public MyTaskResults Run(string outputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, List <CrosslinkSpectralMatch> allPsms, CommonParameters commonParameters, XlSearchParameters xlSearchParameters, List <Protein> proteinList, List <Modification> variableModifications, List <Modification> fixedModifications, List <string> localizeableModificationTypes, MyTaskResults MyTaskResults)
{
// inter-crosslinks; different proteins are linked
List <CrosslinkSpectralMatch> interCsms = allPsms.Where(p => p.CrossType == PsmCrossType.Inter).OrderByDescending(p => p.XLTotalScore).ToList();
// intra-crosslinks; crosslinks within a protein
List <CrosslinkSpectralMatch> intraCsms = allPsms.Where(p => p.CrossType == PsmCrossType.Intra).OrderByDescending(p => p.XLTotalScore).ToList();
var singlePsms = allPsms.Where(p => p.CrossType == PsmCrossType.Single).OrderByDescending(p => p.Score).ToList();
var loopPsms = allPsms.Where(p => p.CrossType == PsmCrossType.Loop).OrderByDescending(p => p.Score).ToList();
var deadendPsms = allPsms.Where(p => p.CrossType == PsmCrossType.DeadEnd ||
p.CrossType == PsmCrossType.DeadEndH2O ||
p.CrossType == PsmCrossType.DeadEndNH2 ||
p.CrossType == PsmCrossType.DeadEndTris).OrderByDescending(p => p.Score).ToList();
ComputeXlinkQandPValues(allPsms, intraCsms, interCsms, commonParameters, taskId);
WriteCsvFiles(outputFolder, interCsms, intraCsms, singlePsms, loopPsms, deadendPsms, taskId, xlSearchParameters);
MyTaskResults.AddTaskSummaryText("Target inter-crosslinks within 1% FDR: " + interCsms.Count(p => p.FdrInfo.QValue <= 0.01 && !p.IsDecoy && !p.BetaPeptide.IsDecoy));
MyTaskResults.AddTaskSummaryText("Target intra-crosslinks within 1% FDR: " + intraCsms.Count(p => p.FdrInfo.QValue <= 0.01 && !p.IsDecoy && !p.BetaPeptide.IsDecoy));
MyTaskResults.AddTaskSummaryText("Target single peptides within 1% FDR: " + singlePsms.Count(p => p.FdrInfo.QValue <= 0.01 && !p.IsDecoy));
MyTaskResults.AddTaskSummaryText("Target loop-linked peptides within 1% FDR: " + loopPsms.Count(p => p.FdrInfo.QValue <= 0.01 && !p.IsDecoy));
MyTaskResults.AddTaskSummaryText("Target deadend peptides within 1% FDR: " + deadendPsms.Count(p => p.FdrInfo.QValue <= 0.01 && !p.IsDecoy));
// write pepXML
if (xlSearchParameters.WritePepXml)
{
List <CrosslinkSpectralMatch> writeToXml = new List <CrosslinkSpectralMatch>();
writeToXml.AddRange(intraCsms.Where(p => !p.IsDecoy && !p.BetaPeptide.IsDecoy && p.FdrInfo.QValue <= 0.05));
writeToXml.AddRange(interCsms.Where(p => !p.IsDecoy && !p.BetaPeptide.IsDecoy && p.FdrInfo.QValue <= 0.05));
writeToXml.AddRange(singlePsms.Where(p => !p.IsDecoy && p.FdrInfo.QValue <= 0.05));
writeToXml.AddRange(loopPsms.Where(p => !p.IsDecoy && p.FdrInfo.QValue <= 0.05));
writeToXml.AddRange(deadendPsms.Where(p => !p.IsDecoy && p.FdrInfo.QValue <= 0.05));
writeToXml = writeToXml.OrderBy(p => p.ScanNumber).ToList();
foreach (var fullFilePath in currentRawFileList)
{
string fileNameNoExtension = Path.GetFileNameWithoutExtension(fullFilePath);
