Exemplo n.º 1
0
        public void TestSearching()
        {
            var methodName = MethodBase.GetCurrentMethod().Name;
            TestUtils.ShowStarting(methodName);

            var sw = new System.Diagnostics.Stopwatch();
            sw.Start();

            const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\Short.fasta";
            if (!File.Exists(dbFile))
            {
                Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFile);
            }

            var db = new FastaDatabase(dbFile);
            var searchableDb = new SearchableDatabase(db);
            //const string pattern = "NSGSHFCGGSLINSQWVVSAAH";
            const string pattern = "FPTDDDDK";
            var position = searchableDb.Search(pattern);
            Assert.True(position >= 0);
            Console.WriteLine("Position: {0}", position);
            Console.WriteLine("Matched indices: {0}", string.Join(",", searchableDb.FindAllMatchedSequenceIndices(pattern)));
            Console.WriteLine("Protein indices: {0}", string.Join(",", searchableDb.FindAllMatchedSequenceIndices(pattern).Select(i => db.GetOneBasedPositionInProtein(i))));
            sw.Stop();
            
            Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
        }
Exemplo n.º 2
0
        private void WriteResultsToFile(SortedSet<DatabaseSequenceSpectrumMatch>[] matches, string outputFilePath, FastaDatabase database)
        {
            using (var writer = new StreamWriter(outputFilePath))
            {
                writer.WriteLine("Scan\tPre\tSequence\tPost\tModifications\tComposition\tProteinName\tProteinDesc" +
                             "\tProteinLength\tStart\tEnd\tCharge\tMostAbundantIsotopeMz\tMass\t#MatchedFragments\tIcScore"
                             );
                for (var scanNum = _run.MinLcScan; scanNum <= _run.MaxLcScan; scanNum++)
                {
                    if (matches[scanNum] == null) continue;
                    foreach (var match in matches[scanNum].Reverse())
                    {
                        var sequence = match.Sequence;
                        var offset = match.Offset;
                        var start = database.GetOneBasedPositionInProtein(offset) + 1 + match.NumNTermCleavages;
                        var end = start + sequence.Length - 1;
                        var proteinName = database.GetProteinName(match.Offset);
                        var protLength = database.GetProteinLength(proteinName);
                        var ion = match.Ion;

                        var scores = _bottomUpScorer.GetScores(match, ion.Composition, ion.Charge, scanNum);

                        if (ion == null)
                        {
                            Console.WriteLine(@"Null ion!");
                        }
                        if (scores == null)
                        {
                            Console.WriteLine(@"Null scores");
                        }

                        // Note for DblToString(value, 9, true), by having "9" and "true",
                        // values between 100 and 999 Da will have 7 digits after the decimal place, and
                        // values between 1000 and 9999 will have 6 digits after the decimal place

                        writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}\t{13}\t{14}\t{15}",
                            scanNum,
                            match.Pre,
                            sequence, // Sequence
                            match.Post,
                            scores.Modifications, // Modifications
                            ion.Composition, // Composition
                            proteinName, // ProteinName
                            database.GetProteinDescription(match.Offset), // ProteinDescription
                            protLength, // ProteinLength
                            start, // Start
                            end, // End
                            ion.Charge, // precursorCharge
                            StringUtilities.DblToString(ion.GetMostAbundantIsotopeMz(), 9, true), // MostAbundantIsotopeMz
                            StringUtilities.DblToString(ion.Composition.Mass, 9, true),           // Mass
                            match.Score,
                            scores.Score    // Score (re-scored)
                            );

                    }
                }
            }
        }
Exemplo n.º 3
0
        private void WriteResultsToFile(DatabaseSequenceSpectrumMatch[] matches, string outputFilePath, FastaDatabase database)
        {
            using (var writer = new StreamWriter(outputFilePath))
            {
                writer.WriteLine("Scan\tPre\tSequence\tPost\tModifications\tComposition\tProteinName\tProteinDesc" +
                                 "\tProteinLength\tStart\tEnd\tCharge\tMostAbundantIsotopeMz\tMass\t#MatchedFragments\tProbability\tSpecEValue\tEValue");
                
                foreach(var scanNum in _ms2ScanNums)
                {
                    var match = matches[scanNum];
                    if (match == null) continue;

                    var sequence = match.Sequence;
                    var offset = match.Offset;
                    var start = database.GetOneBasedPositionInProtein(offset) + 1 + match.NumNTermCleavages;
                    var end = start + sequence.Length - 1;
                    var proteinName = database.GetProteinName(match.Offset);
                    var protLength = database.GetProteinLength(proteinName);
                    var ion = match.Ion;
                    var proteinDescription = database.GetProteinDescription(match.Offset);
                    var probability = CompositeScorer.GetProbability(match.Score);

