public XLSearchTask() : base(MyTask.XLSearch)
{
CommonParameters = new CommonParameters();
XlSearchParameters = new XlSearchParameters();
}
public static void WritePepXML_xl(List <CrosslinkSpectralMatch> items, List <Protein> proteinList, string databasePath, List <Modification> variableModifications, List <Modification> fixedModifications, List <string> localizeableModificationTypes, string outputFolder, string fileName, CommonParameters CommonParameters, XlSearchParameters XlSearchParameters)
{
if (!items.Any())
{
return;
}
XmlSerializer _indexedSerializer = new XmlSerializer(typeof(pepXML.Generated.msms_pipeline_analysis));
var _pepxml = new pepXML.Generated.msms_pipeline_analysis();
_pepxml.date = DateTime.Now;
_pepxml.summary_xml = items[0].FullFilePath + ".pep.XML";
string proteaseC = ""; string proteaseNC = "";
foreach (var x in CommonParameters.DigestionParams.Protease.DigestionMotifs.Select(m => m.InducingCleavage))
{
proteaseC += x;
}
foreach (var x in CommonParameters.DigestionParams.Protease.DigestionMotifs.Select(m => m.PreventingCleavage))
{
proteaseNC += x;
}
Crosslinker crosslinker = XlSearchParameters.Crosslinker;
string fileNameNoExtension = Path.GetFileNameWithoutExtension(items[0].FullFilePath);
string filePathNoExtension = Path.ChangeExtension(items[0].FullFilePath, null);
string modSites = crosslinker.CrosslinkerModSites.ToCharArray().Concat(crosslinker.CrosslinkerModSites2.ToCharArray()).Distinct().ToString();
var para = new List <pepXML.Generated.nameValueType>();
{
para.Add(new pepXML.Generated.nameValueType {
name = "threads", value = CommonParameters.MaxThreadsToUsePerFile.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "database", value = databasePath
});
para.Add(new pepXML.Generated.nameValueType {
name = "MS_data_file", value = items[0].FullFilePath
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-link precursor Mass Tolerance", value = CommonParameters.PrecursorMassTolerance.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker type", value = crosslinker.CrosslinkerName
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker mass", value = crosslinker.TotalMass.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker cleavable", value = crosslinker.Cleavable.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker cleavable long mass", value = crosslinker.CleaveMassLong.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker cleavable short mass", value = crosslinker.CleaveMassShort.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker xl site", value = modSites
});
para.Add(new pepXML.Generated.nameValueType {
name = "Generate decoy proteins", value = XlSearchParameters.DecoyType.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "MaxMissed Cleavages", value = CommonParameters.DigestionParams.MaxMissedCleavages.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Protease", value = CommonParameters.DigestionParams.Protease.Name
});
para.Add(new pepXML.Generated.nameValueType {
name = "Initiator Methionine", value = CommonParameters.DigestionParams.InitiatorMethionineBehavior.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Max Modification Isoforms", value = CommonParameters.DigestionParams.MaxModificationIsoforms.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Min Peptide Len", value = CommonParameters.DigestionParams.MinPeptideLength.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Max Peptide Len", value = CommonParameters.DigestionParams.MaxPeptideLength.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Product Mass Tolerance", value = CommonParameters.ProductMassTolerance.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Ions to search", value = String.Join(", ", DissociationTypeCollection.ProductsFromDissociationType[CommonParameters.DissociationType])
});
foreach (var fixedMod in fixedModifications)
{
para.Add(new pepXML.Generated.nameValueType {
name = "Fixed Modifications: " + fixedMod.IdWithMotif, value = fixedMod.MonoisotopicMass.ToString()
});
}
foreach (var variableMod in variableModifications)
{
para.Add(new pepXML.Generated.nameValueType {
name = "Variable Modifications: " + variableMod.IdWithMotif, value = variableMod.MonoisotopicMass.ToString()
});
}
para.Add(new pepXML.Generated.nameValueType {
name = "Localize All Modifications", value = "true"
});
}
_pepxml.msms_run_summary = new pepXML.Generated.msms_pipeline_analysisMsms_run_summary[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summary
{
base_name = filePathNoExtension,
raw_data_type = "raw",
raw_data = ".mzML",
sample_enzyme = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzyme()
{
name = CommonParameters.DigestionParams.Protease.Name,