WriteFile.WritePepXML_xl(writeToXml.Where(p => p.FullFilePath == fullFilePath).ToList(), proteinList, dbFilenameList[0].FilePath, variableModifications, fixedModifications, localizeableModificationTypes, outputFolder, fileNameNoExtension, commonParameters, xlSearchParameters);
FinishedWritingFile(Path.Combine(outputFolder, fileNameNoExtension + ".pep.XML"), new List <string> {
taskId
});
}
}
return(MyTaskResults);
}
public MyTaskResults Run(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList, List <CrosslinkSpectralMatch> allPsms, CommonParameters commonParameters, XlSearchParameters xlSearchParameters, List <Protein> proteinList, List <Modification> variableModifications, List <Modification> fixedModifications, List <string> localizeableModificationTypes, MyTaskResults MyTaskResults)
{
foreach (var csm in allPsms)
{
csm.ResolveProteinPosAmbiguitiesForXl();
}
var allPsmsXL = allPsms.Where(p => p.CrossType == PsmCrossType.Cross).ToList();
// inter-crosslinks; different proteins are linked
var interCsms = allPsmsXL.Where(p => !p.IsIntraCsm()).ToList();
foreach (var item in interCsms)
{
item.CrossType = PsmCrossType.Inter;
}
// intra-crosslinks; crosslinks within a protein
var intraCsms = allPsmsXL.Where(p => p.IsIntraCsm()).ToList();
foreach (var item in intraCsms)
{
item.CrossType = PsmCrossType.Intra;
}
// calculate FDR
DoCrosslinkFdrAnalysis(interCsms);
DoCrosslinkFdrAnalysis(intraCsms);
SingleFDRAnalysis(allPsms, commonParameters, new List <string> {
taskId
});
// write interlink CSMs
if (interCsms.Any())
{
string file = Path.Combine(OutputFolder, "XL_Interlinks.tsv");
WriteFile.WritePsmCrossToTsv(interCsms, file, 2);
FinishedWritingFile(file, new List <string> {
taskId
});
}
MyTaskResults.AddNiceText("Target inter-crosslinks within 1% FDR: " + interCsms.Count(p => p.FdrInfo.QValue <= 0.01 && !p.IsDecoy && !p.BetaPeptide.IsDecoy));
if (xlSearchParameters.WriteOutputForPercolator)
{
var interPsmsXLPercolator = interCsms.Where(p => p.Score >= 2 && p.BetaPeptide.Score >= 2).OrderBy(p => p.ScanNumber).ToList();
WriteFile.WriteCrosslinkToTxtForPercolator(interPsmsXLPercolator, OutputFolder, "XL_Interlinks_Percolator", xlSearchParameters.Crosslinker);
FinishedWritingFile(Path.Combine(OutputFolder, "XL_Interlinks_Percolator.txt"), new List <string> {
taskId
});
}
// write intralink CSMs
if (intraCsms.Any())
{
string file = Path.Combine(OutputFolder, "XL_Intralinks.tsv");
WriteFile.WritePsmCrossToTsv(intraCsms, file, 2);
FinishedWritingFile(file, new List <string> {
taskId
});
}
MyTaskResults.AddNiceText("Target intra-crosslinks within 1% FDR: " + intraCsms.Count(p => p.FdrInfo.QValue <= 0.01 && !p.IsDecoy && !p.BetaPeptide.IsDecoy));
if (xlSearchParameters.WriteOutputForPercolator)
{
var intraPsmsXLPercolator = intraCsms.Where(p => p.Score >= 2 && p.BetaPeptide.Score >= 2).OrderBy(p => p.ScanNumber).ToList();
WriteFile.WriteCrosslinkToTxtForPercolator(intraPsmsXLPercolator, OutputFolder, "XL_Intralinks_Percolator", xlSearchParameters.Crosslinker);
FinishedWritingFile(Path.Combine(OutputFolder, "XL_Intralinks_Percolator.txt"), new List <string> {
taskId
});
}
// write single peptides
