fixing typos

cmd/bioquant.go

@@ -25,7 +25,7 @@ var bioquantCmd = &cobra.Command{
 		// run clustering
 		qua.RunBioQuantification(m)
 
-		// store paramters on meta data
+		// store parameters on meta data
 		m.Serialize()
 
 		// clean tmp

cmd/database.go

@@ -22,7 +22,7 @@ var databaseCmd = &cobra.Command{
 
 		m = dat.Run(m)
 
-		// store paramters on meta data
+		// store parameters on meta data
 		m.Serialize()
 
 		msg.Done()

cmd/freequant.go

@@ -44,7 +44,7 @@ var freequant = &cobra.Command{
 		// run label-free quantification
 		qua.RunLabelFreeQuantification(m.Quantify)
 
-		// store paramters on meta data
+		// store parameters on meta data
 		m.Serialize()
 
 		// clean tmp

cmd/labelquant.go

@@ -47,7 +47,7 @@ var labelquantCmd = &cobra.Command{
 
 		m.Quantify = qua.RunIsobaricLabelQuantification(m.Quantify, m.Filter.Mapmods)
 
-		// store paramters on meta data
+		// store parameters on meta data
 		m.Serialize()
 
 		// clean tmp

cmd/proproph.go

@@ -50,7 +50,7 @@ func init() {
 		proprophCmd.Flags().BoolVarP(&m.ProteinProphet.Fpkm, "fpkm", "", false, "model protein FPKM values")
 		proprophCmd.Flags().BoolVarP(&m.ProteinProphet.NonSP, "nonsp", "", false, "do not use NSP model")
 		proprophCmd.Flags().IntVarP(&m.ProteinProphet.Minindep, "minindep", "", 0, "minimum percentage of independent peptides required for a protein")
-		proprophCmd.Flags().Float64VarP(&m.ProteinProphet.Minprob, "minprob", "", 0.05, "PeptideProphet probabilty threshold")
+		proprophCmd.Flags().Float64VarP(&m.ProteinProphet.Minprob, "minprob", "", 0.05, "PeptideProphet probability threshold")
 		proprophCmd.Flags().IntVarP(&m.ProteinProphet.Maxppmdiff, "maxppmdiff", "", 2000000, "maximum peptide mass difference in ppm")
 		proprophCmd.Flags().BoolVarP(&m.ProteinProphet.Accuracy, "accuracy", "", false, "equivalent to --minprob 0")
 		proprophCmd.Flags().BoolVarP(&m.ProteinProphet.Normprotlen, "normprotlen", "", false, "normalize NSP using protein length")

cmd/root.go

@@ -25,7 +25,7 @@ var (
 // RootCmd represents the base command when called without any subcommands
 var RootCmd = &cobra.Command{
 	Use:   "philosopher",
-	Short: "philospher: a proteomics data analysis toolkit",
+	Short: "philosopher: a proteomics data analysis toolkit",
 	Long:  "Philosopher: A toolkit for Proteomics data analysis and post-processing filtering",
 }
 

lib/dat/dat.go

@@ -249,10 +249,14 @@ func (d *Base) Deploy(temp string) {
 
 	d.CrapDB = fmt.Sprintf("%s%scrap.fas", temp, string(filepath.Separator))
 
-	param, e := Asset("crap.fas")
-	e = ioutil.WriteFile(d.CrapDB, param, sys.FilePermission())
-	if e != nil {
-		msg.WriteFile(e, "fatal")
+	param, e1 := Asset("crap.fas")
+	if e1 != nil {
+		msg.WriteFile(e1, "fatal")
+	}
+
+	e2 := ioutil.WriteFile(d.CrapDB, param, sys.FilePermission())
+	if e2 != nil {
+		msg.WriteFile(e2, "fatal")
 	}
 
 	return
@@ -314,7 +318,7 @@ func (d *Base) Save(home, temp, tag string, isRev, hasIso, noD, Crap bool) strin
 	return outfile
 }
 
-// Serialize saves to disk a msgpack verison of the database data structure
+// Serialize saves to disk a msgpack version of the database data structure
 func (d *Base) Serialize() {
 
 	b, e := msgpack.Marshal(&d)

lib/ext/comet/comet.go

@@ -9,12 +9,13 @@ import (
 	"path/filepath"
 	"strings"
 
