public void TestProMexFilter() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); const string specFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw"; if (!File.Exists(specFilePath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath); } var run = PbfLcMsRun.GetLcMsRun(specFilePath, 0, 0); const string ms1FtPath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_Intact_26Sep14_Bane_C2Column3.ms1ft"; if (!File.Exists(ms1FtPath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, ms1FtPath); } var filter = new Ms1FtFilter(run, new Tolerance(10), ms1FtPath); // Console.WriteLine("ScanNums: {0}", string.Join("\t",filter.GetMatchingMs2ScanNums(8480.327609))); Assert.IsTrue(filter.GetMatchingMs2ScanNums(8480.327609).Contains(5255)); }
public void TestReadingProMexFile(double massToFind, string expectedScanNumbers) { var methodName = MethodBase.GetCurrentMethod().Name; Utils.ShowStarting(methodName); var pbfFilePath = Utils.GetPbfTestFilePath(false); var pbfFile = Utils.GetTestFile(methodName, pbfFilePath); var promexFilePath = Path.Combine(Utils.DEFAULT_SPEC_FILES_FOLDER, "QC_Shew_Intact_26Sep14_Bane_C2Column3_Excerpt.ms1ft"); var promexFile = Utils.GetTestFile(methodName, promexFilePath); var run = PbfLcMsRun.GetLcMsRun(pbfFile.FullName); Console.Write("Reading ProMex results..."); var ms1Filter = new Ms1FtFilter(run, new Tolerance(10), promexFile.FullName); Console.WriteLine(); var matchingScanNums = new SortedSet <int>(); foreach (var item in ms1Filter.GetMatchingMs2ScanNums(massToFind)) { matchingScanNums.Add(item); } var scanNumList = string.Join(",", matchingScanNums); Console.WriteLine("Scans with mass {0}:", massToFind); Console.WriteLine(scanNumList); var expectedScanNumList = expectedScanNumbers.Split(','); var matchCount = 0; foreach (var scanNumText in expectedScanNumList) { var scanNum = int.Parse(scanNumText); if (!matchingScanNums.Contains(scanNum)) { Assert.Fail("Did not find scan {0} for mass {1}", scanNum, massToFind); } matchCount++; } Assert.AreEqual(matchCount, matchingScanNums.Count, "Found extra matching scan nums vs. what was expected"); }
public void TestReadingProMexFile() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); const string rawFilePath = @"\\proto-11\MSXML_Cache\PBF_Gen_1_214\2014_3\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf"; if (!File.Exists(rawFilePath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath); } var run = PbfLcMsRun.GetLcMsRun(rawFilePath); const string promexFileName = @"\\Proto-5\VOrbiETD02\2014_3\QC_Shew_Intact_26Sep14_Bane_C2Column3\MSP201508271107_Auto1226713\QC_Shew_Intact_26Sep14_Bane_C2Column3.ms1ft"; Console.Write("Reading ProMex results..."); var ms1Filter = new Ms1FtFilter(run, new Tolerance(10), promexFileName); Console.WriteLine(string.Join(",", ms1Filter.GetMatchingMs2ScanNums(3016.6583))); }
public void TestFeatureId() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); const string dataSet = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3"; if (!File.Exists(dataSet)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dataSet); } // Feature: 5236-5286 6-12 8480.3681 5 const int minScanNum = 5236; const int maxScanNum = 5286; const double featureMass = 8480.3681; //const int minScanNum = 7251; //const int maxScanNum = 7326; //const double featureMass = 32347.18; // const int minScanNum = 4451; // const int maxScanNum = 4541; // const double featureMass = 31267.95; var tolerance = new Tolerance(10); var relaxedTolerance = new Tolerance(20); const int minTagLength = 5; const int minMergedTagLength = 7; const int minNumTagMatches = 1; var rawFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".raw"); var run = PbfLcMsRun.GetLcMsRun(rawFileName); var aminoAcidSet = AminoAcidSet.GetStandardAminoAcidSet(); var featureFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".ms1ft"); var filter = new Ms1FtFilter(run, tolerance, featureFileName); var ms2ScanNums = filter.GetMatchingMs2ScanNums(featureMass) .Where(scanNum => scanNum > minScanNum && scanNum < maxScanNum) .ToArray(); const string tagFileName = dataSet + ".seqtag"; //"_MinLength3.seqtag"; //Path.ChangeExtension(dataSet, ".seqtag"); const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta"; if (!File.Exists(fastaFilePath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, fastaFilePath); } var fastaDb = new FastaDatabase(fastaFilePath); var searchableDb = new SearchableDatabase(fastaDb); var tagParser = new SequenceTagParser(tagFileName, minTagLength); var proteinsToTags = new Dictionary <string, IList <MatchedTag> >(); foreach (var ms2ScanNum in ms2ScanNums) { var tags = tagParser.GetSequenceTags(ms2ScanNum); foreach (var tag in tags) { var matchedIndices = searchableDb.FindAllMatchedSequenceIndices(tag.Sequence).ToArray(); foreach (var index in matchedIndices) { var protein = fastaDb.GetProteinName(index); var startIndex = fastaDb.GetZeroBasedPositionInProtein(index); var matchedTag = new MatchedTag(tag, startIndex, featureMass); IList <MatchedTag> existingTags; if (proteinsToTags.TryGetValue(protein, out existingTags)) { existingTags.Add(matchedTag); } else { proteinsToTags.Add(protein, new List <MatchedTag> { matchedTag }); } } } } foreach (var entry in proteinsToTags.OrderByDescending(e => e.Value.Count)) { if (entry.Value.Count < minNumTagMatches) { break; } var proteinName = entry.Key; var proteinSequence = fastaDb.GetProteinSequence(proteinName); var protein = new Sequence(proteinSequence, aminoAcidSet); Console.WriteLine(proteinName + "\t" + entry.Value.Count); var matchedTagSet = new MatchedTagSet(proteinSequence, aminoAcidSet, tolerance, relaxedTolerance); Console.WriteLine("********** Before merging"); foreach (var matchedTag in entry.Value) { var seq = proteinSequence.Substring(matchedTag.StartIndex, matchedTag.EndIndex - matchedTag.StartIndex); var nTermMass = protein.GetMass(0, matchedTag.StartIndex); var cTermMass = protein.GetMass(matchedTag.EndIndex, protein.Count); Console.WriteLine("\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}", (matchedTag.NTermFlankingMass - nTermMass), seq, (matchedTag.CTermFlankingMass - cTermMass), matchedTag.StartIndex, matchedTag.IsNTermFlankingMassReliable, matchedTag.IsCTermFlankingMassReliable); matchedTagSet.Add(matchedTag); } Console.WriteLine("********** After merging"); foreach (var matchedTag in matchedTagSet.Tags) { if (matchedTag.Length < minMergedTagLength) { continue; } var seq = proteinSequence.Substring(matchedTag.StartIndex, matchedTag.EndIndex - matchedTag.StartIndex); var nTermMass = protein.GetMass(0, matchedTag.StartIndex); var cTermMass = protein.GetMass(matchedTag.EndIndex, protein.Count); Console.WriteLine("\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}", (matchedTag.NTermFlankingMass - nTermMass), seq, (matchedTag.CTermFlankingMass - cTermMass), matchedTag.StartIndex, matchedTag.IsNTermFlankingMassReliable, matchedTag.IsCTermFlankingMassReliable); } break; } }