Beispiel #1
0
        public void TestFeatureAlignment()
        {
            const string outFilePath = @"\\protoapps\UserData\Jungkap\Lewy\aligned\promex_crosstab_temp.tsv";


            //CPTAC_Intact_CR32A_24Aug15_Bane_15-02-06-RZ
            var prsmReader = new ProteinSpectrumMatchReader();
            var tolerance  = new Tolerance(10);
            var alignment  = new LcMsFeatureAlignment(new AnalysisCompRef.CompRefFeatureComparer(tolerance));

            for (var i = 0; i < NdataSet; i++)
            {
                var rawFile   = string.Format(@"{0}\{1}.pbf", PbfPath, GetDataSetNames(i));
                var mspFile   = string.Format(@"{0}\{1}_IcTda.tsv", MsPfFolder, GetDataSetNames(i));
                var mspFile2  = string.Format(@"{0}\{1}_IcTda.tsv", MsPfFolder2, GetDataSetNames(i));
                var ms1FtFile = string.Format(@"{0}\{1}.ms1ft", Ms1FtFolder, GetDataSetNames(i));
                Console.WriteLine(rawFile);
                var run       = PbfLcMsRun.GetLcMsRun(rawFile);
                var prsmList1 = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
                var prsmList2 = prsmReader.LoadIdentificationResult(mspFile2, ProteinSpectrumMatch.SearchTool.MsPathFinder);
                prsmList1.AddRange(prsmList2);

                var prsmList = MergePrsm(prsmList1);
                var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);

                for (var j = 0; j < prsmList.Count; j++)
                {
                    var match = prsmList[j];
                    match.ProteinId = match.ProteinName;
                }

                // tag features by PrSMs
                for (var j = 0; j < features.Count; j++)
                {
                    //features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
                    var massTol = tolerance.GetToleranceAsTh(features[j].Mass);
                    foreach (var match in prsmList)
                    {
                        if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
                        {
                            features[j].ProteinSpectrumMatches.Add(match);
                        }
                    }
                }

                alignment.AddDataSet(i, features, run);
            }

            alignment.AlignFeatures();

            Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);

            for (var i = 0; i < NdataSet; i++)
            {
                alignment.FillMissingFeatures(i);
                Console.WriteLine("{0} has been processed", GetDataSetNames(i));
            }

            OutputCrossTabWithId(outFilePath, alignment);
        }
Beispiel #2
0
        public void TestFeatureAlignment()
        {
            const string outFilePath = @"\\protoapps\UserData\Jungkap\CompRef\aligned\promex_crosstab_temp.tsv";

            var runLabels = new[] { "32A", "32B", "32C", "32D", "32E", "32F", "32G", "33A", "33B", "33C", "33D", "33E", "33F", "33G" };
            var nDataset  = runLabels.Length;

            var prsmReader = new ProteinSpectrumMatchReader();
            var tolerance  = new Tolerance(10);
            var alignment  = new LcMsFeatureAlignment(new CompRefFeatureComparer(tolerance));

            for (var i = 0; i < nDataset; i++)
            {
                var rawFile   = string.Format(@"{0}\CPTAC_Intact_CR{1}_24Aug15_Bane_15-02-06-RZ.pbf", RawFolder, runLabels[i]);
                var mspFile   = string.Format(@"{0}\CPTAC_Intact_CR{1}_24Aug15_Bane_15-02-06-RZ_IcTda.tsv", MsPfFolder, runLabels[i]);
                var ms1FtFile = string.Format(@"{0}\CPTAC_Intact_CR{1}_24Aug15_Bane_15-02-06-RZ.ms1ft", Ms1FtFolder, runLabels[i]);

                var run      = PbfLcMsRun.GetLcMsRun(rawFile);
                var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);

                if (File.Exists(mspFile))
                {
                    var prsmList = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);

                    for (var j = 0; j < prsmList.Count; j++)
                    {
                        var match = prsmList[j];
                        match.ProteinId = match.ProteinName;
                    }

