Merge pull request #137 from Nesvilab/dev

Dev

Changelog

@@ -2,4 +2,6 @@
 ### Changed
 
 ### Fixed
-- Pipeline functions were restored.
+- Pipeline functions were restored.
+- Ion Purity calculation was fixed, and now supports msconvert 3.20
+- Fixed file discovery for filtering on Windows

Makefile

@@ -6,7 +6,7 @@ BINARY = philosopher
 VERSION = $(shell date +%Y%m%d)
 BUILD = $(shell  date +%Y%m%d%H%M)
 
-TAG = v3.2.5
+TAG = v3.2.6
 
 LDFLAGS = -ldflags "-w -s -X main.version=${TAG} -X main.build=${BUILD}"
 

cmd/labelquant.go

@@ -32,9 +32,7 @@ var labelquantCmd = &cobra.Command{
 			msg.InputNotFound(errors.New("You need to specify the experiment Plex"), "fatal")
 		}
 
-		// hardcoded tmt for now
 		msg.Executing("Isobaric-label quantification ", Version)
-		//m.Quantify.Brand = "tmt"
 
 		if strings.EqualFold(strings.ToLower(m.Quantify.Format), "mzml") {
 			m.Quantify.Format = "mzML"

lib/aba/pep.go

@@ -47,27 +47,36 @@ func peptideLevelAbacus(m met.Data, args []string) {
 		var labels DataSetLabelNames
 		labels.LabelName = make(map[string]string)
 
-		// collect interact full file names
 		files, _ := ioutil.ReadDir(i)
+
+		// collect interact full file names
 		for _, f := range files {
 			if strings.Contains(f.Name(), "pep.xml") {
 				interactFile := fmt.Sprintf("%s%s%s", i, string(filepath.Separator), f.Name())
 				absPath, _ := filepath.Abs(interactFile)
 				xmlFiles = append(xmlFiles, absPath)
 			}
-		}
+			if strings.Contains(f.Name(), "annotation") {
+				var annot = fmt.Sprintf("%s%s%s", i, string(filepath.Separator), f.Name())
+				labels.Name = annot
 
-		var annot = fmt.Sprintf("%s%sannotation.txt", i, string(filepath.Separator))
-		if strings.Contains(i, string(filepath.Separator)) {
-			i = strings.Replace(i, string(filepath.Separator), "", -1)
-			labels.Name = i
-		} else {
-			labels.Name = i
+				if len(m.Quantify.Annot) > 0 {
+					labels.LabelName = getLabelNames(annot)
+				}
+			}
 		}
 
-		if len(m.Quantify.Annot) > 0 {
-			labels.LabelName = getLabelNames(annot)
-		}
+		// var annot = fmt.Sprintf("%s%sannotation.txt", i, string(filepath.Separator))
+		// if strings.Contains(i, string(filepath.Separator)) {
+		// 	i = strings.Replace(i, string(filepath.Separator), "", -1)
+		// 	labels.Name = i
+		// } else {
+		// 	labels.Name = i
+		// }
+
+		// if len(m.Quantify.Annot) > 0 {
+		// 	labels.LabelName = getLabelNames(annot)
+		// }
 
 		// collect project names
 		prjName := i

lib/aba/pro.go

@@ -63,19 +63,27 @@ func proteinLevelAbacus(m met.Data, args []string) {
 				absPath, _ := filepath.Abs(interactFile)
 				xmlFiles = append(xmlFiles, absPath)
 			}
-		}
+			if strings.Contains(f.Name(), "annotation") {
+				var annot = fmt.Sprintf("%s%s%s", i, string(filepath.Separator), f.Name())
+				labels.Name = annot
 
-		var annot = fmt.Sprintf("%s%sannotation.txt", i, string(filepath.Separator))
-		if strings.Contains(i, string(filepath.Separator)) {
-			i = strings.Replace(i, string(filepath.Separator), "", -1)
-			labels.Name = i
-		} else {
-			labels.Name = i
+				if len(m.Quantify.Annot) > 0 {
+					labels.LabelName = getLabelNames(annot)
+				}
+			}
 		}
 
