Merge pull request #336 from Nesvilab/rc-v4.2.1

removing raw reader

Changelog

@@ -1,8 +1,13 @@
 ### Added
-
+- Added support for TMT 18
+- Added option for contaminant tags in the database.
 
 ### Changed
 - Added the parsing rules from the Prophets to the protein description.
+- Removed RawReader because of licensing issues.
+- Improved processing speed and resource usage.
+- Reduced binariy size.
 
 ### Fixed
-
+- Several bugs and code fizes added.
+- Fixed issue with TMT 6 plex quantification.

cmd/freequant.go

@@ -64,7 +64,7 @@ func init() {
 		freequant.Flags().StringVarP(&m.Quantify.Dir, "dir", "", "", "folder path containing the raw files")
 		freequant.Flags().Float64VarP(&m.Quantify.Tol, "tol", "", 10, "m/z tolerance in ppm")
 		freequant.Flags().Float64VarP(&m.Quantify.PTWin, "ptw", "", 0.4, "specify the time windows for the peak (minute)")
-		freequant.Flags().BoolVarP(&m.Quantify.Raw, "raw", "", false, "read raw files instead of converted XML")
+		//freequant.Flags().BoolVarP(&m.Quantify.Raw, "raw", "", false, "read raw files instead of converted XML")
 		freequant.Flags().BoolVarP(&m.Quantify.Faims, "faims", "", false, "Use FAIMS information for the quantification")
 	}
 

cmd/labelquant.go

@@ -72,7 +72,7 @@ func init() {
 		labelquantCmd.Flags().Float64VarP(&m.Quantify.RemoveLow, "removelow", "", 0.0, "ignore the lower % of PSMs based on their summed abundances. 0 means no removal, entry value must be a decimal")
 		labelquantCmd.Flags().BoolVarP(&m.Quantify.Unique, "uniqueonly", "", false, "report quantification based only on unique peptides")
 		labelquantCmd.Flags().BoolVarP(&m.Quantify.BestPSM, "bestpsm", "", false, "select the best PSMs for protein quantification")
-		labelquantCmd.Flags().BoolVarP(&m.Quantify.Raw, "raw", "", false, "read raw files instead of converted XML")
+		//labelquantCmd.Flags().BoolVarP(&m.Quantify.Raw, "raw", "", false, "read raw files instead of converted XML")
 
 	}
 

lib/qua/lfq.go

@@ -5,14 +5,12 @@ import (
 	"fmt"
 	"math"
 	"path/filepath"
+	"philosopher/lib/bio"
 	"philosopher/lib/id"
+	"philosopher/lib/msg"
 	"sort"
 	"strings"
 
-	"philosopher/lib/bio"
-	"philosopher/lib/ext/rawfilereader"
-	"philosopher/lib/msg"
-
 	"philosopher/lib/mzn"
 	"philosopher/lib/rep"
 
@@ -86,9 +84,9 @@ func peakIntensity(evi rep.Evidence, dir, format string, rTWin, pTWin, tol float
 		var fileName string
 
 		if isRaw {
-			fileName = fmt.Sprintf("%s%s%s.raw", dir, string(filepath.Separator), s)
-			stream := rawfilereader.Run(fileName, "")
-			mz.ReadRaw(s, stream)
+			//fileName = fmt.Sprintf("%s%s%s.raw", dir, string(filepath.Separator), s)
+			//stream := rawfilereader.Run(fileName, "")
+			//mz.ReadRaw(s, stream)
 		} else {
 			fileName = fmt.Sprintf("%s%s%s.mzML", dir, string(filepath.Separator), s)
 			mz.Read(fileName)

lib/qua/qua.go

@@ -9,7 +9,6 @@ import (
 	"sort"
 	"strings"
 
-	"philosopher/lib/ext/rawfilereader"
 	"philosopher/lib/iso"
 	"philosopher/lib/met"
 	"philosopher/lib/msg"
@@ -100,10 +99,9 @@ func RunIsobaricLabelQuantification(p met.Quantify, mods bool) met.Quantify {
 		logrus.Info("Processing ", sourceList[i])
 
 		if p.Raw {
-
-			fileName = fmt.Sprintf("%s%s%s.raw", p.Dir, string(filepath.Separator), sourceList[i])
-			stream := rawfilereader.Run(fileName, "")
-			mz.ReadRaw(fileName, stream)
+			//fileName = fmt.Sprintf("%s%s%s.raw", p.Dir, string(filepath.Separator), sourceList[i])
+			//stream := rawfilereader.Run(fileName, "")
+			//mz.ReadRaw(fileName, stream)
 
 		} else {