Add a new open/mass-offset search related column.

Nesvilab · Feb 2, 2024 · 833984b · 833984b
1 parent 1e289e7
commit 833984b
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Showing 3 changed files with 6 additions and 1 deletion.
diff --git a/lib/id/pep.go b/lib/id/pep.go
@@ -117,6 +117,7 @@ type MSFraggerLoc struct {
 	IonsSecondBestPosition   string
 	IonsAllUnshifted         string
 	IonsShiftedAllPositioins string
+	BestPosition             string
 }
 
 // PepIDList is a list of PeptideSpectrumMatch
@@ -510,6 +511,7 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
 				IonsSecondBestPosition:   i.PTMResult.IonsSecondBestPosition,
 				IonsAllUnshifted:         i.PTMResult.IonsAllUnshifted,
 				IonsShiftedAllPositioins: i.PTMResult.IonsShiftedAllPositions,
+				BestPosition:             i.PTMResult.BestPosition,
 			}
 		}
 

diff --git a/lib/rep/psm.go b/lib/rep/psm.go
@@ -238,6 +238,7 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 	if hasLoc {
 		header += "\tMSFragger Localization" +
 			"\tPosition Scores" +
+			"\tBest Position" +
 			"\tScore Best Position" +
 			"\tIons Best Position" +
 			"\tScore Second Best Position" +
@@ -629,10 +630,11 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 			if MSFraggerLoc == nil {
 				MSFraggerLoc = &id.MSFraggerLoc{}
 			}
-			line = fmt.Sprintf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
+			line = fmt.Sprintf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
 				line,
 				MSFraggerLoc.LocalizationPeptide,
 				MSFraggerLoc.PositionScores,
+				MSFraggerLoc.BestPosition,
 				MSFraggerLoc.ScoreBestPosition,
 				MSFraggerLoc.IonsBestPosition,
 				MSFraggerLoc.ScoreSecondBestPosition,

diff --git a/lib/spc/pepxml.go b/lib/spc/pepxml.go
@@ -228,4 +228,5 @@ type PTMResult struct {
 	IonsShiftedAllPositions  string `xml:"ions_shifted_all_positions,attr"`
 	ScoreShiftedBestPosition string `xml:"score_shifted_best_position,attr"`
 	IonsShiftedBestPosition  string `xml:"ions_shifted_best_position,attr"`
+	BestPosition             string `xml:"best_position,attr"`
 }