Changes to be committed:

modified:   go.mod
	modified:   go.sum
	modified:   pkg/obilua/obilib.go
	modified:   pkg/obilua/obiseq.go
	modified:   pkg/obilua/obiseqslice.go
	new file:   pkg/obilua/obitaxon.go
	new file:   pkg/obilua/obitaxonomy.go
	modified:   pkg/obioptions/version.go

go.mod

@@ -26,6 +26,7 @@ require (
 require (
 	github.com/Clever/csvlint v0.3.0 // indirect
 	github.com/buger/jsonparser v1.1.1 // indirect
+	github.com/chzyer/readline v0.0.0-20180603132655-2972be24d48e // indirect
 	github.com/davecgh/go-spew v1.1.1 // indirect
 	github.com/goombaio/orderedmap v0.0.0-20180924084748-ba921b7e2419 // indirect
 	github.com/kr/pretty v0.3.0 // indirect

go.sum

@@ -12,6 +12,8 @@ github.com/buger/jsonparser v1.1.1 h1:2PnMjfWD7wBILjqQbt530v576A/cAbQvEW9gGIpYMU
 github.com/buger/jsonparser v1.1.1/go.mod h1:6RYKKt7H4d4+iWqouImQ9R2FZql3VbhNgx27UK13J/0=
 github.com/chen3feng/stl4go v0.1.1 h1:0L1+mDw7pomftKDruM23f1mA7miavOj6C6MZeadzN2Q=
 github.com/chen3feng/stl4go v0.1.1/go.mod h1:5ml3psLgETJjRJnMbPE+JiHLrCpt+Ajc2weeTECXzWU=
+github.com/chzyer/readline v0.0.0-20180603132655-2972be24d48e h1:fY5BOSpyZCqRo5OhCuC+XN+r/bBCmeuuJtjz+bCNIf8=
+github.com/chzyer/readline v0.0.0-20180603132655-2972be24d48e/go.mod h1:nSuG5e5PlCu98SY8svDHJxuZscDgtXS6KTTbou5AhLI=
 github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E=
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=

pkg/obilua/obilib.go

@@ -4,4 +4,5 @@ import lua "github.com/yuin/gopher-lua"
 
 func RegisterObilib(luaState *lua.LState) {
 	RegisterObiSeq(luaState)
+	RegisterObiTaxonomy(luaState)
 }

pkg/obilua/obiseq.go

@@ -1,7 +1,9 @@
 package obilua
 
 import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	lua "github.com/yuin/gopher-lua"
 )
 
@@ -16,6 +18,7 @@ func registerBioSequenceType(luaState *lua.LState) {
 	bioSequenceType := luaState.NewTypeMetatable(luaBioSequenceTypeName)
 	luaState.SetGlobal(luaBioSequenceTypeName, bioSequenceType)
 	luaState.SetField(bioSequenceType, "new", luaState.NewFunction(newObiSeq))
+	luaState.SetField(bioSequenceType, "nil", obiseq2Lua(luaState, nil))
 
 	luaState.SetField(bioSequenceType, "__index",
 		luaState.SetFuncs(luaState.NewTable(),
@@ -53,6 +56,7 @@ var bioSequenceMethods = map[string]lua.LGFunction{
 	"definition":         bioSequenceGetSetDefinition,
 	"count":              bioSequenceGetSetCount,
 	"taxid":              bioSequenceGetSetTaxid,
+	"taxon":              bioSequenceGetSetTaxon,
 	"attribute":          bioSequenceGetSetAttribute,
 	"len":                bioSequenceGetLength,
 	"has_sequence":       bioSequenceHasSequence,
@@ -62,6 +66,9 @@ var bioSequenceMethods = map[string]lua.LGFunction{
 	"md5_string":         bioSequenceGetMD5String,
 	"subsequence":        bioSequenceGetSubsequence,
 	"reverse_complement": bioSequenceGetRevcomp,
+	"fasta":              bioSequenceGetFasta,
+	"fastq":              bioSequenceGetFastq,
+	"string":             bioSequenceAsString,
 }
 
