public static void MergeUbiSites(string csvFileA, string csvFileB, string csvOut)
{
int[] ubiPos = new int[] { 34, 36, 38, 40, 42, 44 };
vsCSV csvA = new vsCSV(csvFileA);
vsCSV csvB = new vsCSV(csvFileB);
vsCSVWriter writer = new vsCSVWriter(csvOut);
int posUbiA = -1;
int posUbiB = -1;
foreach (string lineA in csvA.LINES_LIST)
{
string[] splitsA = lineA.Split(vsCSV._Generic_Separator);
foreach (int indexUbiPos in ubiPos)
{
if (splitsA.Length > indexUbiPos && int.TryParse(splitsA[indexUbiPos], out posUbiA))
{
foreach (string lineB in csvB.LINES_LIST)
{
string[] splitsB = lineB.Split(vsCSV._Generic_Separator);
if (splitsB.Length > indexUbiPos && int.TryParse(splitsB[indexUbiPos], out posUbiB))
{
if (splitsA[3].CompareTo(splitsB[3]) == 0 && posUbiA == posUbiB)
{
writer.AddLine(splitsA[3] + "," + vsCSV.GetFileName_NoExtension(csvFileA) + "," + splitsA[13] + "," +
vsCSV.GetFileName_NoExtension(csvFileB) + "," + splitsB[13] + "," +
posUbiA + "," + splitsA[indexUbiPos + 1]);
}
}
}
}
}
}
writer.WriteToFile();
}
}//*/
public static void LIR(string fasta, string csvOut)
{
vsCSVWriter writer = new vsCSVWriter(csvOut);
foreach (string[] protein in Fasta.FastaRead.GetSequences(fasta))
//string header = "Known LIR";
//foreach (string sequence in LIR_Peptides)
{
string header = protein[0];
string sequence = protein[1];
//if("W/F/Y" && pos+2 == "L/I/V" && "Enough E,D,S or T at +1 to -3")
for (int i = 2; i + 3 < sequence.Length; i++)
{
if (Score_LIR(sequence, i))
{
//double score = Score_LIR(sequence, i);
//int nbDest = NbDEST(sequence, i);
//if (score >= 2.6 && nbDest >= 3 && nbDest <= 7)
//{
writer.AddLine('"' + header + "\"," + i + "," + sequence.Substring(Math.Max(i - 9, 0), Math.Min(12, sequence.Length - Math.Max(i - 9, 0))) + "," + NbDEST(sequence, i));
}
}
}
writer.WriteToFile();
}
public static void ScoreSequences(string csvFileOut)
{
vsCSVWriter writer = new vsCSVWriter(csvFileOut);
foreach (string motif in GetAllLIRSequences("DESTx", "WFY", "LIV", 12, ""))
{
double score = 0;
foreach (string lir in LIR_Peptides)
{
for (int i = 0; i < LIR_Peptides.Length; i++)
{
if (lir[i] == motif[i] || motif[i] == 'x')
{
score += 1;
}
}
}
if (score > 2)
{
writer.AddLine(motif + "," + score);
}
}
writer.WriteToFile();
}