Merge pull request #335 from Nesvilab/rc-v4.2.1

Rc v4.2.1

cmd/inspect.go

@@ -13,10 +13,10 @@ import (
 	"philosopher/lib/msg"
 	"philosopher/lib/qua"
 	"philosopher/lib/rep"
+	"philosopher/lib/sys"
 
 	"github.com/davecgh/go-spew/spew"
 	"github.com/spf13/cobra"
-	"github.com/vmihailenco/msgpack"
 )
 
 var object string
@@ -34,90 +34,54 @@ var inspectCmd = &cobra.Command{
 			var o met.Data
 
 			target := fmt.Sprintf(".meta%smeta.bin", string(filepath.Separator))
-			file, _ := os.Open(target)
-
-			dec := msgpack.NewDecoder(file)
-			e := dec.Decode(&o)
-			if e != nil {
-				msg.DecodeMsgPck(e, "fatal")
-			}
+			sys.Restore(&o, target, false)
 
 			if key == "session" {
 				fmt.Println(o.UUID)
 			} else {
 				spew.Dump(o)
 			}
+
 		case "psm":
 			var o rep.PSMEvidenceList
 
 			target := fmt.Sprintf(".meta%spsm.bin", string(filepath.Separator))
-			file, _ := os.Open(target)
-
-			dec := msgpack.NewDecoder(file)
-			e := dec.Decode(&o)
-			if e != nil {
-				msg.DecodeMsgPck(e, "fatal")
-			}
+			sys.Restore(&o, target, false)
 			spew.Dump(o)
+
 		case "peptide":
 			var o rep.PeptideEvidenceList
 
 			target := fmt.Sprintf(".meta%spep.bin", string(filepath.Separator))
-			file, _ := os.Open(target)
-
-			dec := msgpack.NewDecoder(file)
-			e := dec.Decode(&o)
-			if e != nil {
-				msg.DecodeMsgPck(e, "fatal")
-			}
+			sys.Restore(&o, target, false)
 			spew.Dump(o)
+
 		case "db":
 			var o dat.Base
 
 			target := fmt.Sprintf(".meta%sdb.bin", string(filepath.Separator))
-			file, _ := os.Open(target)
-
-			dec := msgpack.NewDecoder(file)
-			e := dec.Decode(&o)
-			if e != nil {
-				msg.DecodeMsgPck(e, "fatal")
-			}
+			sys.Restore(&o, target, false)
 			spew.Dump(o.Records)
+
 		case "lfq":
 			var o qua.LFQ
 
 			target := fmt.Sprintf(".meta%slfq.bin", string(filepath.Separator))
-			file, _ := os.Open(target)
-
-			dec := msgpack.NewDecoder(file)
-			e := dec.Decode(&o)
-			if e != nil {
-				msg.DecodeMsgPck(e, "fatal")
-			}
+			sys.Restore(&o, target, false)
 			spew.Dump(o.Intensities)
+
 		case "razor":
 			var o fil.RazorMap
 
 			target := fmt.Sprintf(".meta%srazor.bin", string(filepath.Separator))
-			file, _ := os.Open(target)
-
-			dec := msgpack.NewDecoder(file)
-			e := dec.Decode(&o)
-			if e != nil {
-				msg.DecodeMsgPck(e, "fatal")
-			}
+			sys.Restore(&o, target, false)
 			spew.Dump(o)
+
 		case "protein":
 			var o rep.ProteinEvidenceList
 
 			target := fmt.Sprintf(".meta%spro.bin", string(filepath.Separator))
-			file, _ := os.Open(target)
-
-			dec := msgpack.NewDecoder(file)
-			e := dec.Decode(&o)
-			if e != nil {
-				msg.DecodeMsgPck(e, "fatal")
-			}
+			sys.Restore(&o, target, false)
 
 			if len(key) > 0 {
 
@@ -130,6 +94,7 @@ var inspectCmd = &cobra.Command{
 			} else {
 				spew.Dump(o)
 			}
+
 		default:
 			msg.Custom(errors.New("the option is not available"), "fatal")
 		}

