Merge pull request #403 from Nesvilab/dev

Dev

Changelog

@@ -1,12 +1,7 @@
 ### Added
-- Adjusted the peptide-to-protein mapping due to I/L replacement rules
-- Adjusted the protein FDR caclulation rules.
+
 
 ### Changed
-- Removed the normalization done at the protein level in labelquant
-- Improved the protein filter for small scale analyses
 
-### Fixed
-- Adjusted the msstats file format, added Purity to all plex sizes
-- Fixed the protein coverage calculations
-- Fixed repeated isobaric values that would eventually show up in the protein table
+
+### Fixed

Makefile

@@ -6,8 +6,8 @@ BINARY = philosopher
 VERSION = $(shell date +%Y%m%d)
 BUILD = $(shell  date +%Y%m%d%H%M)
 
-TAG = v4.7.0
-RC = RC-6
+TAG = v4.7.1
+RC = RC-2
 
 LDFLAGS = -ldflags "-w -s -extldflags -static -X main.version=${TAG} -X main.build=${BUILD}"
 

lib/id/pep.go

@@ -90,7 +90,7 @@ type PeptideIdentification struct {
 	Intensity                        float64
 	PrevAA                           []byte
 	NextAA                           []byte
-	AlternativeProteins              map[string]int
+	AlternativeProteins              map[string]string
 	MSFragerLoc                      *MSFraggerLoc
 	PTM                              *PTM
 	Modifications                    mod.ModificationsSlice
@@ -399,7 +399,7 @@ func ReadPepXMLInput(xmlFile, decoyTag, temp string, models bool) (PepIDListPtrs
 func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag, FileName string) PeptideIdentification {
 
 	var psm PeptideIdentification
-	psm.AlternativeProteins = make(map[string]int)
+	psm.AlternativeProteins = make(map[string]string)
 
 	psm.Index = sq.Index
 	psm.SpectrumFile = FileName
@@ -462,7 +462,7 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
 		}
 
 		for _, j := range i.AlternativeProteins {
-			psm.AlternativeProteins[string(j.Protein)]++
+			psm.AlternativeProteins[string(j.Protein)] = string(j.PepPrevAA) + "#" + string(j.PepNextAA)
 		}
 
 		for _, j := range i.Score {
@@ -643,62 +643,74 @@ func (p *PepXML4Serialiazation) PromoteProteinIDs() {
 
 		var current string
 		var alt string
-		var list = make(map[string]int)
+		var list = make(map[string]string)
 		var isUniProt bool
 
 		if strings.Contains(p.PeptideIdentification[i].Protein, p.DecoyTag) {
 
 			current = p.PeptideIdentification[i].Protein
 
-			for j := range p.PeptideIdentification[i].AlternativeProteins {
+			for k, v := range p.PeptideIdentification[i].AlternativeProteins {
 
-				if strings.Contains(j, "sp|") {
+				if strings.Contains(k, "sp|") {
 					isUniProt = true
 				}
 
-				if !strings.HasPrefix(j, p.DecoyTag) {
-					list[j]++
+				if !strings.HasPrefix(k, p.DecoyTag) {
+					list[k] = v
 				}
 			}
 
 		}
 
 		if len(list) > 0 {
 
+			var prevAA string
+			var nextAA string
+
 			// if a Uniprot database is used we give preference to SwissProt proteins
 			if isUniProt {
-				for k := range list {
+				for k, v := range list {
+
+					pna := strings.Split(v, "#")
+
 					if strings.HasPrefix(k, "sp|") {
 						alt = k
+						prevAA = pna[0]
+						nextAA = pna[1]
 						break
 					} else {
 						alt = k
+						prevAA = pna[0]
+						nextAA = pna[1]
 					}
 				}
-				p.PeptideIdentification[i].Protein = alt
-
-				// remove the replaces protein from the alternative proteins list
-				//p.PeptideIdentification[i].AlternativeProteins[list[alt]] = p.PeptideIdentification[i].AlternativeProteins[len(p.PeptideIdentification[i].AlternativeProteins)-1]
-				//p.PeptideIdentification[i].AlternativeProteins[len(p.PeptideIdentification[i].AlternativeProteins)-1] = ""
-				//p.PeptideIdentification[i].AlternativeProteins = p.PeptideIdentification[i].AlternativeProteins[:len(p.PeptideIdentification[i].AlternativeProteins)-1]
 
