public static void Generate(DegradomeType dType, int length, int index)
{
string dotBracket = GetStruct(dType, length, index);
string outputFile = RnaPlotWrapper.Plot(dotBracket);
File.Copy(outputFile, $"{Config.WorkingFolder}\\cs_rna_struct\\plot\\{dType}_{length}_{index}.svg");
Svg.SvgDocument doc = SvgDocument.Open(outputFile);
doc.Draw().Save($"{Config.WorkingFolder}\\cs_rna_struct\\plot\\{dType}_{length}_{index}.png");
}
public static float GetEfficiency(string gene, int position, DegradomeType dType)
{
var dict = LoadDict(dType);
if (!dict[gene].ContainsKey(position))
{
return(0);
}
return(dict[gene][position]);
}
private static Dictionary <string, Dictionary <int, float> > LoadDict(DegradomeType type)
{
if (dict.ContainsKey(type))
{
return(dict[type]);
}
var subdict = Serializer.Deserialize <Dictionary <string, Dictionary <int, float> > >($"ce_{type}_dict.bin");
dict[type] = subdict;
return(subdict);
}
public static bool HasEfficiency_21(CleavageSite site, DegradomeType dType)
{
var dict = LoadDict(dType);
for (int i = 0; i <= 21; i++)
{
if (dict[site.Gene].ContainsKey(site.StartAt - 1 + i))
{
return(true);
}
}
return(false);
}
public static float GetEfficiency(string gene, int start, int endAt, DegradomeType dType)
{
var dict = LoadDict(dType);
float sum = 0;
for (int i = start; i <= endAt; i++)
{
if (dict[gene].ContainsKey(i))
{
sum += dict[gene][i];
}
}
return(sum);
}
public static string GetDegradomeFile(DegradomeType dType)
{
switch (dType)
{
case DegradomeType.wt:
return(DegradomeWTFile);
case DegradomeType.xrn4:
return(DegradomeXrn4File);
default:
throw new Exception("wrong degradome type");
}
}
private static string GetStruct(DegradomeType dType, int length, int index)
{
string structFolder = $"{Config.WorkingFolder}\\cs_rna_struct\\";
string structFile = $"{structFolder}\\cs_structure_{length}_{dType}.txt";
string dotBracket = "";
using (StreamReader sr = new StreamReader(structFile))
{
for (int i = 0; i < index; i++)
{
sr.ReadLine();
}
dotBracket = sr.ReadLine();
}
return(dotBracket);
}
private static float[][] GetAverageAndStandardDeviation(int datasetIndex, DegradomeType dType)
{
var list = ReadCleavageSite($"{Config.WorkingFolder}\\cleavage_sites_{dType}_{datasetIndex}.csv");
float[][] matrix = new float[21][];
float[][] stats = new float[2][];
//average
stats[AVG] = new float[21];
//StandardDeviation
stats[SD] = new float[21];
for (int col = 0; col < 21; col++)
{
matrix[col] = new float[list.Count];
for (int row = 0; row < list.Count; row++)
{
try
{
var site = list[row];
matrix[col][row] = Reactivity.GetReactivity(site.Gene, site.StartAt - 1 + col);
}
catch
{
}
}
}
for (int col = 0; col < 21; col++)
{
stats[AVG][col] = matrix[col].Average();
stats[SD][col] = (float)matrix[col].StandardDeviation();
}
return(stats);
}
public static bool HasEfficiency_Gene(CleavageSite site, DegradomeType dType)
{
var dict = LoadDict(dType);
return(dict[site.Gene].Count > 0);
}
public static float GetEfficiency(CleavageSite site, DegradomeType dType)
{
return(GetEfficiency(site.Gene, site.StartAt - 1 + 10, site.StartAt - 1 + 11, dType));
}
private static string GetSequence(DegradomeType deg, int length, int index)
{
string seqFile = $"{Config.WorkingFolder}\\cs_rna_struct\\{deg}\\{length}\\{index}.seq";
return(FileExtension.ReadList(seqFile).Last());
}
