コード例 #1
0
        public static void GenerateMatrix()
        {
            var sites = CleavageSiteUtility.Deserialize();

            float[,] matrix = new float[sites.Count, 21];

            for (int i = 0; i < sites.Count; i++)
            {
                System.Console.WriteLine(sites[i].Gene);
                for (int j = 0; j < 21; j++)
                {
                    matrix[i, j] = Reactivity.GetReactivity(sites[i].Gene, sites[i].StartAt + j - 1);
                }
            }

            //print
            string content = string.Empty;

            for (int i = 0; i < matrix.GetLength(0); i++)
            {
                for (int j = 0; j < matrix.GetLength(1); j++)
                {
                    content += matrix[i, j].ToString() + ",";
                }
                content = content.TrimEnd(',') + "\n";
            }

            FileExtension.Save(content, Config.WorkingFolder + "cs_21_reactivity.csv");
        }
コード例 #2
0
        public static void GenerateEfficiencies()
        {
            var sites = CleavageSiteUtility.Deserialize();

            foreach (var type in EnumUtil.GetValues <DegradomeType>())
            {
                float[] efficiencies = new float[sites.Count];

                for (int i = 0; i < sites.Count; i++)
                {
                    efficiencies[i] = Efficiency.GetEfficiency(sites[i].Gene, sites[i].StartAt - 1 + 10, sites[i].StartAt - 1 + 20, type);
                }

                //print
                string content = string.Empty;
                for (int i = 0; i < efficiencies.Length; i++)
                {
                    content += efficiencies[i].ToString() + "\n";
                }

                FileExtension.Save(content, Config.WorkingFolder + "cs_efficiencies_" + type.ToString() + ".csv");
            }
        }
コード例 #3
0
        public static void Filter()
        {
            var    sites = CleavageSiteUtility.Deserialize();
            string deletedCleavageSite   = string.Empty;
            List <CleavageSite> toDelete = new List <CleavageSite>();

            foreach (var site in sites)
            {
                if (!Reactivity.HasReactivity(site.Gene))
                {
                    toDelete.Add(site);
                    deletedCleavageSite += site.ToString() + "\r\n";
                }
            }

            foreach (var site in toDelete)
            {
                sites.Remove(site);
            }
            FileExtension.Save(deletedCleavageSite, "CleavageSite_Filtered_by_Reactivity.txt");

            Serializer.Serialize("cleavage_sites.bin", sites);
            //return sites;
        }