def draw_boxPlotPeptideIntensity(self,category_intensityList,exptCycle,nbrframes=7,nbrchannels=2): """ Makes a series of boxplot where the intensity of the peptides are applied. """ edmanCycle = exptCycle - 2 #(nbrMock=4;) desired_category = peptracks.getDesiredCategory('staggered',nbrframes) category = desired_category[exptCycle] all_peptrack_intensity = category_intensityList[tuple(category)] title = 'intensity_edman_'+str(edmanCycle) iTracks.plot_boxPlots(self.pathDir,self.peptracks_destDir,all_peptrack_intensity,title) return True
def writeTracks(self,category_dict_ch1,category_dict_ch2,nbrframes=7,nbrchannels=2): if len(category_dict_ch2) <= 1: assert nbrchannels == 1 desired_category = peptracks.getDesiredCategory('staggered',nbrframes) if nbrchannels == 2: self.desired_categoryList_ch1 = peptracks.getIntensityList_category(category_dict_ch1,desired_category) self.desired_categoryList_ch2 = peptracks.getIntensityList_category(category_dict_ch2,desired_category) ofname = peptracks.writeCountsFile([self.desired_categoryList_ch1,self.desired_categoryList_ch2],self.peptracks_destDir,nbrchannels) else: self.desired_categoryList_ch1 = peptracks.getIntensityList_category(category_dict_ch1,desired_category) self.desired_categoryList_ch2 = None ofname = peptracks.writeCountsFile([self.desired_categoryList_ch1],self.peptracks_destDir,nbrchannels) print "Peptide track counts and intensity file created ",ofname return self.desired_categoryList_ch1, self.desired_categoryList_ch2,ofname
def writeTracks_quartilesCutoff(self,ofname,nbrframes=7,nbrchannels=2,cycle=3): cycle = 2 desired_category = peptracks.getDesiredCategory('staggered',nbrframes) ofname = ofname[:-4]+'.quartileCutoff.tab' ofile = open(ofname,'w') ofile.write('#Category \t Counts \n') ofile.write('\n Cycle used for cutoff - \t '+str(cycle)+'\n') if nbrchannels == 2: print len(self.desired_categoryList_ch1) print len(self.desired_categoryList_ch2) else: all_trackCounts = list() for q_range in ([0,25],[25,50],[50,75],[75,100]): trackCounts = peptracks.applyCutoff(self.desired_categoryList_ch1,desired_category,q_range, cycle) ofile.write('\n \n Quartile '+str(q_range)+ '\n') for cat, counts_qTracks,q_intensityList in trackCounts: ofile.write(str(cat)+'\t'+str(counts_qTracks)+'\n') ofile.close() print ofname return True