                    // tag features by PrSMs
                    for (var j = 0; j < features.Count; j++)
                    {
                        //features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
                        var massTol = tolerance.GetToleranceAsMz(features[j].Mass);
                        foreach (var match in prsmList)
                        {
                            if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
                            {
                                features[j].ProteinSpectrumMatches.Add(match);
                            }
                        }
                    }
                }

                alignment.AddDataSet(i, features, run);
            }

            alignment.AlignFeatures();

            Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);

            for (var i = 0; i < nDataset; i++)
            {
                alignment.FillMissingFeatures(i);
                Console.WriteLine("{0} has been processed", runLabels[i]);
            }

            OutputCrossTabWithId(outFilePath, alignment, runLabels);
        }
Beispiel #3
0
        private void AlignFeatures(List <string> datasets, string mspfFolder, string ms1ftFolder, string outFilePath)
        {
            var nDataset   = datasets.Count;
            var prsmReader = new ProteinSpectrumMatchReader();
            var tolerance  = new Tolerance(12);
            var alignment  = new LcMsFeatureAlignment(new AnalysisCompRef.CompRefFeatureComparer(tolerance));

            for (var i = 0; i < nDataset; i++)
            {
                var rawFile    = string.Format(@"{0}\{1}.pbf", PbfPath, datasets[i]);
                var mspFile    = string.Format(@"{0}\{1}_IcTda.tsv", mspfFolder, datasets[i]);
                var ms1FtFile  = string.Format(@"{0}\{1}.ms1ft", ms1ftFolder, datasets[i]);
                var ms1FtFile2 = string.Format(@"{0}\{1}.seqtag.ms1ft", ms1ftFolder, datasets[i]);

                var run       = PbfLcMsRun.GetLcMsRun(rawFile);
                var features  = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);
                var features2 = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile2, run);
                features.AddRange(features2);

                if (File.Exists(mspFile))
                {
                    var prsmList = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
                    //var prsmFeatureMatch = new bool[prsmList.Count];

                    foreach (var match in prsmList)
                    {
                        match.ProteinId = match.ProteinName;
                    }

                    // tag features by PrSMs
                    foreach (var feature in features)
                    {
                        //features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
                        var massTol = tolerance.GetToleranceAsMz(feature.Mass);
                        foreach (var match in prsmList)
                        {
                            if (feature.MinScanNum < match.ScanNum && match.ScanNum < feature.MaxScanNum && Math.Abs(feature.Mass - match.Mass) < massTol)
                            {
                                feature.ProteinSpectrumMatches.Add(match);
                                //prsmFeatureMatch[k] = true;
                            }
                        }
                    }
                }

                alignment.AddDataSet(i, features, run);
            }

            alignment.AlignFeatures();

            Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);

            for (var i = 0; i < nDataset; i++)
            {
                alignment.FillMissingFeatures(i);
                Console.WriteLine("{0} has been processed", datasets[i]);
            }

            AnalysisCompRef.OutputCrossTabWithId(outFilePath, alignment, datasets);
        }
Beispiel #4
0
        public void TestFeatureAlignment()
        {
            const string outFilePath = @"\\protoapps\UserData\Jungkap\Lewy\aligned\promex_crosstab_temp.tsv";
            
            
            //CPTAC_Intact_CR32A_24Aug15_Bane_15-02-06-RZ
            var prsmReader = new ProteinSpectrumMatchReader();
            var tolerance = new Tolerance(10);
            var alignment = new LcMsFeatureAlignment(new AnalysisCompRef.CompRefFeatureComparer(tolerance));

            for (var i = 0; i < NdataSet; i++)
            {
                var rawFile = string.Format(@"{0}\{1}.pbf", PbfPath, GetDataSetNames(i));
                var mspFile = string.Format(@"{0}\{1}_IcTda.tsv", MsPfFolder, GetDataSetNames(i));
                var mspFile2 = string.Format(@"{0}\{1}_IcTda.tsv", MsPfFolder2, GetDataSetNames(i));
                var ms1FtFile = string.Format(@"{0}\{1}.ms1ft", Ms1FtFolder, GetDataSetNames(i));
                Console.WriteLine(rawFile);
                var run = PbfLcMsRun.GetLcMsRun(rawFile);
                var prsmList1 = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
                var prsmList2 = prsmReader.LoadIdentificationResult(mspFile2, ProteinSpectrumMatch.SearchTool.MsPathFinder);
                prsmList1.AddRange(prsmList2);
                
                var prsmList = MergePrsm(prsmList1);
                var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);

                for (var j = 0; j < prsmList.Count; j++)
                {
                    var match = prsmList[j];
                    match.ProteinId = match.ProteinName;
                }

