Esempio n. 1
0
        private static void Main(string[] args)
        {
            if (args.Length != 4)
            {
                Console.Out.Write("参数不正确");
                return;
            }
            int    cycleLengthThreshold = 20;       //环长度
            int    dustLengthThreshold  = 20;
            string infile = args[0];
            string outdir = args[1];

            if (!Directory.Exists(outdir))
            {
                Directory.CreateDirectory(outdir);
            }
            cycleLengthThreshold = int.Parse(args[2]);
            dustLengthThreshold  = int.Parse(args[3]);

            //步数15
            int          simplificationSteps = 15;
            IGraphTool   graphTool           = new GraphTool();             //创建图池子
            ABruijnGraph aBruijnGraph        = new ABruijnGraph(graphTool); //AB图
            IDataReader  dataReader          = new SyntenyDataReader(infile, ' ');
            IDataWriter  dataWriter          = new SyntenyDataWriter(outdir + "/synteny.txt", ' ', outdir + "/sequenceColor.txt", infile,
                                                                     outdir + "/modifiedSequence.txt");
            IColorTracker    colorTracker  = new ColorTracker();                                                             //颜色标记
            ISequenceSmother smother       = new SequenceSmother(2, cycleLengthThreshold);                                   //序列平滑
            ISyntenyFinder   syntenyFinder = new SyntenyFinder(dataReader, dataWriter, aBruijnGraph, smother, colorTracker); //核心函数

            syntenyFinder.Run(cycleLengthThreshold, 2, 3, simplificationSteps, true, dustLengthThreshold, outdir);
        }
Esempio n. 2
0
        private static void Main(string[] args)
        {
            int cycleLengthThreshold = 30;          //环长度

            string infile = INFILE;

            string outdir = OUTDIR;

            int dustLengthThreshold = 8;

            int simplificationSteps = 15;        //步数15


            IGraphTool   graphTool    = new GraphTool();             //创建图池子
            ABruijnGraph aBruijnGraph = new ABruijnGraph(graphTool); //AB图
            IDataReader  dataReader   = new SyntenyDataReader(infile, ' ');
            IDataWriter  dataWriter   = new SyntenyDataWriter(outdir + "/synteny.txt", ' ', outdir + "/sequenceColor.txt", infile,
                                                              outdir + "/modifiedSequence.txt");
            IColorTracker    colorTracker  = new ColorTracker();                                                             //颜色标记
            ISequenceSmother smother       = new SequenceSmother(2, cycleLengthThreshold);                                   //序列平滑
            ISyntenyFinder   syntenyFinder = new SyntenyFinder(dataReader, dataWriter, aBruijnGraph, smother, colorTracker); //核心函数

            syntenyFinder.Run(cycleLengthThreshold, 2, 3, simplificationSteps, true, dustLengthThreshold, outdir);
        }