cmd/proproph.go

@@ -48,6 +48,7 @@ func init() {
 		proprophCmd.Flags().BoolVarP(&m.ProteinProphet.Glyc, "glyc", "", false, "highlight peptide N-glycosylation motif")
 		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().BoolVarP(&m.ProteinProphet.Subgroups, "subgroups", "", false, "do not use NOGROUPS")
 		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 probability threshold")
 		proprophCmd.Flags().IntVarP(&m.ProteinProphet.Maxppmdiff, "maxppmdiff", "", 2000000, "maximum peptide mass difference in ppm")

go.mod

@@ -5,7 +5,6 @@ go 1.13
 require (
 	github.com/ajstarks/svgo v0.0.0-20200204031535-0cbcf57ea1d8 // indirect
 	github.com/davecgh/go-spew v1.1.1
-	github.com/golang/protobuf v1.3.4 // indirect
 	github.com/gorilla/websocket v1.4.1 // indirect
 	github.com/jpillora/go-ogle-analytics v0.0.0-20161213085824-14b04e0594ef
 	github.com/jung-kurt/gofpdf v1.16.2 // indirect
@@ -22,15 +21,12 @@ require (
 	github.com/sirupsen/logrus v1.4.2
 	github.com/spf13/cobra v0.0.6
 	github.com/spf13/pflag v1.0.5 // indirect
-	github.com/stretchr/testify v1.5.1 // indirect
-	github.com/vmihailenco/msgpack v4.0.4+incompatible
+	github.com/vmihailenco/msgpack/v5 v5.3.5
 	golang.org/x/exp v0.0.0-20200228211341-fcea875c7e85 // indirect
 	golang.org/x/image v0.0.0-20200119044424-58c23975cae1 // indirect
-	golang.org/x/net v0.0.0-20200301022130-244492dfa37a // indirect
 	golang.org/x/sys v0.0.0-20200302150141-5c8b2ff67527 // indirect
 	gonum.org/v1/netlib v0.0.0-20200229103305-d71f404090bf // indirect
 	gonum.org/v1/plot v0.7.0
-	google.golang.org/appengine v1.6.5 // indirect
 	gopkg.in/check.v1 v1.0.0-20200227125254-8fa46927fb4f // indirect
 	gopkg.in/yaml.v2 v2.2.8
 )

