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();
}
