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ProForma-Exporters/20210819-ProForma-formatter-pTop.cs

+using System;
+using System.IO;
+using System.Data;
+using System.Text;
+
+class PTM {
+    public int Position=0;
+    public string Name="";
+    public PTM Next=null;
+
+    public void PrintAll() {
+	PTM Runner = this.Next;
+	Console.WriteLine("PrintAll");
+	while (Runner != null) {
+	    Console.Write(Runner.Position);
+	    Console.Write("\t");
+	    Console.WriteLine(Runner.Name);
+	    Runner = Runner.Next;
+	}
+    }
+
+    public void InsertSorted(int NewPos, string NewString) {
+	PTM Runner = this;
+	while (Runner.Next != null && Runner.Next.Position < NewPos) {
+	    Runner = Runner.Next;
+	}
+	PTM PlaceHolder = Runner.Next;
+	Runner.Next = new PTM();
+	Runner = Runner.Next;
+	Runner.Position = NewPos;
+	Runner.Name = NewString;
+	Runner.Next = PlaceHolder;
+    }
+}
+
+namespace ProFormaFormatter {
+    class Program {
+	static void Main(string[] args)
+	{
+	    if (args.Length==0) {
+		Console.WriteLine("Supply the name of the search_task _filter.csv or pTop_filtered.csv file for processing.");
+		Environment.Exit(1);
+	    }
+	    DataTable datatable = new DataTable();
+	    string FileString = args[0];
+	    StreamReader streamreader = new StreamReader(FileString);
+	    char[] delimiter = new char[] { ',' };
+	    string[] columnheaders = streamreader.ReadLine().Split(delimiter);
+	    foreach (string columnheader in columnheaders)
+	    {
+		datatable.Columns.Add(columnheader);
+	    }
+	    
+	    while (streamreader.Peek() > 0)
+	    {
+		DataRow datarow = datatable.NewRow();
+		datarow.ItemArray = streamreader.ReadLine().Split(delimiter);
+		datatable.Rows.Add(datarow);
+	    }
+	    PTM ThesePTMs = new PTM();
+	    // Loop through all the different PrSMs in this table
+	    foreach (DataRow row in datatable.Rows) {
+		string FName = Convert.ToString(row["Title"]);
+		string Seq;
+		// This column changes names between pTop 1 and pTop 2
+		if (datatable.Columns.Contains("Sequence"))
+		    Seq = Convert.ToString(row["Sequence"]);
+		else
+		    Seq = Convert.ToString(row["Protein Sequence"]);
+		string OutSeq = Seq;
+		int    OutMassAdded = 0;
+		string PTMs = Convert.ToString(row["PTMs"]);
+		//pTop output table lacks Q-values
+		double EVal;
+		if (datatable.Columns.Contains(" Evalue"))
+		    EVal = -Math.Log(Convert.ToDouble(row[" Evalue"]));
+		else
+		    EVal = -Math.Log(Convert.ToDouble(row["Final Score"]));
+		string[] FNameChunks = FName.Split('.');
+		//This code will break the first time someone uses a period in their RAW file names...
+		string OutFile = FNameChunks[0];
+		string OutScan = FNameChunks[1];
+		string OutCharge = Convert.ToString(row["Charge State"]);
+		string OutAccession = Convert.ToString(row["Protein AC"]);
+		string[] PTMArray = PTMs.Split(';');
+		// Clean away the extra fields for accessions
+		OutAccession = OutAccession.Split('|')[1];
+		foreach (string ThisPTM in PTMArray) {
+		    if (ThisPTM.Length > 0) {
+			string[] PTMFields = ThisPTM.Split(')');
+			if (PTMFields[0]!="NULL") {
+			    int Pos = Convert.ToInt32(PTMFields[0].Substring(1));
+			    string[] NameSplitter = PTMFields[1].Split('[');
+			    string ModName = NameSplitter[0];
+			    if (ModName == "Oxidation")
+				OutMassAdded += 16;
+			    else if (ModName == "Methyl")
+				OutMassAdded += 14;
+			    else if (ModName == "Acetyl")
+				OutMassAdded += 42;
+			    else if (ModName == "Carbamidomethyl")
+				OutMassAdded += 57;
+			    else if (ModName == "Phospho")
+				OutMassAdded += 80;
+			    // Add to the sorted linked list of PTMs
+			    ThesePTMs.InsertSorted(Pos, ModName);
+			}
+		    }
+		}
+		// ThesePTMs.PrintAll();
+		// Create a decorated sequence by incorporating PTM string data.
+		int CurrentSeqPos = 0;
+		StringBuilder DecoratedSeq = new StringBuilder();
+		PTM ThisPTMinLL = ThesePTMs.Next;
+		while (ThisPTMinLL != null) {
+		    if (ThisPTMinLL.Position == 0) {
+			DecoratedSeq.Append("[");
+			DecoratedSeq.Append(ThisPTMinLL.Name);
+			DecoratedSeq.Append("]-");
+			DecoratedSeq.Append(Seq.Substring(CurrentSeqPos, ThisPTMinLL.Position-CurrentSeqPos));
+		    }
+		    else {
+			DecoratedSeq.Append(Seq.Substring(CurrentSeqPos, ThisPTMinLL.Position-CurrentSeqPos));
+			DecoratedSeq.Append("[");
+			DecoratedSeq.Append(ThisPTMinLL.Name);
+			DecoratedSeq.Append("]");
+		    }
+		    CurrentSeqPos = ThisPTMinLL.Position;
+		    ThisPTMinLL = ThisPTMinLL.Next;
+		}
+		DecoratedSeq.Append(Seq.Substring(CurrentSeqPos));
+		string OutProForma = Convert.ToString(DecoratedSeq);
+		// I feel guilty for dumping garbage collection on the interpreter.
+		ThesePTMs.Next=null;
+		
+		Console.Write(OutFile);
+		Console.Write("\t");
+		Console.Write(OutScan);
+		Console.Write("\t");
+		Console.Write(OutCharge);
+		Console.Write("\t");
+		Console.Write(OutAccession);
+		Console.Write("\t");
+		Console.Write(OutSeq);
+		Console.Write("\t");
+		Console.Write(OutMassAdded);
+		Console.Write("\t");
+		Console.Write(OutProForma);
+		Console.Write("\t");
+		Console.WriteLine(EVal);
+	    }
+	}
+    }
+}