 // checkBioSequence checks if the first argument in the Lua stack is a *obiseq.BioSequence.
@@ -254,3 +261,88 @@ func bioSequenceGetRevcomp(luaState *lua.LState) int {
 	luaState.Push(obiseq2Lua(luaState, revcomp))
 	return 1
 }
+
+func bioSequenceGetSetTaxon(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+
+	if luaState.GetTop() > 1 {
+		taxon := checkTaxon(luaState, 2)
+
+		s.SetTaxon(taxon)
+
+		return 0
+	}
+
+	taxon := s.Taxon(obitax.DefaultTaxonomy())
+	luaState.Push(taxon2Lua(luaState, taxon))
+
+	return 1
+}
+
+func bioSequenceGetFasta(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+
+	formater := obiformats.FormatFastSeqJsonHeader
+
+	if luaState.GetTop() > 1 {
+		format := luaState.CheckString(2)
+		switch format {
+		case "json":
+			formater = obiformats.FormatFastSeqJsonHeader
+		case "obi":
+			formater = obiformats.FormatFastSeqOBIHeader
+		}
+	}
+
+	txt := obiformats.FormatFasta(s, formater)
+
+	luaState.Push(lua.LString(txt))
+	return 1
+}
+
+func bioSequenceGetFastq(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+
+	formater := obiformats.FormatFastSeqJsonHeader
+
+	if luaState.GetTop() > 1 {
+		format := luaState.CheckString(2)
+		switch format {
+		case "json":
+			formater = obiformats.FormatFastSeqJsonHeader
+		case "obi":
+			formater = obiformats.FormatFastSeqOBIHeader
+		}
+	}
+
+	txt := obiformats.FormatFastq(s, formater)
+
+	luaState.Push(lua.LString(txt))
+	return 1
+}
+
+func bioSequenceAsString(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+
+	formater := obiformats.FormatFastSeqJsonHeader
+	format := obiformats.FormatFasta
+
+	if s.HasQualities() {
+		format = obiformats.FormatFastq
+	}
+
+	if luaState.GetTop() > 1 {
+		format := luaState.CheckString(2)
+		switch format {
+		case "json":
+			formater = obiformats.FormatFastSeqJsonHeader
+		case "obi":
+			formater = obiformats.FormatFastSeqOBIHeader
+		}
+	}
+
+	txt := format(s, formater)
+
+	luaState.Push(lua.LString(txt))
+	return 1
+}

pkg/obilua/obiseqslice.go

@@ -1,6 +1,9 @@
 package obilua
 
 import (
+	"strings"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	lua "github.com/yuin/gopher-lua"
 )
@@ -11,6 +14,7 @@ func registerBioSequenceSliceType(luaState *lua.LState) {
 	bioSequenceSliceType := luaState.NewTypeMetatable(luaBioSequenceSliceTypeName)
 	luaState.SetGlobal(luaBioSequenceSliceTypeName, bioSequenceSliceType)
 	luaState.SetField(bioSequenceSliceType, "new", luaState.NewFunction(newObiSeqSlice))
+	luaState.SetField(bioSequenceSliceType, "nil", obiseqslice2Lua(luaState, nil))
 
 	luaState.SetField(bioSequenceSliceType, "__index",
 		luaState.SetFuncs(luaState.NewTable(),
@@ -37,6 +41,9 @@ var bioSequenceSliceMethods = map[string]lua.LGFunction{
 	"pop":      bioSequenceSlicePop,
 	"sequence": bioSequenceSliceGetSetSequence,
 	"len":      bioSequenceSliceGetLength,
+	"fasta":    bioSequenceSliceGetFasta,
+	"fastq":    bioSequenceSliceGetFastq,
+	"string":   bioSequenceSliceAsString,
 }
 
 func checkBioSequenceSlice(L *lua.LState) *obiseq.BioSequenceSlice {
@@ -105,3 +112,96 @@ func bioSequenceSlicePop(luaState *lua.LState) int {
 	return 1
 
 }
+
+func bioSequenceSliceGetFasta(luaState *lua.LState) int {
+	s := checkBioSequenceSlice(luaState)
+
+	formater := obiformats.FormatFastSeqJsonHeader
+
+	if luaState.GetTop() > 1 {
+		format := luaState.CheckString(2)
+		switch format {
+		case "json":
+			formater = obiformats.FormatFastSeqJsonHeader
+		case "obi":
+			formater = obiformats.FormatFastSeqOBIHeader
+		}
+	}
+
+	txts := make([]string, len(*s))
+
+	for i, seq := range *s {
+		txts[i] = obiformats.FormatFasta(seq, formater)
+	}
+
+	txt := strings.Join(txts, "\n")
+
+	luaState.Push(lua.LString(txt))
+	return 1
+}
+
+func bioSequenceSliceGetFastq(luaState *lua.LState) int {
+	s := checkBioSequenceSlice(luaState)
+
+	formater := obiformats.FormatFastSeqJsonHeader
+
+	if luaState.GetTop() > 1 {
+		format := luaState.CheckString(2)
+		switch format {
+		case "json":
+			formater = obiformats.FormatFastSeqJsonHeader
+		case "obi":
+			formater = obiformats.FormatFastSeqOBIHeader
+		}
+	}
+
+	txts := make([]string, len(*s))
+
+	for i, seq := range *s {
+		txts[i] = obiformats.FormatFastq(seq, formater)
+	}
+
+	txt := strings.Join(txts, "\n")
+
+	luaState.Push(lua.LString(txt))
+	return 1
+}
+
+func bioSequenceSliceAsString(luaState *lua.LState) int {
+	s := checkBioSequenceSlice(luaState)
+
+	formater := obiformats.FormatFastSeqJsonHeader
+
+	if luaState.GetTop() > 1 {
+		format := luaState.CheckString(2)
+		switch format {
+		case "json":
+			formater = obiformats.FormatFastSeqJsonHeader
+		case "obi":
+			formater = obiformats.FormatFastSeqOBIHeader
+		}
+	}
+
+	txts := make([]string, len(*s))
+
+	format := obiformats.FormatFasta
+
+	allQual := true
+
+	for _, s := range *s {
+		allQual = allQual && s.HasQualities()
+	}
+
+	if allQual {
+		format = obiformats.FormatFastq
+	}
+
+	for i, seq := range *s {
+		txts[i] = format(seq, formater)
+	}
+
+	txt := strings.Join(txts, "\n")
+
+	luaState.Push(lua.LString(txt))
+	return 1
+}