-	"github.com/sirupsen/logrus"
 	ucomet "philosopher/lib/ext/comet/unix"
 	wcomet "philosopher/lib/ext/comet/win"
 	"philosopher/lib/met"
 	"philosopher/lib/msg"
 	"philosopher/lib/sys"
+
+	"github.com/sirupsen/logrus"
 )
 
 // Comet represents the tool configuration
@@ -132,7 +133,7 @@ func (c *Comet) Deploy(os, arch string) {
 	return
 }
 
-// Execute is the main fucntion to execute Comet
+// Execute is the main function to execute Comet
 func (c *Comet) Execute(cmdArgs []string, param string) {
 
 	par := fmt.Sprintf("-P%s", param)

lib/ext/comet/unix/unix.go

@@ -13,13 +13,12 @@ func UnixParameterFile(unixParam string) {
 
 	param, e1 := Asset("comet.params")
 	if e1 != nil {
-		msg.DeployAsset(errors.New("Unimod"), "Cannot read Comet parameter bin")
-	} else {
+		msg.DeployAsset(errors.New("Comet Parameter File"), "Cannot read Comet parameter bin")
+	}
 
-		e2 := ioutil.WriteFile(unixParam, param, sys.FilePermission())
-		if e2 != nil {
-			msg.DeployAsset(errors.New("Unimod"), "Cannot deploy Comet parameter")
-		}
+	e2 := ioutil.WriteFile(unixParam, param, sys.FilePermission())
+	if e2 != nil {
+		msg.DeployAsset(errors.New("Comet Parameter File"), "Cannot deploy Comet parameter")
 	}
 
 	return

lib/ext/comet/win/win.go

@@ -11,14 +11,14 @@ import (
 // WinParameterFile writes the parameter file to the disk
 func WinParameterFile(winParam string) {
 
-	param, e := Asset("comet.params.txt")
-	if e != nil {
-		msg.DeployAsset(errors.New("Comet parameter file"), "fatal")
+	param, e1 := Asset("comet.params.txt")
+	if e1 != nil {
+		msg.DeployAsset(errors.New("Comet Parameter File"), "Cannot read Comet parameter bin")
 	}
 
-	e = ioutil.WriteFile(winParam, param, sys.FilePermission())
-	if e != nil {
-		msg.DeployAsset(errors.New("Comet parameter file"), "fatal")
+	e2 := ioutil.WriteFile(winParam, param, sys.FilePermission())
+	if e2 != nil {
+		msg.DeployAsset(errors.New("Comet Parameter File"), "Cannot deploy Comet parameter")
 	}
 
 	return

lib/ext/interprophet/win/win.go

@@ -12,11 +12,14 @@ import (
 // WinInterProphetParser accessor
 func WinInterProphetParser(s string) {
 
-	bin, e := Asset("InterProphetParser.exe")
-	e = ioutil.WriteFile(s, bin, sys.FilePermission())
+	bin, e1 := Asset("InterProphetParser.exe")
+	if e1 != nil {
+		msg.DeployAsset(errors.New("InterProphetParser.exe"), "Cannot read InterProphetParser.exe bin")
+	}
 
-	if e != nil {
-		msg.DeployAsset(errors.New("InterProphetParser"), "trace")
+	e2 := ioutil.WriteFile(s, bin, sys.FilePermission())
+	if e2 != nil {
+		msg.DeployAsset(errors.New("InterProphetParser.exe"), "Cannot deploy InterProphetParser.exe")
 	}
 
 	return
@@ -25,11 +28,14 @@ func WinInterProphetParser(s string) {
 // LibgccDLL accessor
 func LibgccDLL(s string) {
 
-	bin, e := Asset("libgcc_s_dw2-1.dll")
-	e = ioutil.WriteFile(s, bin, sys.FilePermission())
+	bin, e1 := Asset("libgcc_s_dw2-1.dll")
+	if e1 != nil {
+		msg.DeployAsset(errors.New("LibgccDLL"), "Cannot read LibgccDLL bin")
+	}
 
-	if e != nil {
-		msg.DeployAsset(errors.New("libgcc_s_dw2"), "trace")
+	e2 := ioutil.WriteFile(s, bin, sys.FilePermission())
+	if e2 != nil {
+		msg.DeployAsset(errors.New("LibgccDLL"), "Cannot deploy LibgccDLL")
 	}
 
 	return
@@ -38,11 +44,14 @@ func LibgccDLL(s string) {
 // Zlib1DLL accessor
 func Zlib1DLL(s string) {
 
