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

+using System;
+using System.IO;
+using System.Data;
+using System.Text;
+
+namespace ProFormaFormatter {
+
+    class PTM {
+	public int Position=0;
+	public string Name="";
+	public PTM Next=null;
+	
+	public void PrintAll() {
+	    PTM Runner = this.Next;
+	    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;
+	}
+	
+    }
+    
+    class Program {
+	static void Main(string[] args)
+	{
+	    bool SuppressUnknowns = false;
+	    if (args.Length==0) {
+		Console.WriteLine("Supply the name of the _ms2_toppic_prsm.tsv file for processing.");
+		Console.WriteLine("If you want to exclude unknown mass PTM-containing PrSMs, add the argument \"--suppress\".");
+		Environment.Exit(1);
+	    }
+	    if (args.Length==2) {
+		if (args[1] == "--suppress") {
+		    SuppressUnknowns = true;
+		}
+	    }
+	    DataTable datatable = new DataTable();
+	    StreamReader streamreader = new StreamReader(args[0]);
+	    //skip the header
+	    string Linebuffer=streamreader.ReadLine();
+	    while ((Linebuffer.Length == 0) || (Linebuffer.Substring(0,9) != "Data file")) {
+		Linebuffer=streamreader.ReadLine();
+	    }
+	    char[] delimiter = new char[] { '\t' };
+	    char[] PathDelimiters = new char[] { '\\','/' };
+	    string FNameTrailer = "_ms2.msalign";
+	    string[] columnheaders = Linebuffer.Split(delimiter);
+	    foreach (string columnheader in columnheaders)
+	    {
+		datatable.Columns.Add(columnheader); // I've added the column headers here.
+	    }
+	    
+	    while (streamreader.Peek() > 0)
+	    {
+		DataRow datarow = datatable.NewRow();
+		Linebuffer = streamreader.ReadLine();
+		datarow.ItemArray = Linebuffer.Split(delimiter);
+		datatable.Rows.Add(datarow);
+	    }
+
+	    string LastPrsmID = "NoneSoFar";
+	    foreach (DataRow row in datatable.Rows) {
+		bool   ContainsUnknown = false;
+		string ThisPrsmID = Convert.ToString(row["Prsm ID"]);
+		if (ThisPrsmID != LastPrsmID) {
+		    LastPrsmID = ThisPrsmID;
+		    string OutFile = Convert.ToString(row["Data file name"]);
+		    string OutScan = Convert.ToString(row["Scan(s)"]);
+		    string OutCharge = Convert.ToString(row["Charge"]);
+		    string OutAccession = Convert.ToString(row["Protein accession"]);
+		    string Seq = Convert.ToString(row["Proteoform"]);
+		    string OutSequence;
+		    int    OutMassAdded = 0;
+		    double OutEVal = -Math.Log(Convert.ToDouble(row["E-value"]));
+		    string[] FNameChunks = OutFile.Split(PathDelimiters);
+		    OutFile = FNameChunks[FNameChunks.Length-1];
+		    if (OutFile.EndsWith(FNameTrailer)) {
+			OutFile = OutFile.Substring(0,OutFile.Length-FNameTrailer.Length);
+		    }
+		    //FChunk is now the input mzML / RAW without suffix
+		    OutAccession = OutAccession.Split('|')[1];
+		    //Scan numbers are fine as is
+		    //Remove the sequence context characters (and double-quotes) from N-terminus
+		    if (Seq[1] == '.')
+			Seq = Seq.Substring(2);
+		    else
+			Seq = Seq.Substring(3);
+		    //Remove the sequence context characters from C-terminus
+		    if (Seq[Seq.Length-2] == '.')
+			Seq = Seq.Substring(0,Seq.Length-2);
+		    else
+			Seq = Seq.Substring(0,Seq.Length-3);
+		    StringBuilder OutSeqBuilder = new StringBuilder();
+		    StringBuilder UnkPTMLabel;
+		    float ObsMass;
+		    PTM ThesePTMs = new PTM();
+		    // THIS CODE ASSOCIATES EACH PTM WITH THE LAST SEQUENCE LETTER IN THE RANGE TO WHICH IT MIGHT BE ATTACHED; LOCALIZATION INFORMATION IS DESTROYED HERE.
