public void TestVennDiagram() { var methodName = MethodBase.GetCurrentMethod().Name; Utils.ShowStarting(methodName); const string result1Path = @"C:\cygwin\home\kims336\Data\QCShewQE\NoMod_NTT1.tsv"; const string result2Path = @"C:\cygwin\home\kims336\Data\QCShewQE\Ic_NTT1_Test\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28_IcTda.tsv"; if (!File.Exists(result1Path)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, result1Path); } if (!File.Exists(result2Path)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, result2Path); } const double pepQValueThreshold = 0.01; var result1 = new TsvFileParser(result1Path); var result2 = new TsvFileParser(result2Path); var vennDiagram = new VennDiagram <string>(result1.GetPeptides(pepQValueThreshold), result2.GetPeptides(pepQValueThreshold)); var intersectionPeptides = vennDiagram.Intersection; Console.WriteLine(vennDiagram.Set1 + " " + vennDiagram.Set2); Console.WriteLine(vennDiagram.Set1 + " " + vennDiagram.Intersection + " " + vennDiagram.Set2Only); }
public void CompareIpaIc() { var methodName = MethodBase.GetCurrentMethod().Name; Utils.ShowStarting(methodName); const string resultDir = @"D:\Research\Data\UW\QExactive\Ic_NTT2_03"; if (!Directory.Exists(resultDir)) { Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, resultDir); } var targetPeptides = new HashSet <string>(); foreach (var icResultFilePath in Directory.GetFiles(resultDir, "*DIA*IcTarget.tsv")) { var icParser = new TsvFileParser(icResultFilePath); foreach (var peptide in icParser.GetData("Sequence")) { targetPeptides.Add(peptide); } } const string ipaResultPath = @"D:\Research\Data\UW\QExactive\DIA_All_Summary.tsv"; if (!File.Exists(ipaResultPath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, methodName); } var parser = new TsvFileParser(ipaResultPath); var ipaPeptides = parser.GetPeptides(0.005).Select(p => p.Replace("C+57.021", "C")); var ipaOnly = 0; var both = 0; foreach (var ipaPeptide in ipaPeptides) { if (targetPeptides.Contains(ipaPeptide)) { ++both; } else { ++ipaOnly; Console.WriteLine(ipaPeptide); } } Console.WriteLine("Both: {0}, IpaOnly: {1}, Sum: {2}", both, ipaOnly, both + ipaOnly); }
public void CompareRtFusion() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); // Fusion const string qeDdaResult = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv"; const string qeDiaResult = @"D:\Research\Data\UW\Fusion\DIA_Summary.tsv"; const string specFileDda = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw"; var ddaReader = new XCaliburReader(specFileDda); const string specFileDia = @"D:\Research\Data\UW\Fusion\WT_D_DIA_130412091220.raw"; var diaReader = new XCaliburReader(specFileDia); const string resultPath1 = qeDdaResult; const string resultPath2 = qeDiaResult; var result1 = new TsvFileParser(resultPath1); var result2 = new TsvFileParser(resultPath2); const double pepQValueThreshold = 0.01; var vennDiagram = new VennDiagram <string>(result1.GetPeptides(pepQValueThreshold), result2.GetPeptides(pepQValueThreshold)); var intersectionPeptides = vennDiagram.Intersection; var result1Peptides = result1.GetData("Peptide"); var result1ScanNums = result1.GetData("ScanNum"); var result2Peptides = result2.GetData("Peptide"); var result2ScanNums = result2.GetData("ScanNum"); Console.WriteLine("Peptide\tScanNum1\tScanNum2\tRt1\tRt2"); foreach (var peptide in intersectionPeptides) { var index1 = result1Peptides.IndexOf(peptide); var index2 = result2Peptides.IndexOf(peptide); var scanNum1 = Convert.ToInt32(result1ScanNums[index1]); var scanNum2 = Convert.ToInt32(result2ScanNums[index2]); var reader1 = ddaReader; var reader2 = diaReader; Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", peptide.Replace("C+57.021", "C"), scanNum1, scanNum2, reader1.RtFromScanNum(scanNum1), reader2.RtFromScanNum(scanNum2)); } }