var singlePsms = allPsms.Where(p => p.CrossType == PsmCrossType.Single).ToList();
if (singlePsms.Any())
{
string writtenFileSingle = Path.Combine(OutputFolder, "SinglePeptides" + ".tsv");
WriteFile.WritePsmCrossToTsv(singlePsms, writtenFileSingle, 1);
FinishedWritingFile(writtenFileSingle, new List <string> {
taskId
});
}
MyTaskResults.AddNiceText("Target single peptides within 1% FDR: " + singlePsms.Count(p => p.FdrInfo.QValue <= 0.01 && !p.IsDecoy));
// write loops
var loopPsms = allPsms.Where(p => p.CrossType == PsmCrossType.Loop).ToList();
if (loopPsms.Any())
{
string writtenFileLoop = Path.Combine(OutputFolder, "Looplinks" + ".tsv");
WriteFile.WritePsmCrossToTsv(loopPsms, writtenFileLoop, 1);
FinishedWritingFile(writtenFileLoop, new List <string> {
taskId
});
}
MyTaskResults.AddNiceText("Target loop-linked peptides within 1% FDR: " + loopPsms.Count(p => p.FdrInfo.QValue <= 0.01 && !p.IsDecoy));
// write deadends
var deadendPsms = allPsms.Where(p => p.CrossType == PsmCrossType.DeadEnd ||
p.CrossType == PsmCrossType.DeadEndH2O ||
p.CrossType == PsmCrossType.DeadEndNH2 ||
p.CrossType == PsmCrossType.DeadEndTris).ToList();
if (deadendPsms.Any())
{
string writtenFileDeadend = Path.Combine(OutputFolder, "Deadends" + ".tsv");
WriteFile.WritePsmCrossToTsv(deadendPsms, writtenFileDeadend, 1);
FinishedWritingFile(writtenFileDeadend, new List <string> {
taskId
});
}
MyTaskResults.AddNiceText("Target deadend peptides within 1% FDR: " + deadendPsms.Count(p => p.FdrInfo.QValue <= 0.01 && !p.IsDecoy));
// write pepXML
if (xlSearchParameters.WritePepXml)
{
List <CrosslinkSpectralMatch> writeToXml = new List <CrosslinkSpectralMatch>();
writeToXml.AddRange(intraCsms.Where(p => !p.IsDecoy && !p.BetaPeptide.IsDecoy && p.FdrInfo.QValue <= 0.05));
writeToXml.AddRange(interCsms.Where(p => !p.IsDecoy && !p.BetaPeptide.IsDecoy && p.FdrInfo.QValue <= 0.05));
writeToXml.AddRange(singlePsms.Where(p => !p.IsDecoy && p.FdrInfo.QValue <= 0.05));
writeToXml.AddRange(loopPsms.Where(p => !p.IsDecoy && p.FdrInfo.QValue <= 0.05));
writeToXml.AddRange(deadendPsms.Where(p => !p.IsDecoy && p.FdrInfo.QValue <= 0.05));
writeToXml = writeToXml.OrderBy(p => p.ScanNumber).ToList();
foreach (var fullFilePath in currentRawFileList)
{
string fileNameNoExtension = Path.GetFileNameWithoutExtension(fullFilePath);
WriteFile.WritePepXML_xl(writeToXml.Where(p => p.FullFilePath == fullFilePath).ToList(), proteinList, dbFilenameList[0].FilePath, variableModifications, fixedModifications, localizeableModificationTypes, OutputFolder, fileNameNoExtension, commonParameters, xlSearchParameters);
FinishedWritingFile(Path.Combine(OutputFolder, fileNameNoExtension + ".pep.XML"), new List <string> {
taskId
});
}
}
return(MyTaskResults);
}
public MyTaskResults Run(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList, List <GlycoSpectralMatch> allPsms, CommonParameters commonParameters, GlycoSearchParameters glycoSearchParameters, List <Protein> proteinList, List <Modification> variableModifications, List <Modification> fixedModifications, List <string> localizeableModificationTypes, MyTaskResults MyTaskResults)