+		    // Note that TopMG results frequently include multiple PTMs in the same ambiguous sequence range; all PTMs for that range are attributed to the last residue in it.
+		    foreach (string sElement in Seq.Split('(',')','[',']',';')) {
+			if (sElement == "Xlink:Disulfide") {
+			    OutMassAdded -= 2;
+			    ThesePTMs.InsertSorted(OutSeqBuilder.Length,sElement);
+			}
+			else if (sElement == "Methyl") {
+			    OutMassAdded += 14;
+			    ThesePTMs.InsertSorted(OutSeqBuilder.Length,sElement);
+			}
+			else if (sElement == "Oxidation") {
+			    OutMassAdded += 16;
+			    ThesePTMs.InsertSorted(OutSeqBuilder.Length,sElement);
+			}
+			else if (sElement == "Acetyl") {
+			    OutMassAdded += 42;
+			    // We force N-terminal acetyls to the N-terminus rather than the first side chain
+			    ThesePTMs.InsertSorted(0,sElement);
+			}
+			else if (sElement == "Phospho") {
+			    OutMassAdded += 80;
+			    ThesePTMs.InsertSorted(OutSeqBuilder.Length,sElement);
+			}
+			else if (sElement == "Carbamidomethyl") {
+			    OutMassAdded += 57;
+			    ThesePTMs.InsertSorted(OutSeqBuilder.Length,sElement);
+			}
+			else if (sElement.Length > 0) {
+			    try {
+				ObsMass = Convert.ToSingle(sElement);
+				// sElement IS a number if you reach this
+				ContainsUnknown = true;
+				OutMassAdded += (int)Math.Round(ObsMass);
+				UnkPTMLabel = new StringBuilder();
+				if (sElement[0]!='-') {
+				    UnkPTMLabel.Append("Obs:+");
+				}
+				else {
+				    UnkPTMLabel.Append("Obs:");
+				}
+				UnkPTMLabel.Append(ObsMass);
+				ThesePTMs.InsertSorted(OutSeqBuilder.Length,Convert.ToString(UnkPTMLabel));
+			    }
+			    catch (FormatException) {
+				// sElement is NOT a number; it is therefore sequence we can simply append to what is already captured.
+				OutSeqBuilder.Append(sElement);
+			    }
+			}
+		    }
+		    // ThesePTMs.PrintAll();
+		    OutSequence = Convert.ToString(OutSeqBuilder);
+		    // 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(OutSequence.Substring(CurrentSeqPos, ThisPTMinLL.Position-CurrentSeqPos));
+			}
+			else {
+			    DecoratedSeq.Append(OutSequence.Substring(CurrentSeqPos, ThisPTMinLL.Position-CurrentSeqPos));
+			    DecoratedSeq.Append("[");
+			    DecoratedSeq.Append(ThisPTMinLL.Name);
+			    DecoratedSeq.Append("]");
+			}
+			CurrentSeqPos = ThisPTMinLL.Position;
+			ThisPTMinLL = ThisPTMinLL.Next;
+		    }
+		    DecoratedSeq.Append(OutSequence.Substring(CurrentSeqPos));
+		    string OutProForma = Convert.ToString(DecoratedSeq);
+		    // I feel guilty for dumping garbage collection on the interpreter.
+		    ThesePTMs.Next=null;
+		    //If a named PTM has ambiguous localization, mark specific AAs that might hit it: "(KRGLKIVSLKMVKMSRDIAEK)[Methyl]" becomes "K[Methyl #g1]RGLK[#g1]IVSLK[#g1]MVK[#g1]MSRDIAEK[#g1]"
+		    //NOT IMPLEMENTED YET
+		    
+		    if (SuppressUnknowns && ContainsUnknown) {
+		    // Output Nothing
+		    }
+		    else {
+			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(OutSequence);
+			Console.Write("\t");
+			Console.Write(OutMassAdded);
+			Console.Write("\t");
+			Console.Write(OutProForma);
+			Console.Write("\t");
+			Console.WriteLine(OutEVal);
+		    }
+		}
+	    }
+	}
+    }
+}