-	bin, e := Asset("zlib1.dll")
-	e = ioutil.WriteFile(s, bin, sys.FilePermission())
+	bin, e1 := Asset("zlib1.dll")
+	if e1 != nil {
+		msg.DeployAsset(errors.New("Zlib1DLL"), "Cannot read Zlib1DLL bin")
+	}
 
-	if e != nil {
-		msg.DeployAsset(errors.New("Zlib1DLL"), "trace")
+	e2 := ioutil.WriteFile(s, bin, sys.FilePermission())
+	if e2 != nil {
+		msg.DeployAsset(errors.New("Zlib1DLL"), "Cannot deploy Zlib1DLL")
 	}
 
 	return

lib/ext/msfragger/msfragger.go

@@ -57,7 +57,7 @@ func Run(m met.Data, args []string) met.Data {
 	return m
 }
 
-// Execute is the main fucntion to execute MSFragger
+// Execute is the main function to execute MSFragger
 func (c *MSFragger) Execute(params met.MSFragger, cmdArgs []string) {
 
 	cmd := appendParams(params)
@@ -79,7 +79,7 @@ func (c *MSFragger) Execute(params met.MSFragger, cmdArgs []string) {
 	return
 }
 
-// ExecutewithParameter is the main fucntion to execute MSFragger
+// ExecutewithParameter is the main function to execute MSFragger
 func (c *MSFragger) ExecutewithParameter(params met.MSFragger, cmdArgs []string) {
 
 	mem := fmt.Sprintf("-Xmx%dG", params.Memory)

lib/ext/proteinprophet/proteinprophet.go

@@ -258,7 +258,7 @@ func (p ProteinProphet) appendParams(params met.ProteinProphet, cmd *exec.Cmd) *
 
 	// // there is an error in the way how the modified version was implemented.
 	// // The mod version is *always* active, and the tag makes it normal again.
-	// // it should be the oposite, so thats why this block looks like that.
+	// // it should be the opposite, so thats why this block looks like that.
 	// if c.Excludemods == true {
 	// 	// the program is always trying to process os'es
 	// 	//cmd.Args = append(cmd.Args, "ALLOWDIFFPROBS")

lib/ext/tmtintegrator/tmtintegrator.go

@@ -53,7 +53,7 @@ func Run(m met.Data, args []string) met.Data {
 	return m
 }
 
-// Execute is the main fucntion to execute TMTIntegrator
+// Execute is the main function to execute TMTIntegrator
 func (c *TMTIntegrator) Execute(params met.TMTIntegrator, cmdArgs []string) {
 
 	cmd := appendParams(params)

lib/fil/fdr.go

@@ -737,7 +737,7 @@ func mirrorProteinList(p id.ProtIDList, decoyTag string) id.ProtIDList {
 	}
 
 	// add decoys correspondent to the given targets.
-	// first check if the oposite list doesn't have an entry already.
+	// first check if the opposite list doesn't have an entry already.
 	// if not, search for the mirror entry on the original list, if found
 	// move it to the mirror list, otherwise add fake entry.
 	for _, k := range list {

lib/fil/fil.go

@@ -428,7 +428,7 @@ func chargeProfile(p id.PepIDList, charge uint8, decoyTag string) (t, d int) {
 	return t, d
 }
 
-//GetUniquePSMs selects only unique pepetide ions for the given data stucture
+//GetUniquePSMs selects only unique pepetide ions for the given data structure
 func GetUniquePSMs(p id.PepIDList) map[string]id.PepIDList {
 
 	uniqMap := make(map[string]id.PepIDList)
@@ -440,7 +440,7 @@ func GetUniquePSMs(p id.PepIDList) map[string]id.PepIDList {
 	return uniqMap
 }
 
-//getUniquePeptideIons selects only unique pepetide ions for the given data stucture
+//getUniquePeptideIons selects only unique pepetide ions for the given data structure
 func getUniquePeptideIons(p id.PepIDList) map[string]id.PepIDList {
 
 	uniqMap := ExtractIonsFromPSMs(p)
@@ -466,7 +466,7 @@ func ExtractIonsFromPSMs(p id.PepIDList) map[string]id.PepIDList {
 	return uniqMap
 }
 
-// GetUniquePeptides selects only unique pepetide for the given data stucture
+// GetUniquePeptides selects only unique pepetide for the given data structure
 func GetUniquePeptides(p id.PepIDList) map[string]id.PepIDList {
 
 	uniqMap := make(map[string]id.PepIDList)
@@ -566,7 +566,7 @@ func processProteinIdentifications(p id.ProtXML, ptFDR, pepProb, protProb float6
 }
 