 				// add the replaces current to the list
-				p.PeptideIdentification[i].AlternativeProteins[current]++
+				p.PeptideIdentification[i].AlternativeProteins[current] = string(p.PeptideIdentification[i].PrevAA) + "#" + string(p.PeptideIdentification[i].NextAA)
+
+				p.PeptideIdentification[i].Protein = alt
+				p.PeptideIdentification[i].PrevAA = []byte(prevAA)
+				p.PeptideIdentification[i].NextAA = []byte(nextAA)
 
 			} else {
-				for k := range list {
+				for k, v := range list {
+
+					pna := strings.Split(v, "#")
+
 					alt = k
+					prevAA = pna[0]
+					nextAA = pna[1]
 					break
 				}
-				p.PeptideIdentification[i].Protein = alt
-
-				// remove the replaces protein from the alternative proteins list
-				//p.PeptideIdentification[i].AlternativeProteins[list[alt]] = p.PeptideIdentification[i].AlternativeProteins[len(p.PeptideIdentification[i].AlternativeProteins)-1]
-				//p.PeptideIdentification[i].AlternativeProteins[len(p.PeptideIdentification[i].AlternativeProteins)-1] = ""
-				//p.PeptideIdentification[i].AlternativeProteins = p.PeptideIdentification[i].AlternativeProteins[:len(p.PeptideIdentification[i].AlternativeProteins)-1]
 
 				// add the replaces current to the list
-				p.PeptideIdentification[i].AlternativeProteins[current]++
+				p.PeptideIdentification[i].AlternativeProteins[current] = string(p.PeptideIdentification[i].PrevAA) + "#" + string(p.PeptideIdentification[i].NextAA)
+
+				p.PeptideIdentification[i].Protein = alt
+				p.PeptideIdentification[i].PrevAA = []byte(prevAA)
+				p.PeptideIdentification[i].NextAA = []byte(nextAA)
+
 			}
 
 		}

lib/inf/inf.go

@@ -197,7 +197,7 @@ func ProteinInference(psm id.PepIDList) (id.PepIDList, map[string]string, map[st
 
 			if pt != psm[i].Protein {
 
-				psm[i].AlternativeProteins[psm[i].Protein]++
+				psm[i].AlternativeProteins[psm[i].Protein] = string(psm[i].PrevAA) + "#" + string(psm[i].NextAA)
 
 				var toRemove string
 				for j := range psm[i].AlternativeProteins {
@@ -207,7 +207,7 @@ func ProteinInference(psm id.PepIDList) (id.PepIDList, map[string]string, map[st
 					}
 				}
 
-				psm[i].AlternativeProteins[psm[i].Protein]++
+				psm[i].AlternativeProteins[psm[i].Protein] = string(psm[i].PrevAA) + "#" + string(psm[i].NextAA)
 				delete(psm[i].AlternativeProteins, toRemove)
 
 				psm[i].Protein = pt

lib/rep/ion.go

@@ -53,18 +53,18 @@ func (evi *Evidence) AssembleIonReport(ion id.PepIDList, decoyTag string) {
 	for idx, i := range ion {
 		pr := &evi.Ions[idx]
 
