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());
}
}
}
public static MZMLFile parseMSFile(String fileName, int _mslevel)
{
List <Spectra> spectraArray = new List <Spectra>();
log.Info("Parsing the ms2 file: " + fileName);
log.Debug("File path: " + fileName);
StreamReader reader = new StreamReader(fileName);
String line = reader.ReadLine();
while (line != null)
{
if (!line.Substring(0, 1).Equals("H"))
{
break;
}
line = reader.ReadLine();
}
int index = 1;
while (!String.IsNullOrEmpty(line))
{
int scanNum = 0;
int msLevel = _mslevel;
int peakCount = 0;
double startTime = 0;
double precursorMz = 0;
int precursorCharge = 0;
//parse header
while (line != null)
{
String[] str = line.Split("\t".ToCharArray());
if (str[0].Equals("S"))
{
scanNum = int.Parse(str[1]);
precursorMz = double.Parse(str[3]);
}
else if (str[0].Equals("I"))
{
if (str[1].Equals("RTime"))
{
startTime = double.Parse(str[2]);
}
}
else if (str[0].Equals("Z"))
{
precursorCharge = int.Parse(str[1]);
break;
}
line = reader.ReadLine();
}
line = reader.ReadLine();
List <String[]> peaks = new List <String[]>();
while (!line.Substring(0, 1).Equals("S"))
{
peaks.Add(line.Split(" ".ToCharArray()));
line = reader.ReadLine();
if (String.IsNullOrEmpty(line))
{
break;
}
}
peakCount = peaks.Count;
double[] peakMz = new double[peakCount];
double[] peakIntensity = new double[peakCount];
for (int i = 0; i < peakCount; i++)
{
peakMz[i] = double.Parse(peaks[i][0]);
peakIntensity[i] = double.Parse(peaks[i][1]);
}
Spectra spec = new Spectra(index, scanNum, msLevel, peakCount, peakMz, peakIntensity,
startTime, precursorMz, precursorCharge);
spectraArray.Add(spec);
index++;
}
MZMLFile mzml = new MZMLFile(fileName, spectraArray);
return(mzml);
}
