From 4d270a22d36dcf9a7b7766762a499e7940ffbac2 Mon Sep 17 00:00:00 2001
From: Karen DRUART <karen.druart@pasteur.fr>
Date: Thu, 6 Oct 2022 15:48:02 +0200
Subject: [PATCH] Upload New File
---
.../20210819-ProForma-formatter-pTop.cs | 154 ++++++++++++++++++
1 file changed, 154 insertions(+)
create mode 100644 ProForma-Exporters/20210819-ProForma-formatter-pTop.cs
diff --git a/ProForma-Exporters/20210819-ProForma-formatter-pTop.cs b/ProForma-Exporters/20210819-ProForma-formatter-pTop.cs
new file mode 100644
index 0000000..4dd743d
--- /dev/null
+++ b/ProForma-Exporters/20210819-ProForma-formatter-pTop.cs
@@ -0,0 +1,154 @@
+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);
+ }
+ }
+ }
+}
--
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