specificity = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzymeSpecificity[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzymeSpecificity
{
cut = proteaseC,
no_cut = proteaseNC,
}
}
},
search_summary = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summary[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summary
{
base_name = filePathNoExtension,
search_engine_version = GlobalVariables.MetaMorpheusVersion,
precursor_mass_type = pepXML.Generated.massType.monoisotopic,
fragment_mass_type = pepXML.Generated.massType.monoisotopic,
search_id = 1,
search_database = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summarySearch_database
{
local_path = databasePath,
type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summarySearch_databaseType.AA,
},
enzymatic_search_constraint = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summaryEnzymatic_search_constraint
{
enzyme = CommonParameters.DigestionParams.Protease.Name,
max_num_internal_cleavages = CommonParameters.DigestionParams.MaxMissedCleavages.ToString(),
//min_number_termini = "2"
},
parameter = para.ToArray()
}
},
}
};
_pepxml.msms_run_summary[0].spectrum_query = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_query[items.Count];
var searchHits = new List <pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit>();
for (int i = 0; i < items.Count; i++)
{
var mods = new List <pepXML.Generated.modInfoDataTypeMod_aminoacid_mass>();
var alphaPeptide = items[i].BestMatchingPeptides.First().Peptide;
foreach (var modification in alphaPeptide.AllModsOneIsNterminus)
{
var mod = new pepXML.Generated.modInfoDataTypeMod_aminoacid_mass
{
mass = modification.Value.MonoisotopicMass.Value,
// convert from one-based to zero-based (N-term is zero in the pepXML output)
position = (modification.Key - 1).ToString()
};
mods.Add(mod);
}
if (items[i].CrossType == PsmCrossType.Single)
{
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = alphaPeptide.BaseSequence,
peptide_prev_aa = alphaPeptide.PreviousAminoAcid.ToString(),
peptide_next_aa = alphaPeptide.NextAminoAcid.ToString(),
protein = alphaPeptide.Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMass,
massdiff = (items[i].ScanPrecursorMass - items[i].PeptideMonisotopicMass.Value).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.na,
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
},
};
searchHits.Add(searchHit);
}
else if (items[i].CrossType == PsmCrossType.DeadEnd || items[i].CrossType == PsmCrossType.DeadEndH2O || items[i].CrossType == PsmCrossType.DeadEndNH2 || items[i].CrossType == PsmCrossType.DeadEndTris)
{
double crosslinkerDeadEndMass = 0;
switch (items[i].CrossType)
{
case PsmCrossType.DeadEndNH2:
crosslinkerDeadEndMass = crosslinker.DeadendMassNH2;
break;
case PsmCrossType.DeadEndTris:
crosslinkerDeadEndMass = crosslinker.DeadendMassTris;
break;
default:
crosslinkerDeadEndMass = crosslinker.DeadendMassH2O;
break;
}
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = alphaPeptide.BaseSequence,
peptide_prev_aa = alphaPeptide.PreviousAminoAcid.ToString(),
peptide_next_aa = alphaPeptide.NextAminoAcid.ToString(),
protein = alphaPeptide.Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMass,
massdiff = (items[i].ScanPrecursorMass - items[i].PeptideMonisotopicMass.Value - crosslinkerDeadEndMass).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.na,
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
},
};
searchHits.Add(searchHit);
}
else if (items[i].CrossType == PsmCrossType.Inter || items[i].CrossType == PsmCrossType.Intra || items[i].CrossType == PsmCrossType.Cross)
{
var betaPeptide = items[i].BetaPeptide.BestMatchingPeptides.First().Peptide;
var modsBeta = new List <pepXML.Generated.modInfoDataTypeMod_aminoacid_mass>();
foreach (var mod in betaPeptide.AllModsOneIsNterminus)
{
var modBeta = new pepXML.Generated.modInfoDataTypeMod_aminoacid_mass
{
mass = mod.Value.MonoisotopicMass.Value,
// convert from one-based to zero-based (N-term is zero in the pepXML output)
position = (mod.Key - 1).ToString()
};
modsBeta.Add(modBeta);
}
var alpha = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide
{
peptide = alphaPeptide.BaseSequence,
peptide_prev_aa = alphaPeptide.PreviousAminoAcid.ToString(),
peptide_next_aa = alphaPeptide.NextAminoAcid.ToString(),
protein = alphaPeptide.Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].PeptideMonisotopicMass.Value,
complement_mass = (float)(items[i].ScanPrecursorMass - alphaPeptide.MonoisotopicMass),
designation = "alpha",
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
xlink_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlscore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "link", value = items[i].LinkPositions.First().ToString()
},
}
};
