Propagate new localization scores to psm.tsv

Nesvilab · Jan 21, 2024 · 1abf182 · 1abf182
1 parent 7c1cb3d
commit 1abf182
Show file tree

Hide file tree

Showing 3 changed files with 11 additions and 3 deletions.
diff --git a/lib/id/pep.go b/lib/id/pep.go
@@ -111,10 +111,12 @@ type MSFraggerLoc struct {
 	MSFraggerLocalizationScoreWithoutPTM        string
 	MSFraggerLocalizationScores                 string
 	MSFraggerScoreAll                           string
+	MSFraggerScoreOnlyShifted                   string
 	MSFraggerLocalizationScoreWithPTMIons       string
 	MSFraggerLocalizationSecondScoreWithPTMIons string
 	MSFraggerLocalizationScoreWithoutPTMIons    string
 	MSFraggerScoreAllIons                       string
+	MSFraggerScoreOnlyShiftedIons               string
 }
 
 // PepIDList is a list of PeptideSpectrumMatch
@@ -502,10 +504,12 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
 				MSFraggerLocalizationScoreWithoutPTM:        i.PTMResult.ScoreWithoutPTM,
 				MSFraggerLocalizationScores:                 i.PTMResult.LocalizationScores,
 				MSFraggerScoreAll:                           i.PTMResult.ScoreAll,
+				MSFraggerScoreOnlyShifted:                   i.PTMResult.ScoreOnlyShifted,
 				MSFraggerLocalizationScoreWithPTMIons:       i.PTMResult.BestScoreWithPTMIons,
 				MSFraggerLocalizationSecondScoreWithPTMIons: i.PTMResult.SecondBestScoreWithPTMIons,
 				MSFraggerLocalizationScoreWithoutPTMIons:    i.PTMResult.ScoreWithoutPTMIons,
 				MSFraggerScoreAllIons:                       i.PTMResult.ScoreAllIons,
+				MSFraggerScoreOnlyShiftedIons:               i.PTMResult.ScoreOnlyShiftedIons,
 			}
 		}
 

diff --git a/lib/rep/psm.go b/lib/rep/psm.go
@@ -236,7 +236,7 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 	}
 
 	if hasLoc {
-		header += "\tMSFragger Localization\tBest Score with Delta Mass\tBest Matched Ions with Delta Mass\tSecond Best Score with Delta Mass\tSecond Best Matched Ions with Delta Mass\tBest Score without Delta Mass\tMatched Ions without Delta mass\tLocalization Scores\tScore All\tMatched Ions All"
+		header += "\tMSFragger Localization\tBest Score with Delta Mass\tBest Matched Ions with Delta Mass\tSecond Best Score with Delta Mass\tSecond Best Matched Ions with Delta Mass\tBest Score without Delta Mass\tMatched Ions without Delta mass\tLocalization Scores\tScore All\tMatched Ions All\tScore Delta Mass Only\tMatched Ions Delta Mass Only"
 	}
 
 	if hasIonMob {
@@ -618,7 +618,7 @@ 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",
+			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,
 				MSFraggerLoc.MSFragerLocalization,
 				MSFraggerLoc.MSFraggerLocalizationScoreWithPTM,
@@ -629,7 +629,9 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 				MSFraggerLoc.MSFraggerLocalizationScoreWithoutPTMIons,
 				MSFraggerLoc.MSFraggerLocalizationScores,
 				MSFraggerLoc.MSFraggerScoreAll,
-				MSFraggerLoc.MSFraggerScoreAllIons)
+				MSFraggerLoc.MSFraggerScoreAllIons,
+				MSFraggerLoc.MSFraggerScoreOnlyShifted,
+				MSFraggerLoc.MSFraggerScoreOnlyShiftedIons)
 		}
 
 		if hasIonMob {

diff --git a/lib/spc/pepxml.go b/lib/spc/pepxml.go
@@ -226,4 +226,6 @@ type PTMResult struct {
 	LocalizationScores         string `xml:"localization_scores,attr"`
 	ScoreAll                   string `xml:"score_all,attr"`
 	ScoreAllIons               string `xml:"score_all_matched_ions,attr"`
+	ScoreOnlyShifted           string `xml:"score_only_shifted,attr"`
+	ScoreOnlyShiftedIons       string `xml:"score_only_shifted_matched_ions,attr"`
 }