private static void PostExperimentProcessing(Experiment e) { //WriterClass.writeln(exclusionProfile.ReportFailedCometSearchStatistics()); WriterClass.Flush(); if (GlobalVar.IsSimulation) { ProteinProphetResult ppr; if (GlobalVar.isSimulationForFeatureExtraction) { ppr = ProteinProphetEvaluator.getProteinProphetResult(InputFileOrganizer.OriginalProtXMLFile); } else { String proteinProphetResultFileName = e.experimentNumber + GlobalVar.experimentName; ppr = PostProcessingScripts.postProcessing(e.exclusionProfile, proteinProphetResultFileName, true); } e.totalRunTime = getCurrentTime() - e.experimentStartTime; String result = e.exclusionProfile.getPerformanceVector(e.experimentName, e.exclusionProfile.getAnalysisType().getDescription() , e.analysisTime, e.totalRunTime, ppr, 12, e.exclusionProfile); Console.WriteLine(result); Console.WriteLine("Protein groups: " + ppr.getFilteredProteinGroups().Count); WriterClass.writeln(result); //WriterClass.writeln("Protein groups: "+ ppr.getFilteredProteinGroups().Count) ; e.ppr = ppr; } else { WriterClass.writeln(e.exclusionProfile.GetPerformanceEvaluator().outputPerformance()); } }
public static void DoJob() { String comet = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\MS_QC_120min.pep.xml"; String output = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\"; ProteinProphetResult ppr = PostProcessingScripts.RunProteinProphet(comet, output, true); Console.WriteLine(ppr.ToString()); }
public static void DoJob() { InputFileOrganizer.FASTA_FILE = "C:\\Coding\\2019LavalleeLab\\temp2\\ExampleDataSet\\uniprot_SwissProt_Human_1_11_2017.fasta"; //String outputCometFile = "C:\\Coding\\2019LavalleeLab\\temp2\\ModifiedDBSearchFiles\\Result\\ModdedSearch_MLGEGolden_nonCheat_peptideSearchResultIncluded\\PartialCometFile\\1ModdedSearch_MLGE_nonCheat_peptideSearchResultIncluded_partial.pep.xml"; String outputCometFile = "C:\\Coding\\2019LavalleeLab\\temp2\\ModifiedDBSearchFiles\\Result\\Modded_MLGEGolden_rtCheatpeptideSearchResultIncluded\\PartialCometFile\\1Modded_MLGEGolden_rtCheat_partial.pep.xml"; ProteinProphetResult ppr = PostProcessingScripts.RunProteinProphet(outputCometFile, InputFileOrganizer.OutputFolderOfTheRun, true); //String proteinProphetFile = "C:\\Coding\\2019LavalleeLab\\temp2\\Output\\ProteinGroup_Combined_rtCheat\\protein_prophet_output\\ProteinGroup_Combined_rtCheat_partial_interact.prot.xml"; //ProteinProphetResult ppr = ProteinProphetEvaluator.getProteinProphetResult(proteinProphetFile); Console.WriteLine(ppr.ToString()); Console.WriteLine("Protein groups " + ppr.getFilteredProteinGroups().Count); }
private static void FullPepXMLAndProteinProphetSetup() { if (GlobalVar.IsSimulation) { if (!GlobalVar.usePepXMLComputedFile) { //comet log.Info("Performing Comet search on full ms2 data"); String fullCometFile = PostProcessingScripts.CometStandardSearch(InputFileOrganizer.MS2SimulationTestFile, InputFileOrganizer.preExperimentFilesFolder, true); InputFileOrganizer.OriginalCometOutput = fullCometFile; } //protein prophet log.Info("Perform a protein prophet search on full pepxml"); String fullProteinProphetFile = PostProcessingScripts.ProteinProphetSearch(InputFileOrganizer.OriginalCometOutput, InputFileOrganizer.OutputFolderOfTheRun, true); ExecuteShellCommand.MoveFile(fullProteinProphetFile, InputFileOrganizer.preExperimentFilesFolder); InputFileOrganizer.OriginalProtXMLFile = Path.Combine(InputFileOrganizer.preExperimentFilesFolder, IOUtils.getBaseName(IOUtils.getBaseName(fullProteinProphetFile)) + ".prot.xml"); } }
static String mzml = "C:\\Coding\\2019LavalleeLab\\RealTest_Results_20200219\\MSQC_QE_200ng_HEK_2hr_to_run_200219172225.mzML"; //"C:\\Coding\\2019LavalleeLab\\GoldStandardData\\MZML_Files\\MS_QC_120min.mzml"; public static void DoJob() { //comet Console.WriteLine("Performing Comet search on full ms2 data"); String fullCometFile = PostProcessingScripts.CometStandardSearch(ms2File, InputFileOrganizer.OutputFolderOfTheRun, true); InputFileOrganizer.OriginalCometOutput = fullCometFile; //protein prophet Console.WriteLine("Perform a protein prophet search on full pepxml"); String fullProteinProphetFile = PostProcessingScripts.ProteinProphetSearch(fullCometFile, InputFileOrganizer.OutputFolderOfTheRun, true); InputFileOrganizer.OriginalProtXMLFile = fullProteinProphetFile; ProteinProphetResult baseLinePpr = ProteinProphetEvaluator.getProteinProphetResult(InputFileOrganizer.OriginalProtXMLFile); //load spectra Console.WriteLine("loading spectra array"); List <Spectra> ls = Loader.parseMS2File(ms2File).getSpectraArray(); List <int> includedSpectra = new List <int>(); List <int> excludedSpectra = new List <int>(); StreamReader sr = new StreamReader(excludedSpectraFile); String line = sr.ReadLine(); while (line != null) { int excluded = int.Parse(line); excludedSpectra.Add(excluded); line = sr.ReadLine(); } foreach (Spectra sp in ls) { if (!excludedSpectra.Contains(sp.getScanNum())) { includedSpectra.Add(sp.getScanNum()); } } String outputCometFile = Path.Combine(InputFileOrganizer.OutputFolderOfTheRun, "realTestpartialOut.pep.xml"); //"C:\\Coding\\2019LavalleeLab\\GoldStandardData\\pepxml\\MS_QC_120min_partial.pep.xml"; String fastaFile = InputFileOrganizer.FASTA_FILE; //"C:\\Coding\\2019LavalleeLab\\GoldStandardData\\Database\\uniprot_SwissProt_Human_1_11_2017.fasta"; PartialPepXMLWriter.writePartialPepXMLFile(fullCometFile, includedSpectra, outputCometFile, mzml, fastaFile, outputCometFile); String partialProt = PostProcessingScripts.ProteinProphetSearch(outputCometFile, InputFileOrganizer.OutputFolderOfTheRun, true); ProteinProphetResult partialPpr = ProteinProphetEvaluator.getProteinProphetResult(partialProt); double partialNum = partialPpr.getNum_proteins_identified(); double totalNum = baseLinePpr.getNum_proteins_identified(); double idSens = partialNum / totalNum * 100.0; double includedScanNum = includedSpectra.Count; double totalScanNum = ls.Count; double usedResource = includedScanNum / totalScanNum * 100; String line1 = String.Format("includedScans {0} \t totalScanNum {1} \tUsedResources {2}", includedScanNum, totalScanNum, usedResource); String line2 = String.Format("partialNum {0} \t totalNum {1} \tidsens {2}", partialNum, totalNum, idSens); Console.WriteLine(line1); Console.WriteLine(line2); WriterClass.writeln(line1); WriterClass.writeln(line2); WriterClass.CloseWriter(); }