go.sum

@@ -45,8 +45,6 @@ github.com/golang/groupcache v0.0.0-20190129154638-5b532d6fd5ef/go.mod h1:cIg4er
 github.com/golang/mock v1.1.1/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A=
 github.com/golang/protobuf v1.2.0/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
 github.com/golang/protobuf v1.3.1/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
-github.com/golang/protobuf v1.3.4 h1:87PNWwrRvUSnqS4dlcBU/ftvOIBep4sYuBLlh6rX2wk=
-github.com/golang/protobuf v1.3.4/go.mod h1:vzj43D7+SQXF/4pzW/hwtAqwc6iTitCiVSaWz5lYuqw=
 github.com/google/btree v1.0.0/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ=
 github.com/google/go-cmp v0.2.0/go.mod h1:oXzfMopK8JAjlY9xF4vHSVASa0yLyX7SntLO5aqRK0M=
 github.com/gorilla/websocket v1.2.0/go.mod h1:E7qHFY5m1UJ88s3WnNqhKjPHQ0heANvMoAMk2YaljkQ=
@@ -100,6 +98,8 @@ github.com/pkg/errors v0.8.0/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINE
 github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
 github.com/pkg/errors v0.9.1 h1:FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4=
 github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
+github.com/pkg/profile v1.6.0 h1:hUDfIISABYI59DyeB3OTay/HxSRwTQ8rB/H83k6r5dM=
+github.com/pkg/profile v1.6.0/go.mod h1:qBsxPvzyUincmltOk6iyRVxHYg4adc0OFOv72ZdLa18=
 github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
 github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
 github.com/prometheus/client_golang v0.9.1/go.mod h1:7SWBe2y4D6OKWSNQJUaRYU/AaXPKyh/dDVn+NZz0KFw=
@@ -139,12 +139,14 @@ github.com/spf13/viper v1.4.0/go.mod h1:PTJ7Z/lr49W6bUbkmS1V3by4uWynFiR9p7+dSq/y
 github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
 github.com/stretchr/objx v0.1.1/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
 github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs=
-github.com/stretchr/testify v1.5.1 h1:nOGnQDM7FYENwehXlg/kFVnos3rEvtKTjRvOWSzb6H4=
-github.com/stretchr/testify v1.5.1/go.mod h1:5W2xD1RspED5o8YsWQXVCued0rvSQ+mT+I5cxcmMvtA=
+github.com/stretchr/testify v1.6.1 h1:hDPOHmpOpP40lSULcqw7IrRb/u7w6RpDC9399XyoNd0=
+github.com/stretchr/testify v1.6.1/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
 github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U=
 github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc=
-github.com/vmihailenco/msgpack v4.0.4+incompatible h1:dSLoQfGFAo3F6OoNhwUmLwVgaUXK79GlxNBwueZn0xI=
-github.com/vmihailenco/msgpack v4.0.4+incompatible/go.mod h1:fy3FlTQTDXWkZ7Bh6AcGMlsjHatGryHQYUTf1ShIgkk=
+github.com/vmihailenco/msgpack/v5 v5.3.5 h1:5gO0H1iULLWGhs2H5tbAHIZTV8/cYafcFOr9znI5mJU=
+github.com/vmihailenco/msgpack/v5 v5.3.5/go.mod h1:7xyJ9e+0+9SaZT0Wt1RGleJXzli6Q/V5KbhBonMG9jc=
+github.com/vmihailenco/tagparser/v2 v2.0.0 h1:y09buUbR+b5aycVFQs/g70pqKVZNBmxwAhO7/IwNM9g=
+github.com/vmihailenco/tagparser/v2 v2.0.0/go.mod h1:Wri+At7QHww0WTrCBeu4J6bNtoV6mEfg5OIWRZA9qds=
 github.com/xiang90/probing v0.0.0-20190116061207-43a291ad63a2/go.mod h1:UETIi67q53MR2AWcXfiuqkDkRtnGDLqkBTpCHuJHxtU=
 github.com/xordataexchange/crypt v0.0.3-0.20170626215501-b2862e3d0a77/go.mod h1:aYKd//L2LvnjZzWKhF00oedf4jCCReLcmhLdhm1A27Q=
 go.etcd.io/bbolt v1.3.2/go.mod h1:IbVyRI1SCnLcuJnV2u8VeU0CEYM7e686BmAb1XKL+uU=
@@ -179,10 +181,7 @@ golang.org/x/net v0.0.0-20181220203305-927f97764cc3/go.mod h1:mL1N/T3taQHkDXs73r
 golang.org/x/net v0.0.0-20190311183353-d8887717615a/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
 golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
 golang.org/x/net v0.0.0-20190522155817-f3200d17e092/go.mod h1:HSz+uSET+XFnRR8LxR5pz3Of3rY3CfYBVs4xY44aLks=
-golang.org/x/net v0.0.0-20190603091049-60506f45cf65/go.mod h1:HSz+uSET+XFnRR8LxR5pz3Of3rY3CfYBVs4xY44aLks=
 golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
-golang.org/x/net v0.0.0-20200301022130-244492dfa37a h1:GuSPYbZzB5/dcLNCwLQLsg3obCJtX9IJhpXkvY7kzk0=
-golang.org/x/net v0.0.0-20200301022130-244492dfa37a/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
 golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be/go.mod h1:N/0e6XlmueqKjAGxoOufVs8QHGRruUQn6yWY3a++T0U=
 golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
 golang.org/x/sync v0.0.0-20181108010431-42b317875d0f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
@@ -202,11 +201,9 @@ golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae/go.mod h1:h1NjWce9XRLGQEsW7w
 golang.org/x/sys v0.0.0-20200302150141-5c8b2ff67527 h1:uYVVQ9WP/Ds2ROhcaGPeIdVq0RIXVLwsHlnvJ+cT1So=
 golang.org/x/sys v0.0.0-20200302150141-5c8b2ff67527/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
-golang.org/x/text v0.3.2/go.mod h1:bEr9sfX3Q8Zfm5fL9x+3itogRgK3+ptLWKqgva+5dAk=
 golang.org/x/time v0.0.0-20190308202827-9d24e82272b4/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ=
 golang.org/x/tools v0.0.0-20180221164845-07fd8470d635/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
 golang.org/x/tools v0.0.0-20180525024113-a5b4c53f6e8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
-golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
 golang.org/x/tools v0.0.0-20190114222345-bf090417da8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
 golang.org/x/tools v0.0.0-20190206041539-40960b6deb8e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
 golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=
@@ -223,8 +220,6 @@ gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b/go.mod h1:Wt8AAjI+ypCyYX3nZ
 gonum.org/v1/plot v0.7.0 h1:Otpxyvra6Ie07ft50OX5BrCfS/BWEMvhsCUHwPEJmLI=
 gonum.org/v1/plot v0.7.0/go.mod h1:2wtU6YrrdQAhAF9+MTd5tOQjrov/zF70b1i99Npjvgo=
 google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM=
-google.golang.org/appengine v1.6.5 h1:tycE03LOZYQNhDpS27tcQdAzLCVMaj7QT2SXxebnpCM=
-google.golang.org/appengine v1.6.5/go.mod h1:8WjMMxjGQR8xUklV/ARdw2HLXBOI7O7uCIDZVag1xfc=
 google.golang.org/genproto v0.0.0-20180817151627-c66870c02cf8/go.mod h1:JiN7NxoALGmiZfu7CAH4rXhgtRTLTxftemlI0sWmxmc=
 google.golang.org/grpc v1.19.0/go.mod h1:mqu4LbDTu4XGKhr4mRzUsmM4RtVoemTSY81AxZiDr8c=
 google.golang.org/grpc v1.21.0/go.mod h1:oYelfM1adQP15Ek0mdvEgi9Df8B9CZIaU1084ijfRaM=
@@ -239,6 +234,8 @@ gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
 gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
 gopkg.in/yaml.v2 v2.2.8 h1:obN1ZagJSUGI0Ek/LBmuj4SNLPfIny3KsKFopxRdj10=
 gopkg.in/yaml.v2 v2.2.8/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
+gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c h1:dUUwHk2QECo/6vqA44rthZ8ie2QXMNeKRTHCNY2nXvo=
+gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
 honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
 modernc.org/cc v1.0.0/go.mod h1:1Sk4//wdnYJiUIxnW8ddKpaOJCF37yAdqYnkxUpaYxw=
 modernc.org/golex v1.0.0/go.mod h1:b/QX9oBD/LhixY6NDh+IdGv17hgB+51fET1i2kPSmvk=

