Esempio n. 1
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        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);
            }
        }
Esempio n. 2
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        public void TestGettingProteinLengthAndPosition()
        {
            var methodName = MethodBase.GetCurrentMethod().Name;

            Utils.ShowStarting(methodName);

            var fastaFile = Utils.GetTestFile(methodName, Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"MSPathFinderT\Short.fasta"));

            var db = new FastaDatabase(fastaFile.FullName);

            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);
            }
        }
Esempio n. 3
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        public void CreateTargetList()
        {
            var methodName = MethodBase.GetCurrentMethod().Name;

            TestUtils.ShowStarting(methodName);

            const string databaseFilePath = @"D:\Research\Data\IPRG2014\database\SpikedInPeptides.fasta";

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

            var database = new FastaDatabase(databaseFilePath);

            database.Read();
            var indexedDatabase = new IndexedDatabase(database);
            var numTargets      = 0;

            var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);

            Console.WriteLine("Peptide\tFormula\tProtein");
            foreach (var annotationAndOffset in indexedDatabase.AnnotationsAndOffsets(6, 30, 1, 1, Enzyme.Trypsin))
            {
                var annotation = annotationAndOffset.Annotation;
                var peptide    = annotation.Substring(2, annotation.Length - 4);
                var offset     = annotationAndOffset.Offset;

                Console.WriteLine("{0}\t{1}\t{2}", peptide, (aaSet.GetComposition(peptide) + Composition.H2O).ToPlainString(), database.GetProteinName(offset));
                numTargets++;
            }
            Console.WriteLine("NumTargets: {0}", numTargets);
        }
Esempio n. 4
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        private IEnumerable <AnnotationAndOffset> GetAnnotationsAndOffsets(FastaDatabase database)
        {
            var indexedDbTarget = new IndexedDatabase(database);
            IEnumerable <AnnotationAndOffset> annotationsAndOffsets;

            if (NumTolerableTermini == 0)
            {
                annotationsAndOffsets = indexedDbTarget.AnnotationsAndOffsetsNoEnzyme(MinSequenceLength, MaxSequenceLength);
            }
            else
            {
                annotationsAndOffsets = indexedDbTarget.AnnotationsAndOffsets(MinSequenceLength, MaxSequenceLength,
                                                                              NumTolerableTermini, 2, Enzyme);
            }

            return(annotationsAndOffsets);
        }
Esempio n. 5
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        private static void TestCountingPeptides()
        {
            var aaSet = new AminoAcidSet();

            var sw = new Stopwatch();

            sw.Start();

            //const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_002166_F86E3B2F.fasta";
            const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_003456_9B916A8B.fasta";
            //            const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_004208_295531A4.fasta";
            var db        = new FastaDatabase(dbFile);
            var indexedDb = new IndexedDatabase(db);

            indexedDb.Read();
            //var numPeptides = indexedDb.AnnotationsAndOffsetsNoEnzyme(7, 150).LongCount();
            var peptides =
                indexedDb.AnnotationsAndOffsets(7, 40, 2, 2, Enzyme.Trypsin);

            Parallel.ForEach(peptides, annotationAndOffset =>
                             //foreach(var annotationAndOffset in peptides)
            {
                var annotation = annotationAndOffset.Annotation;
                var offset     = annotationAndOffset.Offset;

                var graph = SequenceGraph.CreateGraph(aaSet, annotation);
            }
                             )
            ;

//            Console.WriteLine("NumPeptides: {0}", numPeptides);
            sw.Stop();
            var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;

            Console.WriteLine(@"{0:f4} sec", sec);
        }
Esempio n. 6
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        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);
        }