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);
}