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();
}
public static void parseMZML()
{
String mzmlPath = "/Users/lavalleelab/Desktop/JoshLab/Temp/60minMZML.csv";
MZMLFile mzml = Loader.parseMZMLCSV(mzmlPath);
for (int i = 0; i < 7000; i++)
{
if (i % 500 == 0)
{
Spectra spec = mzml.getSpectraArray()[i];
Console.WriteLine("ID {0} scanNum{1} RT{2} Mass{3} MSLevel{4}", spec.getIndex(), spec.getScanNum(), spec.getStartTime(),
spec.getCalculatedPrecursorMass(), spec.getMSLevel());
}
}
}
protected virtual bool processMS2(Spectra spec)
{
performanceEvaluator.countMS2();
log.Debug(spec);
// check if mass is on exclusion list
double spectraMass = spec.getCalculatedPrecursorMass();
Boolean isExcluded = exclusionList.isExcluded(spectraMass); //checks if the mass should've been excluded,
//in a real experiment, this should never equal to true
//since the mass should not have been scanned in the first place
//if MS exclusion table was updated correctly through API
if (isExcluded)
{
#if (SIMULATION)
IDs id = performDatabaseSearch(spec);
log.Debug("Mass " + spectraMass + " is on the exclusion list. Scan " + spec.getScanNum() + " excluded.");
evaluateExclusion(id);
WriterClass.LogScanTime("Excluded", (int)spec.getIndex());
#endif
performanceEvaluator.countExcludedSpectra();
excludedSpectra.Add(spec.getScanNum());
return(false);
}
else
{
IDs id = performDatabaseSearch(spec);
performanceEvaluator.countAnalyzedSpectra();
log.Debug("Mass " + spectraMass + " was not on the exclusion list. Scan " + spec.getScanNum() + " analyzed.");
evaluateIdentification(id);
includedSpectra.Add(spec.getScanNum());
// calibrate peptide if the observed retention time doesn't match the predicted
//WriterClass.LogScanTime("Processed", (int)spec.getIndex());
return(true);
}
}
