Merge pull request #179 from Nesvilab/dev

Dev

Changelog

@@ -1,10 +1,8 @@
 ### Added
-- Fix to PTProphet mod_nterm_mass change when using TMT-16 plex.
+- Added support to compensation Voltage. 
 
 ### Changed
-- Updated parallelization for PeptideProphet.
-- Updated pipeline configuration file.
--When using a GENCODe database, the Gene name will now be the ENSG key from the header.
+- Tabular spaces in FASTA headers will be replaced by a simple space character.
 
 ### Fixed
-- Fixed issue with empty custom database.
+- Fix a bug that would miscalculate the number of peptides to be reported.

lib/dat/dat_test.go

@@ -73,8 +73,8 @@ func TestBase_ProcessDB(t *testing.T) {
 			}
 			d.ProcessDB(tt.args.file, tt.args.decoyTag)
 
-			if len(d.Records) != 20370 {
-				t.Errorf("Number of FASTA entries is incorrect, got %d, want %d", len(d.Records), 20370)
+			if len(d.Records) != 20379 {
+				t.Errorf("Number of FASTA entries is incorrect, got %d, want %d", len(d.Records), 20379)
 			}
 		})
 	}

lib/fas/fas.go

@@ -30,6 +30,7 @@ func ParseFile(filename string) map[string]string {
 		if strings.HasPrefix(scanner.Text(), ">") {
 			header := reHeader.FindStringSubmatch(scanner.Text())
 			fastaHeader = header[1]
+			fastaHeader = strings.Replace(fastaHeader, "\t", " ", -1)
 			fastaMap[fastaHeader] = ""
 		} else {
 			fastaSeq = fastaMap[fastaHeader]

lib/id/pep.go

@@ -86,6 +86,7 @@ type PeptideIdentification struct {
 	Intensity                        float64
 	IonMobility                      float64
 	IsRejected                       uint8
+	CompesationVoltage               float64
 	Modifications                    mod.Modifications
 }
 
@@ -347,6 +348,7 @@ func processSpectrumQuery(sq spc.SpectrumQuery, massDeviation float64, mods mod.
 	psm.AssumedCharge = sq.AssumedCharge
 	psm.RetentionTime = sq.RetentionTimeSec
 	psm.IonMobility = sq.IonMobility
+	psm.CompesationVoltage = sq.CompensationVoltage
 
 	if sq.UncalibratedPrecursorNeutralMass > 0 {
 		psm.PrecursorNeutralMass = sq.PrecursorNeutralMass

lib/mod/mod.go

@@ -8,7 +8,7 @@ import (
 	"github.com/vmihailenco/msgpack"
 )
 
-// Modifications is a collections of modification
+// Modifications is a collection of modifications
 type Modifications struct {
 	Index map[string]Modification
 }

lib/qua/iso.go

@@ -519,7 +519,8 @@ func correctUnlabelledSpectra(evi rep.Evidence) rep.Evidence {
 			evi.PSM[i].Labels.Channel16.Intensity = 0
 		} else {
 			for _, j := range evi.PSM[i].Modifications.Index {
-				if j.MassDiff == 144.1020 || j.MassDiff == 229.1629 || j.MassDiff == 304.2072 {
+				//if j.MassDiff == 144.1020 || j.MassDiff == 229.1629 || j.MassDiff == 304.2072 {
+				if j.MassDiff > 144 {
 					flag++
 				}
 			}

lib/rep/psm.go

@@ -70,6 +70,7 @@ func (evi *Evidence) AssemblePSMReport(pep id.PepIDList, decoyTag string) {
 		p.DiscriminantValue = i.DiscriminantValue
 		p.Intensity = i.Intensity
 		p.IonMobility = i.IonMobility
+		p.CompensationVoltage = i.CompesationVoltage
 		p.MappedGenes = make(map[string]int)
 		p.MappedProteins = make(map[string]int)
 		p.Modifications = i.Modifications
@@ -151,7 +152,7 @@ func (evi Evidence) MetaPSMReport(brand string, channels int, hasDecoys, isComet
 		header += "\tXCorr\tDeltaCN\tDeltaCNStar\tSPScore\tSPRank"
 	}
 
-	header += "\tExpectation\tHyperscore\tNextscore\tPeptideProphet Probability\tNumber of Enzymatic Termini\tNumber of Missed Cleavages\tIntensity\tIon Mobility\tAssigned Modifications\tObserved Modifications"
+	header += "\tExpectation\tHyperscore\tNextscore\tPeptideProphet Probability\tNumber of Enzymatic Termini\tNumber of Missed Cleavages\tIntensity\tIon Mobility\tCompensation Voltage\tAssigned Modifications\tObserved Modifications"
 
 	if hasLoc == true {
 		header += "\tNumber of Phospho Sites\tPhospho Site Localization"
@@ -286,7 +287,7 @@ func (evi Evidence) MetaPSMReport(brand string, channels int, hasDecoys, isComet
 			)
 		}
 
-		line = fmt.Sprintf("%s\t%.14f\t%.4f\t%.4f\t%.4f\t%d\t%d\t%.4f\t%.4f\t%s\t%s",
+		line = fmt.Sprintf("%s\t%.14f\t%.4f\t%.4f\t%.4f\t%d\t%d\t%.4f\t%.4f\t%.4f\t%s\t%s",
 			line,
 			i.Expectation,
 			i.Hyperscore,
@@ -296,6 +297,7 @@ func (evi Evidence) MetaPSMReport(brand string, channels int, hasDecoys, isComet
 			i.NumberOfMissedCleavages,
 			i.Intensity,
 			i.IonMobility,
+			i.CompensationVoltage,
 			strings.Join(assL, ", "),
 			strings.Join(obs, ", "),
 		)

lib/rep/rep.go

@@ -151,6 +151,7 @@ type PSMEvidence struct {
 	Intensity                        float64
 	IonMobility                      float64
 	Purity                           float64
+	CompensationVoltage              float64
 	IsDecoy                          bool
 	IsUnique                         bool
 	IsURazor                         bool

lib/rep/updater.go

@@ -59,6 +59,7 @@ func (evi *Evidence) UpdateIonStatus(decoyTag string) {
 	var uniqueSeqMap = make(map[string]string)
 
 	for _, i := range evi.Proteins {
+
 		for _, j := range i.TotalPeptideIons {
 			if j.IsUnique == true {
 				uniqueMap[j.IonForm] = true
@@ -151,7 +152,8 @@ func (evi *Evidence) UpdateIonStatus(decoyTag string) {
 	}
 
 	for i := range evi.Peptides {
-		v, ok := uniqueSeqMap[evi.Peptides[i].Sequence]
+		//v, ok := uniqueSeqMap[evi.Peptides[i].Sequence]
+		v, ok := sequenceMap[evi.Peptides[i].Sequence]
 		if ok {
 			evi.Peptides[i].MappedProteins[evi.Peptides[i].Protein] = 0
 			delete(evi.Peptides[i].MappedProteins, v)

lib/spc/pepxml.go

@@ -192,6 +192,7 @@ type SpectrumQuery struct {
 	Index                            uint32       `xml:"index,attr"`
 	RetentionTimeSec                 float64      `xml:"retention_time_sec,attr"`
 	IonMobility                      float64      `xml:"ion_mobility,attr"`
+	CompensationVoltage              float64      `xml:"compensation_voltage,attr"`
 	SearchResult                     SearchResult `xml:"search_result"`
 }