public PeptideMatches SearchClusters(List <Cluster> clusters, List <Precursor> precursors, bool DiffByMod = true)
{
options.ConSole.WriteLine("Creating the list of peptide found...");
Dictionary <string, PeptideMatch> peptideMatches = new Dictionary <string, PeptideMatch>();
foreach (Precursor prec in precursors)
{
foreach (PeptideSpectrumMatch psm in prec.OptimizedBestPsms())
{
Peptide pep = psm.Peptide;
string seq = (DiffByMod ? pep.Sequence : pep.BaseSequence);
if (!peptideMatches.ContainsKey(seq))
{
peptideMatches.Add(seq, new PeptideMatch(pep));
}
else if (pep.Target)
{
peptideMatches[seq].peptide = pep;
}
}
}
int nbClusterNewSeq = 0;
foreach (Cluster cl in clusters)
{
foreach (clCondition condition in cl.conditions)
{
if (condition != null)
{
foreach (clReplicate replicate in condition.replicates)
{
if (replicate != null)
{
foreach (Precursor precursor in replicate.precursors)
{
foreach (PeptideSpectrumMatch psm in precursor.OptimizedBestPsms())
{
string seq = (DiffByMod ? psm.Peptide.Sequence : psm.Peptide.BaseSequence);
if (peptideMatches.ContainsKey(seq))
{
peptideMatches[seq].AddOnlyOnce(cl);
}
else
{
nbClusterNewSeq++;
}
}
}
}
}
}
}
}
PeptideMatches TotalList = new PeptideMatches(peptideMatches.Values);
options.ConSole.WriteLine(TotalList.Count + " distinct peptides (based on sequence" + (DiffByMod ? " and modifications)" : ")") + " [" + nbClusterNewSeq + " not unmapped clusters]");
return(TotalList);
}
public Result()
{
queries = new Queries();
precursors = new Precursors();
matchedPrecursors = new Precursors();
clusters = new GraphML_List <Cluster>();
peptides = new PeptideMatches(new PeptideMatch[0]);
peptideSequences = new PeptideMatches(new PeptideMatch[0]);
proteins = new ProteinGroupMatches();
dbOptions = new DBOptions("");
samples = new Samples();
}
public void Export(double fdr, string keyword = "", bool onlyPrecursors = false)
{
dbOptions.ConSole.WriteLine("Exporting at " + (fdr * 100) + "% FDR (Decoy/Target)...");
List <Precursor> prec = null;
if (precursors != null)
{
if (matchedPrecursors == null)
{
this.matchedPrecursors = new Precursors();
foreach (Precursor precursor in precursors)
{
if (precursor.psms.Count > 0)
{
matchedPrecursors.Add(precursor);
}
}
}/*
* List<Precursor> prec = FDR.PrecursorsV2(precursors, fdr, 1);
* Sol.CONSOLE.OutputLine("> " + prec.Count + " Precursors");
* MSSearcher.Export(dbOptions.outputFolder + keyword + "precursors.csv", prec);//*/
/*
* prec = Optimizer.PrecursorOptimizer(matchedPrecursors, fdr);
* Sol.CONSOLE.OutputLine("> " + prec.Count + " Optimized Precursors");
* MSSearcher.Export(dbOptions.outputFolder + keyword + "Optimized_precursors.csv", prec);//*/
prec = matchedPrecursors.ComputeAtFDR(fdr);
dbOptions.ConSole.WriteLine("> " + prec.Count + " Uptimized V5 Precursors");
MSSearcher.Export(dbOptions.OutputFolder + keyword + "UptimizedV5_precursors.csv", prec);
}
if (!onlyPrecursors)
{
if (queries != null)
{
List <Query> qs = queries.ComputeAtFDR(fdr);
dbOptions.ConSole.WriteLine("> " + qs.Count + " PSMs (Top 10)");
MSSearcher.Export(dbOptions.OutputFolder + keyword + "queries.csv", qs);
}
if (clusters != null)
{
//List<PeptideSpectrumMatch> psms = FDR.PSMs(clusters, fdr, 1, 10);
//dbOptions.ConSole.WriteLine("> " + psms.Count + " PSMs (Top 10)");
//MSSearcher.Export(dbOptions.outputFolder + keyword + "psms_Top10.csv", psms);
//psms = FDR.PSMs(clusters, fdr, 1, 1);
//dbOptions.ConSole.WriteLine("> " + psms.Count + " PSMs");
