Merge pull request #406 from Nesvilab/dev

Dev

Changelog

@@ -1,4 +1,8 @@
+### Added
+- FASTA header verification for IonQuant
+
+### Changed
+- New version annoucements will happpen for all updates, including minor changes
+
 ### Fixed
-- Fixed the protein coverage calculations with partially overlapping and subsumed peptides
-- Fixed an issue where peptides would map to multiple locations in the protein after having I/L converted (Needs to be used with MSFragger v3.6.1 or higher)
-- Fixed an issue with report tables having no isobaric labels being reported
+- Fixed an issue that would not udpate PSMs with razor IDs and description

Makefile

@@ -6,8 +6,8 @@ BINARY = philosopher
 VERSION = $(shell date +%Y%m%d)
 BUILD = $(shell  date +%Y%m%d%H%M)
 
-TAG = v4.8.0
-RC = RC
+TAG = v4.8.1
+RC = RC2
 
 LDFLAGS = -ldflags "-w -s -extldflags -static -X main.version=${TAG} -X main.build=${BUILD}"
 

lib/aba/aba.go

@@ -12,13 +12,8 @@ type DataSetLabelNames struct {
 }
 
 // Run abacus
-// TODO update error methos on the abacus function
 func Run(m met.Data, args []string) {
 
-	// if !m.Abacus.Peptide && !m.Abacus.Protein {
-	// 	msg.Custom(errors.New("you need to specify a peptide or protein combined file for the Abacus analysis"), "fatal")
-	// }
-
 	psmLevelAbacus(m, args)
 
 	if m.Abacus.Peptide {
@@ -29,30 +24,3 @@ func Run(m met.Data, args []string) {
 		proteinLevelAbacus(m, args)
 	}
 }
-
-// addCustomNames adds to the label structures user-defined names to be used on the TMT labels
-// func getLabelNames(dataSet, annot string) map[string]string {
-
-// 	var labels = make(map[string]string)
-
-// 	file, e := os.Open(annot)
-// 	if e != nil {
-// 		msg.ReadFile(errors.New("cannot open annotation file"), "error")
-// 	}
-// 	defer file.Close()
-
-// 	scanner := bufio.NewScanner(file)
-// 	for scanner.Scan() {
-// 		names := strings.Fields(scanner.Text())
-
-// 		name := dataSet + " " + names[0]
-
-// 		labels[name] = names[1]
-// 	}
-
-// 	if e = scanner.Err(); e != nil {
-// 		msg.Custom(errors.New("the annotation file looks to be empty"), "fatal")
-// 	}
-
-// 	return labels
-// }

lib/aba/pep.go

@@ -54,17 +54,13 @@ func peptideLevelAbacus(m met.Data, args []string) {
 
 		// 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())
 
 				file, e := os.Open(annot)
 				if e != nil {
-					msg.ReadFile(errors.New("cannot open annotation file"), "error")
+					msg.ReadFile(errors.New("cannot open annotation file"), "fatal")
 				}
 				defer file.Close()
 
@@ -78,7 +74,7 @@ func peptideLevelAbacus(m met.Data, args []string) {
 				}
 
 				if e = scanner.Err(); e != nil {
-					msg.Custom(errors.New("the annotation file looks to be empty"), "fatal")
+					msg.Custom(errors.New("the annotation file looks to be empty"), "error")
 				}
 			}
 
@@ -117,7 +113,7 @@ func processPeptideCombinedFile(a met.Abacus) {
 
 	if _, e := os.Stat("combined.pep.xml"); os.IsNotExist(e) {
 
-		msg.NoParametersFound(errors.New("cannot find the combined.pep.xml file"), "fatal")
+		msg.NoParametersFound(errors.New("cannot find the combined.pep.xml file"), "error")
 
 	} else {
 
@@ -272,7 +268,7 @@ func savePeptideAbacusResult(session string, evidences rep.CombinedPeptideEviden
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(e, "error")
+		msg.WriteFile(e, "fatal")
 	}
 	defer file.Close()
 
@@ -286,7 +282,7 @@ func savePeptideAbacusResult(session string, evidences rep.CombinedPeptideEviden
 	line += "\n"
 	_, e = io.WriteString(file, line)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	// organize by group number
@@ -328,7 +324,7 @@ func savePeptideAbacusResult(session string, evidences rep.CombinedPeptideEviden
 		line += "\n"
 		_, e = io.WriteString(file, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 
 	}

lib/aba/pro.go

@@ -60,7 +60,7 @@ func proteinLevelAbacus(m met.Data, args []string) {
 
 				file, e := os.Open(annot)
 				if e != nil {
-					msg.ReadFile(errors.New("cannot open annotation file"), "error")
+					msg.ReadFile(errors.New("cannot open annotation file"), "fatal")
 				}
 				defer file.Close()
 
@@ -74,7 +74,7 @@ func proteinLevelAbacus(m met.Data, args []string) {
 				}
 
 				if e = scanner.Err(); e != nil {
-					msg.Custom(errors.New("the annotation file looks to be empty"), "fatal")
+					msg.Custom(errors.New("the annotation file looks to be empty"), "error")
 				}
 			}
 		}
@@ -157,7 +157,7 @@ func processProteinCombinedFile(a met.Abacus, database dat.Base) rep.CombinedPro
 
 	if _, e := os.Stat("combined.prot.xml"); os.IsNotExist(e) {
 
-		msg.Custom(errors.New("cannot find combined.prot.xml file"), "fatal")
+		msg.Custom(errors.New("cannot find combined.prot.xml file"), "error")
 