-		if len(m.Quantify.Annot) > 0 {
-			labels.LabelName = getLabelNames(annot)
-		}
+		// var annot = fmt.Sprintf("%s%sannotation.txt", i, string(filepath.Separator))
+		// if strings.Contains(i, string(filepath.Separator)) {
+		// 	i = strings.Replace(i, string(filepath.Separator), "", -1)
+		// 	labels.Name = i
+		// } else {
+		// 	labels.Name = i
+		// }
+
+		// if len(m.Quantify.Annot) > 0 {
+		// 	labels.LabelName = getLabelNames(annot)
+		// }
 
 		// collect project names
 		prjName := i

lib/fil/fil.go

@@ -200,7 +200,7 @@ func readPepXMLInput(xmlFile, decoyTag, temp string, models bool, calibratedMass
 		fileCheckList = append(fileCheckList, xmlFile)
 		files[xmlFile] = 0
 	} else {
-		glob := fmt.Sprintf("%s/*pep.xml", xmlFile)
+		glob := fmt.Sprintf("%s%s*pep.xml", xmlFile, string(filepath.Separator))
 		list, _ := filepath.Glob(glob)
 
 		if len(list) == 0 {

lib/mzn/mzn.go

@@ -13,8 +13,9 @@ import (
 
 	"philosopher/lib/msg"
 
-	"github.com/sirupsen/logrus"
 	"philosopher/lib/psi"
+
+	"github.com/sirupsen/logrus"
 )
 
 // MsData top struct
@@ -46,8 +47,9 @@ type Precursor struct {
 	ParentScan                 string
 	ChargeState                int
 	SelectedIon                float64
+	SelectedIonIntensity       float64
 	TargetIon                  float64
-	PeakIntensity              float64
+	TargetIonIntensity         float64
 	IsolationWindowLowerOffset float64
 	IsolationWindowUpperOffset float64
 }
@@ -228,7 +230,7 @@ func processSpectrum(mzSpec psi.Spectrum) Spectrum {
 				if e != nil {
 					msg.CastFloatToString(e, "fatal")
 				}
-				spec.Precursor.PeakIntensity = val
+				spec.Precursor.SelectedIonIntensity = val
 			}
 		}
 	}

lib/mzn/mzn_test.go

@@ -100,8 +100,8 @@ func TestMS2Spectra(t *testing.T) {
 		t.Errorf("Spectrum target ion is incorrect, got %f, want %f", spec.Precursor.TargetIon, 391.2)
 	}
 
-	if spec.Precursor.PeakIntensity != 3.58558525e+06 {
-		t.Errorf("Spectrum precursor intensity is incorrect, got %f, want %f", spec.Precursor.PeakIntensity, 3.58558525e+06)
+	if spec.Precursor.SelectedIonIntensity != 3.58558525e+06 {
+		t.Errorf("Spectrum precursor intensity is incorrect, got %f, want %f", spec.Precursor.SelectedIonIntensity, 3.58558525e+06)
 	}
 
 	if spec.Precursor.IsolationWindowLowerOffset != 0.34999999404 {

lib/qua/iso.go

@@ -24,6 +24,9 @@ func calculateIonPurity(d, f string, mz mzn.MsData, evi []rep.PSMEvidence) []rep
 	var indexedMS1 = make(map[string]mzn.Spectrum)
 	var indexedMS2 = make(map[string]mzn.Spectrum)
 
+	var MS1Peaks = make(map[string][]float64)
+	var MS1Int = make(map[string][]float64)
+
 	for i := range mz.Spectra {
 
 		if mz.Spectra[i].Level == "1" {
@@ -39,6 +42,9 @@ func calculateIonPurity(d, f string, mz mzn.MsData, evi []rep.PSMEvidence) []rep
 
 			indexedMS1[paddedScan] = mz.Spectra[i]
 
+			MS1Peaks[paddedScan] = mz.Spectra[i].Mz.DecodedStream
+			MS1Int[paddedScan] = mz.Spectra[i].Intensity.DecodedStream
+
 		} else if mz.Spectra[i].Level == "2" {
 
 			if mz.Spectra[i].Precursor.IsolationWindowLowerOffset == 0 && mz.Spectra[i].Precursor.IsolationWindowUpperOffset == 0 {
@@ -63,10 +69,17 @@ func calculateIonPurity(d, f string, mz mzn.MsData, evi []rep.PSMEvidence) []rep
 			mz.Spectra[i].Precursor.ParentIndex = paddedPI
 			mz.Spectra[i].Precursor.ParentScan = paddedPS
 
