protected override MyTaskResults RunSpecific(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList)
{
MyTaskResults = new MyTaskResults(this);
List <PsmCross> allPsms = new List <PsmCross>();
var compactPeptideToProteinPeptideMatch = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >();
Status("Loading modifications...", taskId);
List <ModificationWithMass> variableModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsVariable.Contains((b.modificationType, b.id))).ToList();
List <ModificationWithMass> fixedModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsFixed.Contains((b.modificationType, b.id))).ToList();
List <string> localizeableModificationTypes = GlobalVariables.AllModTypesKnown.ToList();
// load proteins
List <Protein> proteinList = LoadProteins(taskId, dbFilenameList, true, XlSearchParameters.DecoyType, localizeableModificationTypes, CommonParameters);
List <ProductType> ionTypes = new List <ProductType>();
if (CommonParameters.BIons)
{
ionTypes.Add(ProductType.BnoB1ions);
}
if (CommonParameters.YIons)
{
ionTypes.Add(ProductType.Y);
}
if (CommonParameters.ZdotIons)
{
ionTypes.Add(ProductType.Zdot);
}
if (CommonParameters.CIons)
{
ionTypes.Add(ProductType.C);
}
TerminusType terminusType = ProductTypeMethods.IdentifyTerminusType(ionTypes);
var crosslinker = new CrosslinkerTypeClass();
crosslinker.SelectCrosslinker(XlSearchParameters.CrosslinkerType);
if (XlSearchParameters.CrosslinkerType == CrosslinkerType.UserDefined)
{
crosslinker = GenerateUserDefinedCrosslinker(XlSearchParameters);
}
MyFileManager myFileManager = new MyFileManager(XlSearchParameters.DisposeOfFileWhenDone);
var fileSpecificCommonParams = fileSettingsList.Select(b => SetAllFileSpecificCommonParams(CommonParameters, b));
HashSet <DigestionParams> ListOfDigestionParams = new HashSet <DigestionParams>(fileSpecificCommonParams.Select(p => p.DigestionParams));
int completedFiles = 0;
object indexLock = new object();
object psmLock = new object();
Status("Searching files...", taskId);
ProseCreatedWhileRunning.Append("The following crosslink discovery were used: ");
ProseCreatedWhileRunning.Append("crosslinker name = " + crosslinker.CrosslinkerName + "; ");
ProseCreatedWhileRunning.Append("crosslinker type = " + crosslinker.Cleavable + "; ");
ProseCreatedWhileRunning.Append("crosslinker mass = " + crosslinker.TotalMass + "; ");
ProseCreatedWhileRunning.Append("crosslinker modification site(s) = " + crosslinker.CrosslinkerModSites + "; ");
ProseCreatedWhileRunning.Append("protease = " + CommonParameters.DigestionParams.Protease + "; ");
ProseCreatedWhileRunning.Append("maximum missed cleavages = " + CommonParameters.DigestionParams.MaxMissedCleavages + "; ");
ProseCreatedWhileRunning.Append("minimum peptide length = " + CommonParameters.DigestionParams.MinPeptideLength + "; ");
ProseCreatedWhileRunning.Append(CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ?