 	} else {
 
@@ -409,7 +409,7 @@ func saveProteinAbacusResult(session, plex string, evidences rep.CombinedProtein
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(e, "error")
+		msg.WriteFile(e, "fatal")
 	}
 	defer file.Close()
 
@@ -464,7 +464,7 @@ func saveProteinAbacusResult(session, plex string, evidences rep.CombinedProtein
 	} else if plex == "18" {
 		chs = append(chs, "126", "127N", "127C", "128N", "128C", "129N", "129C", "130N", "130C", "131N", "131C", "132N", "132C", "133N", "133C", "134N", "134C", "135N")
 	} else {
-		msg.Custom(errors.New("unsupported number of labels"), "fatal")
+		msg.Custom(errors.New("unsupported number of labels"), "error")
 	}
 
 	if hasLabels {
@@ -486,7 +486,7 @@ func saveProteinAbacusResult(session, plex string, evidences rep.CombinedProtein
 	header += "\n"
 	_, e = io.WriteString(file, header)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	for _, i := range evidences {
@@ -631,7 +631,7 @@ func saveProteinAbacusResult(session, plex string, evidences rep.CombinedProtein
 			line += "\n"
 			_, e := io.WriteString(file, line)
 			if e != nil {
-				msg.WriteToFile(e, "fatal")
+				msg.WriteToFile(e, "error")
 			}
 
 		}
@@ -651,7 +651,7 @@ func saveReprintSpCResults(session, plex string, evidences rep.CombinedProteinEv
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(errors.New("cannot create reprint SpC report"), "error")
+		msg.WriteFile(errors.New("cannot create reprint SpC report"), "fatal")
 	}
 	defer file.Close()
 
@@ -672,7 +672,7 @@ func saveReprintSpCResults(session, plex string, evidences rep.CombinedProteinEv
 
 	_, e = io.WriteString(file, line)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	// organize by group number
@@ -691,7 +691,7 @@ func saveReprintSpCResults(session, plex string, evidences rep.CombinedProteinEv
 		line += "\n"
 		_, e := io.WriteString(file, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 
 	}
@@ -710,7 +710,7 @@ func saveReprintIntResults(session, plex string, evidences rep.CombinedProteinEv
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(errors.New("cannot create reprint Int. report"), "error")
+		msg.WriteFile(errors.New("cannot create reprint Int. report"), "fatal")
 	}
 	defer file.Close()
 
@@ -731,7 +731,7 @@ func saveReprintIntResults(session, plex string, evidences rep.CombinedProteinEv
 
 	_, e = io.WriteString(file, line)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	// organize by group number
@@ -750,7 +750,7 @@ func saveReprintIntResults(session, plex string, evidences rep.CombinedProteinEv
 		line += "\n"
 		_, e := io.WriteString(file, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 
 	}

lib/aba/psm.go

@@ -43,7 +43,7 @@ func psmLevelAbacus(m met.Data, args []string) {
 
 				file, e := os.Open(annot)
 				if e != nil {
-					msg.ReadFile(errors.New("cannot open annotation file"), "error")
+					msg.ReadFile(errors.New("cannot open annotation file"), "fatal")
 				}
 				defer file.Close()
 
@@ -57,7 +57,7 @@ func psmLevelAbacus(m met.Data, args []string) {
 				}
 
 				if e = scanner.Err(); e != nil {
-					msg.Custom(errors.New("the annotation file looks to be empty"), "fatal")
+					msg.Custom(errors.New("the annotation file looks to be empty"), "error")
 				}
 			}
 		}
@@ -122,7 +122,7 @@ func savePSMAbacusResult(session, plex string, evidences rep.CombinedPSMEvidence
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(e, "error")
+		msg.WriteFile(e, "fatal")
 	}
 	defer file.Close()
 
@@ -144,7 +144,7 @@ func savePSMAbacusResult(session, plex string, evidences rep.CombinedPSMEvidence
 	} else if plex == "18" {
 		chs = append(chs, "126", "127N", "127C", "128N", "128C", "129N", "129C", "130N", "130C", "131N", "131C", "132N", "132C", "133N", "133C", "134N", "134C", "135N")
 	} else {
-		msg.Custom(errors.New("unsupported number of labels"), "fatal")
+		msg.Custom(errors.New("unsupported number of labels"), "error")
 	}
 
 	if hasLabels {
@@ -164,7 +164,7 @@ func savePSMAbacusResult(session, plex string, evidences rep.CombinedPSMEvidence
 	header += "\n"
 	_, e = io.WriteString(file, header)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	for _, i := range evidences {
@@ -267,7 +267,7 @@ func savePSMAbacusResult(session, plex string, evidences rep.CombinedPSMEvidence
 		line += "\n"
 		_, e := io.WriteString(file, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 	}
 

lib/bio/bio_test.go

@@ -112,13 +112,6 @@ func TestAminoAcids(t *testing.T) {
 
 }
 
-// func TestProtonMass(t *testing.T) {
-// 	p := Proton
-// 	if p != float64(1.007276) {
-// 		t.Errorf("Proton mass is incorrect, got %f, want %f", p, 1.007276)
-// 	}
-// }
-
 func TestEnzymes(t *testing.T) {
 
 	tes.SetupTestEnv()