-			indexedMS2[paddedScan] = mz.Spectra[i]
+			stream := MS1Peaks[paddedPS]
 
-		}
+			for j := range stream {
+				if stream[j] >= (mz.Spectra[i].Precursor.TargetIon-mz.Spectra[i].Precursor.IsolationWindowLowerOffset) && stream[j] <= (mz.Spectra[i].Precursor.TargetIon+mz.Spectra[i].Precursor.IsolationWindowUpperOffset) {
+					mz.Spectra[i].Precursor.TargetIonIntensity = MS1Int[mz.Spectra[i].Precursor.ParentScan][j]
+					break
+				}
+			}
 
+			indexedMS2[paddedScan] = mz.Spectra[i]
+		}
 	}
 
 	for i := range evi {
@@ -98,14 +111,16 @@ func calculateIonPurity(d, f string, mz mzn.MsData, evi []rep.PSMEvidence) []rep
 
 			var isotopePackage = make(map[float64]float64)
 
-			isotopePackage[v2.Precursor.TargetIon] = v2.Precursor.PeakIntensity
-			isotopesInt := v2.Precursor.PeakIntensity
+			isotopePackage[v2.Precursor.TargetIon] = v2.Precursor.TargetIonIntensity
+			isotopesInt := v2.Precursor.TargetIonIntensity
 
 			for k, v := range ions {
 				for _, m := range mzRatio {
 					if math.Abs(v2.Precursor.TargetIon-k) <= (m+0.02) && math.Abs(v2.Precursor.TargetIon-k) >= (m-0.02) {
-						isotopePackage[k] = v
-						isotopesInt += v
+						if v != v2.Precursor.TargetIonIntensity {
+							isotopePackage[k] = v
+							isotopesInt += v
+						}
 						break
 					}
 				}
@@ -117,11 +132,7 @@ func calculateIonPurity(d, f string, mz mzn.MsData, evi []rep.PSMEvidence) []rep
 				evi[i].Purity = uti.Round((isotopesInt / isolationWindowSummedInt), 5, 2)
 			}
 
-			if evi[i].Purity > 1 {
-				evi[i].Purity = 1
-			}
 		}
-
 	}
 
 	return evi

lib/qua/lfq.go

@@ -8,16 +8,16 @@ import (
 	"sort"
 	"strings"
 
+	"philosopher/lib/bio"
 	"philosopher/lib/msg"
+	"philosopher/lib/uti"
 
-	"philosopher/lib/bio"
 	"philosopher/lib/mzn"
 	"philosopher/lib/rep"
 
 	"github.com/sirupsen/logrus"
 )
 
-// // peakIntensity collects PSM intensities from the apex peak
 func peakIntensity(evi rep.Evidence, dir, format string, rTWin, pTWin, tol float64, isIso bool) rep.Evidence {
 
 	logrus.Info("Indexing PSM information")
@@ -31,8 +31,10 @@ func peakIntensity(evi rep.Evidence, dir, format string, rTWin, pTWin, tol float
 	var retentionTime = make(map[string]float64)
 	var intensity = make(map[string]float64)
 
-	for _, i := range evi.PSM {
+	var charges = make(map[string]int)
 
+	// collect attributes from PSM
+	for _, i := range evi.PSM {
 		partName := strings.Split(i.Spectrum, ".")
 		sourceMap[partName[0]] = 0
 		spectra[partName[0]] = append(spectra[partName[0]], i.Spectrum)
@@ -42,13 +44,15 @@ func peakIntensity(evi rep.Evidence, dir, format string, rTWin, pTWin, tol float
 		minRT[i.Spectrum] = (i.RetentionTime / 60) - rTWin
 		maxRT[i.Spectrum] = (i.RetentionTime / 60) + rTWin
 		retentionTime[i.Spectrum] = i.RetentionTime
+
+		charges[i.Spectrum] = int(i.AssumedCharge)
 	}
 
+	// get a sorted list of spectrum names
 	var sourceMapList []string
 	for source := range sourceMap {
 		sourceMapList = append(sourceMapList, source)
 	}
-
 	sort.Strings(sourceMapList)
 
 	logrus.Info("Reading spectra and tracing peaks")
@@ -59,7 +63,8 @@ func peakIntensity(evi rep.Evidence, dir, format string, rTWin, pTWin, tol float
 
 		fileName := fmt.Sprintf("%s%s%s.mzML", dir, string(filepath.Separator), s)
 
