コード例 #1
0
ファイル: Program.cs プロジェクト: weizhiting/canvas
        static void Main(string[] args)
        {
            if (args.Length < 4)
            {
                Console.WriteLine("EvaluateCNV {0}",
                                  System.Reflection.Assembly.GetExecutingAssembly().GetName().Version);
                Console.WriteLine("For more info see: http://confluence.illumina.com/display/BIOINFO/EvaluateCNV");
                Console.WriteLine();
                Console.WriteLine("Usage info:");
                Console.WriteLine("EvaluateCNV $TruthSetPath $CNV.vcf $ExcludedRegionsBed $OutputPath [$RegionOfInterestBed]");
                return;
            }
            CNVChecker checker = new CNVChecker();
            string     ROIBed  = null;
            double     heterogeneityFraction = 1;

            if (args.Length > 4)
            {
                ROIBed = args[4];
            }
            if (args.Length > 5)
            {
                heterogeneityFraction = double.Parse(args[5]);
            }
            checker.Evaluate(args[0], args[1], args[2], args[3], ROIBed, heterogeneityFraction);
        }
コード例 #2
0
ファイル: Program.cs プロジェクト: zhang919/canvas
        private static int MainHelper(string[] args)
        {
            EvaluateCnvOptionsParser optionsParser = new EvaluateCnvOptionsParser();

            if (args.Length < 4)
            {
                ShowHelp(optionsParser, Console.Error);
                return(1);
            }
            var parsingResult = optionsParser.Parse(args.Skip(4));

            if (!parsingResult.Success)
            {
                Console.Error.WriteLine(parsingResult.ErrorMessage);
                ShowHelp(optionsParser, Console.Error);
                return(1);
            }
            var options = parsingResult.Result;

            if (options.Help)
            {
                ShowHelp(optionsParser, Console.Out);
                return(0);
            }
            CNVChecker.Evaluate(args[0], args[1], args[2], args[3], options);
            return(0);
        }
コード例 #3
0
ファイル: Program.cs プロジェクト: abladon/canvas
 static void Main(string[] args)
 {
     if (args.Length < 4)
     {
         Console.WriteLine("EvaluateCNV {0}",
             System.Reflection.Assembly.GetExecutingAssembly().GetName().Version);
         Console.WriteLine("For more info see: http://confluence.illumina.com/display/BIOINFO/EvaluateCNV");
         Console.WriteLine();
         Console.WriteLine("Usage info:");
         Console.WriteLine("EvaluateCNV $TruthSetPath $CNV.vcf $ExcludedRegionsBed $OutputPath [$RegionOfInterestBed]");
         return;
     }
     CNVChecker checker = new CNVChecker();
     string ROIBed = null;
     if (args.Length > 4) ROIBed = args[4];
     checker.Evaluate(args[0], args[1], args[2], args[3], ROIBed);
 }
コード例 #4
0
ファイル: CNVEvaluator.cs プロジェクト: zhang919/canvas
        private const int MaxCn = 5; // Currently the max copynum is 5

        #endregion

        public CnvEvaluator(CNVChecker cnvChecker)
        {
            _cnvChecker = cnvChecker;
        }
コード例 #5
0
        public static void Evaluate(string truthSetPath, string cnvCallsPath, string excludedBed, string outputPath, EvaluateCnvOptions options)
        {
            double heterogeneityFraction = options.HeterogeneityFraction;
            var    knownCn = LoadKnownCn(truthSetPath, heterogeneityFraction);

            knownCn = knownCn.SelectValues(
                truthEntries => truthEntries.Where(truthEntry => truthEntry.Length >= options.MinEntrySize).ToList());
            var calls = GetCnvCallsFromVcf(cnvCallsPath, options.DQscoreThreshold);

            calls = calls.SelectValues(
                chromosomeCalls => chromosomeCalls.Where(call => call.Length >= options.MinEntrySize).ToList());

            // LoadRegionsOfInterest(options.RoiBed?.FullName);
            var excludeIntervals = new Dictionary <string, List <CNInterval> >();

            if (!string.IsNullOrEmpty(excludedBed))
            {
                var           excludeIntervalsTmp = LoadIntervalsFromBed(excludedBed, false, 1.0);
                List <string> keys = excludeIntervalsTmp.Keys.ToList();
                foreach (string key in keys)
                {
                    string chr = key;
                    if (!calls.ContainsKey(chr))
                    {
                        chr = key.Replace("chr", "");
                    }
                    if (!calls.ContainsKey(chr))
                    {
                        chr = "chr" + key;
                    }
                    if (!calls.ContainsKey(chr))
                    {
                        Console.WriteLine($"Error: Skipping exclude intervals for chromosome {key} with no truth data." +
                                          $"Check that chromosome names are spelled correctly for exclude intervals");
                        continue;
                    }
                    excludeIntervals[chr] = excludeIntervalsTmp[key];
                }
            }
            Console.WriteLine("TruthSet\t{0}", truthSetPath);
            Console.WriteLine("CNVCalls\t{0}", cnvCallsPath);

            bool includePassingOnly = Path.GetFileName(cnvCallsPath).ToLower().Contains("vcf");
            var  logger             = new Logger(new[] { Console.Out }, new[] { Console.Error });
            var  settings           = IsasConfigurationSettings.GetConfigSettings();
            var  output             = new DirectoryLocation(outputPath);
            var  workerDirectory    = new DirectoryLocation(Isas.Framework.Utilities.Utilities.GetAssemblyFolder(typeof(CNVChecker)));
            var  commandManager     = new CommandManager(new ExecutableProcessor(settings, logger, workerDirectory));

            WorkDoerFactory.RunWithWorkDoer(logger, settings, output, workDoer =>
            {
                var tabixWrapper    = TabixWrapperFactory.GetTabixWrapper(logger, workDoer, commandManager);
                var ploidyCorrector = new PloidyCorrector(logger, workDoer,
                                                          new PloidyEstimator(logger, workDoer, null, false, commandManager), tabixWrapper, false);
                var checker = new CNVChecker(options.DQscoreThreshold, excludeIntervals, ploidyCorrector);
                if (options.PloidyInfo.SexPloidyInfo != null)
                {
                    Console.WriteLine($">>>Getting reference ploidy from provided ploidy information and PAR bed file '{options.PloidyInfo.ParBed}'");

                    var ploidy          = checker.GetPloidy(options.PloidyInfo, output);
                    var referencePloidy = LoadReferencePloidy(options.PloidyInfo.SexPloidyInfo, options.PloidyInfo.ParBed);
                    knownCn             = GetKnownCopyNumberWithReferencePloidy(referencePloidy, knownCn);
                    calls = GetCallsWithRefPloidy(calls, ploidy);
                }
                var cnvEvaluator = new CnvEvaluator(checker);

                if (checker.DQscoreThreshold.HasValue && !Path.GetFileName(cnvCallsPath).ToLower().Contains("vcf"))
                {
                    throw new ArgumentException("CNV.vcf must be in a vcf format when --dqscore option is used");
                }
                cnvEvaluator.ComputeAccuracy(knownCn, cnvCallsPath, outputPath, includePassingOnly, options, calls);
                if (includePassingOnly)
                {
                    cnvEvaluator.ComputeAccuracy(knownCn, cnvCallsPath, outputPath, false, options, calls);
                }
                ComputeCallability(logger, calls, options, output);
                Console.WriteLine(">>>Done - results written to {0}", outputPath);
            });
        }