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");
}
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");
}
}
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;
}