def test(): pathDir = '/home/jaggu/marcotte_project/boulgakov/microscope/2015-Oct/2015-10-27_forHopper' outputDirname = "output_2015-11-02" outputDir = os.path.join(pathDir,outputDirname) destDir = '/home/jaggu/marcotte_project/current/project2/jaggu/dataAnalysis/microscope1/2015-Oct/2015-10-27' trackPhotometryFile = 'track_photometries_nx8t5v.csv' trackFile = os.path.join(outputDir,trackPhotometryFile) #category_trackDetails_ch1 = makeIntensityCategory(trackFile,ch=1) #category_trackDetails_ch2 = makeIntensityCategory(trackFile,ch=2) #print "Categories Dictionaries pickled" category_dict_ch1 = loadPkl('category_trackDetails.ch1.dict.pkl',pathDir) category_dict_ch2 = loadPkl('category_trackDetails.ch2.dict.pkl',pathDir) print "Categories Dictionaries loaded " desired_category = getDesiredCategory('staggered') desired_categoryList_ch1 = getIntensityList_category(category_dict_ch1,desired_category) desired_categoryList_ch2 = getIntensityList_category(category_dict_ch2,desired_category) writeCountsFile([desired_categoryList_ch1,desired_categoryList_ch2]) print "Peptide track counts and intensity file created" edmanframe_ch1 = 3 edmanframe_ch2 = 4 allCounts_ch1 = [item[1] for item in desired_categoryList_ch1] allCounts_ch2 = [item[1] for item in desired_categoryList_ch2] eff1_ch1,eff2_ch1 = calculateEdmanEfficiency(allCounts_ch1,edmanframe_ch1) eff1_ch2,eff2_ch2 = calculateEdmanEfficiency(allCounts_ch2,edmanframe_ch2) print "Overall Edman efficiency - \n Ch1 : ",eff1_ch1,eff2_ch1," \n Ch2 : ",eff1_ch2,eff2_ch2
def countTracks(self, pickle_exists=False,nbrframes=7,nbrchannels=2): trackFile = self.trackFile if pickle_exists: category_dict_ch1 = loadPkl('category_trackDetails.ch1.dict.pkl',self.pathDir) category_dict_ch2 = loadPkl('category_trackDetails.ch2.dict.pkl',self.pathDir) print "Categories Dictionaries loaded " else: category_dict_ch1,category_peakDetails_ch1 = peptracks.makeIntensityCategory(trackFile,ch=1) category_dict_ch2,category_peakDetails_ch2 = peptracks.makeIntensityCategory(trackFile,ch=2) self.pickle_categoryDict(category_dict_ch1,'category_trackDetails.ch',1) self.pickle_categoryDict(category_dict_ch2,'category_trackDetails.ch',2) self.pickle_categoryDict(category_peakDetails_ch1,'category_peakDetails.ch',1) self.pickle_categoryDict(category_peakDetails_ch2,'category_peakDetails.ch',2) print "Categories Dictionaries pickled" return category_dict_ch1, category_dict_ch2