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Add a new open/mass-offset search related column.
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fcyu committed Feb 2, 2024

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d2iq-dispatch D2iQ Dispatch
1 parent 1e289e7 commit 833984b
Showing 3 changed files with 6 additions and 1 deletion.
2 changes: 2 additions & 0 deletions lib/id/pep.go
Original file line number Diff line number Diff line change
@@ -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,
}
}

4 changes: 3 additions & 1 deletion lib/rep/psm.go
Original file line number Diff line number Diff line change
@@ -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,
1 change: 1 addition & 0 deletions lib/spc/pepxml.go
Original file line number Diff line number Diff line change
@@ -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"`
}

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