-		mz.Read(fileName, false, true, true)
+		// load MS1, ignore MS2 and MS3
+		mz.Read(fileName, false, false, true)
 
 		for i := range mz.Spectra {
 			if mz.Spectra[i].Level == "1" {
@@ -68,6 +73,7 @@ func peakIntensity(evi rep.Evidence, dir, format string, rTWin, pTWin, tol float
 				spectrum := fmt.Sprintf("%s.%05s.%05s.%d", s, mz.Spectra[i].Scan, mz.Spectra[i].Scan, mz.Spectra[i].Precursor.ChargeState)
 				_, ok := mzMap[spectrum]
 				if ok {
+					// update the MZ with the desired Precursor value from mzML
 					if isIso == true {
 						mzMap[spectrum] = mz.Spectra[i].Precursor.TargetIon
 					} else {
@@ -81,12 +87,21 @@ func peakIntensity(evi rep.Evidence, dir, format string, rTWin, pTWin, tol float
 		if ok {
 			for _, j := range v {
 
-				//var measured = make(map[float64]float64)
-				//var retrieved bool
-
 				measured, retrieved := xic(mz.Spectra, minRT[j], maxRT[j], ppmPrecision[j], mzMap[j])
 
+				// if j == "20180209_03_TP_1A.03130.03130.2#interact.pep.xml" {
+				// 	fmt.Println(measured)
+				// }
+
 				if retrieved == true {
+
+					// create the list of mz differences for each peak
+					var mzRatio []float64
+					for k := 1; k <= 6; k++ {
+						r := float64(k) * (float64(1) / float64(charges[j]))
+						mzRatio = append(mzRatio, uti.ToFixed(r, 2))
+					}
+
 					var timeW = retentionTime[j] / 60
 					var topI = 0.0
 
@@ -102,7 +117,6 @@ func peakIntensity(evi rep.Evidence, dir, format string, rTWin, pTWin, tol float
 				}
 			}
 		}
-
 	}
 
 	for i := range evi.PSM {

lib/qua/qua.go

@@ -122,7 +122,6 @@ func RunIsobaricLabelQuantification(p met.Quantify, mods bool) met.Quantify {
 				psmMap[j.Spectrum] = psm
 			}
 		}
-		//mappedPurity = nil
 
 		for _, j := range mappedPSM {
 			v, ok := psmMap[j.Spectrum]
@@ -132,7 +131,6 @@ func RunIsobaricLabelQuantification(p met.Quantify, mods bool) met.Quantify {
 				psmMap[j.Spectrum] = psm
 			}
 		}
-		//mappedPSM = nil
 
 	}
 

lib/rep/rep.go

@@ -401,11 +401,9 @@ func Run(m met.Data) {
 
 	// get the labels from the annotation file
 	if len(m.Quantify.Annot) > 0 {
-		if len(m.Quantify.Annot) > 0 {
-			annotfile := fmt.Sprintf(".%sannotation.txt", string(filepath.Separator))
-			annotfile, _ = filepath.Abs(annotfile)
-			labels = uti.GetLabelNames(annotfile)
-		}
+		annotfile := fmt.Sprintf(".%sannotation.txt", string(filepath.Separator))
+		annotfile, _ = filepath.Abs(annotfile)
+		labels = uti.GetLabelNames(annotfile)
 	}
 
 	logrus.Info("Creating reports")

lib/uti/uti.go

@@ -3,8 +3,10 @@ package uti
 
 import (
 	"bufio"
+	"fmt"
 	"math"
 	"os"
+	"path/filepath"
 	"philosopher/lib/msg"
 	"regexp"
 	"strconv"
@@ -110,3 +112,15 @@ func GetLabelNames(annot string) map[string]string {
 
 	return labels
 }
+
+// FindFile locates a file based on a name pattern
+func FindFile(targetDir string, pattern string) string {
+
+	match, e := filepath.Glob(targetDir + string(filepath.Separator) + pattern)
+
+	if e != nil {
+		fmt.Println(e)
+	}
+
+	return match[0]
+}