-		//pr.IonForm() = fmt.Sprintf("%s#%d#%.4f", i.Peptide, i.AssumedCharge, i.CalcNeutralPepMass)
-
 		pr.Spectra = make(map[id.SpectrumType]int)
 		pr.MappedGenes = make(map[string]struct{})
 		pr.MappedProteins = make(map[string]int)
-		//pr.Modifications.Index = make(map[string]mod.Modification)
-
 		pr.Sequence = i.Peptide
 		pr.ModifiedSequence = i.ModifiedPeptide
 		pr.MZ = uti.Round(((i.CalcNeutralPepMass + (float64(i.AssumedCharge) * bio.Proton)) / float64(i.AssumedCharge)), 5, 4)
 		pr.ChargeState = i.AssumedCharge
 		pr.PeptideMass = i.CalcNeutralPepMass
+
+		pr.PrevAA = string(i.PrevAA)
+		pr.NextAA = string(i.NextAA)
+
 		if v, ok := psmIonMap[pr.IonForm()]; ok {
 			for _, j := range v {
 				pr.Spectra[j]++
@@ -92,6 +92,7 @@ func (evi *Evidence) AssembleIonReport(ion id.PepIDList, decoyTag string) {
 			}
 		}
 		pr.Modifications = prModifications.ToSlice()
+
 		// is this bservation a decoy ?
 		if cla.IsDecoyPSM(i, decoyTag) {
 			pr.IsDecoy = true
@@ -146,7 +147,7 @@ func (evi IonEvidenceList) IonReport(workspace, brand, decoyTag string, channels
 
 	var headerIndex int
 	for i := range printSet {
-		if printSet[i].Labels != nil && len(printSet[i].Labels.Channel1.Name) > 0 {
+		if printSet[i].Labels != nil && len(printSet[i].Labels.Channel1.CustomName) > 0 {
 			headerIndex = i
 			break
 		}

lib/rep/peptide.go

@@ -23,12 +23,14 @@ func (evi *Evidence) AssemblePeptideReport(pep id.PepIDList, decoyTag string) {
 
 	var pepSeqMap = make(map[string]bool) //is this a decoy
 	var pepCSMap = make(map[string][]uint8)
-	var pepInt = make(map[string]float64)
 	var pepProt = make(map[string]string)
-	var spectra = make(map[string][]id.SpectrumType)
 	var mappedGenes = make(map[string][]string)
 	var mappedProts = make(map[string][]string)
+	var pepInt = make(map[string]float64)
 	var bestProb = make(map[string]float64)
+	var prevAA = make(map[string]string)
+	var nextAA = make(map[string]string)
+	var spectra = make(map[string][]id.SpectrumType)
 	var pepMods = make(map[string][]mod.Modification)
 
 	for _, i := range pep {
@@ -42,6 +44,8 @@ func (evi *Evidence) AssemblePeptideReport(pep id.PepIDList, decoyTag string) {
 			pepCSMap[i.Peptide] = append(pepCSMap[i.Peptide], i.AssumedCharge)
 			spectra[i.Peptide] = append(spectra[i.Peptide], i.SpectrumFileName())
 			pepProt[i.Peptide] = i.Protein
+			prevAA[i.Peptide] = i.PrevAA
+			nextAA[i.Peptide] = i.NextAA
 
 			if i.Intensity > pepInt[i.Peptide] {
 				pepInt[i.Peptide] = i.Intensity
@@ -83,6 +87,9 @@ func (evi *Evidence) AssemblePeptideReport(pep id.PepIDList, decoyTag string) {
 
 		pep.Probability = bestProb[k]
 
+		pep.PrevAA = prevAA[k]
+		pep.NextAA = nextAA[k]
+
 		for _, i := range spectra[k] {
 			pep.Spectra[i] = 0
 		}
@@ -166,7 +173,7 @@ func (evi PeptideEvidenceList) PeptideReport(workspace, brand, decoyTag string,
 
 	var headerIndex int
 	for i := range printSet {
-		if printSet[i].Labels != nil && len(printSet[i].Labels.Channel1.Name) > 0 {
+		if printSet[i].Labels != nil && len(printSet[i].Labels.Channel1.CustomName) > 0 {
 			headerIndex = i
 			break
 		}

lib/rep/protein.go

@@ -282,7 +282,7 @@ func (eviProteins ProteinEvidenceList) ProteinReport(workspace, brand, decoyTag
 
 	var headerIndex int
 	for i := range printSet {
-		if printSet[i].UniqueLabels != nil && len(printSet[i].UniqueLabels.Channel1.Name) > 0 {
+		if printSet[i].UniqueLabels != nil && len(printSet[i].UniqueLabels.Channel1.CustomName) > 0 {
 			headerIndex = i
 			break
 		}

