public static Dictionary <string, GlycoProteinParsimony> ProteinLevelGlycoParsimony(List <GlycoSpectralMatch> allPsmsGly)
{
//key: proPosId
Dictionary <string, GlycoProteinParsimony> localizedGlycan = new Dictionary <string, GlycoProteinParsimony>();
foreach (var gsm in allPsmsGly)
{
if (gsm.IsContaminant || gsm.IsDecoy)
{
continue;
}
if (gsm.LocalizedGlycan.Count > 0)
{
foreach (var local in gsm.LocalizedGlycan)
{
int proteinPos = local.Item1 + gsm.OneBasedStartResidueInProtein.Value - 2;
string proPosId = gsm.ProteinAccession + "-" + proteinPos.ToString() + "-" + local.Item2;
double prob = -1;
if (gsm.SiteSpeciLocalProb != null && gsm.SiteSpeciLocalProb.ContainsKey(local.Item1))
{
prob = gsm.SiteSpeciLocalProb[local.Item1].Where(p => p.Item1 == local.Item2).FirstOrDefault().Item2;
}
if (!localizedGlycan.ContainsKey(proPosId))
{
GlycoProteinParsimony gpp = new GlycoProteinParsimony(gsm.ProteinAccession, proteinPos, gsm.BaseSequence[local.Item1 - 2], local.Item3, gsm.FdrInfo.QValue, gsm.LocalizationLevel, prob);
localizedGlycan.Add(proPosId, gpp);
}
else
{
bool islocalized = (local.Item3 || localizedGlycan[proPosId].IsLocalized);
double minQValue = localizedGlycan[proPosId].MinQValue > gsm.FdrInfo.QValue ? gsm.FdrInfo.QValue : localizedGlycan[proPosId].MinQValue;
double maxProb = localizedGlycan[proPosId].MaxProbability > prob ? localizedGlycan[proPosId].MaxProbability : prob;
var localLevel = localizedGlycan[proPosId].BestLocalizeLevel < gsm.LocalizationLevel ? localizedGlycan[proPosId].BestLocalizeLevel : gsm.LocalizationLevel;
localizedGlycan[proPosId].IsLocalized = islocalized;
localizedGlycan[proPosId].MinQValue = minQValue;
localizedGlycan[proPosId].BestLocalizeLevel = localLevel;
localizedGlycan[proPosId].MaxProbability = maxProb;
}
}
}
}
return(localizedGlycan);
}
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);
}
}