lib/aba/pep.go

@@ -8,6 +8,7 @@ import (
 	"io/ioutil"
 	"os"
 	"path/filepath"
+	"philosopher/lib/mod"
 	"sort"
 	"strconv"
 	"strings"
@@ -104,9 +105,6 @@ func peptideLevelAbacus(m met.Data, args []string) {
 // processPeptideCombinedFile reads and filter the combined peptide report
 func processPeptideCombinedFile(a met.Abacus) {
 
-	var pepID id.PepIDList
-	var filteredPeptides id.PepIDList
-
 	if _, e := os.Stat("combined.pep.xml"); os.IsNotExist(e) {
 
 		msg.NoParametersFound(errors.New("cannot find the combined.pep.xml file"), "fatal")
@@ -116,13 +114,12 @@ func processPeptideCombinedFile(a met.Abacus) {
 		var pep id.PepXML
 		pep.DecoyTag = a.Tag
 
-		pepID, _ = id.ReadPepXMLInput("combined.pep.xml", a.Tag, sys.GetTemp(), false)
-
+		pepID, _ := id.ReadPepXMLInput("combined.pep.xml", a.Tag, sys.GetTemp(), false)
 		//uniqPsms := fil.GetUniquePSMs(pepID)
 		uniqPeps := fil.GetUniquePeptides(pepID)
 
 		//filteredPSMs, _ := fil.PepXMLFDRFilter(uniqPsms, 0.01, "PSM", a.Tag)
-		filteredPeptides, _ = fil.PepXMLFDRFilter(uniqPeps, 0.01, "Peptide", a.Tag)
+		filteredPeptides, _ := fil.PepXMLFDRFilter(uniqPeps, 0.01, "Peptide", a.Tag)
 		filteredPeptides.Serialize("pep")
 
 	}
@@ -179,8 +176,8 @@ func SummarizeAttributes(evidences rep.CombinedPeptideEvidenceList, datasets map
 
 		for _, j := range evi.Peptides {
 
-			for _, k := range j.Modifications.Index {
-				if k.Type == "Assigned" {
+			for _, k := range j.Modifications.IndexSlice {
+				if k.Type == mod.Assigned {
 					mass := strconv.FormatFloat(k.MassDiff, 'f', 6, 64)
 					ModsMap[j.Sequence] = append(ModsMap[j.Sequence], mass)
 				}

lib/aba/pro.go

@@ -9,7 +9,6 @@ import (
 	"os"
 	"path/filepath"
 	"sort"
-	"strconv"
 	"strings"
 
