Eliminate extra tab from chromatographic peak (#749)

* correct Within calculation * update unit tests * this is the spot * add space * remove tab * remove extra tab from peptides and proteins output of flashlfq --------- Co-authored-by: MICHAEL SHORTREED <[email protected]>
smith-chem-wisc · Dec 12, 2023 · 79207f3 · 79207f3
1 parent 167fa9b
commit 79207f3
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Showing 3 changed files with 14 additions and 2 deletions.
diff --git a/mzLib/FlashLFQ/Peptide.cs b/mzLib/FlashLFQ/Peptide.cs
@@ -40,7 +40,7 @@ public static string TabSeparatedHeader(List<SpectraFileInfo> rawFiles)
             {
                 sb.Append("Detection Type_" + rawfile.FilenameWithoutExtension + "\t");
             }
-            return sb.ToString();
+            return sb.ToString().TrimEnd('\t');
         }
 
         public double GetIntensity(SpectraFileInfo fileInfo)

diff --git a/mzLib/FlashLFQ/ProteinGroup.cs b/mzLib/FlashLFQ/ProteinGroup.cs
@@ -70,7 +70,7 @@ public static string TabSeparatedHeader(List<SpectraFileInfo> spectraFiles)
                 }
             }
 
-            return sb.ToString();
+            return sb.ToString().TrimEnd('\t');
         }
 
         public string ToString(List<SpectraFileInfo> spectraFiles)

diff --git a/mzLib/TestFlashLFQ/TestFlashLFQ.cs b/mzLib/TestFlashLFQ/TestFlashLFQ.cs
@@ -1180,6 +1180,8 @@ public static void TestFlashLfqQoutputRealData()
             var engine = new FlashLfqEngine(ids, matchBetweenRuns: true, requireMsmsIdInCondition: false, useSharedPeptidesForProteinQuant: true, maxThreads: -1);
             var results = engine.Run();
 
+            results.WriteResults(Path.Combine(outputDirectory,"peaks.tsv"), Path.Combine(outputDirectory, "peptides.tsv"), Path.Combine(outputDirectory, "proteins.tsv"), Path.Combine(outputDirectory, "bayesian.tsv"),true);
+
             var peaks = results.Peaks.Values.ToList();
             var peptides = results.PeptideModifiedSequences.Values.ToList();
             var proteins = results.ProteinGroups.Values.ToList();
@@ -1194,6 +1196,16 @@ public static void TestFlashLfqQoutputRealData()
             CollectionAssert.AreEquivalent(new string[] { "Q7KZF4", "P52298", "Q15149", "Q15149", "Q7KZF4", "P52298" }, peptides.Select(g => g.ProteinGroups.First()).Select(m => m.ProteinGroupName).ToArray());
 
             Assert.AreEqual(3, proteins.Count);
+
+            List<string> peaksList = File.ReadAllLines(Path.Combine(outputDirectory, "peaks.tsv")).ToList();
+            List<string> peptidesList = File.ReadAllLines(Path.Combine(outputDirectory, "peptides.tsv")).ToList();
+            List<string> proteinsList = File.ReadAllLines(Path.Combine(outputDirectory, "proteins.tsv")).ToList();
+
+            //check that all rows including header have the same number of elements
+            Assert.AreEqual(1, peaksList.Select(l => l.Split('\t').Length).Distinct().ToList().Count);
+            Assert.AreEqual(1, peptidesList.Select(l => l.Split('\t').Length).Distinct().ToList().Count);
+            Assert.AreEqual(1, proteinsList.Select(l => l.Split('\t').Length).Distinct().ToList().Count);
+
             CollectionAssert.AreEquivalent(new string[] { "P52298", "Q15149", "Q7KZF4" }, proteins.Select(p => p.ProteinGroupName.ToArray()));
 
             Directory.Delete(outputDirectory, true);