diff --git a/lib/id/pep.go b/lib/id/pep.go index 3030ef40..6ce78f22 100644 --- 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 index ebda5fb0..fb7e9d13 100644 --- 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 index 6c3184c1..5662d329 100644 --- 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"` }