroups(ionLists, file_name4)
#
## ionLists = iglearner.generateIonGroup(subspects, orginalpois)
###
################################ Test 5#####################################
filename1 = "SubSpectrumData/" + "new_CHPP_LM3_RP3_2_atype_intensity_20160120"
subparser = SubSpectrumGenerator()
atypesubspects = list(subparser.generateSubSpecfile(
filename1, 'intensity'))
filename2 = "SubSpectrumData/" + "IonPostion"
iglearner = IonGroupLearner()
orginalpois = iglearner.generateIonPoitionFile(
filename2) # directly get original pois from file
print orginalpois
# file_name = 'data/new_CHPP_LM3_RP3_2.mgf'
# parser = SpectrumParser()
# specs = list(parser.readSpectrum(file_name)) # orignal datas file
#
# spectMaxInt = iglearner.generateMaxIntentity(specs)