{
if (glycoSearchParameters.GlycoSearchType == GlycoSearchType.NGlycanSearch)
{
var allPsmsSingle = allPsms.Where(p => p.NGlycan == null).OrderByDescending(p => p.Score).ToList();
SingleFDRAnalysis(allPsmsSingle, commonParameters, new List <string> {
taskId
});
var writtenFileSingle = Path.Combine(OutputFolder, "single" + ".psmtsv");
WriteFile.WritePsmGlycoToTsv(allPsmsSingle, writtenFileSingle, 1);
FinishedWritingFile(writtenFileSingle, new List <string> {
taskId
});
var allPsmsGly = allPsms.Where(p => p.NGlycan != null).OrderByDescending(p => p.Score).ToList();
SingleFDRAnalysis(allPsmsGly, commonParameters, new List <string> {
taskId
});
var writtenFileNGlyco = Path.Combine(OutputFolder, "nglyco" + ".psmtsv");
WriteFile.WritePsmGlycoToTsv(allPsmsGly, writtenFileNGlyco, 3);
FinishedWritingFile(writtenFileNGlyco, new List <string> {
taskId
});
return(MyTaskResults);
}
else if (glycoSearchParameters.GlycoSearchType == GlycoSearchType.OGlycanSearch)
{
var allPsmsSingle = allPsms.Where(p => p.Routes == null).OrderByDescending(p => p.Score).ToList();
SingleFDRAnalysis(allPsmsSingle, commonParameters, new List <string> {
taskId
});
var writtenFileSingle = Path.Combine(OutputFolder, "single" + ".psmtsv");
WriteFile.WritePsmGlycoToTsv(allPsmsSingle, writtenFileSingle, 1);
FinishedWritingFile(writtenFileSingle, new List <string> {
taskId
});
var allPsmsGly = allPsms.Where(p => p.Routes != null).OrderByDescending(p => p.Score).ToList();
SingleFDRAnalysis(allPsmsGly, commonParameters, new List <string> {
taskId
});
var writtenFileOGlyco = Path.Combine(OutputFolder, "oglyco" + ".psmtsv");
WriteFile.WritePsmGlycoToTsv(allPsmsGly, writtenFileOGlyco, 2);
FinishedWritingFile(writtenFileOGlyco, new List <string> {
taskId
});
var ProteinLevelLocalization = GlycoProteinParsimony.ProteinLevelGlycoParsimony(allPsmsGly.Where(p => p.ProteinAccession != null && p.OneBasedStartResidueInProtein.HasValue).ToList());
var seen_oglyco_localization_file = Path.Combine(OutputFolder, "seen_oglyco_localization" + ".tsv");
WriteFile.WriteSeenProteinGlycoLocalization(ProteinLevelLocalization, seen_oglyco_localization_file);
FinishedWritingFile(seen_oglyco_localization_file, new List <string> {
taskId
});
var protein_oglyco_localization_file = Path.Combine(OutputFolder, "protein_oglyco_localization" + ".tsv");
WriteFile.WriteProteinGlycoLocalization(ProteinLevelLocalization, protein_oglyco_localization_file);
FinishedWritingFile(protein_oglyco_localization_file, new List <string> {
taskId
});
return(MyTaskResults);
}
else
{
var allPsmsSingle = allPsms.Where(p => p.NGlycan == null && p.Routes == null).OrderByDescending(p => p.Score).ToList();
SingleFDRAnalysis(allPsmsSingle, commonParameters, new List <string> {
taskId
});
var writtenFileSingle = Path.Combine(OutputFolder, "single" + ".psmtsv");
WriteFile.WritePsmGlycoToTsv(allPsmsSingle, writtenFileSingle, 1);
FinishedWritingFile(writtenFileSingle, new List <string> {
taskId
});
var allPsmsNGly = allPsms.Where(p => p.NGlycan != null).OrderByDescending(p => p.Score).ToList();