                // tag features by PrSMs
                for (var j = 0; j < features.Count; j++)
                {
                    //features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
                    var massTol = tolerance.GetToleranceAsTh(features[j].Mass);
                    foreach (var match in prsmList)
                    {
                        if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
                        {
                            features[j].ProteinSpectrumMatches.Add(match);
                        }
                    }
                }

                alignment.AddDataSet(i, features, run);
            }

            alignment.AlignFeatures();

            Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);
            
            for (var i = 0; i < NdataSet; i++)
            {
                alignment.FillMissingFeatures(i);
                Console.WriteLine("{0} has been processed", GetDataSetNames(i));
            }
            
            OutputCrossTabWithId(outFilePath, alignment);
        }
Beispiel #5
0
        public void TestIMERFeatureAlignment()
        {
            const string outFilePath = @"D:\MassSpecFiles\IMER\promex_crosstab.tsv";
            const string rawFolder   = @"D:\MassSpecFiles\IMER";
            var          runLabels   = new string[] { "1", "2", "3", "4", "5", "6" };

            var nDataset = runLabels.Length;
            //CPTAC_Intact_CR32A_24Aug15_Bane_15-02-06-RZ
            var prsmReader = new ProteinSpectrumMatchReader();
            var tolerance  = new Tolerance(10);
            var alignment  = new LcMsFeatureAlignment(new CompRefFeatureComparer(tolerance));

            for (var i = 0; i < nDataset; i++)
            {
                var k         = runLabels[i].Equals("2") || runLabels[i].Equals("3") ? 14 : 13;
                var rawFile   = string.Format(@"{0}\Diabetes_iPSC_Beta_{1}_IMER_{2}May14_Alder_14-01-33.pbf", rawFolder, runLabels[i], k);
                var mspFile   = string.Format(@"{0}\Diabetes_iPSC_Beta_{1}_IMER_{2}May14_Alder_14-01-33_msgfdb_syn.txt", rawFolder, runLabels[i], k);
                var ms1FtFile = string.Format(@"{0}\Diabetes_iPSC_Beta_{1}_IMER_{2}May14_Alder_14-01-33.ms1ft", rawFolder, runLabels[i], k);

                Console.WriteLine(rawFile);
                Console.WriteLine(File.Exists(rawFile));

                var run      = PbfLcMsRun.GetLcMsRun(rawFile);
                var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run, 500, 15000);

                if (File.Exists(mspFile))
                {
                    var prsmList = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsGfPlus);

                    for (var j = 0; j < prsmList.Count; j++)
                    {
                        var match = prsmList[j];
                        match.ProteinId = match.ProteinName;
                    }

                    // tag features by PrSMs
                    for (var j = 0; j < features.Count; j++)
                    {
                        //features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
                        var massTol = tolerance.GetToleranceAsTh(features[j].Mass);
                        foreach (var match in prsmList)
                        {
                            if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
                            {
                                features[j].ProteinSpectrumMatches.Add(match);
                            }
                        }
                    }
                }


                alignment.AddDataSet(i, features, run);
            }

            alignment.AlignFeatures();

            Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);

            for (var i = 0; i < nDataset; i++)
            {
                alignment.FillMissingFeatures(i);
                Console.WriteLine("{0} has been processed", runLabels[i]);
            }

