public void ExportPSMs(int nbPsmPerQuery, string filename)
{
//List<Query> qs = queries.ComputeAtFDR(1);
MSSearcher.Export(filename, queries);
}
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);
}
}
}