public void TestGetChrom() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); const string rafFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf"; if (!File.Exists(rafFilePath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath); } var pbfRun = new PbfLcMsRun(rafFilePath); Console.WriteLine(@"Chromatogram"); // chromatogram comparison const double targetMz = 655.01; var tolerance = new Tolerance(10); var xic = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance); const int MAX_POINTS = 50; xic.Display(MAX_POINTS); Console.WriteLine(@"Done"); }
public void TestGetChrom() { var methodName = MethodBase.GetCurrentMethod().Name; Utils.ShowStarting(methodName); var pbfFilePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf"); if (!File.Exists(pbfFilePath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFilePath); } var pbfRun = new PbfLcMsRun(pbfFilePath); Console.WriteLine(@"Chromatogram"); // chromatogram comparison const double targetMz = 655.01; var tolerance = new Tolerance(10); var xic = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance); const int MAX_POINTS = 50; xic.Display(MAX_POINTS); Console.WriteLine(@"Done"); }
public void TestReadingPbfFile() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); const string pbfFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf"; if (!File.Exists(pbfFilePath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFilePath); } var pbfRun = new PbfLcMsRun(pbfFilePath); var specFilePath = Path.ChangeExtension(pbfFilePath, "raw"); if (!File.Exists(specFilePath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath); } Console.WriteLine(@"Loading .pbf into memory"); var run = InMemoryLcMsRun.GetLcMsRun(specFilePath); Console.WriteLine(@"Comparing spectra between .pbf and in-memory spectra"); // spectrum comparison for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++) { var spec1 = run.GetSpectrum(scanNum); var spec2 = pbfRun.GetSpectrum(scanNum); Assert.IsTrue(spec1.Peaks.Length == spec2.Peaks.Length); for (var i = 0; i < spec1.Peaks.Length; i++) { var p1 = spec1.Peaks[i]; var p2 = spec2.Peaks[i]; Assert.True(p1.Equals(p2)); Assert.True(Math.Abs(p1.Mz - p2.Mz) < 1e-8); Assert.True(Math.Abs(p1.Intensity - p2.Intensity) < 0.001); } } Console.WriteLine(@"Comparing XICs"); // chromatogram comparison const double targetMz = 655.01; var tolerance = new Tolerance(10); var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance); var xic2 = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance); Assert.True(xic1.Count == xic2.Count); for (var i = 0; i < xic1.Count; i++) { if (!xic1[i].Equals(xic2[i])) { Console.WriteLine(@"{0} {1} {2}", i, xic1[i], xic2[i]); } Assert.True(xic1[i].Equals(xic2[i])); } Console.WriteLine(@"Done"); }
public void TestRunningTimeChromGen() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf"; if (!File.Exists(rafFilePath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath); } var rafRun = new PbfLcMsRun(rafFilePath); var tolerance = new Tolerance(10); const string dbFile = @"D:\Research\Data\CommonContaminants\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta"; if (!File.Exists(dbFile)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFile); } var db = new FastaDatabase(dbFile); var indexedDb = new IndexedDatabase(db); var aaSet = new AminoAcidSet(Modification.Carbamidomethylation); var sw = new System.Diagnostics.Stopwatch(); sw.Start(); var numPeptides = 0; foreach (var peptide in indexedDb.AnnotationsAndOffsets(6, 30, 2, 2, Enzyme.Trypsin)) { ++numPeptides; var comp = new Sequence(peptide.Annotation.Substring(2, peptide.Annotation.Length - 4), aaSet).Composition + Composition.H2O; var mz = new Ion(comp, 2).GetMonoIsotopicMz(); //Console.WriteLine(peptide.Annotation + " " + mz); rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance); //run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance); //var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance); //var xic2 = rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance); //Assert.True(xic1.Count == xic2.Count); //for (var i = 0; i < xic1.Count; i++) //{ // if (!xic1[i].Equals(xic2[i])) // { // Console.WriteLine("{0} {1} {2}", i, xic1[i], xic2[i]); // } // Assert.True(xic1[i].Equals(xic2[i])); //} if (numPeptides == 100000) { break; } } sw.Stop(); Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds); }
public void TestRunningTimeChromGen() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf"; if (!File.Exists(rafFilePath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath); } var rafRun = new PbfLcMsRun(rafFilePath); var tolerance = new Tolerance(10); const string dbFile = @"D:\Research\Data\CommonContaminants\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta"; if (!File.Exists(dbFile)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFile); } var db = new FastaDatabase(dbFile); var indexedDb = new IndexedDatabase(db); var aaSet = new AminoAcidSet(Modification.Carbamidomethylation); var sw = new System.Diagnostics.Stopwatch(); sw.Start(); var numPeptides = 0; foreach (var peptide in indexedDb.AnnotationsAndOffsets(6, 30, 2, 2, Enzyme.Trypsin)) { ++numPeptides; var comp = new Sequence(peptide.Annotation.Substring(2, peptide.Annotation.Length-4), aaSet).Composition + Composition.H2O; var mz = new Ion(comp, 2).GetMonoIsotopicMz(); //Console.WriteLine(peptide.Annotation + " " + mz); rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance); //run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance); //var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance); //var xic2 = rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance); //Assert.True(xic1.Count == xic2.Count); //for (var i = 0; i < xic1.Count; i++) //{ // if (!xic1[i].Equals(xic2[i])) // { // Console.WriteLine("{0} {1} {2}", i, xic1[i], xic2[i]); // } // Assert.True(xic1[i].Equals(xic2[i])); //} if (numPeptides == 100000) break; } sw.Stop(); Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds); }