 // processProteinInferenceIdentifications checks if pickedFDR ar razor options should be applied to given data set, if they do,
-// the inputed Philospher inference data is processed before filtered.
+// the inputed Philosopher inference data is processed before filtered.
 func processProteinInferenceIdentifications(psm id.PepIDList, razorMap map[string]string, coverMap map[string]float64, ptFDR, pepProb, protProb float64, isPicked bool, decoyTag string) {
 
 	var t int

lib/fin/fin.go

@@ -1241,15 +1241,15 @@ func binaryread(r io.Reader, data interface{}) {
 // data, and returns the position in the file afterwards
 func readAt(rs io.ReadSeeker, pos uint64, v Version, data reader) uint64 {
 
-	spos, e := rs.Seek(int64(pos), 0)
-	if e != nil {
+	spos, e1 := rs.Seek(int64(pos), 0)
+	if e1 != nil {
 		msg.Custom(errors.New("error seeking file"), "fatal")
 	}
 
 	data.Read(rs, v)
 
-	spos, e = rs.Seek(0, 1)
-	if e != nil {
+	spos, e2 := rs.Seek(0, 1)
+	if e2 != nil {
 		msg.Custom(errors.New("error determining position in file"), "fatal")
 	}
 

lib/id/pep.go

@@ -325,31 +325,24 @@ func processSpectrumQuery(sq spc.SpectrumQuery, massDeviation float64, mods mod.
 			} else if string(j.Name) == "xcorr" {
 				value, _ := strconv.ParseFloat(j.Value, 64)
 				psm.Xcorr = value
-				value = -99
 			} else if string(j.Name) == "deltacn" {
 				value, _ := strconv.ParseFloat(j.Value, 64)
 				psm.DeltaCN = value
-				value = -99
 			} else if string(j.Name) == "deltacnstar" {
 				value, _ := strconv.ParseFloat(j.Value, 64)
 				psm.DeltaCNStar = value
-				value = -99
 			} else if string(j.Name) == "spscore" {
 				value, _ := strconv.ParseFloat(j.Value, 64)
 				psm.SPScore = value
-				value = -99
 			} else if string(j.Name) == "sprank" {
 				value, _ := strconv.ParseFloat(j.Value, 64)
 				psm.SPRank = value
-				value = -99
 			} else if string(j.Name) == "hyperscore" {
 				value, _ := strconv.ParseFloat(j.Value, 64)
 				psm.Hyperscore = value
-				value = -99
 			} else if string(j.Name) == "nextscore" {
 				value, _ := strconv.ParseFloat(j.Value, 64)
 				psm.Nextscore = value
-				value = -99
 			}
 		}
 

lib/psi/mzid.go

@@ -509,14 +509,14 @@ type FilterType struct {
 	UserParam []UserParam `xml:"userParam"`
 }
 
-// Include is all sequences fulfilling the specifed criteria are included
+// Include is all sequences fulfilling the specified criteria are included
 type Include struct {
 	XMLName   xml.Name    `xml:"Include"`
 	CVParam   []CVParam   `xml:"cvParam"`
 	UserParam []UserParam `xml:"userParam"`
 }
 
-// Exclude all sequences fulfilling the specifed criteria are excluded
+// Exclude all sequences fulfilling the specified criteria are excluded
 type Exclude struct {
 	XMLName   xml.Name    `xml:"Exclude"`
 	CVParam   []CVParam   `xml:"cvParam"`

lib/qua/bqt.go

@@ -83,7 +83,7 @@ func execute(level float64) (string, string) {
 	cd.ClusterFasta = cd.FileName + ".fasta"
 	cd.ClusterFile = cd.ClusterFasta + ".clstr"
 
-	// deploy binary and paramter to workdir
+	// deploy binary and parameter to workdir
 	cd.Deploy()
 
 	// run cdhit and create the clusters

lib/qua/iso.go

@@ -1242,7 +1242,7 @@ func NormToTotalProteins(evi rep.Evidence) rep.Evidence {
 		channelSum[15] += i.URazorLabels.Channel16.Intensity
 	}
 
-	// find the higest value amongst channels
+	// find the highest value amongst channels
 	for _, i := range channelSum {
 		if i > topValue {
 			topValue = i