"maximum peptide length = unspecified; " :
"maximum peptide length = " + CommonParameters.DigestionParams.MaxPeptideLength + "; ");
ProseCreatedWhileRunning.Append("initiator methionine behavior = " + CommonParameters.DigestionParams.InitiatorMethionineBehavior + "; ");
ProseCreatedWhileRunning.Append("max modification isoforms = " + CommonParameters.DigestionParams.MaxModificationIsoforms + "; ");
ProseCreatedWhileRunning.Append("fixed modifications = " + string.Join(", ", fixedModifications.Select(m => m.id)) + "; ");
ProseCreatedWhileRunning.Append("variable modifications = " + string.Join(", ", variableModifications.Select(m => m.id)) + "; ");
ProseCreatedWhileRunning.Append("parent mass tolerance(s) = " + XlSearchParameters.XlPrecusorMsTl + "; ");
ProseCreatedWhileRunning.Append("product mass tolerance = " + CommonParameters.ProductMassTolerance + "; ");
ProseCreatedWhileRunning.Append("The combined search database contained " + proteinList.Count + " total entries including " + proteinList.Where(p => p.IsContaminant).Count() + " contaminant sequences. ");
for (int spectraFileIndex = 0; spectraFileIndex < currentRawFileList.Count; spectraFileIndex++)
{
if (GlobalVariables.StopLoops)
{
break;
}
var origDataFile = currentRawFileList[spectraFileIndex];
CommonParameters combinedParams = SetAllFileSpecificCommonParams(CommonParameters, fileSettingsList[spectraFileIndex]);
List <PsmCross> newPsms = new List <PsmCross>();
var thisId = new List <string> {
taskId, "Individual Spectra Files", origDataFile
};
NewCollection(Path.GetFileName(origDataFile), thisId);
Status("Loading spectra file...", thisId);
MsDataFile myMsDataFile = myFileManager.LoadFile(origDataFile, combinedParams.TopNpeaks, combinedParams.MinRatio, combinedParams.TrimMs1Peaks, combinedParams.TrimMsMsPeaks, combinedParams);
Status("Getting ms2 scans...", thisId);
Ms2ScanWithSpecificMass[] arrayOfMs2ScansSortedByMass = GetMs2Scans(myMsDataFile, origDataFile, combinedParams.DoPrecursorDeconvolution, combinedParams.UseProvidedPrecursorInfo, combinedParams.DeconvolutionIntensityRatio, combinedParams.DeconvolutionMaxAssumedChargeState, combinedParams.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
for (int currentPartition = 0; currentPartition < CommonParameters.TotalPartitions; currentPartition++)
{
List <CompactPeptide> peptideIndex = null;
List <Protein> proteinListSubset = proteinList.GetRange(currentPartition * proteinList.Count() / combinedParams.TotalPartitions, ((currentPartition + 1) * proteinList.Count() / combinedParams.TotalPartitions) - (currentPartition * proteinList.Count() / combinedParams.TotalPartitions));
Status("Getting fragment dictionary...", new List <string> {
taskId
});
var indexEngine = new IndexingEngine(proteinListSubset, variableModifications, fixedModifications, ionTypes, currentPartition, UsefulProteomicsDatabases.DecoyType.Reverse, ListOfDigestionParams, combinedParams, 30000.0, new List <string> {
taskId
});
List <int>[] fragmentIndex = null;
lock (indexLock)
GenerateIndexes(indexEngine, dbFilenameList, ref peptideIndex, ref fragmentIndex, taskId);
Status("Searching files...", taskId);
new TwoPassCrosslinkSearchEngine(newPsms, arrayOfMs2ScansSortedByMass, peptideIndex, fragmentIndex, ionTypes, currentPartition, combinedParams, false, XlSearchParameters.XlPrecusorMsTl, crosslinker, XlSearchParameters.CrosslinkSearchTop, XlSearchParameters.CrosslinkSearchTopNum, XlSearchParameters.XlQuench_H2O, XlSearchParameters.XlQuench_NH2, XlSearchParameters.XlQuench_Tris, XlSearchParameters.XlCharge_2_3, XlSearchParameters.XlCharge_2_3_PrimeFragment, thisId).Run();