//MSSearcher.Export(dbOptions.outputFolder + keyword + "psms_Best.csv", psms);
}
if (peptides != null)
{
List <PeptideMatch> pep = peptideSequences.ComputeAtFDR(fdr);
dbOptions.ConSole.WriteLine("> " + pep.Count + " Peptides Sequences (Version 5)");
PeptideSearcher.Export(dbOptions.OutputFolder + keyword + "peptideSequencesV5_.csv", pep);
PeptideSearcher sr = new PeptideSearcher(dbOptions);
PeptideMatches seqs = sr.Search(clusters, prec, false);
pep = seqs.ComputeAtFDR(fdr);
dbOptions.ConSole.WriteLine("> " + pep.Count + " Peptides Sequences (Version 5b)");
PeptideSearcher.Export(dbOptions.OutputFolder + keyword + "peptideSequencesV5b_PrecursorFDRed.csv", pep);
pep = peptides.ComputeAtFDR(fdr);
dbOptions.ConSole.WriteLine("> " + pep.Count + " Peptides (Version 5)");
PeptideSearcher.Export(dbOptions.OutputFolder + keyword + "peptidesV5_.csv", pep);
}
if (proteins != null)
{
List <ProteinGroupMatch> prots = proteins.ComputeAtFDR(fdr);
dbOptions.ConSole.WriteLine("> " + prots.Count + " Proteins");
ProteinSearcher.Export(dbOptions.OutputFolder + keyword + "proteins_.csv", prots);
}
}
}
/// <summary>
/// Updates scores for the PeptideSpectrumMatches based on newly computed elements (such as protein sequences, peptides, newly computed tolerances)
/// </summary>
/// <param name="protein_groups"></param>
public static PeptideMatches UpdatePsmScores(PeptideMatches peptides, Result result)
{
Dictionary <Precursor, PeptideMatch> dicOfUsedPrecursors = new Dictionary <Precursor, PeptideMatch>();
peptides.Sort(PeptideMatches.CompareScore);
foreach (Precursor precursor in result.precursors)
{
precursor.psms.Clear();
}
double maxPeptideProbScore = 0;
foreach (PeptideMatch peptide in peptides)
{
foreach (Cluster cluster in peptide.clusters)
{
foreach (clCondition condition in cluster.conditions)
{
if (condition != null)
{
foreach (clReplicate replicate in condition.replicates)
{
if (replicate != null)
{
foreach (Precursor precursor in replicate.precursors)
{
if (!dicOfUsedPrecursors.ContainsKey(precursor))
{
bool found = false;
foreach (PeptideSpectrumMatch psm in precursor.psms_AllPossibilities)
{
if (psm.Peptide.IsSamePeptide(peptide.peptide, true))
{
precursor.psms.Add(psm);
found = true;
}
}
if (found)
{
dicOfUsedPrecursors.Add(precursor, peptide);
}
}
}
}
}
}
}
}
double peptideScore = peptide.ProbabilityScore();
if (peptideScore > maxPeptideProbScore)
{
maxPeptideProbScore = peptideScore;
}
}
peptides.Sort(PeptideMatches.CompareScore);
foreach (PeptideMatch peptide in peptides)
{
double peptideScore = peptide.ProbabilityScore() / maxPeptideProbScore;
foreach (Cluster cluster in peptide.clusters)
{
foreach (clCondition condition in cluster.conditions)
{
if (condition != null)
{
foreach (clReplicate replicate in condition.replicates)
{
if (replicate != null)
{
foreach (Precursor precursor in replicate.precursors)
{
foreach (PeptideSpectrumMatch psm in precursor.psms)
{
if (peptide.peptide.IsSamePeptide(psm.Peptide, true))
{
if (psm.PeptideScore < peptideScore)
{
psm.PeptideScore = peptideScore;
}
}
}
foreach (Precursor isotope in precursor.Isotopes)
{
foreach (PeptideSpectrumMatch psm in isotope.psms)
{
if (peptide.peptide.IsSamePeptide(psm.Peptide, true))
{
if (psm.PeptideScore < peptideScore)
{
psm.PeptideScore = peptideScore;
}
}
}
}
precursor.psms.Sort(PeptideSpectrumMatch.DescendingOptimizedScoreComparison);
if (precursor.psms.Count == 0)
{
result.dbOptions.ConSole.WriteLine("Precursor with no match"); // = precursor;
}
}
}
}
}
}
}
}
return(peptides);
}