public GlycoSearchTask() : base(MyTask.GlycoSearch)
{
//Default parameter setting which is different from SearchTask, can be overwriten
var digestPara = new DigestionParams(
minPeptideLength: 5,
maxPeptideLength: 60
);
CommonParameters = new CommonParameters(
precursorMassTolerance: new PpmTolerance(10),
ms2childScanDissociationType: DissociationType.EThcD,
scoreCutoff: 3,
trimMsMsPeaks: false,
numberOfPeaksToKeepPerWindow: 1000,
minimumAllowedIntensityRatioToBasePeak: 0.01,
digestionParams: digestPara
);
_glycoSearchParameters = new GlycoSearchParameters();
}
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);
}
}
