diff --git a/ProForma-Exporters/20210819-ProForma-formatter-PSPD.cs b/ProForma-Exporters/20210819-ProForma-formatter-PSPD.cs
new file mode 100644
index 0000000000000000000000000000000000000000..353efcdc6e4be6d913dec5257f5cba6109197902
--- /dev/null
+++ b/ProForma-Exporters/20210819-ProForma-formatter-PSPD.cs
@@ -0,0 +1,275 @@
+using System;
+using System.IO;
+using System.Data;
+using System.Text;
+using System.Text.RegularExpressions;
+
+namespace ProFormaFormatter {
+
+ class PSImod {
+ public string PSImodName="";
+ public string UniProtName="";
+ public string OutputName="";
+ public int RoundedMass=0;
+ public PSImod Next=null;
+
+ public void PrintAll() {
+ PSImod Runner = this.Next;
+ Console.WriteLine("PSImodName\tUniProtName\tOutputName\tRoundedMass");
+ while (Runner != null) {
+ Console.Write(Runner.PSImodName);
+ Console.Write("\t");
+ Console.Write(Runner.UniProtName);
+ Console.Write("\t");
+ Console.Write(Runner.OutputName);
+ Console.Write("\t");
+ Console.WriteLine(Runner.RoundedMass);
+ Runner = Runner.Next;
+ }
+ }
+
+ public PSImod FindByString(string Key) {
+ PSImod TailRunner = this.Next;
+ while (TailRunner != null) {
+ if (string.Equals(TailRunner.UniProtName,Key) || string.Equals(TailRunner.PSImodName,Key)) {
+ return TailRunner;
+ }
+ TailRunner = TailRunner.Next;
+ }
+ return null;
+ }
+
+ public void LoadFromFile() {
+ PSImod TailRunner = this;
+ StreamReader SRead = new StreamReader("PSI-MOD.obo.txt");
+ string WholeLine;
+ string[] Chunks;
+ float Mass;
+ int FirstSpace;
+ while (SRead.Peek() > 0) {
+ WholeLine = SRead.ReadLine();
+ if (WholeLine.StartsWith("id:")) {
+ TailRunner.Next = new PSImod();
+ TailRunner = TailRunner.Next;
+ }
+ else if (WholeLine.StartsWith("name:")) {
+ TailRunner.PSImodName = WholeLine.Substring(6);
+ }
+ else if (WholeLine.StartsWith("synonym:")) {
+ if (WholeLine.EndsWith("RELATED PSI-MS-label []")) {
+ Chunks = WholeLine.Split('\"');
+ TailRunner.OutputName = Chunks[1];
+ }
+ else if (WholeLine.EndsWith("EXACT UniProt-feature []")) {
+ Chunks = WholeLine.Split('\"');
+ FirstSpace = Chunks[1].IndexOf(' ')+1;
+ //We would really rather keep only those starting with MOD_RES, no?
+ TailRunner.UniProtName = Chunks[1].Substring(FirstSpace);
+ }
+ }
+ else if (WholeLine.StartsWith("xref: DiffMono:")) {
+ Chunks = WholeLine.Split('\"');
+ if (Chunks[1] != "none") {
+ Mass = Convert.ToSingle(Chunks[1]);
+ TailRunner.RoundedMass = (int)Math.Round(Mass);
+ }
+ }
+ }
+ }
+
+ public void FillEmptyOutputNames() {
+ PSImod TailRunner=this.Next;
+ while (TailRunner != null) {
+ if (TailRunner.OutputName.Length == 0) {
+ // I am unsure why, but the PSI-MS name "Acetyl" isn't connected with the term below.
+ if (TailRunner.PSImodName == "alpha-amino acetylated residue") {
+ TailRunner.OutputName = "Acetyl";
+ }
+ else {
+ TailRunner.OutputName = "M:" + TailRunner.PSImodName;
+ }
+ }
+ TailRunner = TailRunner.Next;
+ }
+ }
+ }
+
+ 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;
+ }
+
+ }
+
+ class Program {
+ static void Main(string[] args) {
+ if (args.Length==0) {
+ Console.Error.WriteLine("Please be sure that this directory contains a copy of PSI-MOD.obo.txt from https://github.com/HUPO-PSI/psi-mod-CV/blob/master/PSI-MOD.obo.");
+ Console.Error.WriteLine("Supply the name of the exported *_PrSMs.txt file for processing.");
+ Console.Error.WriteLine("If you would like to restrict to medium or high PrSMs, append --medium or --high to the command line.");
+ Environment.Exit(1);
+ }
+ float MinNegLogEVal = -700;
+ if (args.Length==2) {
+ if (args[1] == "--high") {
+ MinNegLogEVal = 5;
+ }
+ else if (args[1] == "--medium") {
+ MinNegLogEVal = 2;
+ }
+ }
+ DataTable datatable = new DataTable();
+ PSImod PSIModTable = new PSImod();
+ PSImod ThisPSIMod;
+ PSIModTable.LoadFromFile();
+ PSIModTable.FillEmptyOutputNames();
+ string FileString = args[0];
+ StreamReader streamreader = new StreamReader(FileString);
+ string FNameTrailer = ".raw";
+ string WholeLine = streamreader.ReadLine();
+ // Console.WriteLine(WholeLine);
+ string[] columnheaders = WholeLine.Split('\t');
+ foreach (string columnheader in columnheaders) {
+ datatable.Columns.Add(columnheader);
+ }
+ while (streamreader.Peek() > 0) {
+ DataRow datarow = datatable.NewRow();
+ datarow.ItemArray = streamreader.ReadLine().Split('\t');
+ datatable.Rows.Add(datarow);
+ }
+ // Remove the coloumn that is the bane of my existence.