pkg/obilua/obitaxon.go

@@ -0,0 +1,139 @@
+package obilua
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+	lua "github.com/yuin/gopher-lua"
+)
+
+const luaTaxonTypeName = "Taxon"
+
+func registerTaxonType(luaState *lua.LState) {
+	taxonType := luaState.NewTypeMetatable(luaTaxonTypeName)
+	luaState.SetGlobal(luaTaxonTypeName, taxonType)
+	luaState.SetField(taxonType, "new", luaState.NewFunction(newTaxon))
+	luaState.SetField(taxonType, "nil", taxonomy2Lua(luaState, nil))
+
+	luaState.SetField(taxonType, "__index",
+		luaState.SetFuncs(luaState.NewTable(),
+			taxonMethods))
+}
+
+func taxon2Lua(interpreter *lua.LState,
+	taxon *obitax.Taxon) lua.LValue {
+	ud := interpreter.NewUserData()
+	ud.Value = taxon
+	interpreter.SetMetatable(ud, interpreter.GetTypeMetatable(luaTaxonTypeName))
+
+	return ud
+}
+
+func newTaxon(luaState *lua.LState) int {
+	taxonomy := checkTaxonomy(luaState)
+	taxid := luaState.CheckString(2)
+	parent := luaState.CheckString(3)
+	sname := luaState.CheckString(4)
+	rank := luaState.CheckString(5)
+
+	isroot := false
+
+	if luaState.GetTop() > 5 {
+		isroot = luaState.CheckBool(6)
+	}
+
+	taxon, err := taxonomy.AddTaxon(taxid, parent, rank, isroot, false)
+
+	if err != nil {
+		luaState.RaiseError("(%v,%v,%v) : Error on taxon creation: %v", taxid, parent, sname, err)
+		return 0
+	}
+
+	taxon.SetName(sname, "scientific name")
+
+	luaState.Push(taxon2Lua(luaState, taxon))
+	return 1
+}
+
+var taxonMethods = map[string]lua.LGFunction{
+	"string":          taxonAsString,
+	"scientific_name": taxonGetSetScientificName,
+	"parent":          taxonGetParent,
+	"taxon_at_rank":   taxGetTaxonAtRank,
+	"species":         taxonGetSpecies,
+	"genus":           taxonGetGenus,
+	"family":          taxonGetFamily,
+}
+
+func checkTaxon(L *lua.LState, i int) *obitax.Taxon {
+	ud := L.CheckUserData(i)
+	if v, ok := ud.Value.(*obitax.Taxon); ok {
+		return v
+	}
+	L.ArgError(i, "obitax.Taxon expected")
+	return nil
+}
+
+func taxonAsString(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+	luaState.Push(lua.LString(taxon.String()))
+	return 1
+}
+
+func taxonGetSetScientificName(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+
+	if luaState.GetTop() > 1 {
+		sname := luaState.CheckString(2)
+		taxon.SetName(sname, "scientific name")
+		return 0
+	}
+
+	luaState.Push(lua.LString(taxon.ScientificName()))
+	return 1
+}
+
+func taxonGetParent(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+
+	parent := taxon.Parent()
+	luaState.Push(taxon2Lua(luaState, parent))
+
+	return 1
+}
+
+func taxonGetSpecies(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+
+	species := taxon.Species()
+	luaState.Push(taxon2Lua(luaState, species))
+
+	return 1
+}
+
+func taxonGetGenus(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+
+	genus := taxon.Genus()
+	luaState.Push(taxon2Lua(luaState, genus))
+
+	return 1
+}
+
+func taxonGetFamily(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+
+	family := taxon.Family()
+	luaState.Push(taxon2Lua(luaState, family))
+
+	return 1
+}
+
+func taxGetTaxonAtRank(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+	rank := luaState.CheckString(2)
+
+	taxonAt := taxon.TaxonAtRank(rank)
+
+	luaState.Push(taxon2Lua(luaState, taxonAt))
+
+	return 1
+}

