Merge pull request #291 from Nesvilab/dev

Dev

.goreleaser.yml

@@ -111,68 +111,4 @@ release:
     # If set to auto, the release will not be pushed to the docker repository
     # in case there is an indicator for prerelease in the tag e.g. v1.0.0-rc1
     # Defaults to false.
-    #    skip_push: true
-
-
-snapcrafts:
-  # You can change the name of the package.
-  # Default: `{{ .ProjectName }}_{{ .Version }}_{{ .Os }}_{{ .Arch }}{{ if .Arm }}v{{ .Arm }}{{ end }}`
- - name_template: "{{ .ProjectName }}_{{ .Os }}_{{ .Arch }}"
-
-   # Wether to publish the snap to the snapcraft store.
-   # Remember you need to `snapcraft login` first.
-   # Defaults to false.
-   publish: true
-
-   # Single-line elevator pitch for your amazing snap.
-   # 79 char long at most.
-   summary: A complete toolkit for shotgun proteomics data analysis.
-
-   # This the description of your snap. You have a paragraph or two to tell the
-   # most important story about your snap. Keep it under 100 words though,
-   # we live in tweetspace and your description wants to look good in the snap
-   # store.
-   description:
-    Philosopher is a software designed for proteome bioinformatics analysis.
-
-   # A guardrail to prevent you from releasing a snap to all your users before
-   # it is ready.
-   # `devel` will let you release only to the `edge` and `beta` channels in the
-   # store. `stable` will let you release also to the `candidate` and `stable`
-   # channels. More info about channels here:
-   # https://snapcraft.io/docs/reference/channels
-   grade: stable
-
-   # Snaps can be setup to follow three different confinement policies:
-   # `strict`, `devmode` and `classic`. A strict confinement where the snap
-   # can only read and write in its own namespace is recommended. Extra
-   # permissions for strict snaps can be declared as `plugs` for the app, which
-   # are explained later. More info about confinement here:
-   # https://snapcraft.io/docs/reference/confinement
-   confinement: strict
-
-   # Your app's license, based on SPDX license expressions: https://spdx.org/licenses
-   # Default is empty.
-   license: GPL-3.0
-
-   # A snap of type base to be used as the execution environment for this snap.
-   # Valid values are:
-   # * bare - Empty base snap;
-   # * core - Ubuntu Core 16;
-   # * core18 - Ubuntu Core 18.
-   # Default is empty.
-   #base: core18
-
-   # Each binary built by GoReleaser is an app inside the snap. In this section
-   # you can declare extra details for those binaries. It is optional.
-   apps:
-
-    # The name of the app must be the same name as the binary built or the snapcraft name.
-    philosopher:
-
-      # If your app requires extra permissions to work outside of its default
-      # confined space, declare them here.
-      # You can read the documentation about the available plugs and the
-      # things they allow:
-      # https://snapcraft.io/docs/reference/interfaces.
-      plugs: ["home", "network"]
+    #    skip_push: true

Changelog

@@ -1,10 +1,9 @@
 ### Added
-- Support for TMTPro (18-plex)
+
 
 ### Changed
-- Decoys have NextAA and PrevAA
-- Improved the filtering process
+
 
 ### Fixed
-- Fixed an issue with the labelling of the TMT-6 channels
-- Minor bugs and issues
+- Fixed an issue with the ion mobility column not showing in empty PSM tables.
+- Fixed an issue where high-scoring peptides mapping to complicated razor cases where not showing in the reports.