+ // datatable.Columns.Remove("\"External Top Down Displays\"");
+ PTM ThesePTMs = new PTM();
+ foreach (DataRow row in datatable.Rows) {
+ string FName = Convert.ToString(row["\"Spectrum File\""]);
+ // The scan numbers do not appear in the default export from PSPD
+ string Scan = Convert.ToString(row["\"Fragmentation Scan(s)\""]);
+ string Seq = Convert.ToString(row["\"Annotated Sequence\""]);
+ string PTMs = Convert.ToString(row["\"Modifications\""]);
+ string OutCharge = Convert.ToString(row["\"Original Precursor Charge\""]);
+ string OutAccession = Convert.ToString(row["\"Protein Accessions\""]);
+ string OutEVal = Convert.ToString(row["\"-Log E-Value\""]);
+ //Since we need the next field as a number, we need to strip away its double-quotes.
+ string FScans = Convert.ToString(row["\"# Fragmentation Scans\""]);
+ int FragScans = Convert.ToInt32(FScans.Split('\"')[1]);
+ // Truncate the double quotes from the Filename field
+ string OutFile = FName.Split('\"')[1];
+ // Truncate the double quotes from the Accession field
+ OutAccession = OutAccession.Split('\"')[1];
+ if (OutFile.EndsWith(FNameTrailer)) {
+ OutFile = OutFile.Substring(0,OutFile.Length-FNameTrailer.Length);
+ }
+ // Truncate the double quotes from the scans field
+ Scan = Scan.Split('\"')[1];
+ string[] ScanNumbers = Scan.Split(';');
+ // Truncate the double quotes from the sequence field, and
+ // force all characters in proteoform sequence to uppercase
+ string OutSeq = Seq.ToUpperInvariant().Split('\"')[1];
+ // Truncate the double quotes from the PTM field
+ PTMs = PTMs.Split('\"')[1];
+ // Truncate the double quotes from the Charge field
+ OutCharge = OutCharge.Split('\"')[1];
+ int OutMassAdded = 0;
+ // Truncate the double quotes from the EVal field
+ OutEVal = OutEVal.Split('\"')[1];
+ // Create a decorated sequence by incorporating PTM string data.
+ string[] PTMArray = PTMs.Split(';');
+ foreach (string ThisPTM in PTMArray) {
+ if (ThisPTM.Length > 0) {
+ string[] PTMFields = ThisPTM.Split('(');
+ string PosString = Regex.Replace(PTMFields[0], "[^0-9]","");
+ int FirstLeft = ThisPTM.IndexOf('(')+1;
+ int LastRight = ThisPTM.LastIndexOf(')');
+ string PTMName = ThisPTM.Substring(FirstLeft, LastRight-FirstLeft);
+ string UniModName = "default";
+ // For translating ProSight PD PTM names to masses, you will want https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo.
+ // I am rounding DiffMono values and prefering PSI-MS labels (though the variable is called "UniModName").
+ ThisPSIMod = PSIModTable.FindByString(PTMName);
+ if (ThisPSIMod == null) {
+ Console.Error.WriteLine("Your PSI-MOD.obo.txt does not contain this PTM: ");
+ Console.Error.WriteLine(PTMName);
+ Environment.Exit(1);
+ }
+ UniModName = ThisPSIMod.OutputName;
+ OutMassAdded += ThisPSIMod.RoundedMass;
+ // When acetylation is positioned on the first side chain, move it to the N-term instead.
+ if (PTMName=="alpha-amino acetylated residue" && PosString == "1") {
+ PosString = "0";
+ }
+ int Pos = Convert.ToInt32(PosString);
+ // Add to the sorted linked list of PTMs for this row of file
+ ThesePTMs.InsertSorted(Pos,UniModName);
+ }
+ }
+ // 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(OutSeq.Substring(CurrentSeqPos, ThisPTMinLL.Position-CurrentSeqPos));
+ }
+ else {
+ DecoratedSeq.Append(OutSeq.Substring(CurrentSeqPos, ThisPTMinLL.Position-CurrentSeqPos));
+ DecoratedSeq.Append("[");
+ DecoratedSeq.Append(ThisPTMinLL.Name);
+ DecoratedSeq.Append("]");
+ }
+ CurrentSeqPos = ThisPTMinLL.Position;
+ ThisPTMinLL = ThisPTMinLL.Next;
+ }
+ DecoratedSeq.Append(OutSeq.Substring(CurrentSeqPos));
+ string OutProForma = Convert.ToString(DecoratedSeq);
+ ThesePTMs.Next=null;
+ // To make the number of rows of output equal to the number of PrSMs, we will need to write some rows repeatedly.
+ if (Convert.ToSingle(OutEVal)>= MinNegLogEVal) {
+ foreach (string OutScan in ScanNumbers) {
+ 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(OutEVal);
+ }
+ }
+ }
+ }
+ }
+}