 	"philosopher/lib/iso"
@@ -196,7 +195,7 @@ func processProteinCombinedFile(a met.Abacus, database dat.Base) rep.CombinedPro
 
 				ce.SupportingSpectra = make(map[string]string)
 				ce.ProteinName = j.ProteinName
-				ce.Length, _ = strconv.Atoi(j.Length)
+				ce.Length = j.Length
 				ce.Coverage = j.PercentCoverage
 				ce.GroupNumber = j.GroupNumber
 				ce.SiblingID = j.GroupSiblingID
@@ -312,9 +311,9 @@ func getProteinLabelIntensities(combined rep.CombinedProteinEvidenceList, datase
 		for i := range combined {
 			for _, j := range v.Proteins {
 				if combined[i].ProteinID == j.ProteinID && !strings.Contains(j.OriginalHeader, decoyTag) {
-					combined[i].TotalLabels[k] = j.TotalLabels
-					combined[i].UniqueLabels[k] = j.UniqueLabels
-					combined[i].URazorLabels[k] = j.URazorLabels
+					combined[i].TotalLabels[k] = *j.TotalLabels
+					combined[i].UniqueLabels[k] = *j.UniqueLabels
+					combined[i].URazorLabels[k] = *j.URazorLabels
 					break
 				}
 			}
@@ -330,9 +329,9 @@ func sumProteinIntensities(combined rep.CombinedProteinEvidenceList, datasets ma
 
 	for k, v := range datasets {
 
-		var ions = make(map[string]float64)
+		var ions = make(map[id.IonFormType]float64)
 		for _, i := range v.Ions {
-			ions[i.IonForm] = i.Intensity
+			ions[i.IonForm()] = i.Intensity
 		}
 
 		for _, i := range combined {

lib/dat/dat.go

@@ -21,7 +21,7 @@ import (
 	"philosopher/lib/sys"
 
 	"github.com/sirupsen/logrus"
-	"github.com/vmihailenco/msgpack"
+	"github.com/vmihailenco/msgpack/v5"
 )
 
 // Base main structure
@@ -234,7 +234,7 @@ func (d *Base) Create(temp, add, enz, tag string, crap, noD, cTag bool) {
 
 			for k, v := range crapMap {
 
-				if cTag {
+				if cTag && !strings.Contains(k, "_HUMAN") && !strings.Contains(k, "OX=9606") {
 					k = "contam_" + k
 				}
 
@@ -361,33 +361,15 @@ func (d *Base) Serialize() {
 
 // Restore reads philosopher results files and restore the data sctructure
 func (d *Base) Restore() {
-
-	b, e := ioutil.ReadFile(sys.DBBin())
-	if e != nil {
-		msg.MarshalFile(e, "warning")
-	}
-
-	e = msgpack.Unmarshal(b, &d)
-	if e != nil {
-		msg.SerializeFile(e, "warning")
-	}
-
+	sys.Restore(d, sys.DBBin(), false)
 }
 
 // RestoreWithPath reads philosopher results files and restore the data sctructure
 func (d *Base) RestoreWithPath(p string) {
 
 	path := fmt.Sprintf("%s%s%s", p, string(filepath.Separator), sys.DBBin())
 	path, _ = filepath.Abs(path)
-
-	file, _ := os.Open(path)
-
-	dec := msgpack.NewDecoder(file)
-	e := dec.Decode(&d)
-	if e != nil {
-		msg.DecodeMsgPck(e, "fatal")
-	}
-
+	sys.Restore(d, path, false)
 }
 
 // reverseSeq returns its argument string reversed rune-wise left to right.

lib/dat/dat_test.go

@@ -73,7 +73,7 @@ func TestBase_ProcessDB(t *testing.T) {
 			}
 			d.ProcessDB(tt.args.file, tt.args.decoyTag)
 
-			if len(d.Records) != 20360 {
+			if len(d.Records) != 20361 {
 				t.Errorf("Number of FASTA entries is incorrect, got %d, want %d", len(d.Records), 20360)
 			}
 		})