/// <summary> /// Generate the cleavage sites and sort it by the extendability /// </summary> public static void GenerateCleavegeSites() { string[] lines = FileExtension.ReadList(Config.AllCleavegSiteFile); Console.WriteLine($"Total Cleavage Sites:{lines.Length}"); List <CleavageSite> sites = new List <CleavageSite>(); foreach (string line in lines) { var arr = line.Split('_'); if (!arr[2].IsDigit()) { continue; } if (!Config.ValidNames.Contains(arr[1])) { continue; } CleavageSite site = new CleavageSite(); site.MiRNA = arr[0]; site.Gene = arr[1]; site.StartAt = int.Parse(arr[2]); int extendLeft = site.StartAt - 1; int extendRight = Gene.GetCount(site.Gene) - (site.StartAt - 1 + 21); site.Extendability = Math.Min(extendLeft, extendRight); sites.Add(site); } sites.Sort((a, b) => - a.Extendability.CompareTo(b.Extendability)); //create file StringBuilder site_content = new StringBuilder(); foreach (var site in sites) { site_content.AppendLine(site.ToString()); } FileExtension.Save(site_content.ToString(), Config.WorkingFolder + "\\cleavage_sites_repeat.csv"); List <CleavageSite> combinedSites = Combine(sites); //create file StringBuilder combined_site_content = new StringBuilder(); foreach (var site in combinedSites) { combined_site_content.AppendLine(site.ToString()); } FileExtension.Save(combined_site_content.ToString(), Config.WorkingFolder + "\\cleavage_sites.csv"); }
public static void GenerateCleavageSiteFiles() { List <CleavageSite> sites = new List <CleavageSite>(); string[] lines = FileExtension.ReadList(Config.WorkingFolder + "cleavage_sites.csv"); Console.WriteLine($"Total Cleavage Sites:{lines.Length}"); foreach (string line in lines) { var arr = line.Split('_'); CleavageSite site = CleavageSite.Parse(line); sites.Add(site); } Console.WriteLine($"After filtered by cleavage efficiency and reactivity:{sites.Count}"); //Generate 4 files filtered by 4 degradome datasets. foreach (DegradomeType dType in EnumUtil.GetValues <DegradomeType>()) { string site_content = string.Empty; string efficiency_content = string.Empty; string efficiency_log_content = string.Empty; string reactivity_content = string.Empty; string reactivity_25_content = string.Empty; string reactivity_50_content = string.Empty; //string reactivity_75_content = string.Empty; //string reactivity_100_content = string.Empty; foreach (CleavageSite site in sites) { if (site.Extendability < 50) { break; } //if the cleavage efficiency is zero, //we can say that this is not a cleavage site. //filter it out. float efficiency = Efficiency.GetEfficiency(site, dType); if (efficiency == 0) { continue; } site_content += site.ToString() + "\n"; efficiency_content += efficiency.ToString() + "\n"; efficiency_log_content += Math.Log(efficiency).ToString() + "\n"; for (int j = 0; j < 21; j++) { reactivity_content += Reactivity.GetReactivity(site.Gene, site.StartAt - 1 + j) + ","; } for (int j = 0 - 25; j < 21 + 25; j++) { reactivity_25_content += Reactivity.GetReactivity(site.Gene, site.StartAt - 1 + j) + ","; } for (int j = 0 - 50; j < 21 + 50; j++) { reactivity_50_content += Reactivity.GetReactivity(site.Gene, site.StartAt - 1 + j) + ","; } reactivity_content = reactivity_content.TrimEnd(',') + "\n"; reactivity_25_content = reactivity_25_content.TrimEnd(',') + "\n"; reactivity_50_content = reactivity_50_content.TrimEnd(',') + "\n"; } FileExtension.Save(site_content, Config.WorkingFolder + "\\cleavage_site_" + dType + ".csv"); FileExtension.Save(efficiency_content, Config.WorkingFolder + "\\cs_efficiencies_" + dType + ".csv"); FileExtension.Save(efficiency_log_content, Config.WorkingFolder + "\\cs_efficiencies_log_" + dType + ".csv"); FileExtension.Save(reactivity_content, Config.WorkingFolder + "\\cs_reactivity_" + dType + ".csv"); FileExtension.Save(reactivity_25_content, Config.WorkingFolder + "\\cs_reactivity_" + dType + "_25.csv"); FileExtension.Save(reactivity_50_content, Config.WorkingFolder + "\\cs_reactivity_" + dType + "_50.csv"); //FileExtension.Save(reactivity_75_content, Config.WorkingFoler + "\\cs_reactivity_" + dType + "_75.csv"); //FileExtension.Save(reactivity_100_content, Config.WorkingFoler + "\\cs_reactivity_" + dType + "_100.csv"); } }