private void TestQExactiveDdaDataPostProcessingPerFile(string range)
{
var resultPath = @"D:\Research\Data\UW\QExactive\DIA_Results\DIA_" + range + ".tsv";
var specFilePath = @"D:\Research\Data\UW\QExactive\82593_lv_mcx_DIA_5mz_" + range + ".raw";
var outputFilePath = @"D:\Research\Data\UW\QExactive\DIA_" + range + "_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFilePath, resultPath, new Tolerance(20), new Tolerance(10));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void TestQExactiveDiaDataPostProcessingNoEdgeNtt2()
{
const string resultPath = @"D:\Research\Data\UW\QExactive\NoEdge\DIA_All.tsv";
var specFiles = Directory.GetFiles(@"D:\Research\Data\UW\QExactive\", "*_DIA_*.raw");
const string outputFilePath = @"D:\Research\Data\UW\QExactive\DIA_All_Edge_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFiles, resultPath, new Tolerance(20), new Tolerance(10));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void RunIpa()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\EDRN\Replicates_Frac7\343513_EDRN_Serum_07_DIA_1_05_18Nov13_Samwise_13-07-28.tsv";
const string specFilePath = @"D:\Research\Data\EDRN\RawFiles\DIA_Replicate\343513_EDRN_Serum_07_DIA_1_05_18Nov13_Samwise_13-07-28.raw";
const string outputFilePath = @"D:\Research\Data\EDRN\Replicates_Frac7\Rep5_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFilePath, resultPath, new Tolerance(20), new Tolerance(10));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void RunIpa()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\EDRN\Replicates_Frac7\343513_EDRN_Serum_07_DIA_1_05_18Nov13_Samwise_13-07-28.tsv";
const string specFilePath = @"D:\Research\Data\EDRN\RawFiles\DIA_Replicate\343513_EDRN_Serum_07_DIA_1_05_18Nov13_Samwise_13-07-28.raw";
const string outputFilePath = @"D:\Research\Data\EDRN\Replicates_Frac7\Rep5_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFilePath, resultPath, new Tolerance(20), new Tolerance(10));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void ProcessPemmrData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\PEMMR\Ox\iTRAQ_N33T34_10ug_100cm_300min_C2_061213_All.tsv";
const string outputFilePath = @"D:\Research\Data\PEMMR\Ox\IPA_Summary.tsv";
const string specFilePath = @"D:\Research\Data\PEMMR\Spectra\iTRAQ_N33T34_10ug_100cm_300min_C2_061213.raw";;
var postProcessor = new MsGfPostProcessor(specFilePath, resultPath, new Tolerance(5), new Tolerance(5));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void TestFusionDdaDataPostProcessing()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\UW\Fusion\DDA_Results\DDA_C_1_To_4.tsv";
const string specFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
const string outputFilePath = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFilePath, resultPath, new Tolerance(5), new Tolerance(3));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void TestQExactiveDiaDataPostProcessing()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\UW\QExactive\DIA_Results\DIA_All.tsv";
var specFiles = Directory.GetFiles(@"D:\Research\Data\UW\QExactive\", "*_DIA_*.raw");
const string outputFilePath = @"D:\Research\Data\UW\QExactive\DIA_All_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFiles, resultPath, new Tolerance(20), new Tolerance(10));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void TestQExactiveDdaDataPostProcessing()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\UW\QExactive\DDA_Results\DDA_All.tsv";
const string specFile = @"D:\Research\Data\UW\QExactive\82593_lv_mcx_DDA_NoCharge.raw";
const string outputFilePath = @"D:\Research\Data\UW\QExactive\DDA_All_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFile, resultPath, new Tolerance(20), new Tolerance(10));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void ProcessMhcData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\ImmunoPeptidomics\Benchmarking\IPA\carone_C1309_All.tsv";