pkg/obilua/obitaxonomy.go

@@ -0,0 +1,110 @@
+package obilua
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+	lua "github.com/yuin/gopher-lua"
+)
+
+func RegisterObiTaxonomy(luaState *lua.LState) {
+	registerTaxonomyType(luaState)
+	registerTaxonType(luaState)
+}
+
+const luaTaxonomyTypeName = "Taxonomy"
+
+func registerTaxonomyType(luaState *lua.LState) {
+	taxonomyType := luaState.NewTypeMetatable(luaTaxonomyTypeName)
+	luaState.SetGlobal(luaTaxonomyTypeName, taxonomyType)
+	luaState.SetField(taxonomyType, "new", luaState.NewFunction(newTaxonomy))
+	luaState.SetField(taxonomyType, "default", luaState.NewFunction(defaultTaxonomy))
+	luaState.SetField(taxonomyType, "has_default", luaState.NewFunction(hasDefaultTaxonomy))
+	luaState.SetField(taxonomyType, "nil", taxon2Lua(luaState, nil))
+	luaState.SetField(taxonomyType, "__index",
+		luaState.SetFuncs(luaState.NewTable(),
+			taxonomyMethods))
+}
+
+func taxonomy2Lua(interpreter *lua.LState,
+	taxonomy *obitax.Taxonomy) lua.LValue {
+	ud := interpreter.NewUserData()
+	ud.Value = taxonomy
+	interpreter.SetMetatable(ud, interpreter.GetTypeMetatable(luaTaxonomyTypeName))
+
+	return ud
+}
+
+func newTaxonomy(luaState *lua.LState) int {
+	name := luaState.CheckString(1)
+	code := luaState.CheckString(2)
+
+	charset := obiutils.AsciiAlphaNumSet
+	if luaState.GetTop() > 2 {
+		charset = obiutils.AsciiSetFromString(luaState.CheckString(3))
+	}
+
+	taxonomy := obitax.NewTaxonomy(name, code, charset)
+
+	luaState.Push(taxonomy2Lua(luaState, taxonomy))
+	return 1
+}
+
+func defaultTaxonomy(luaState *lua.LState) int {
+	taxonomy := obitax.DefaultTaxonomy()
+
+	if taxonomy == nil {
+		luaState.RaiseError("No default taxonomy")
+		return 0
+	}
+
+	luaState.Push(taxonomy2Lua(luaState, taxonomy))
+	return 1
+}
+
+func hasDefaultTaxonomy(luaState *lua.LState) int {
+	taxonomy := obitax.DefaultTaxonomy()
+
+	luaState.Push(lua.LBool(taxonomy != nil))
+	return 1
+}
+
+var taxonomyMethods = map[string]lua.LGFunction{
+	"name":  taxonomyGetName,
+	"code":  taxonomyGetCode,
+	"taxon": taxonomyGetTaxon,
+}
+
+func checkTaxonomy(L *lua.LState) *obitax.Taxonomy {
+	ud := L.CheckUserData(1)
+	if v, ok := ud.Value.(*obitax.Taxonomy); ok {
+		return v
+	}
+	L.ArgError(1, "obitax.Taxonomy expected")
+	return nil
+}
+
+func taxonomyGetName(luaState *lua.LState) int {
+	taxo := checkTaxonomy(luaState)
+	luaState.Push(lua.LString(taxo.Name()))
+	return 1
+}
+
+func taxonomyGetCode(luaState *lua.LState) int {
+	taxo := checkTaxonomy(luaState)
+	luaState.Push(lua.LString(taxo.Code()))
+	return 1
+}
+
+func taxonomyGetTaxon(luaState *lua.LState) int {
+	taxo := checkTaxonomy(luaState)
+	taxid := luaState.CheckString(2)
+	taxon, err := taxo.Taxon(taxid)
+
+	if err != nil {
+		luaState.RaiseError("%s : Error on taxon taxon: %v", taxid, err)
+		return 0
+	}
+
+	luaState.Push(taxon2Lua(luaState, taxon))
+	return 1
+}

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "d3dac1b"
+var _Commit = "c10df07"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.