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Merged
rrad42 merged 2 commits into from
Nov 23, 2025
Merged

read peptide ID as string. correctly override cli input paths. additi… #4

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704f352
read peptide ID as string. correctly override cli input paths. additi…
Nov 23, 2025
0994cc1
Merge branch 'main' into 3-input-string-format
Nov 23, 2025
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4 changes: 2 additions & 2 deletions src/AScorePro/Interface/PeptidesFile.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ public struct PeptidesFileEntry {
/// Not used in AScore, can be any unique number for
/// identification purposes.
/// </summary>
public int Id;
public string Id;

/// <summary>
/// The scan number is used to look up the scan from the
Expand Down Expand Up @@ -73,7 +73,7 @@ public IEnumerator GetEnumerator()
private PeptidesFileEntry ParsePeptide(string line) {
var entry = new PeptidesFileEntry();
string[] pieces = line.Split("\t");
entry.Id = int.Parse(pieces[0]);
entry.Id = pieces[0];
entry.ScanNumber = int.Parse(pieces[1]);
entry.Peptide = pieces[2];
entry.PrecursorMz = double.Parse(pieces[3]);
Expand Down
72 changes: 41 additions & 31 deletions src/AScorePro/Program.cs
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Expand Up @@ -53,13 +53,15 @@ static void Main(string[] args)
}
else
{
AScoreMulti(aScore, scans, peptideParser, ascoreOptions);
AScoreMulti(aScore, scans, peptideParser, peptidesPath, ascoreOptions);
}
}
catch (Exception ex)
{
if (ex.Message.Length > 0) {
Console.WriteLine("An error occurred: " + ex.Message);
Console.WriteLine("Stack trace:");
Console.WriteLine(ex.StackTrace);
try {
using (StreamWriter writer = new StreamWriter("error.log", true)) {
writer.WriteLine("[" + DateTime.Now.ToString() + "]");
Expand Down Expand Up @@ -96,8 +98,9 @@ private static void AScoreSingle(AScoreCalculator aScore, Peptide peptide, Scan
/// <param name="aScore">Instance of AScore used on all peptides</param>
/// <param name="scans">Collection of scans</param>
/// <param name="parser">Unserializes peptides from the text input</param>
/// <param name="peptidesPath">Path to peptides file (may override options)</param>
/// <param name="options">AScore options</param>
private static void AScoreMulti(AScoreCalculator aScore, ScanCache scans, PeptideParser parser, AScoreOptions options)
private static void AScoreMulti(AScoreCalculator aScore, ScanCache scans, PeptideParser parser, string peptidesPath, AScoreOptions options)
{
var stream = new FileStream(options.Out, FileMode.Create, FileAccess.Write);
using (var writer = new StreamWriter(stream))
Expand All @@ -111,41 +114,48 @@ private static void AScoreMulti(AScoreCalculator aScore, ScanCache scans, Peptid
}
writer.Write("\n");

var peptides = new PeptidesFile(options.PeptidesFile);
var peptides = new PeptidesFile(peptidesPath);
foreach (PeptidesFileEntry entry in peptides)
{
var peptide = parser.Parse(entry.Peptide);
peptide.PrecursorMz = entry.PrecursorMz;
peptide.Id = entry.Id;
peptide.ScanNumber = entry.ScanNumber;
var scan = scans.GetScan(peptide.ScanNumber);
var result = aScore.Run(peptide, scan);
try
{
var peptide = parser.Parse(entry.Peptide);
peptide.PrecursorMz = entry.PrecursorMz;
peptide.Id = entry.Id;
peptide.ScanNumber = entry.ScanNumber;
var scan = scans.GetScan(peptide.ScanNumber);
var result = aScore.Run(peptide, scan);

Peptide topPeptide = result.Peptides[0];
writer.Write(topPeptide.Id);
writer.Write("\t");
writer.Write(result.ModCount);
writer.Write("\t");
writer.Write(result.Peptides.Count);
writer.Write("\t");
writer.Write(topPeptide.ToString());
writer.Write("\t");
writer.Write(topPeptide.Score.ToString("F9"));
Peptide topPeptide = result.Peptides[0];
writer.Write(topPeptide.Id);
writer.Write("\t");
writer.Write(result.ModCount);
writer.Write("\t");
writer.Write(result.Peptides.Count);
writer.Write("\t");
writer.Write(topPeptide.ToString());
writer.Write("\t");
writer.Write(topPeptide.Score.ToString("F9"));

// Flatten output. Show up to six mods.
for (int i = 0; i < 6; ++i) {
if (i < result.Sites.Count) {
var site = result.Sites[i];
writer.Write("\t");
writer.Write(site.Position);
writer.Write("\t");
writer.Write(site.Score.ToString("F9"));
}
else {
writer.Write("\t\\N\t\\N");
// Flatten output. Show up to six mods.
for (int i = 0; i < 6; ++i) {
if (i < result.Sites.Count) {
var site = result.Sites[i];
writer.Write("\t");
writer.Write(site.Position);
writer.Write("\t");
writer.Write(site.Score.ToString("F9"));
}
else {
writer.Write("\t\\N\t\\N");
}
}
writer.Write("\n");
}
catch (Exception ex)
{
Console.WriteLine($"Warning: Skipping peptide {entry.Id} scan {entry.ScanNumber}: {ex.Message}");
}
writer.Write("\n");
}
}
}
Expand Down
2 changes: 1 addition & 1 deletion src/Common/Sequence/Peptide.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ public class Peptide
/// <summary>
/// A unique number used to identify the peptide.
/// </summary>
public int Id;
public string Id;

/// <summary>
/// The scan number for the peptide
Expand Down
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