ReportProgress(new ProgressEventArgs(100, "Done with search " + (currentPartition + 1) + "/" + CommonParameters.TotalPartitions + "!", thisId));
}
lock (psmLock)
{
allPsms.AddRange(newPsms.Where(p => p != null));
}
completedFiles++;
ReportProgress(new ProgressEventArgs(completedFiles / currentRawFileList.Count, "Searching...", new List <string> {
taskId, "Individual Spectra Files"
}));
}
ReportProgress(new ProgressEventArgs(100, "Done with all searches!", new List <string> {
taskId, "Individual Spectra Files"
}));
Status("Crosslink analysis engine", taskId);
MetaMorpheusEngineResults allcrosslinkanalysisResults;
allcrosslinkanalysisResults = new CrosslinkAnalysisEngine(allPsms, compactPeptideToProteinPeptideMatch, proteinList, variableModifications, fixedModifications, ionTypes, OutputFolder, crosslinker, terminusType, CommonParameters, new List <string> {
taskId
}).Run();
allPsms = allPsms.ToList();
if (XlSearchParameters.XlOutAll)
{
try
{
WriteAllToTsv(allPsms, OutputFolder, "allPsms", new List <string> {
taskId
});
}
catch (Exception)
{
throw;
}
}
var allPsmsXL = allPsms.Where(p => p.CrossType == PsmCrossType.Cross).Where(p => p.XLBestScore >= CommonParameters.ScoreCutoff && p.BetaPsmCross.XLBestScore >= CommonParameters.ScoreCutoff).ToList();
foreach (var item in allPsmsXL)
{
if (item.OneBasedStartResidueInProtein.HasValue)
{
item.XlProteinPos = item.OneBasedStartResidueInProtein.Value + item.XlPos - 1;
}
if (item.BetaPsmCross.OneBasedStartResidueInProtein.HasValue)
{
item.BetaPsmCross.XlProteinPos = item.BetaPsmCross.OneBasedStartResidueInProtein.Value + item.BetaPsmCross.XlPos - 1;
}
}
//Write Inter Psms FDR
var interPsmsXL = allPsmsXL.Where(p => !p.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First().Contains(p.BetaPsmCross.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First()) &&
!p.BetaPsmCross.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First().Contains(p.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First())).OrderByDescending(p => p.XLQvalueTotalScore).ToList();
foreach (var item in interPsmsXL)
{
item.CrossType = PsmCrossType.Inter;
}
var interPsmsXLFDR = CrosslinkDoFalseDiscoveryRateAnalysis(interPsmsXL).ToList();
//var interPsmsXLFDR = CrosslinkFDRAnalysis(interPsmsXL).ToList();
if (XlSearchParameters.XlOutCrosslink)
{
WriteCrosslinkToTsv(interPsmsXLFDR, OutputFolder, "xl_inter_fdr", new List <string> {
taskId
});
}
if (XlSearchParameters.XlOutPercolator)
{
try
{
var interPsmsXLPercolator = interPsmsXL.Where(p => p.XLBestScore >= 2 && p.BetaPsmCross.XLBestScore >= 2).OrderBy(p => p.ScanNumber).ToList();
WriteCrosslinkToTxtForPercolator(interPsmsXLPercolator, OutputFolder, "xl_inter_perc", crosslinker, new List <string> {
taskId
});
}
catch (Exception)
{
throw;
}
}
//Write Intra Psms FDR
var intraPsmsXL = allPsmsXL.Where(p => p.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First() == p.BetaPsmCross.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First() ||
p.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First().Contains(p.BetaPsmCross.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First()) ||
p.BetaPsmCross.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First().Contains(p.CompactPeptides.First().Value.Item2.Select(b => b.Protein.Accession).First())).OrderByDescending(p => p.XLQvalueTotalScore).ToList();
foreach (var item in intraPsmsXL)
{
item.CrossType = PsmCrossType.Intra;
}
var intraPsmsXLFDR = CrosslinkDoFalseDiscoveryRateAnalysis(intraPsmsXL).ToList();
//var intraPsmsXLFDR = CrosslinkFDRAnalysis(intraPsmsXL).ToList();
if (XlSearchParameters.XlOutCrosslink)
{
