/// <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");
}
}
