public void ParseDirs(List <DirectoryClassDescription> myDirectoryDescriptionDictionary) { MyDirectoryDescriptionDictionary = myDirectoryDescriptionDictionary; MyResultPackages = new List <ResultEntry>(); foreach (DirectoryClassDescription dcd in myDirectoryDescriptionDictionary) { //Get all Sepro Files in this and in deeper directories //FileInfo[] fileInfo = dcd.MyDirectory.GetFiles("*.sepr"); FileInfo[] fileInfo = new DirectoryInfo(dcd.MyDirectoryFullName).GetFiles("*.sepr", SearchOption.AllDirectories); foreach (FileInfo file in fileInfo) { //First lets unserialize the object Console.WriteLine("Loading .. " + file.FullName); ResultPackage rp = ResultPackage.Load(file.FullName); //Lets free um some ram foreach (SQTScan s in rp.MyProteins.AllSQTScans) { s.MSLight = null; } MyResultPackages.Add(new ResultEntry(rp, file, dcd.ClassLabel)); } Console.WriteLine("Done loading."); } }
private static void PrintHead(ResultPackage resultPackage, System.IO.StreamWriter sw) { string versionNo = "NT"; try { string[] stuff = Regex.Split(AppDomain.CurrentDomain.SetupInformation.ActivationArguments.ActivationContext.Identity.FullName, ","); versionNo = stuff[1]; } catch { } sw.WriteLine("Search Engine Processor v" + versionNo); sw.WriteLine("Input directory: {0}", resultPackage.SQTDirectory); sw.WriteLine("Database searched: {0}", resultPackage.Database); sw.WriteLine(""); sw.WriteLine("{0}\tComposite score considers primary score", resultPackage.MyParameters.CompositeScorePrimaryScore); sw.WriteLine("{0}\tComposite score considers secondary score", resultPackage.MyParameters.CompositeScoreSecondaryScore); sw.WriteLine("{0}\tComposite score considers deltaCN", resultPackage.MyParameters.CompositeScoreDeltaCN); sw.WriteLine("{0}\tComposite score considers peaks matched", resultPackage.MyParameters.CompositeScorePeaksMatched); sw.WriteLine("{0}\tCompostie score considers deltaMass", resultPackage.MyParameters.CompositeScoreDeltaMassPPM); sw.WriteLine("{0}\tSpectra max FDR", resultPackage.MyParameters.SpectraFDR); sw.WriteLine("{0}\tPeptide max FDR", resultPackage.MyParameters.PeptideFDR); sw.WriteLine("{0}\tProtein max FDR", resultPackage.MyParameters.ProteinFDR); sw.WriteLine("{0}\tQualityFilterMinSequenceLength", resultPackage.MyParameters.QFilterMinSequenceLength); string qdDeltaPPM = "False"; if (resultPackage.MyParameters.QFilterDeltaMassPPM) { qdDeltaPPM = resultPackage.MyParameters.QFilterDeltaMassPPMValue.ToString(); } sw.WriteLine("{0}\tQualityFilterDeltaMassPPM", qdDeltaPPM); double primScore = 0; if (resultPackage.MyParameters.QFilterPrimaryScore) { primScore = resultPackage.MyParameters.QFilterPrimaryScoreValue; } sw.WriteLine("{0}\tQualityFilterPrimaryScore", primScore); double secScore = 0; if (resultPackage.MyParameters.QFilterSecondaryScore) { secScore = resultPackage.MyParameters.QFilterSecondaryScoreValue; } sw.WriteLine("{0}\tQualityFilterSecondaryScore", secScore); sw.WriteLine("{0}\tQualityFilterDiscardNonTryptic", resultPackage.MyParameters.QFilterMinNoEnzymaticTermini); sw.WriteLine("{0}\tQualityFilterIncludeOnlyLociWithUniquePeptide", resultPackage.MyParameters.QFilterDiscardProteinsWithNoUniquePeptides); sw.WriteLine("{0}\tQualityFilterIncludeOnlyLociWithTwoOrMorePeptides", resultPackage.MyParameters.QFilterProteinsMinNoPeptides); sw.WriteLine(""); }