SingleFDRAnalysis(allPsmsNGly, commonParameters, new List <string> {
taskId
});
var writtenFileNGlyco = Path.Combine(OutputFolder, "nglyco" + ".psmtsv");
WriteFile.WritePsmGlycoToTsv(allPsmsNGly, writtenFileNGlyco, 3);
FinishedWritingFile(writtenFileNGlyco, new List <string> {
taskId
});
var allPsmsOGly = allPsms.Where(p => p.Routes != null).OrderByDescending(p => p.Score).ToList();
SingleFDRAnalysis(allPsmsOGly, commonParameters, new List <string> {
taskId
});
var writtenFileOGlyco = Path.Combine(OutputFolder, "oglyco" + ".psmtsv");
WriteFile.WritePsmGlycoToTsv(allPsmsOGly, writtenFileOGlyco, 2);
FinishedWritingFile(writtenFileOGlyco, new List <string> {
taskId
});
return(MyTaskResults);
}
}
public void WriteCsvFiles(string outputFolder, List <CrosslinkSpectralMatch> interCsms, List <CrosslinkSpectralMatch> intraCsms, List <CrosslinkSpectralMatch> singlePsms,
List <CrosslinkSpectralMatch> loopPsms, List <CrosslinkSpectralMatch> deadendPsms, string taskId, XlSearchParameters xlSearchParameters)
{
// write interlink CSMs
if (interCsms.Any())
{
string file = Path.Combine(outputFolder, "XL_Interlinks.tsv");
WriteFile.WritePsmCrossToTsv(interCsms, file, 2);
FinishedWritingFile(file, new List <string> {
taskId
});
}
if (xlSearchParameters.WriteOutputForPercolator)
{
var interPsmsXLPercolator = interCsms.Where(p => p.Score >= 2 && p.BetaPeptide.Score >= 2).OrderBy(p => p.ScanNumber).ToList();
WriteFile.WriteCrosslinkToTxtForPercolator(interPsmsXLPercolator, outputFolder, "XL_Interlinks_Percolator", xlSearchParameters.Crosslinker);
FinishedWritingFile(Path.Combine(outputFolder, "XL_Interlinks_Percolator.txt"), new List <string> {
taskId
});
}
// write intralink CSMs
if (intraCsms.Any())
{
string file = Path.Combine(outputFolder, "XL_Intralinks.tsv");
WriteFile.WritePsmCrossToTsv(intraCsms, file, 2);
FinishedWritingFile(file, new List <string> {
taskId
});
}
if (xlSearchParameters.WriteOutputForPercolator)
{
var intraPsmsXLPercolator = intraCsms.Where(p => p.Score >= 2 && p.BetaPeptide.Score >= 2).OrderBy(p => p.ScanNumber).ToList();
WriteFile.WriteCrosslinkToTxtForPercolator(intraPsmsXLPercolator, outputFolder, "XL_Intralinks_Percolator", xlSearchParameters.Crosslinker);
FinishedWritingFile(Path.Combine(outputFolder, "XL_Intralinks_Percolator.txt"), new List <string> {
taskId
});
}
// write single peptides
if (singlePsms.Any())
{
string writtenFileSingle = Path.Combine(outputFolder, "SinglePeptides" + ".tsv");
WriteFile.WritePsmCrossToTsv(singlePsms, writtenFileSingle, 1);
FinishedWritingFile(writtenFileSingle, new List <string> {
taskId
});
}
// write loops
if (loopPsms.Any())
{
string writtenFileLoop = Path.Combine(outputFolder, "Looplinks" + ".tsv");
WriteFile.WritePsmCrossToTsv(loopPsms, writtenFileLoop, 1);
FinishedWritingFile(writtenFileLoop, new List <string> {
taskId
});
}
// write deadends
if (deadendPsms.Any())
{
string writtenFileDeadend = Path.Combine(outputFolder, "Deadends" + ".tsv");
WriteFile.WritePsmCrossToTsv(deadendPsms, writtenFileDeadend, 1);
FinishedWritingFile(writtenFileDeadend, new List <string> {
taskId
});
}
}
