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");
}
public static void CometSingleSearchTest()
{
String idx = "C:\\Coding\\2019LavalleeLab\\GitProjectRealTimeMS\\TestData\\PreComputedFiles\\uniprot_SwissProt_Human_1_11_2017_decoyConcacenated.fasta.idx";
//String idx = "C:\\temp\\comet_2019015\\comet_source_2019015\\IDXMake\\uniprot_SwissProt_Human_1_11_2017_decoyConcacenated.fasta.idx";
String param = "C:\\Coding\\2019LavalleeLab\\temp2\\ExampleDataSet\\2019.comet.params";
CometSingleSearch.InitializeComet(idx, param);
CometSingleSearch.QualityCheck();
Program.ExitProgram(1);
String dataRoot = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\MealTimeMS_APITestRun\\Data\\";
String outputRoot = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\MealTimeMS_APITestRun\\Output\\";
//String mzmlPath = dataRoot+"60minMZMLShrink.csv";
String mzmlPath = dataRoot + "8001.ms2.txt";
String dbPath = dataRoot + "tinyDB.fasta.idx"; //
String outputPath = outputRoot + "output.txt";
String paramsPath = dataRoot + "comet.params";
MZMLFile mzml = Loader.parseMS2File(mzmlPath);
//MZMLFile mzml = null;
CometSingleSearch.InitializeComet(dbPath, paramsPath);
var watch = System.Diagnostics.Stopwatch.StartNew();
int counter = 0;
Console.WriteLine("Starting comet search");
WriterClass.initiateWriter(outputPath);
for (int i = 0; i < 1; i++)
{
if (i % 1 == 0)
{
Spectra spec = mzml.getSpectraArray()[i];
if (spec.getMSLevel() != 2)
{
continue;
}
Console.WriteLine("scanNum {0} RT {2} Mass {2} MSLevel {3}", spec.getScanNum(), spec.getStartTime(),
spec.getCalculatedPrecursorMass(), spec.getMSLevel());
IDs id = null;
if (CometSingleSearch.Search(spec, out id))
{
String outLine = String.Format("{0}\t{1}\txcorr\t{2}\tdcn\t{3}", id.getScanNum(), id.getPeptideSequence(), id.getXCorr(), id.getDeltaCN());
Console.WriteLine(outLine);
WriterClass.writeln(outLine);
}
else
{
Console.WriteLine("Spectrum cannot be matched\n");
}
counter++;
}
}
watch.Stop();
Console.WriteLine("Comet search of " + counter + " spectra took " + watch.ElapsedMilliseconds + " milliseconds");
WriterClass.CloseWriter();
}
protected IDs performDatabaseSearch(Spectra spec)
{
IDs id = null;
if (CometSingleSearch.Search(spec, out id))
{
log.Debug("MS2 scan was identified.");
log.Debug(id);
performanceEvaluator.countMS2Identified();
PSMTSVReaderWriter.WritePSM(id);
}
else
{
// scan cannot be matched to a peptide
log.Debug("MS2 scan {0} was not identified by a comet search", spec.getScanNum());
performanceEvaluator.countMS2Unidentified();
}
return(id);
}
public static void reset()
{
isListening = true;
CometSingleSearch.reset();
}
public String ReportFailedCometSearchStatistics()
{
return(CometSingleSearch.ReportFailedStatistics());
}
public static void TestValidity()
{
HashSet <String> set = new HashSet <String> {
"sd", "qq", "sdd"
};
Console.WriteLine(set);
String logOutput = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\Output\\CometValidationOutput.txt";
StreamWriter sw = new StreamWriter(logOutput);
String TSVFile = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\MS_QC_120min.tsv\\MSQC120min.tsv"; //obtained from standard comet search
List <IDs> idList = PSMTSVReaderWriter.ParseTSV(TSVFile);
sw.WriteLine("OriginalCometOutput has {0} PSMs", idList.Count);
int sdDecoyCount = 0;
foreach (IDs id in idList)
{
if (id.isDecoy())
{
sdDecoyCount++;
}
}
Console.WriteLine("sdDecoy count: {0}", sdDecoyCount);
sw.WriteLine("sdDecoy count: {0}", sdDecoyCount);
String ms2File = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\MS_QC_120min.ms2";
List <Spectra> spectra = Loader.parseMS2File(ms2File).getSpectraArray();
String dbPath = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\PreComputedFiles\\uniprot_SwissProt_Human_1_11_2017_decoyConcacenated.fasta.idx";
String paramsPath = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\2019.comet.params";
CometSingleSearch.InitializeComet(dbPath, paramsPath);
List <IDs> realTimeIDList = new List <IDs>();
foreach (Spectra spec in spectra)
{
IDs id = null;
if (CometSingleSearch.Search(spec, out id))
{
realTimeIDList.Add(id);
}
}
sw.WriteLine("RealTimeOutput has {0} PSMs", realTimeIDList.Count);
sw.WriteLine(CometSingleSearch.ReportFailedStatistics());
sw.WriteLine("ScanNum\tSeq_sd\tSeq_rt\txcorr_sd\txcorr_rt");
sw.Flush();
int sameSeq = 0;
int diffSeq = 0;
foreach (IDs standardID in idList)
{
Boolean matched = false;
foreach (IDs realTimeID in realTimeIDList)
{
if (standardID.getScanNum() == realTimeID.getScanNum())
{
matched = true;
String output = String.Format("{0}\t{1}\t{2}\t{3}\t{4}", standardID.getScanNum(), standardID.getPeptideSequence(), realTimeID.getPeptideSequence(), standardID.getXCorr(), realTimeID.getXCorr());
sw.WriteLine(output);
if (standardID.getPeptideSequence().Equals(realTimeID.getPeptideSequence()))
{
sameSeq++;
}
else
{
diffSeq++;
}
break;
}
}
if (!matched && !standardID.isDecoy())
{
String output = String.Format("{0}\t{1}\t{2}\t{3}\t{4}\t{5}", standardID.getScanNum(), standardID.getPeptideSequence(), "", standardID.getXCorr(), "", standardID.getParentProteinAccessionsAsString());
sw.WriteLine(output);
}
}
sw.WriteLine("sameSequence: {0}\t diffSeq: {1}", sameSeq, diffSeq);
}
