示例#1
0
        public void TestChaoChao(string specFilePath)
        {
            var methodName = MethodBase.GetCurrentMethod().Name;
            TestUtils.ShowStarting(methodName);

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

            const string dbFilePath = @"D:\Research\Data\ChaoChao\database\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
            if (!File.Exists(dbFilePath))
            {
                Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
            }

            const string outputDir = @"D:\Research\Data\ChaoChao\Ic\";

            // Configure amino acid set
            //var carbamidomethylC = new SearchModification(Modification.Carbamidomethylation, 'C', SequenceLocation.Everywhere, true);
            //var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
            //var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
            //var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.Everywhere, false);
            //var deamdN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
            //var deamdQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);

            const int numMaxModsPerProtein = 0;
            var searchModifications = new List<SearchModification>
            {
                //carbamidomethylC,
                //acetylN,
                //oxM
            };
            var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);

            bool? tda = true;   // true: target & decoy, false: target, null: decoy

            const int minSequenceLength = 7; // 7
            const int maxSequenceLength = 150; // 1000
            const int minPrecursorIonCharge = 1; // 3
            const int maxPrecursorIonCharge = 30; // 67
            const int minProductIonCharge = 1; // 1
            const int maxProductIonCharge = 15; // 15
            const double precursorIonTolerancePpm = 10;
            const double productIonTolerancePpm = 10;
            const double corrThreshold = 0.7;

            var bottomUpLauncher = new IcBottomUpLauncher(
                specFilePath,
                dbFilePath,
                outputDir,
                aaSet,
                null)
            {
                MinSequenceLength = minSequenceLength,
                MaxSequenceLength = maxSequenceLength,
                MinPrecursorIonCharge = minPrecursorIonCharge,
                MaxPrecursorIonCharge = maxPrecursorIonCharge,
                MinProductIonCharge = minProductIonCharge,
                MaxProductIonCharge = maxProductIonCharge,
                PrecursorIonTolerancePpm = precursorIonTolerancePpm,
                ProductIonTolerancePpm = productIonTolerancePpm,
                RunTargetDecoyAnalysisBool = tda,
                NumTolerableTermini = 0
            };

            bottomUpLauncher.RunSearch(corrThreshold);
        }
示例#2
0
文件: Program.cs 项目: javamng/GitHUB
        private static void Main(string[] args)
        {
            var handle = Process.GetCurrentProcess().MainWindowHandle;
            SetConsoleMode(handle, EnableExtendedFlags);

            if (args.Length % 2 != 0)
            {
                PrintUsageInfo("The number of arguments must be even.");
                return;
            }

            // initialize parameters
            var paramDic = new Dictionary<string, string>
            {
                {"-s", null},
                {"-d", null},
                {"-o", null},
                {"-e", "1"},
                {"-ntt", "2"},
                {"-mod", null},
                {"-t", "10"},
                {"-f", "10"},
                {"-tda", "0"},
                {"-minLength", "6"},
                {"-maxLength", "40"},
                {"-minCharge", "1"},
                {"-maxCharge", "4"},
                {"-minFragCharge", "1"},
                {"-maxFragCharge", "3"}
            };

            for (var i = 0; i < args.Length / 2; i++)
            {
                var key = args[2 * i];
                var value = args[2 * i + 1];
                if (!paramDic.ContainsKey(key))
                {
                    PrintUsageInfo("Invalid parameter: " + key);
                    return;
                }
                paramDic[key] = value;
            }

            var parameters = new BottomUpInputParameters();
            var message = parameters.Parse(paramDic);
            if (message != null)
            {
                PrintUsageInfo(message);
                return;
            }

            Console.WriteLine(Name + " " + Version);
            parameters.Display();
            parameters.Write();

            foreach (string specFilePath in parameters.SpecFilePaths)
            {
                var bottomUpLauncher = new IcBottomUpLauncher(
                    specFilePath,
                    parameters.DatabaseFilePath,
                    parameters.OutputDir,
                    parameters.AminoAcidSet,
                    parameters.Enzyme)
                {
                    MinSequenceLength = parameters.MinSequenceLength,
                    MaxSequenceLength = parameters.MaxSequenceLength,
                    MinPrecursorIonCharge = parameters.MinPrecursorIonCharge,
                    MaxPrecursorIonCharge = parameters.MaxPrecursorIonCharge,
                    MinProductIonCharge = parameters.MinProductIonCharge,
                    MaxProductIonCharge = parameters.MaxProductIonCharge,
                    PrecursorIonTolerancePpm = parameters.PrecursorIonTolerancePpm,
                    ProductIonTolerancePpm = parameters.ProductIonTolerancePpm,
                    //RunTargetDecoyAnalysisBool = parameters.TdaBool,
                    RunTargetDecoyAnalysis = parameters.Tda,
                    NumTolerableTermini = parameters.NumTolerableTermini,
                };

                bottomUpLauncher.RunSearch(CorrThreshold);
            }
        }
示例#3
0
        public void TestBottomUpSearch(string specFilePath, string dbFilePath, string outputDir, AminoAcidSet aaSet, bool? tda, int ntt, double corrThreshold = 0.3)
        {
            var methodName = MethodBase.GetCurrentMethod().Name;
            TestUtils.ShowStarting(methodName);

            // Search parameters
            const int minSequenceLength = 6; // 7
            const int maxSequenceLength = 40; // 1000
            const int minPrecursorIonCharge = 1; // 3
            const int maxPrecursorIonCharge = 4; // 67
            const int minProductIonCharge = 1; // 1
            const int maxProductIonCharge = 2; // 15
            const int precursorIonTolerancePpm = 10;
            const int productIonTolerancePpm = 10;

            var enzyme = Enzyme.Trypsin;

            var bottomUpLauncher = new IcBottomUpLauncher(
                specFilePath,
                dbFilePath,
                outputDir,
                aaSet,
                enzyme)
            {
                MinSequenceLength = minSequenceLength,
                MaxSequenceLength = maxSequenceLength,
                MinPrecursorIonCharge = minPrecursorIonCharge,
                MaxPrecursorIonCharge = maxPrecursorIonCharge,
                MinProductIonCharge = minProductIonCharge,
                MaxProductIonCharge = maxProductIonCharge,
                PrecursorIonTolerancePpm = precursorIonTolerancePpm,
                ProductIonTolerancePpm = productIonTolerancePpm,
                RunTargetDecoyAnalysisBool = tda,
                NumTolerableTermini = ntt
            };

            bottomUpLauncher.RunSearch(corrThreshold);
            //topDownLauncher.RunIntactProteinSearch();
        }