protected bool processMS2(Spectra spec)
{
performanceEvaluator.countMS2();
log.Debug(spec);
IDs id = performDatabaseSearch(spec);
Boolean isExcluded = false;
if (id != null)
{
Peptide pep = getPeptideFromIdentification(id);
isExcluded = exclusionList.containsPeptide(pep);
}
if (isExcluded)
{
#if SIMULATION
//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
{
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);
}
}
protected bool processMS2(Spectra spec)
{
performanceEvaluator.countMS2();
log.Debug(spec);
IDs id = performDatabaseSearch(spec);
// check if mass is on exclusion list
Boolean isExcluded = false;
if (id != null)
{
Peptide pep = getPeptideFromIdentification(id);
isExcluded = exclusionList.containsPeptide(pep); //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 (!peptideRT.Keys.Contains(pep.getSequence()))
{
peptideRT.Add(pep.getSequence(), spec.getStartTime());
}
}
if (isExcluded)
{
#if SIMULATION
//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
{
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);
}
}
protected void processMS1(Spectra spec)
{
log.Debug("MS1 scan, unused");
performanceEvaluator.countMS1();
includedSpectra.Add(spec.getScanNum());
}
public InfoContainer(bool common, Spectra spec)
{
table = new Dictionary <string, string>();
String msLevel = "MS";
if (spec.getMSLevel() == 2)
{
msLevel = "MS2";
}
if (common)
{
table.Add(GlobalVar.MSLevelHeader, msLevel);
table.Add(GlobalVar.PrecursorChargeHeader, spec.getPrecursorCharge().ToString());
table.Add(GlobalVar.PrecursorMZHeader, spec.getPrecursorMz().ToString());
table.Add(GlobalVar.ScanNumHeader, spec.getScanNum().ToString());
table.Add(GlobalVar.ScanTimeHeader, spec.getStartTime().ToString());
}
else
{
table.Add("specificInfo1", "aa");
table.Add("specificInfo2", "pp");
}
Names = table.Keys;
}
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 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);
}
}
private void setUpRandomlyExcludedMS2_NoneDDA(List <Spectra> ms2SpectraArray, int numExcluded, int numAnalyzed,
int maximumNumberOfMS2Spectra)
{
ms2SpectraArray = CloneList(ms2SpectraArray); //just removes the reference to the original variable, so any operation to the new list doesn't mess with the original list up outside of this function
randomlyExcludedScans = new List <int>();
Random r = new Random();
while (ms2SpectraArray.Count > numAnalyzed)
{
int pos = r.Next(ms2SpectraArray.Count);
Spectra spectraToBeExcluded = ms2SpectraArray[pos];
randomlyExcludedScans.Add(spectraToBeExcluded.getScanNum());
ms2SpectraArray.RemoveAt(pos);
}
}
protected bool processMS2(Spectra spec)
{
log.Debug(spec);
performanceEvaluator.countMS2();
//IDs id = performDatabaseSearch(spec);
bool isExcluded = randomlyExcludedScans.Contains(spec.getScanNum());
if (isExcluded)
{
log.Debug("MS2 spectra was randomly excluded");
performanceEvaluator.countExcludedSpectra();
//evaluateExclusion(id);
excludedSpectra.Add(spec.getScanNum());
return(false);
}
else
{
log.Debug("MS2 spectra was analyzed");
performanceEvaluator.countAnalyzedSpectra();
//evaluateIdentification(id);
includedSpectra.Add(spec.getScanNum());
return(true);
}
}
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);
}
/*
* Alex Stuff: Accounted for DDA
* Goes through the spectra array and randomly excludes numExcluded of these
* scans
*/
private void setUpRandomlyExcludedMS2(List <Spectra> spectraArray, int numExcluded, int numAnalyzed,
int maximumNumberOfMS2Spectra)
{
List <List <Spectra> > groupedByMS1 = GroupedByMS1(spectraArray);
Dictionary <int, List <Spectra> > ms1ScanNumberToRemainingMS2 = new Dictionary <int, List <Spectra> >();
List <Spectra> spectraEligibleForExclusion = new List <Spectra>();
foreach (List <Spectra> groupedSpectra in groupedByMS1)
{
int ms1ScanNum = groupedSpectra[0].getScanNum();
// remove the MS1 spectra
groupedSpectra.RemoveAt(0);
// keep adding MS2 until max number of MS2 added or no more MS2
int numMS2Added = 0;
while (groupedSpectra.Count != 0)
{
Spectra s = groupedSpectra[0];
groupedSpectra.RemoveAt(0);
spectraEligibleForExclusion.Add(s);
if (++numMS2Added >= maximumNumberOfMS2Spectra)
{
break;
}
}
ms1ScanNumberToRemainingMS2.Add(ms1ScanNum, groupedSpectra);
}
// Keep adding randomly selected spectra to randomly excluded list
randomlyExcludedScans = new List <int>();
Random r = new Random();
while (spectraEligibleForExclusion.Count > numAnalyzed)
{
int pos = r.Next(spectraEligibleForExclusion.Count);
Spectra randomlyExcludedSpectra = spectraEligibleForExclusion[pos];
spectraEligibleForExclusion.RemoveAt(pos);
randomlyExcludedScans.Add(randomlyExcludedSpectra.getScanNum());
/* update spectraEligibleForExclusion */
int specArrIndex = spectraArray.IndexOf(randomlyExcludedSpectra);
Spectra parentMS1 = null;
// find the parent MS1 spectra by backtracking in spectraArray
while (specArrIndex >= 0)
{
Spectra prevSpectra = spectraArray[specArrIndex];
if (prevSpectra.getMSLevel() == 1)
{
parentMS1 = prevSpectra;
break;
}
}
// add newly eligible MS2 to candidate list
List <Spectra> ms2RemainingToAdd = ms1ScanNumberToRemainingMS2[parentMS1.getScanNum()];
if (ms2RemainingToAdd.Count != 0)
{
Spectra specToAdd = ms2RemainingToAdd[0];
spectraEligibleForExclusion.Add(specToAdd);
ms2RemainingToAdd.RemoveAt(0);
}
}
}
//Called by DataProcessor, entry point to Alex's program
public bool evaluate(Spectra spec)
{
currentTime = spec.getStartTime();
updateExclusionList(spec);
if (spec.getMSLevel() == 1)
{
log.Debug("Evaluating ms1 scan");
processMS1(spec);
}
else if (spec.getMSLevel() == 2)
{
log.Debug("evaluating ms2 scan");
if (spec.getIndex() % GlobalVar.ScansPerOutput == 0)
{
#if SIMULATION
double progressPercent = spec.getIndex() / GlobalVar.ExperimentTotalScans * 100;
log.Info("Progress: {0:F2}% Processing ID: {1}\t ScanNum: {2} \t Excluded: {3}", progressPercent, spec.getIndex(), spec.getScanNum(),
excludedSpectra.Count);
#else
log.Info("Progress: {0}\t{1} excluded------------------------", spec.getIndex(), excludedSpectra.Count);
log.Info("ExclusionListSize: {0}\tRTOffset: {1}", exclusionList.getExclusionList().Count, RetentionTime.getRetentionTimeOffset());
#endif
}
return(processMS2(spec));
}
else
{
log.Debug("unrecognized msScan");
}
return(true);
}
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());
}
}
}
