public void TestVennDiagram()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.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;
TestUtils.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));
}
}
