def getBOWfeature(file,num):
hydrophobicity =[]
peptide_length = []
psmDescriptions, aaAlphabet = el.processTrainData(file)
Index = rm.buildRetentionIndex(aaAlphabet,psmDescriptions,True)
customIndex = dict(zip(aaAlphabet, Index))
for i, psmd in enumerate(psmDescriptions):
aas = dm.getAminoAcidList(psmd.peptide)
peptide_length.append(len(psmd.peptide))
hydrophobicity.append(bowindexSum(aas, customIndex))
peptide,rt = dg.extract(psmDescriptions,len(psmDescriptions))
bow_feature = BOW(peptide,hydrophobicity,peptide_length,aaAlphabet,num)
return psmDescriptions ,bow_feature
def get_elude_model(self):
aaAlphabet = self.amino_acid_list()
normalizeRetentionTimes = True
customIndex = rm.buildRetentionIndex(aaAlphabet, self.peptides, normalizeRetentionTimes)
return elute_model(aaAlphabet, customIndex)
def trainRetentionModel(aaAlphabet, psmDescriptions): customIndex = rm.buildRetentionIndex(aaAlphabet, psmDescriptions, normalizeRetentionTimes) return dict(zip(aaAlphabet, customIndex))
