def merge(self,rmout):
for rawspectrum in self.rt_all.keys():
for peptide in self.rt_all[rawspectrum]:
rt = []
for idx in all_indices(sorted(self.prob_all[rawspectrum][peptide], reverse=True)[0],self.prob_all[rawspectrum][peptide]):
rt.append(self.rt_all[rawspectrum][peptide][idx])
if rmout and len(rt) > 2:
self.rt[rawspectrum][peptide] = lmedian(array(rt)[chauvenet(array(rt),array(rt))])
self.rt_run[rawspectrum][peptide] = array(rt)[chauvenet(array(rt),array(rt))]
else:
self.rt[rawspectrum][peptide] = lmedian(rt)
self.rt_run[rawspectrum][peptide] = rt
def merge(self,rmout):
for rawspectrum in self.rt_all:
for peptide in self.rt_all[rawspectrum]:
rt = []
for idx in all_indices(sorted(self.prob_all[rawspectrum][peptide], reverse=True)[0],self.prob_all[rawspectrum][peptide]):
rt.append(self.rt_all[rawspectrum][peptide][idx])
if rmout and len(rt) > 2:
self.rt[rawspectrum][peptide] = lmedian(array(rt)[chauvenet(array(rt),array(rt))])
self.rt_run[rawspectrum][peptide] = array(rt)[chauvenet(array(rt),array(rt))]
else:
self.rt[rawspectrum][peptide] = lmedian(rt)
self.rt_run[rawspectrum][peptide] = rt
def transform(self, rmout):
irt = {}
for rawspectrum in self.rt:
for peptide in self.rt[rawspectrum]:
self.irt[rawspectrum][peptide] = scipy.polyval(
[self.a[rawspectrum], self.b[rawspectrum]],
self.rt[rawspectrum][peptide])
if peptide not in irt:
irt[peptide] = []
irt[peptide].append(self.irt[rawspectrum][peptide])
for peptide in irt:
if len(irt) == 1:
self.irt_merged[peptide] = round(irt[peptide][0], 5)
else:
if rmout and len(irt) > 2:
self.irt_merged[peptide] = round(
lmedian(
array(irt[peptide])[invert(
chauvenet(array(irt[peptide]),
array(irt[peptide])))]), 5)
else:
self.irt_merged[peptide] = round(lmedian(irt[peptide]), 5)
for i in range(0, len(self.blocks)):
self.blocks[i].replace(self.irt_merged[self.blocks[i].peptide])
def transform(self,rmout):
irt = {}
for rawspectrum in self.rt.keys():
for peptide in self.rt[rawspectrum].keys():
self.irt[rawspectrum][peptide] = scipy.polyval([self.a[rawspectrum],self.b[rawspectrum]],self.rt[rawspectrum][peptide])
if peptide not in irt.keys():
irt[peptide] = []
irt[peptide].append(self.irt[rawspectrum][peptide])
for peptide in irt.keys():
if len(irt) == 1:
self.irt_merged[peptide] = round(irt[peptide][0],5)
else:
if rmout and len(irt) > 2:
self.irt_merged[peptide] = round(lmedian(array(irt[peptide])[invert(chauvenet(array(irt[peptide]),array(irt[peptide])))]),5)
else:
self.irt_merged[peptide] = round(lmedian(irt[peptide]),5)
for i in range(0,len(self.blocks)):
self.blocks[i].replace(self.irt_merged[self.blocks[i].peptide])