            OutputCrossTabWithId(outFilePath, alignment, runLabels);
        }
        public void AlignFeatures(List<string> datasets, string mspfFolder, string ms1ftFolder, string outFilePath)
        {
            var nDataset = datasets.Count;
            var prsmReader = new ProteinSpectrumMatchReader();
            var tolerance = new Tolerance(12);
            var alignment = new LcMsFeatureAlignment(new AnalysisCompRef.CompRefFeatureComparer(tolerance));
            for (var i = 0; i < nDataset; i++)
            {
                var rawFile = string.Format(@"{0}\{1}.pbf", PbfPath, datasets[i]);
                var mspFile = string.Format(@"{0}\{1}_IcTda.tsv", mspfFolder, datasets[i]);
                var ms1FtFile = string.Format(@"{0}\{1}.ms1ft", ms1ftFolder, datasets[i]);
                var ms1FtFile2 = string.Format(@"{0}\{1}.seqtag.ms1ft", ms1ftFolder, datasets[i]);

                var run = PbfLcMsRun.GetLcMsRun(rawFile);
                var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);
                var features2 = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile2, run);
                features.AddRange(features2);

                if (File.Exists(mspFile))
                {
                    var prsmList = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
                    //var prsmFeatureMatch = new bool[prsmList.Count];

                    for (var j = 0; j < prsmList.Count; j++)
                    {
                        var match = prsmList[j];
                        match.ProteinId = match.ProteinName;
                    }

                    // tag features by PrSMs
                    for (var j = 0; j < features.Count; j++)
                    {
                        //features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
                        var massTol = tolerance.GetToleranceAsTh(features[j].Mass);
                        for(var k = 0; k < prsmList.Count; k++)
                        {
                            var match = prsmList[k];
                            if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
                            {
                                features[j].ProteinSpectrumMatches.Add(match);
                                //prsmFeatureMatch[k] = true;
                            }
                        }
                    }
                }

                alignment.AddDataSet(i, features, run);
            }

            alignment.AlignFeatures();

            Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);

            for (var i = 0; i < nDataset; i++)
            {
                alignment.FillMissingFeatures(i);
                Console.WriteLine("{0} has been processed", datasets[i]);
            }

            AnalysisCompRef.OutputCrossTabWithId(outFilePath, alignment, datasets.ToArray());
        }
Beispiel #7
0
        public static void Main(string[] args)
        {
            // Parse file
            var inputFilePath = args[0];
            var datasets      = DatasetInfo.ParseDatasetInfoFile(inputFilePath);

            var fileName       = Path.GetFileNameWithoutExtension(inputFilePath);
            var directory      = Path.GetDirectoryName(inputFilePath);
            var outputfilePath = Path.Combine(directory, string.Format("{0}_crosstab.tsv", fileName));

            int nDataset   = datasets.Count;
            var prsmReader = new ProteinSpectrumMatchReader();
            var tolerance  = new Tolerance(100);
            var alignment  = new LcMsFeatureAlignment(new CompRefFeatureComparer(tolerance));

            int dataId = 0;

            foreach (var dataset in datasets)
            {
                var run      = PbfLcMsRun.GetLcMsRun(dataset.RawFilePath, 0, 0);
                var features = LcMsFeatureAlignment.LoadProMexResult(dataId++, dataset.Ms1FtFilePath, run);

                if (File.Exists(dataset.MsPfIdFilePath))
                {
                    var prsmList = prsmReader.LoadIdentificationResult(dataset.MsPfIdFilePath, ProteinSpectrumMatch.SearchTool.MsPathFinder);

                    foreach (var match in prsmList)
                    {
                        match.ProteinId = match.ProteinName;
                    }

                    // tag features by PrSMs
                    foreach (LcMsFeature feature in features)
                    {
                        //features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
                        var massTol = tolerance.GetToleranceAsMz(feature.Mass);
                        foreach (var match in prsmList)
                        {
                            if (feature.MinScanNum < match.ScanNum && match.ScanNum < feature.MaxScanNum && Math.Abs(feature.Mass - match.Mass) < massTol)
                            {
                                feature.ProteinSpectrumMatches.Add(match);
                            }
                        }
                    }
                }

                alignment.AddDataSet(dataId, features, run);
            }

            alignment.AlignFeatures();

            Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);

            for (var i = 0; i < nDataset; i++)
            {
                alignment.FillMissingFeatures(i);
                Console.WriteLine("{0} has been processed", datasets[i].Label);
            }