public void GenerateVennDiagramsPeMmr() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); // No PE-MMR //const string noPeMmr = @"D:\Research\Data\PEMMR\iTRAQ_N33T34_10ug_100cm_300min_C2_061213.tsv"; // PE-MMR Scan based FDR //const string scanBasedPeMmr = @"D:\Research\Data\PEMMR\NewSpectra\iTRAQ_N33T34_10ug_100cm_300min_C2_061213_MX_PEMMR_UMCID_ScanFDR.tsv"; // UMC based FDR const string umcBasedPeMmr = @"D:\Research\Data\PEMMR\NewSpectra\iTRAQ_N33T34_10ug_100cm_300min_C2_061213_MX_PEMMR_UMCID_UMCFDR.tsv"; // IPA const string ipa = @"D:\Research\Data\PEMMR\Ox\IPA_Summary_TargetOnly.tsv"; const string resultPath1 = umcBasedPeMmr; const string resultPath2 = ipa; var result1 = new TsvFileParser(resultPath1); var result2 = new TsvFileParser(resultPath2); const double pepQValueThreshold = 0.01; var vennDiagram = new VennDiagram <string>(result1.GetPeptides(pepQValueThreshold), result2.GetPeptides(pepQValueThreshold)); Console.WriteLine("{0}\t{1}\t{2}", vennDiagram.Set1Only.Count + vennDiagram.Intersection.Count, vennDiagram.Intersection.Count, vennDiagram.Set2Only.Count + vennDiagram.Intersection.Count); Console.WriteLine("{0}\t{1}\t{2}", vennDiagram.Set1Only.Count, vennDiagram.Intersection.Count, vennDiagram.Set2Only.Count); foreach (var peptide in vennDiagram.Set2Only) { Console.WriteLine(peptide); var peptides = result2.GetData("Peptide"); } }
public void GenerateVennDiagrams() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); // Fusion //const string fusionMsgfResult = @"D:\Research\Data\UW\Fusion\MSGFPlusResults\TI2.tsv"; const string fusionDdaResult = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv"; //const string fusionDiaResult = @"D:\Research\Data\UW\Fusion\DIA_Summary.tsv"; // Q-Exactive //const string qeDdaMsGfResult = @"D:\Research\Data\UW\QExactive\82593_lv_mcx_DDA.tsv"; //const string qeDdaResult = @"D:\Research\Data\UW\QExactive\DDA_All_Summary.tsv"; //const string qeDiaResult = @"D:\Research\Data\UW\QExactive\DIA_All_Summary.tsv"; // PE-MMR //const string pemmrQeDia = @"D:\Research\Data\UW\PEMMR\QE\allFDR.tsv"; const string pemmrFusionDda = @"D:\Research\Data\UW\PEMMR\Fusion\WT_D_DDA_130412065618_MX_PEMMR.tsv"; //const string pemmrFusionDia = @"D:\Research\Data\UW\PEMMR\Fusion\WT_D_DIA_130412091220_MX_PEMMR.tsv"; const string resultPath1 = pemmrFusionDda; const string resultPath2 = fusionDdaResult; var result1 = new TsvFileParser(resultPath1); var result2 = new TsvFileParser(resultPath2); const double pepQValueThreshold = 0.01; var vennDiagram = new VennDiagram <string>(result1.GetPeptides(pepQValueThreshold), result2.GetPeptides(pepQValueThreshold)); Console.WriteLine("{0}\t{1}\t{2}", vennDiagram.Set1Only.Count + vennDiagram.Intersection.Count, vennDiagram.Intersection.Count, vennDiagram.Set2Only.Count + vennDiagram.Intersection.Count); }
public void CompareRt() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); // Q-Exactive //const string qeDdaResult = @"D:\Research\Data\UW\QExactive\DDA_All_Summary.tsv"; //const string qeDiaResult = @"D:\Research\Data\UW\QExactive\DIA_All_Summary.tsv"; // Fusion const string qeDdaResult = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv"; const string qeDiaResult = @"D:\Research\Data\UW\Fusion\DIA_Summary.tsv"; const string specFileDda = @"D:\Research\Data\UW\QExactive\82593_lv_mcx_DDA.raw"; var ddaReader = new XCaliburReader(specFileDda); var specFileToReader = new Dictionary <string, XCaliburReader>(); var specFilesDia = Directory.GetFiles(@"D:\Research\Data\UW\QExactive\", "*_DIA_*.raw"); foreach (var specFile in specFilesDia) { var specFileNoExt = Path.GetFileNameWithoutExtension(specFile); if (specFileNoExt == null) { continue; } var reader = new XCaliburReader(specFile); specFileToReader.Add(specFileNoExt, reader); } const string resultPath1 = qeDdaResult; const string resultPath2 = qeDiaResult; var result1 = new TsvFileParser(resultPath1); var result2 = new TsvFileParser(resultPath2); const double pepQValueThreshold = 0.01; var vennDiagram = new VennDiagram <string>(result1.GetPeptides(pepQValueThreshold), result2.GetPeptides(pepQValueThreshold)); var intersectionPeptides = vennDiagram.Intersection; var result1Peptides = result1.GetData("Peptide"); var result1ScanNums = result1.GetData("ScanNum"); var result2Peptides = result2.GetData("Peptide"); var result2ScanNums = result2.GetData("ScanNum"); var result2SpecFile = result2.GetData("#SpecFile"); Console.WriteLine("Peptide\tScanNum1\tScanNum2\tRt1\tRt2"); foreach (var peptide in intersectionPeptides) { var index1 = result1Peptides.IndexOf(peptide); var index2 = result2Peptides.IndexOf(peptide); var scanNum1 = Convert.ToInt32(result1ScanNums[index1]); var scanNum2 = Convert.ToInt32(result2ScanNums[index2]); var diaFile = Path.GetFileNameWithoutExtension(result2SpecFile[index2]); var reader1 = ddaReader; var reader2 = specFileToReader[diaFile]; Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", peptide.Replace("C+57.021", "C"), scanNum1, scanNum2, reader1.RtFromScanNum(scanNum1), reader2.RtFromScanNum(scanNum2)); } }