public static void SaveReportByFileName(string fileName, ResultPackage resultPackage) { System.IO.StreamWriter sw = new System.IO.StreamWriter(fileName); //Print the head PrintHead(resultPackage, sw); sw.WriteLine("#Scan Line: Unique\tFileName\tPrimaryScore\tDeltCN\tM+H+\tCalcM+H+\tZScore\tBayesianScore\tRedundancyAtPtnLevel\tSequence"); //Obtain a list of unique file Names List <string> fileNames = (from peptide in resultPackage.MyProteins.MyPeptideList from scan in peptide.MyScans select scan.FileName).Distinct().ToList(); fileNames.Sort(); foreach (var fname in fileNames) { sw.WriteLine("\nFileName: " + fname); List <MyProtein> myProtein = (from protein in resultPackage.MyProteins.MyProteinList from scan in protein.Scans where scan.FileName.Equals(fname) select protein).Distinct().ToList(); foreach (MyProtein prot in myProtein) { sw.WriteLine("\tLocus:" + prot.Locus + "\tGroup No: " + prot.GroupNo + "(" + prot.MyGroupType + ")\t" + prot.Description); List <SQTScan> scans = (from scan in prot.Scans where scan.FileName.Equals(fname) select scan).Distinct().ToList(); foreach (SQTScan scan in scans) { sw.Write("\t\t"); PrintScan(sw, scan); sw.WriteLine(""); } } Console.WriteLine("\n"); } sw.Close(); }
private ResultPackage FusionSEPro(List <ResultPackage> myPackages) { List <SQTScan> allScans = new List <SQTScan>(); SEPRPackage.Parameters theparams = new SEPRPackage.Parameters(); List <string> allProteinIDs = new List <string>(); string database = ""; List <FastaItem> fastaItems = new List <FastaItem>(); foreach (ResultPackage pkg in myPackages) { allScans.AddRange(pkg.MyProteins.AllSQTScans); theparams = pkg.MyParameters; allProteinIDs.AddRange(pkg.MyProteins.MyProteinList.Select(a => a.Locus).ToList()); foreach (MyProtein p in pkg.MyProteins.MyProteinList) { if (!fastaItems.Exists(a => a.SequenceIdentifier.Equals(p.Locus))) { FastaItem fasta = new FastaItem(); fasta.Description = p.Description; fasta.Sequence = p.Sequence; fasta.SequenceIdentifier = p.Locus; fastaItems.Add(fasta); } } database = pkg.Database; } Console.WriteLine("Generating SEPro Fusion"); ProteinManager pm = new ProteinManager(allScans, theparams, allProteinIDs.Distinct().ToList()); pm.CalculateProteinCoverage(fastaItems); pm.GroupProteinsHavingCommonPeptides(1); ResultPackage rp = new ResultPackage(pm, theparams, database, theparams.SeachResultDirectoy, false); rp.MyProteins.RebuildProteinsFromScans(); Console.WriteLine("Done fusioning the SEPro files."); return(rp); }
public static void SaveProteinTable(string outputFile, ResultPackage resultPackage) { System.IO.StreamWriter sw = new System.IO.StreamWriter(outputFile); PrintHead(resultPackage, sw); resultPackage.MyProteins.MyProteinList.Sort((a, b) => a.GroupNo.CompareTo(b.GroupNo)); sw.WriteLine("#Identified Proteins :{0}, Identified Peptides :{1}", resultPackage.MyProteins.MyProteinList.Count, resultPackage.MyProteins.MyPeptideList.Count); sw.WriteLine("#Locus\tGroup\tLength\tMolWt (MH)\tSequenceCount\tSpectrumCount\tCoverage\tProteinScore (i.e., sum of XCorr)\tDescription"); sw.WriteLine("#\tPeptideSequence\tSpecCount\tRedundancy\tMaximumPrimaryScore\tFileName.ScanNumber.ChargeState-At