예제 #1
0
        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);
        }
예제 #2
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        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);
        }
예제 #3
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파일: TestEdrn.cs 프로젝트: javamng/GitHUB
        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);
        }
예제 #4
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        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);
        }
예제 #5
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        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);
        }
예제 #6
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        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);
        }
예제 #7
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        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);
        }
예제 #8
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        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);
        }
예제 #9
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        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);
        }
예제 #10
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        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);
        }
예제 #11
0
        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);
        }
예제 #12
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        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);
        }
예제 #13
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        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);
        }
예제 #14
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        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);
        }
예제 #15
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        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);
        }
예제 #16
0
        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);
        }