WriteCrosslinkToTsv(intraPsmsXLFDR, OutputFolder, "xl_intra_fdr", new List <string> {
taskId
});
}
if (XlSearchParameters.XlOutPercolator)
{
try
{
var intraPsmsXLPercolator = intraPsmsXL.Where(p => p.XLBestScore >= 2 && p.BetaPsmCross.XLBestScore >= 2).OrderBy(p => p.ScanNumber).ToList();
WriteCrosslinkToTxtForPercolator(intraPsmsXLPercolator, OutputFolder, "xl_intra_perc", crosslinker, new List <string> {
taskId
});
}
catch (Exception)
{
throw;
}
}
var singlePsms = allPsms.Where(p => p.CrossType == PsmCrossType.Singe && p.FullSequence != null && !p.FullSequence.Contains("Crosslink")).OrderByDescending(p => p.Score).ToList();
var singlePsmsFDR = SingleFDRAnalysis(singlePsms).ToList();
if (XlSearchParameters.XlOutAll)
{
WriteSingleToTsv(singlePsmsFDR, OutputFolder, "single_fdr", new List <string> {
taskId
});
}
var loopPsms = allPsms.Where(p => p.CrossType == PsmCrossType.Loop).OrderByDescending(p => p.XLTotalScore).ToList();
var loopPsmsFDR = SingleFDRAnalysis(loopPsms).ToList();
if (XlSearchParameters.XlOutAll)
{
WriteSingleToTsv(loopPsmsFDR, OutputFolder, "loop_fdr", new List <string> {
taskId
});
}
var deadendPsms = allPsms.Where(p => p.CrossType == PsmCrossType.DeadEnd || p.CrossType == PsmCrossType.DeadEndH2O || p.CrossType == PsmCrossType.DeadEndNH2 || p.CrossType == PsmCrossType.DeadEndTris).OrderByDescending(p => p.XLTotalScore).ToList();
deadendPsms.AddRange(allPsms.Where(p => p.CrossType == PsmCrossType.Singe && p.FullSequence != null && p.FullSequence.Contains("Crosslink")).ToList());
var deadendPsmsFDR = SingleFDRAnalysis(deadendPsms).ToList();
if (XlSearchParameters.XlOutAll)
{
WriteSingleToTsv(deadendPsmsFDR, OutputFolder, "deadend_fdr", new List <string> {
taskId
});
}
if (XlSearchParameters.XlOutPepXML)
{
List <PsmCross> allPsmsFDR = new List <PsmCross>();
allPsmsFDR.AddRange(intraPsmsXLFDR.Where(p => p.IsDecoy != true && p.BetaPsmCross.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList());
allPsmsFDR.AddRange(interPsmsXLFDR.Where(p => p.IsDecoy != true && p.BetaPsmCross.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList());
allPsmsFDR.AddRange(singlePsmsFDR.Where(p => p.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList());
allPsmsFDR.AddRange(loopPsmsFDR.Where(p => p.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList());
allPsmsFDR.AddRange(deadendPsmsFDR.Where(p => p.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList());
allPsmsFDR = allPsmsFDR.OrderBy(p => p.ScanNumber).ToList();
foreach (var fullFilePath in currentRawFileList)
{
string fileNameNoExtension = Path.GetFileNameWithoutExtension(fullFilePath);
WritePepXML_xl(allPsmsFDR.Where(p => p.FullFilePath == fullFilePath).ToList(), proteinList, dbFilenameList[0].FilePath, variableModifications, fixedModifications, localizeableModificationTypes, OutputFolder, fileNameNoExtension, new List <string> {
taskId
});
}
}
if (XlSearchParameters.XlOutAll)
{
List <PsmCross> allPsmsXLFDR = new List <PsmCross>();
allPsmsXLFDR.AddRange(intraPsmsXLFDR.Where(p => p.IsDecoy != true && p.BetaPsmCross.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList());
allPsmsXLFDR.AddRange(interPsmsXLFDR.Where(p => p.IsDecoy != true && p.BetaPsmCross.IsDecoy != true && p.FdrInfo.QValue <= 0.05).ToList());
try
{
allPsmsXLFDR = allPsmsXLFDR.OrderByDescending(p => p.XLQvalueTotalScore).ToList();
var allPsmsXLFDRGroup = FindCrosslinks(allPsmsXLFDR);
WriteCrosslinkToTsv(allPsmsXLFDRGroup, OutputFolder, "allPsmsXLFDRGroup", new List <string> {
taskId
});
}
catch (Exception)
{
throw;
}
}
return(MyTaskResults);
}
public CrosslinkAnalysisResults(CrosslinkAnalysisEngine s) : base(s)
{
}