Maximum Primary Score"); foreach (MyProtein p in resultPackage.MyProteins.MyProteinList) { sw.WriteLine(p.Locus + "\t" + p.GroupNo + "\t" + p.Sequence.Length + "\t" + p.MolWt + "\t" + p.SequenceCount + "\t" + p.SpectrumCount + "\t" + Math.Round(p.Coverage, 2) + "\t" + Math.Round(p.ProteinScore, 3) + "\t" + p.Description); foreach (PeptideResult pep in p.PeptideResults) { pep.MyScans.Sort((a, b) => b.PrimaryScore.CompareTo(a.PrimaryScore)); sw.WriteLine("\t" + pep.PeptideSequence + "\t" + pep.NoMyScans + "\t" + pep.MyMapableProteins.Count + "\t" + pep.MyScans[0].PrimaryScore + "\t" + pep.MyScans[0].FileName + "." + pep.MyScans[0].ScanNumber + "." + pep.MyScans[0].ChargeState); } } sw.Close(); }
private void buttonGo_Click(object sender, EventArgs e) { //Verify write permission to directory if (!Directory.Exists(textBoxOutputDirectory.Text)) { MessageBox.Show("Please specify a valid output directory"); return; } if (!Regex.IsMatch(textBoxIsobaricMasses.Text, "[0-9]+ [0-9]+")) { MessageBox.Show("Please fill out the masses of the isobaric tags."); return; } if (!PatternTools.pTools.HasWriteAccessToFolder(textBoxOutputDirectory.Text)) { MessageBox.Show("Please specify a valid output directory"); return; } //Obtain class labels if (textBoxClassLabels.Text.Length == 0) { MessageBox.Show("Please input the class labels (eg., for iTRAQ 1,2,3,4"); return; } List <int> labels = Regex.Split(textBoxClassLabels.Text, " ").Select(a => int.Parse(a)).ToList(); //Obtain the isobaric masses string[] im = Regex.Split(textBoxIsobaricMasses.Text, " "); List <double> isobaricMasses = im.Select(a => double.Parse(a)).ToList(); if (labels.Count != isobaricMasses.Count) { MessageBox.Show("Please make sure that the class labels and isobaric masses match"); return; } buttonGo.Text = "Working..."; this.Update(); richTextBoxLog.Clear(); //-------------------------------------------- //Get signal from all signalAllNormalizationDictionary = new Dictionary <string, double[]>(); //if (false) FileInfo fi = new FileInfo(textBoxitraqSEPro.Text); bool extractSignal = false; ResultPackage rp = null; if (checkBoxNormalizationChannelSignal.Checked) { //We should get the MS infor and merge it the the sepro package if (fi.Extension.Equals(".sepr")) { rp = ResultPackage.Load(textBoxitraqSEPro.Text); extractSignal = true; } List <FileInfo> rawFiles = fi.Directory.GetFiles("*.RAW").ToList(); foreach (FileInfo rawFile in rawFiles) { Console.WriteLine("Extracting data for " + rawFile.Name); PatternTools.RawReader.RawReaderParams rParams = new PatternTools.RawReader.RawReaderParams(); rParams.ExtractMS1 = false; rParams.ExtractMS2 = true; rParams.ExtractMS3 = false; PatternTools.RawReader.Reader reader = new PatternTools.RawReader.Reader(rParams); List <MSLight> theMS2 = reader.GetSpectra(rawFile.FullName, new List <int>(), false); theMS2.RemoveAll(a => a.Ions == null); double [] totalSignal = new double[isobaricMasses.Count]; List <SQTScan> theScans = null; //Update the sepro result package with the signal if (extractSignal) { //Get all the scans from this file string rawName = rawFile.Name.Substring(0, rawFile.Name.Length - 4); theScans = rp.MyProteins.AllSQTScans.FindAll(a => a.FileName.Substring(0, a.FileName.Length - 4).Equals(rawName)); } foreach (MSLight ms in theMS2) { double[] thisQuantitation = GetIsobaricSignal(ms.Ions, isobaricMasses); if (extractSignal) { SQTScan scn = theScans.Find(a => a.ScanNumber == ms.ScanNumber); if (scn != null) { scn.MSLight = ms; scn.MSLight.Ions.RemoveAll(a => a.MZ > 400); } } for (int i = 0; i < thisQuantitation.Length; i++) { totalSignal[i] += thisQuantitation[i]; } } string theName = rawFile.Name.Substring(0, rawFile.Name.Length - 3); theName += "sqt"; signalAllNormalizationDictionary.Add(theName, totalSignal); } } Console.WriteLine("Loading SEPro File"); if (!File.Exists(textBoxitraqSEPro.Text)) { MessageBox.Show("Unable to find SEPro file"); return; } #region Load the spero or pepexplorer file theScansToAnalyze = new List <SQTScan>(); List <FastaItem> theFastaItems = new List <FastaItem>(); if (fi.Extension.Equals(".sepr")) { Console.WriteLine("Loading SEPro file"); if (!extractSignal) { rp = ResultPackage.Load(textBoxitraqSEPro.Text); } rp.MyProteins.AllSQTScans.RemoveAll(a => a.MSLight == null); theScansToAnalyze = rp.MyProteins.AllSQTScans; Console.WriteLine("Done reading SEPro result"); theFastaItems = rp.MyProteins.MyProteinList.Select(a => new FastaItem(a.Locus, a.Sequence, a.Description)).ToList(); } else if (fi.Extension.Equals(".mpex")) { Console.WriteLine("Loading PepExplorer file...."); PepExplorer2.Result2.ResultPckg2 result = PepExplorer2.Result2.ResultPckg2.DeserializeResultPackage(textBoxitraqSEPro.Text); theFastaItems = result.MyFasta; theScansToAnalyze = new List <SQTScan>(); foreach (PepExplorer2.Result2.AlignmentResult al in result.Alignments) { foreach (var dnr in al.DeNovoRegistries) { SQTScan sqt = new SQTScan(); sqt.ScanNumber = dnr.ScanNumber; sqt.FileName = dnr.FileName; sqt.PeptideSequence = dnr.PtmSequence; theScansToAnalyze.Add(sqt); } } //And now we need to retrieve the mass spectra. For this, the raw files should be inside the directory containing the mpex file List <string> rawFiles = theScansToAnalyze.Select(a => a.FileName).Distinct().ToList(); for (int i = 0; i < rawFiles.Count; i++) { rawFiles[i] = rawFiles[i].Remove(rawFiles[i].Length - 3, 3); rawFiles[i] = rawFiles[i] += "raw"; } foreach (string fn in rawFiles) { Console.WriteLine("Retrieving spectra for file: " + fn); ParserUltraLightRAW parser = new ParserUltraLightRAW(); string tmpFile = fn.Substring(0, fn.Length - 3); List <SQTScan> scansForThisFile = theScansToAnalyze.FindAll(a => Regex.IsMatch(tmpFile, a.FileName.Substring(0, a.FileName.Length - 3), RegexOptions.IgnoreCase)).ToList(); List <int> scnNumbers = scansForThisFile.Select(a => a.ScanNumber).ToList(); FileInfo theInputFile = new FileInfo(textBoxitraqSEPro.Text); List <MSUltraLight> theSpectra = parser.ParseFile(theInputFile.DirectoryName + "/" + fn, -1, 2, scnNumbers); foreach (SQTScan sqt in scansForThisFile) { MSUltraLight spec = theSpectra.Find(a => a.ScanNumber == sqt.ScanNumber); sqt.MSLight = new MSLight(); sqt.MSLight.MZ = spec.Ions.Select(a => (double)a.Item1).ToList(); sqt.MSLight.Intensity = spec.Ions.Select(a => (double)a.Item2).ToList(); } Console.WriteLine("\tDone processing this file."); } } else { throw new Exception("This file format is not supported."); } #endregion //Obtaining multiplexed spectra SEProQ.IsobaricQuant.YadaMultiplexCorrection.YMC ymc = null; if (textBoxCorrectedYadaDirectory.Text.Length > 0) { Console.WriteLine("Reading Yada results"); ymc = new IsobaricQuant.YadaMultiplexCorrection.YMC(new DirectoryInfo(textBoxCorrectedYadaDirectory.Text)); Console.WriteLine("Done loading Yada results"); } //Remove multiplexed spectra from sepro results if (textBoxCorrectedYadaDirectory.Text.Length > 0) { int removedCounter = 0; foreach (KeyValuePair <string, List <int> > kvp in ymc.fileNameScanNumberMultiplexDictionary) { Console.WriteLine("Removing multiplexed spectra for file :: " + kvp.Key); richTextBoxLog.AppendText("Removing multiplexed spectra for file :: " + kvp.Key + "\n"); string cleanName = kvp.Key.Substring(0, kvp.Key.Length - 4); cleanName += ".sqt"; foreach (int scnNo in kvp.Value) { int index = theScansToAnalyze.FindIndex(a => a.ScanNumber == scnNo && a.FileName.Equals(cleanName)); if (index >= 0) { Console.Write(theScansToAnalyze[index].ScanNumber + " "); richTextBoxLog.AppendText(theScansToAnalyze[index].ScanNumber + " "); removedCounter++; theScansToAnalyze.RemoveAt(index); } } Console.WriteLine("\n"); richTextBoxLog.AppendText("\n"); } Console.WriteLine("Done removing multiplexed spectra :: " + removedCounter); } PatternTools.CSML.Matrix correctionMatrix = new PatternTools.CSML.Matrix(); if (checkBoxApplyPurityCorrection.Checked) { List <List <double> > correctionData = GetPurityCorrectionsFromForm(); correctionMatrix = IsobaricQuant.IsobaricImpurityCorrection.GenerateInverseCorrectionMatrix(correctionData); } //-------------------------------------------------------------------------------------------------------------------- //Prepare normalization Dictionary signalIdentifiedNormalizationDictionary = new Dictionary <string, double[]>(); List <string> fileNames = theScansToAnalyze.Select(a => a.FileName).Distinct().ToList(); foreach (string fileName in fileNames) { signalIdentifiedNormalizationDictionary.Add(fileName, new double[isobaricMasses.Count]); } //------------------------------------- //If necessary, correct for impurity and feed global signal dictionary foreach (SQTScan scn in theScansToAnalyze) { double[] thisQuantitation = GetIsobaricSignal(scn.MSLight.Ions, isobaricMasses); double maxSignal = thisQuantitation.Max(); //We can only correct for signal for those that have quantitation values in all places if (checkBoxApplyPurityCorrection.Checked && (thisQuantitation.Count(a => a > maxSignal * (double)numericUpDownIonCountThreshold.Value) == isobaricMasses.Count)) { thisQuantitation = IsobaricQuant.IsobaricImpurityCorrection.CorrectForSignal(correctionMatrix, thisQuantitation).ToArray(); } if (checkBoxNormalizationChannelSignal.Checked) { for (int k = 0; k < thisQuantitation.Length; k++) { signalIdentifiedNormalizationDictionary[scn.FileName][k] += thisQuantitation[k]; } } scn.Quantitation = new List <List <double> >() { thisQuantitation.ToList() }; } //And now normalize ------------------- if (checkBoxNormalizationChannelSignal.Checked) { Console.WriteLine("Performing channel signal normalization for " + theScansToAnalyze.Count + " scans."); foreach (SQTScan scn2 in theScansToAnalyze) { for (int m = 0; m < isobaricMasses.Count; m++) { scn2.Quantitation[0][m] /= signalIdentifiedNormalizationDictionary[scn2.FileName][m]; } if (scn2.Quantitation[0].Contains(double.NaN)) { Console.WriteLine("Problems on signal of scan " + scn2.FileNameWithScanNumberAndChargeState); } } } comboBoxSelectFileForGraphs.Items.Clear(); foreach (string file in signalIdentifiedNormalizationDictionary.Keys.ToList()) { comboBoxSelectFileForGraphs.Items.Add(file); } tabControlMain.SelectedIndex = 1; if (radioButtonAnalysisPeptideReport.Checked) { //Peptide Analysis //Write Peptide Analysis StreamWriter sw = new StreamWriter(textBoxOutputDirectory.Text + "/" + "PeptideQuantitationReport.txt"); //Eliminate problematic quants int removed = theScansToAnalyze.RemoveAll(a => Object.ReferenceEquals(a.Quantitation, null)); Console.WriteLine("Problematic scans removed: " + removed); var pepDic = from scn in theScansToAnalyze group scn by scn.PeptideSequenceCleaned into groupedSequences select new { PeptideSequence = groupedSequences.Key, TheScans = groupedSequences.ToList() }; foreach (var pep in pepDic) { sw.WriteLine("Peptide:" + pep.PeptideSequence + "\tSpecCounts:" + pep.TheScans.Count); foreach (SQTScan sqt in pep.TheScans) { sw.WriteLine(sqt.FileNameWithScanNumberAndChargeState + "\t" + string.Join("\t", sqt.Quantitation[0])); } } //And now write the Fasta sw.WriteLine("#Fasta Items"); foreach (FastaItem fastaItem in theFastaItems) { sw.WriteLine(">" + fastaItem.SequenceIdentifier + " " + fastaItem.Description); sw.WriteLine(fastaItem.Sequence); } sw.Close(); } else { rp = ResultPackage.Load(textBoxitraqSEPro.Text); //Peptide Level if (true) { PatternTools.SparseMatrixIndexParserV2 ip = new SparseMatrixIndexParserV2(); List <int> allDims = new List <int>(); List <PeptideResult> peptides = rp.MyProteins.MyPeptideList; if (checkBoxOnlyUniquePeptides.Checked) { int removedPeptides = peptides.RemoveAll(a => a.MyMapableProteins.Count > 1); Console.WriteLine("Removing {0} peptides for not being unique.", removedPeptides); } for (int i = 0; i < peptides.Count; i++) { SparseMatrixIndexParserV2.Index index = new SparseMatrixIndexParserV2.Index(); index.Name = peptides[i].PeptideSequence; index.Description = string.Join(" ", peptides[i].MyMapableProteins); index.ID = i; ip.Add(index, true); allDims.Add(i); } SparseMatrix sm = new SparseMatrix(); List <int> dims = ip.allIDs(); for (int l = 0; l < labels.Count; l++) { if (labels[l] < 0) { continue; } sparseMatrixRow smr = new sparseMatrixRow(labels[l]); List <double> values = new List <double>(dims.Count); List <int> dimsWithValues = new List <int>(); foreach (int d in dims) { List <SQTScan> scns = peptides[d].MyScans.FindAll(a => !object.ReferenceEquals(a.Quantitation, null)); if (scns.Count > 0) { double signalSum = scns.FindAll(a => !double.IsNaN(a.Quantitation[0][l])).Sum(a => a.Quantitation[0][l]); values.Add(signalSum); dimsWithValues.Add(d); } } smr.Dims = dimsWithValues; smr.Values = values; smr.FileName = isobaricMasses[l].ToString(); sm.addRow(smr); } PatternLabProject plp = new PatternLabProject(sm, ip, "IsobaricQuant"); plp.Save(textBoxOutputDirectory.Text + "/MyPatternLabProjectPeptides.plp"); } //Protein Level if (true) { //Generate Index PatternTools.SparseMatrixIndexParserV2 ip = new SparseMatrixIndexParserV2(); List <MyProtein> theProteins = rp.MyProteins.MyProteinList; if (checkBoxOnlyUniquePeptides.Checked) { int removedProteins = theProteins.RemoveAll(a => !a.PeptideResults.Exists(b => b.NoMyMapableProteins == 1)); Console.WriteLine("{0} removed proteins for not having unique peptides", removedProteins); } for (int i = 0; i < theProteins.Count; i++) { SparseMatrixIndexParserV2.Index index = new SparseMatrixIndexParserV2.Index(); index.ID = i; index.Name = theProteins[i].Locus; index.Description = theProteins[i].Description; ip.Add(index, false); } //SparseMatrix SparseMatrix sm = new SparseMatrix(); List <int> dims = ip.allIDs(); for (int l = 0; l < labels.Count; l++) { if (labels[l] < 0) { continue; } if (!sm.ClassDescriptionDictionary.ContainsKey(labels[l])) { sm.ClassDescriptionDictionary.Add(labels[l], labels[l].ToString()); } sparseMatrixRow smr = new sparseMatrixRow(labels[l]); List <double> values = new List <double>(dims.Count); List <int> dimsToInclude = new List <int>(); foreach (int d in dims) { double signalSum = 0; List <PeptideResult> thePeptides = theProteins[d].PeptideResults; if (checkBoxOnlyUniquePeptides.Checked) { thePeptides.RemoveAll(a => a.MyMapableProteins.Count > 1); } foreach (PeptideResult pr in thePeptides) { List <SQTScan> scns = pr.MyScans.FindAll(a => !object.ReferenceEquals(a.Quantitation, null)); foreach (SQTScan sqt in scns) { if (!double.IsNaN(sqt.Quantitation[0][l]) && !double.IsInfinity(sqt.Quantitation[0][l])) { signalSum += sqt.Quantitation[0][l]; } } } if (signalSum > 0) { dimsToInclude.Add(d); values.Add(signalSum); } else { Console.WriteLine("No signal found for " + theProteins[d].Locus + " on marker " + l); } } smr.Dims = dims; smr.Values = values; smr.FileName = isobaricMasses[l].ToString(); sm.addRow(smr); } PatternLabProject plp = new PatternLabProject(sm, ip, "IsobaricQuant"); plp.Save(textBoxOutputDirectory.Text + "/MyPatternLabProjectProteins.plp"); } } comboBoxSelectFileForGraphs.Enabled = true; tabControlMain.SelectedIndex = 2; Console.WriteLine("Done"); buttonGo.Text = "Generate Report"; }
public static void SaveReportDTASelectFiltered(string outputFile, ResultPackage resultPackage) { System.IO.StreamWriter sw = new System.IO.StreamWriter(outputFile); //Print the head PrintHead(resultPackage, sw); sw.WriteLine("Locus\tSequence Count\tSpectrum Count\tSequence Coverage\tLength\tMolWt\tDescriptive Name"); sw.WriteLine("Unique\tFileName\tPrimaryScore\tDeltCN\tM+H+\tCalcM+H+\tZScore\tBayesianScore\tRedundancyAtPtnLevel\tSequence"); //Just to make sure we list the better ones on top resultPackage.MyProteins.MyProteinList.Sort((a, b) => b.SequenceCount.CompareTo(a.SequenceCount)); //Now lets begin printing int noGroups = resultPackage.MyProteins.MyProteinList.Max(a => a.GroupNo); for (int i = 1; i <= noGroups; i++) { List <MyProtein> theProteins = resultPackage.MyProteins.MyProteinList.FindAll(a => a.GroupNo == i); //Print the headers List <PeptideResult> thePeptideResults = new List <PeptideResult>(); foreach (MyProtein result in theProteins) { //Print the