                    // Note for DblToString(value, 9, true), by having "9" and "true",
                    // values between 100 and 999 Da will have 7 digits after the decimal place, and
                    // values between 1000 and 9999 will have 6 digits after the decimal place
                    writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}\t{13}\t{14}\t{15}\t{16}\t{17}",
                        scanNum,
                        match.Pre,                 // Pre
                        sequence,                  // Sequence
                        match.Post,                // Post
                        match.ModificationText,    // Modifications
                        ion.Composition,           // Composition
                        proteinName,               // ProteinName
                        proteinDescription,        // ProteinDescription
                        protLength,                // ProteinLength
                        start,                     // Start position in protein
                        end,                       // End position in protein
                        ion.Charge,                // precursorCharge
                        StringUtilities.DblToString(ion.GetMostAbundantIsotopeMz(), 9, true), // MostAbundantIsotopeMz
                        StringUtilities.DblToString(ion.Composition.Mass, 9, true),           // Mass
                        match.NumMatchedFragments,                                          // (Number of matched fragments)
                        StringUtilities.DblToString(probability, 4),                        // Probability
                        StringUtilities.DblToString(ExcelMinValue(match.SpecEvalue), 6, true, 0.001),                             // EValue; will be displayed using scientific notation if the value is less than 0.001
                        StringUtilities.DblToString(ExcelMinValue(match.SpecEvalue * database.GetNumEntries()), 6, true, 0.001)   // SpecEValue; will be displayed using scientific notation if the value is less than 0.001
                        );

                }
            }
        }
Exemplo n.º 4
0
        public void TestGettingProteinLengthAndPosition()
        {
            var methodName = MethodBase.GetCurrentMethod().Name;
            TestUtils.ShowStarting(methodName);

            const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\Short.fasta";
            if (!File.Exists(dbFile))
            {
                Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFile);
            }

            var db = new FastaDatabase(dbFile);
            db.Read();
            var indexedDb = new IndexedDatabase(db);
            foreach (var peptideAnnotationAndOffset in indexedDb.AnnotationsAndOffsets(6, 20, 2, 0, Enzyme.Trypsin))
            {
                var annotation = peptideAnnotationAndOffset.Annotation;
                var offset = peptideAnnotationAndOffset.Offset;
                Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}",
                    annotation, 
                    offset, 
                    db.GetProteinName(offset), 
                    db.GetProteinLength(db.GetProteinName(offset)), 
                    db.GetOneBasedPositionInProtein(offset)+1);
            }
        }
Exemplo n.º 5
0
        public void TestGetProteinsWithTagMatchingSingleSpec()
        {
            var methodName = MethodBase.GetCurrentMethod().Name;
            TestUtils.ShowStarting(methodName);

            const string dataSet = @"H:\Research\Lewy\raw\Lewy_intact_07";
            //            const int scanNum = 5158;
            const int minTagLength = 7;
            const int minNumTagMatches = 1;
            var aminoAcidSet = AminoAcidSet.GetStandardAminoAcidSet();

            const int scanNum = 2;
            // Parse sequence tags
            //const string tagFileName = dataSet + ".seqtag"; //"_MinLength3.seqtag"; //Path.ChangeExtension(dataSet, ".seqtag");

            const string rawFilePath = "";

            const string fastaFilePath = @"H:\Research\Lewy\ID_004858_0EE8CF61.fasta";

            if (!File.Exists(rawFilePath))
            {
                Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
            }

            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 tags = tagParser.GetSequenceTags(scanNum);
            var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
            var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
            var tagFinder = new SequenceTagFinder(spec, new Tolerance(5));
            var tags = tagFinder.GetAllSequenceTagString();

            var proteinsToTags = new Dictionary<string, IList<MatchedTag>>();

            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.GetOneBasedPositionInProtein(index);
                    var matchedTag = new MatchedTag(tag, startIndex, 0.0);
                    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);
                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} ({1})\t{2}\t{3} ({4})\t{5}\t{6}\t{7}",
                        matchedTag.NTermFlankingMass, (matchedTag.NTermFlankingMass - nTermMass), 
                        seq, 
                        matchedTag.CTermFlankingMass, (matchedTag.CTermFlankingMass - cTermMass), 
                        matchedTag.StartIndex,
                        matchedTag.IsNTermFlankingMassReliable, matchedTag.IsCTermFlankingMassReliable);

                }
            }
        }