lib/rep/psm.go

@@ -269,8 +269,9 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 
 	var headerIndex int
 	for i := range printSet {
-		if printSet[i].Labels != nil && len(printSet[i].Labels.Channel1.Name) > 0 {
+		if printSet[i].Labels != nil && len(printSet[i].Labels.Channel1.CustomName) > 0 {
 			headerIndex = i
+			//fmt.Println(headerIndex, printSet[i].Labels.Channel1.Name, printSet[i].Labels.Channel1.CustomName)
 			break
 		}
 	}

lib/rep/updater.go

@@ -427,12 +427,6 @@ func (evi *Evidence) UpdateLayerswithDatabase(decoyTag string) {
 		}
 	}
 
-	type prevNextAA struct {
-		prev string
-		next string
-	}
-	var pepPrevNextAA = make(map[string]prevNextAA)
-
 	replacerIL := strings.NewReplacer("L", "I")
 	for i := range evi.PSM {
 
@@ -449,19 +443,30 @@ func (evi *Evidence) UpdateLayerswithDatabase(decoyTag string) {
 			}
 		}
 
-		peptide := string(evi.PSM[i].PrevAA) + replacerIL.Replace(evi.PSM[i].Peptide) + string(evi.PSM[i].NextAA)
+		var adjustStart = 0
+		var adjustEnd = 0
+		peptide := replacerIL.Replace(evi.PSM[i].Peptide)
 
-		// map the peptide to the protein
-		mstart := strings.Index(replacerIL.Replace(rec.Sequence), peptide)
-		mend := mstart + len(evi.PSM[i].Peptide)
+		if evi.PSM[i].PrevAA != "-" && len(evi.PSM[i].PrevAA) == 1 {
+			peptide = replacerIL.Replace(evi.PSM[i].PrevAA) + peptide
+			adjustStart = +2
+		}
 
-		if mstart != -1 {
-			evi.PSM[i].ProteinStart = mstart + 2
-			evi.PSM[i].ProteinEnd = mend + 1
+		if evi.PSM[i].PrevAA == "-" && len(evi.PSM[i].PrevAA) == 1 {
+			adjustStart = +1
 		}
 
-		pepPrevNextAA[evi.PSM[i].Peptide] = prevNextAA{evi.PSM[i].PrevAA, evi.PSM[i].NextAA}
+		if evi.PSM[i].NextAA != "-" && len(evi.PSM[i].NextAA) == 1 {
+			peptide = peptide + replacerIL.Replace(evi.PSM[i].NextAA)
+			adjustEnd = -1
+		}
+
+		// map the peptide to the protein
+		mstart := strings.Index(replacerIL.Replace(rec.Sequence), peptide)
+		mend := mstart + len(peptide)
 
+		evi.PSM[i].ProteinStart = mstart + adjustStart
+		evi.PSM[i].ProteinEnd = mend + adjustEnd
 	}
 
 	for i := range evi.Ions {
@@ -483,9 +488,6 @@ func (evi *Evidence) UpdateLayerswithDatabase(decoyTag string) {
 				evi.Ions[i].MappedGenes[recordMap[k].GeneNames] = struct{}{}
 			}
 		}
-		pnAA := pepPrevNextAA[evi.Ions[i].Sequence]
-		evi.Ions[i].PrevAA = pnAA.prev
-		evi.Ions[i].NextAA = pnAA.next
 	}
 
 	for i := range evi.Peptides {
@@ -506,9 +508,6 @@ func (evi *Evidence) UpdateLayerswithDatabase(decoyTag string) {
 				evi.Peptides[i].MappedGenes[recordMap[k].GeneNames] = struct{}{}
 			}
 		}
-		pnAA := pepPrevNextAA[evi.Peptides[i].Sequence]
-		evi.Peptides[i].PrevAA = pnAA.prev
-		evi.Peptides[i].NextAA = pnAA.next
 	}
 }