headers sw.Write(result.Locus + "\t"); //Sequence count sw.Write(result.SequenceCount + "\t"); //Spectrum count sw.Write(result.Scans.Count + "\t"); //Sequence coverage sw.Write(result.Coverage * 100 + "%\t"); //Length sw.Write(result.Length + "\t"); //MolWt sw.Write(result.MolWt + "\t"); //Descriptive Name sw.Write(result.Description); sw.WriteLine(""); thePeptideResults.AddRange(result.PeptideResults); } //Print the peptides thePeptideResults = thePeptideResults.Distinct().ToList(); List <string> printedScans = new List <string>(); foreach (PeptideResult pepResult in thePeptideResults) { //Extract peptide info foreach (SQTScan s in pepResult.MyScans) { if (printedScans.Contains(s.FileNameWithScanNumberAndChargeState)) { continue; } printedScans.Add(s.FileNameWithScanNumberAndChargeState); PrintScan(sw, s); //Write the end of the line sw.WriteLine(""); } } } //Write the final summary sw.WriteLine(); sw.WriteLine("Spectra FDR: " + resultPackage.MyFDRResult.SpectraFDRLabel); sw.WriteLine("Peptide FDR: " + resultPackage.MyFDRResult.PeptideFDRLabel); sw.WriteLine("Protein FDR: " + resultPackage.MyFDRResult.ProteinFDRLabel); sw.WriteLine("No Potein Groups: " + noGroups); sw.Close(); }
private void SignalrmanagerOnResultsReceivedEvent(ResultPackage pResults, string pClientID) { _commandManager.SendResults(pResults); }
private void buttonGetGoodHitsFromSEPro_Click(object sender, EventArgs e) { if (!File.Exists(textBoxSEProFileToExtractGoodPeptides.Text)) { MessageBox.Show("Please enter a valid SEPro file."); return; } ResultPackage sepro = ResultPackage.Load(textBoxSEProFileToExtractGoodPeptides.Text); richTextBoxResultScans.Clear(); richTextBoxPeptides.Clear(); richTextBoxResultScans.AppendText("File Name\tCharge\tScan Number\tSequence\tp-value\n"); Dictionary <string, List <double> > peptideScoreDictionary = new Dictionary <string, List <double> >(); List <SQTScan> theScans = sepro.MyProteins.AllSQTScans.Select(a => a).ToList(); if (numericUpDownNoPhosphoSites.Value > 0) { //Calculate an XDScore for each mass spectrum Regex seventyNine = new Regex("79"); theScans = theScans.FindAll(a => seventyNine.Matches(a.PeptideSequence).Count == numericUpDownNoPhosphoSites.Value); } if (numericUpDownModelChargeState.Value > 0) { theScans = theScans.FindAll(a => a.ChargeState == numericUpDownModelChargeState.Value); } foreach (SQTScan sqtScan in theScans) { if (sqtScan.PeptideSequenceCleaned.Contains("79")) { double pValue = xdScore.RetrievePValueForScanNumber(sqtScan.ScanNumber, (double)numericUpDownXCorrPrime.Value); if (pValue == -1) { Console.WriteLine("Shouldn´t be here"); } if (peptideScoreDictionary.ContainsKey(sqtScan.PeptideSequenceCleaned)) { peptideScoreDictionary[sqtScan.PeptideSequenceCleaned].Add(pValue); } else { peptideScoreDictionary.Add(sqtScan.PeptideSequenceCleaned, new List <double>() { pValue }); } richTextBoxResultScans.AppendText(sqtScan.FileName + "\t" + sqtScan.ChargeState + "\t" + sqtScan.ScanNumber + "\t" + sqtScan.PeptideSequenceCleaned + "\t" + Math.Round(pValue, 4) + "\n"); } } foreach (KeyValuePair <string, List <double> > kvp in peptideScoreDictionary) { kvp.Value.Sort(); richTextBoxPeptides.AppendText(kvp.Key + "\t" + kvp.Value[0] + "\n"); } }