            OutputCrossTabWithId(outputfilePath, alignment, datasets.Select(ds => ds.Label).ToArray());
        }
Beispiel #8
0
        public static void Main(string[] args)
        {
            if (args.Length == 0)
            {
                ShowSyntax();
                return;
            }

            // Parse file
            var inputFilePath = args[0];

            if (!File.Exists(inputFilePath))
            {
                ConsoleMsgUtils.ShowError("File not found: " + inputFilePath);
                return;
            }

            var datasets = DatasetInfo.ParseDatasetInfoFile(inputFilePath);

            if (datasets.Count == 0)
            {
                ConsoleMsgUtils.ShowError("No valid data found in the dataset info file");
                ShowSyntax();
                return;
            }

            var fileName  = Path.GetFileNameWithoutExtension(inputFilePath);
            var directory = Path.GetDirectoryName(inputFilePath);

            var crosstabFilename = string.Format("{0}_crosstab.tsv", fileName);

            string outputfilePath;

            if (string.IsNullOrWhiteSpace(directory))
            {
                outputfilePath = crosstabFilename;
            }
            else
            {
                outputfilePath = Path.Combine(directory, crosstabFilename);
            }

            var nDataset   = datasets.Count;
            var prsmReader = new ProteinSpectrumMatchReader();
            var tolerance  = new Tolerance(100);
            var alignment  = new LcMsFeatureAlignment(new CompRefFeatureComparer(tolerance));

            var dataId = 0;

            foreach (var dataset in datasets)
            {
                if (!File.Exists(dataset.RawFilePath))
                {
                    ConsoleMsgUtils.ShowError("Instrument file not found: " + dataset.RawFilePath);
                    continue;
                }

                if (!File.Exists(dataset.Ms1FtFilePath))
                {
                    ConsoleMsgUtils.ShowError("ProMex results file not found: " + dataset.Ms1FtFilePath);
                    continue;
                }

                Console.WriteLine("Opening " + dataset.RawFilePath);
                var run = PbfLcMsRun.GetLcMsRun(dataset.RawFilePath, 0, 0);

                Console.WriteLine("Opening " + dataset.Ms1FtFilePath);
                var features = LcMsFeatureAlignment.LoadProMexResult(dataId++, dataset.Ms1FtFilePath, run);

                if (!string.IsNullOrWhiteSpace(dataset.MsPfIdFilePath) && File.Exists(dataset.MsPfIdFilePath))
                {
                    Console.WriteLine("Opening " + dataset.MsPfIdFilePath);
                    var prsmList = prsmReader.LoadIdentificationResult(dataset.MsPfIdFilePath, ProteinSpectrumMatch.SearchTool.MsPathFinder);

                    foreach (var match in prsmList)
                    {
                        match.ProteinId = match.ProteinName;
                    }

                    // tag features by PrSMs
                    foreach (var feature in features)
                    {
                        //features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
                        var massTol = tolerance.GetToleranceAsMz(feature.Mass);
                        foreach (var match in prsmList)
                        {
                            if (feature.MinScanNum < match.ScanNum && match.ScanNum < feature.MaxScanNum && Math.Abs(feature.Mass - match.Mass) < massTol)
                            {
                                feature.ProteinSpectrumMatches.Add(match);
                            }
                        }
                    }
                }

                alignment.AddDataSet(dataId, features, run);
            }

            alignment.AlignFeatures();

            Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);

            var validResults = 0;

            for (var datasetIndex = 0; datasetIndex < nDataset; datasetIndex++)
            {
                if (datasetIndex >= alignment.CountDatasets)
                {
                    ConsoleMsgUtils.ShowWarning(string.Format("Could not align {0}; features not found", datasets[datasetIndex].Label));
                    continue;
                }

                alignment.FillMissingFeatures(datasetIndex);
                Console.WriteLine("{0} has been processed", datasets[datasetIndex].Label);
                validResults++;
            }

            if (validResults > 0)
            {
                OutputCrossTabWithId(outputfilePath, alignment, datasets.Select(ds => ds.Label).ToArray());
            }
        }