const string outputFilePath = @"D:\Research\Data\ImmunoPeptidomics\Benchmarking\IPA\IPA_Summary.tsv";
var specFiles = Directory.GetFiles(@"D:\Research\Data\ImmunoPeptidomics\Benchmarking\raw", "*.raw");
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var searchModifications = new List <SearchModification>
{
oxM
};
var aaSet = new AminoAcidSet(searchModifications, 2);
var postProcessor = new MsGfPostProcessor(specFiles, resultPath, new Tolerance(5), new Tolerance(3));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void ProcessMhcData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\ImmunoPeptidomics\Benchmarking\IPA\carone_C1309_All.tsv";
const string outputFilePath = @"D:\Research\Data\ImmunoPeptidomics\Benchmarking\IPA\IPA_Summary.tsv";
var specFiles = Directory.GetFiles(@"D:\Research\Data\ImmunoPeptidomics\Benchmarking\raw", "*.raw");
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var searchModifications = new List<SearchModification>
{
oxM
};
var aaSet = new AminoAcidSet(searchModifications, 2);
var postProcessor = new MsGfPostProcessor(specFiles, resultPath, new Tolerance(5), new Tolerance(3));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void ProcessPemmrData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\PEMMR\Ox\iTRAQ_N33T34_10ug_100cm_300min_C2_061213_All.tsv";
const string outputFilePath = @"D:\Research\Data\PEMMR\Ox\IPA_Summary.tsv";
const string specFilePath = @"D:\Research\Data\PEMMR\Spectra\iTRAQ_N33T34_10ug_100cm_300min_C2_061213.raw"; ;
var postProcessor = new MsGfPostProcessor(specFilePath, resultPath, new Tolerance(5), new Tolerance(5));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
private void TestQExactiveDdaDataPostProcessingPerFile(string range)
{
var resultPath = @"D:\Research\Data\UW\QExactive\DIA_Results\DIA_" + range + ".tsv";
var specFilePath = @"D:\Research\Data\UW\QExactive\82593_lv_mcx_DIA_5mz_" + range + ".raw";
var outputFilePath = @"D:\Research\Data\UW\QExactive\DIA_" + range + "_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFilePath, resultPath, new Tolerance(20), new Tolerance(10));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void TestFusionDdaDataPostProcessing()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\UW\Fusion\DDA_Results\DDA_C_1_To_4.tsv";
const string specFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
const string outputFilePath = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFilePath, resultPath, new Tolerance(5), new Tolerance(3));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void TestQExactiveDiaDataPostProcessingNoEdgeNtt2()
{
const string resultPath = @"D:\Research\Data\UW\QExactive\NoEdge\DIA_All.tsv";
var specFiles = Directory.GetFiles(@"D:\Research\Data\UW\QExactive\", "*_DIA_*.raw");
const string outputFilePath = @"D:\Research\Data\UW\QExactive\DIA_All_Edge_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFiles, resultPath, new Tolerance(20), new Tolerance(10));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void TestQExactiveDiaDataPostProcessing()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\UW\QExactive\DIA_Results\DIA_All.tsv";
var specFiles = Directory.GetFiles(@"D:\Research\Data\UW\QExactive\", "*_DIA_*.raw");
const string outputFilePath = @"D:\Research\Data\UW\QExactive\DIA_All_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFiles, resultPath, new Tolerance(20), new Tolerance(10));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}
public void TestQExactiveDdaDataPostProcessing()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultPath = @"D:\Research\Data\UW\QExactive\DDA_Results\DDA_All.tsv";
const string specFile = @"D:\Research\Data\UW\QExactive\82593_lv_mcx_DDA_NoCharge.raw";
const string outputFilePath = @"D:\Research\Data\UW\QExactive\DDA_All_Summary.tsv";
var postProcessor = new MsGfPostProcessor(specFile, resultPath, new Tolerance(20), new Tolerance(10));
var numId = postProcessor.PostProcessing(outputFilePath);
Console.WriteLine("NumId: {0}", numId);
}