From 57849fdd9715c26b6aec88554f17b05dcde081ea Mon Sep 17 00:00:00 2001
From: Karen DRUART <karen.druart@pasteur.fr>
Date: Thu, 6 Oct 2022 15:47:51 +0200
Subject: [PATCH] Upload New File
---
.../20210819-ProForma-formatter-TopPIC.cs | 215 ++++++++++++++++++
1 file changed, 215 insertions(+)
create mode 100644 ProForma-Exporters/20210819-ProForma-formatter-TopPIC.cs
diff --git a/ProForma-Exporters/20210819-ProForma-formatter-TopPIC.cs b/ProForma-Exporters/20210819-ProForma-formatter-TopPIC.cs
new file mode 100644
index 0000000..9ca7123
--- /dev/null
+++ b/ProForma-Exporters/20210819-ProForma-formatter-TopPIC.cs
@@ -0,0 +1,215 @@
+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);
+ }
+ }
+ }
+ }
+ }
+}
--
GitLab