var beta = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide
{
peptide = betaPeptide.BaseSequence,
peptide_prev_aa = betaPeptide.PreviousAminoAcid.ToString(),
peptide_next_aa = betaPeptide.NextAminoAcid.ToString(),
protein = betaPeptide.Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)betaPeptide.MonoisotopicMass,
complement_mass = (float)(items[i].ScanPrecursorMass - betaPeptide.MonoisotopicMass),
designation = "beta",
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = modsBeta.ToArray()
},
xlink_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlscore", value = items[i].BetaPeptide.Score.ToString()
},
new pepXML.Generated.nameValueType {
name = "link", value = items[i].BetaPeptide.LinkPositions.First().ToString()
},
}
};
var cross = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide[2] {
alpha, beta
};
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = "-",
peptide_prev_aa = "-",
peptide_next_aa = "-",
protein = "-",
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMass,
massdiff = (items[i].ScanPrecursorMass - betaPeptide.MonoisotopicMass - alphaPeptide.MonoisotopicMass - crosslinker.TotalMass).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.xl,
xlink = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink
{
identifier = crosslinker.CrosslinkerName,
mass = (float)crosslinker.TotalMass,
linked_peptide = cross
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
}
};
searchHits.Add(searchHit);
}
else if (items[i].CrossType == PsmCrossType.Loop)
{
var thePeptide = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide
{
xlink_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "link", value = items[i].LinkPositions.First().ToString()
},
new pepXML.Generated.nameValueType {
name = "link", value = items[i].LinkPositions[1].ToString()
}
}
};
var cross = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide[1] {
thePeptide
};
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = alphaPeptide.BaseSequence,
peptide_prev_aa = alphaPeptide.PreviousAminoAcid.ToString(),
peptide_next_aa = alphaPeptide.NextAminoAcid.ToString(),
protein = alphaPeptide.Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMass,
massdiff = (items[i].ScanPrecursorMass - alphaPeptide.MonoisotopicMass - crosslinker.LoopMass).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.loop,
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
xlink = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink
{
identifier = crosslinker.CrosslinkerName,
mass = (float)crosslinker.TotalMass,
linked_peptide = cross
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
}
};
searchHits.Add(searchHit);
}
}
for (int i = 0; i < items.Count; i++)
{
_pepxml.msms_run_summary[0].spectrum_query[i] = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_query()
{
spectrum = fileNameNoExtension + "." + items[i].ScanNumber.ToString(),
start_scan = Convert.ToUInt32(items[i].ScanNumber),
end_scan = Convert.ToUInt32(items[i].ScanNumber),
precursor_neutral_mass = (float)items[i].ScanPrecursorMass,
assumed_charge = items[i].ScanPrecursorCharge.ToString(),
index = Convert.ToUInt32(i + 1),
retention_time_sec = (float)(items[i].ScanRetentionTime * 60),
search_result = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_result[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_result
{
search_hit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit[1]
{
searchHits[i]
}
}
}
};
}
TextWriter writer = new StreamWriter(Path.Combine(outputFolder, fileName + ".pep.XML"));
_indexedSerializer.Serialize(writer, _pepxml);
writer.Close();
}
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 List <CrosslinkSpectralMatch> RunSingleFile(string outputFolder, string taskId, List <CrosslinkSpectralMatch> allPsms, XlSearchParameters xlSearchParameters)
{
List <CrosslinkSpectralMatch> allFilterPsms = new List <CrosslinkSpectralMatch>();
if (!Directory.Exists(outputFolder))
{
Directory.CreateDirectory(outputFolder);
}
// 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();
DoCrosslinkFdrAnalysis(interCsms);
DoCrosslinkFdrAnalysis(intraCsms);
DoCrosslinkFdrAnalysis(singlePsms);
DoCrosslinkFdrAnalysis(loopPsms);
DoCrosslinkFdrAnalysis(deadendPsms);
WriteCsvFiles(outputFolder, interCsms, intraCsms, singlePsms, loopPsms, deadendPsms, taskId, xlSearchParameters);
allFilterPsms.AddRange(interCsms.Where(p => p.FdrInfo.QValue <= 0.2));
allFilterPsms.AddRange(intraCsms.Where(p => p.FdrInfo.QValue <= 0.2));
allFilterPsms.AddRange(singlePsms.Where(p => p.FdrInfo.QValue <= 0.2));
allFilterPsms.AddRange(loopPsms.Where(p => p.FdrInfo.QValue <= 0.2));
allFilterPsms.AddRange(deadendPsms.Where(p => p.FdrInfo.QValue <= 0.2));
return(allFilterPsms);
}
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
});
}
}