static void PreExperimentSetUp()
{
ConstructDecoyFasta();
ConstructIDX();
if (GlobalVar.IsSimulation)
//if(false)
{
ms2SpectraList = Loader.parseMS2File(InputFileOrganizer.MS2SimulationTestFile).getSpectraArray();
GlobalVar.ExperimentTotalScans = ms2SpectraList.Count;
FullPepXMLAndProteinProphetSetup();
baseLinePpr = ProteinProphetEvaluator.getProteinProphetResult(InputFileOrganizer.OriginalProtXMLFile);
//so in alex's original code, "original experiment" refers to original experiment without any exclusion or manipulation with this program
//"baseline comparison" refers to the results after "NoExclusion" run, which is a top 6 or top 12 DDA run, which is not implemented in this program
//So the two are the same in thie program
int numMS2Analyzed = (int)GlobalVar.ExperimentTotalScans;
PerformanceEvaluator.setBaselineComparison(baseLinePpr, numMS2Analyzed, 12);
PerformanceEvaluator.setOriginalExperiment(baseLinePpr.getNum_proteins_identified());
}
log.Debug("Setting up Database");
database = databaseSetUp(InputFileOrganizer.ExclusionDBFasta);
log.Debug("Done setting up database.");
CometSingleSearch.InitializeComet(InputFileOrganizer.IDXDataBase, InputFileOrganizer.CometParamsFile);
//CometSingleSearch.InitializeComet_NonRealTime("C:\\Coding\\2019LavalleeLab\\temp2\\ModifiedDBSearchFiles\\NoExclusionRealTimeCometSearch.tsv");
//CometSingleSearch.QualityCheck();
Console.WriteLine("pre-experimental setup finished");
}
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();
}