cmd/msfragger.go

@@ -73,7 +73,7 @@ func init() {
 		msfraggerCmd.Flags().StringVarP(&m.MSFragger.SearchEnzymeCut2, "search_enzyme_cut_2", "", "", "Second enzyme's cutting amino acid.")
 		msfraggerCmd.Flags().StringVarP(&m.MSFragger.SearchEnzymeNocut2, "search_enzyme_nocut_2", "", "", "Second enzyme's protecting amino acid.")
 		msfraggerCmd.Flags().IntVarP(&m.MSFragger.AllowedMissedCleavage2, "allowed_missed_cleavage_2", "", 2, "Second enzyme's allowed number of missed cleavages per peptide. Maximum value is 5.")
-		msfraggerCmd.Flags().StringVarP(&m.MSFragger.SearchEnzymeSense2, "search_enzyme_sense_2", "", "", "Second enzyme's cutting terminal.")
+		msfraggerCmd.Flags().StringVarP(&m.MSFragger.SearchEnzymeSense2, "search_enzyme_sense_2", "", "C", "Second enzyme's cutting terminal.")
 		msfraggerCmd.Flags().IntVarP(&m.MSFragger.NumEnzymeTermini, "num_enzyme_termini", "", 2, "2 for enzymatic, 1 for semi-enzymatic, 0 for nonspecific digestion")
 		msfraggerCmd.Flags().IntVarP(&m.MSFragger.ClipNTermM, "clip_nTerm_M", "", 1, "")
 		msfraggerCmd.Flags().StringVarP(&m.MSFragger.VariableMod01, "variable_mod_01", "", "", "")

cmd/report.go

@@ -43,6 +43,7 @@ func init() {
 		reportCmd.Flags().BoolVarP(&m.Report.Decoys, "decoys", "", false, "add decoy observations to reports")
 		reportCmd.Flags().BoolVarP(&m.Report.MSstats, "msstats", "", false, "create an output compatible with MSstats")
 		reportCmd.Flags().BoolVarP(&m.Report.MZID, "mzid", "", false, "create a mzID output")
+		reportCmd.Flags().BoolVarP(&m.Report.IonMob, "ionmobility", "", false, "forces the printing of the ion mobility column")
 	}
 
 	RootCmd.AddCommand(reportCmd)

lib/aba/pro.go

@@ -214,7 +214,8 @@ func processProteinCombinedFile(a met.Abacus, database dat.Base) rep.CombinedPro
 
 	for i := range list {
 		for _, j := range database.Records {
-			if strings.Contains(j.OriginalHeader, list[i].ProteinName) && !strings.Contains(j.OriginalHeader, a.Tag) {
+			if strings.Contains(j.OriginalHeader, list[i].ProteinName) && strings.HasPrefix(j.OriginalHeader, list[i].ProteinID) && !strings.Contains(j.OriginalHeader, a.Tag) {
+				//if strings.Contains(j.OriginalHeader, list[i].ProteinName) && !strings.Contains(j.OriginalHeader, a.Tag) {
 				list[i].ProteinName = j.PartHeader
 				list[i].ProteinID = j.ID
 				list[i].EntryName = j.EntryName

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) != 20371 {
-				t.Errorf("Number of FASTA entries is incorrect, got %d, want %d", len(d.Records), 20371)
+			if len(d.Records) != 20360 {
+				t.Errorf("Number of FASTA entries is incorrect, got %d, want %d", len(d.Records), 20360)
 			}
 		})
 	}

lib/dat/db.go

@@ -395,8 +395,15 @@ func ProcessGeneric(k, v, decoyTag string) Record {
 	idm := idReg.FindStringSubmatch(k)
 	e.ID = idm[1]
 
-	e.Description = ""
-	e.EntryName = ""
+	part := strings.Split(k, " ")
+
+	if len(part) > 1 {
+		e.Description = part[1]
+	} else {
+		e.Description = k
+	}
+
+	e.EntryName = k
 	e.GeneNames = ""
 	e.Organism = ""
 	e.SequenceVersion = ""
@@ -405,7 +412,6 @@ func ProcessGeneric(k, v, decoyTag string) Record {
 	e.Length = len(v)
 	e.OriginalHeader = k
 
-	part := strings.Split(k, " ")
 	e.PartHeader = part[0]
 
 	if strings.HasPrefix(k, decoyTag) {