mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
b9bee5f426
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
349 lines
8.5 KiB
Go
349 lines
8.5 KiB
Go
package obilua
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import (
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
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lua "github.com/yuin/gopher-lua"
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)
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func RegisterObiSeq(luaState *lua.LState) {
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registerBioSequenceType(luaState)
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registerBioSequenceSliceType(luaState)
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}
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const luaBioSequenceTypeName = "BioSequence"
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func registerBioSequenceType(luaState *lua.LState) {
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bioSequenceType := luaState.NewTypeMetatable(luaBioSequenceTypeName)
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luaState.SetGlobal(luaBioSequenceTypeName, bioSequenceType)
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luaState.SetField(bioSequenceType, "new", luaState.NewFunction(newObiSeq))
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luaState.SetField(bioSequenceType, "nil", obiseq2Lua(luaState, nil))
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luaState.SetField(bioSequenceType, "__index",
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luaState.SetFuncs(luaState.NewTable(),
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bioSequenceMethods))
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}
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func obiseq2Lua(interpreter *lua.LState,
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sequence *obiseq.BioSequence) lua.LValue {
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ud := interpreter.NewUserData()
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ud.Value = sequence
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interpreter.SetMetatable(ud, interpreter.GetTypeMetatable(luaBioSequenceTypeName))
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return ud
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}
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func newObiSeq(luaState *lua.LState) int {
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seqid := luaState.CheckString(1)
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seq := []byte(luaState.CheckString(2))
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definition := ""
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if luaState.GetTop() > 2 {
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definition = luaState.CheckString(3)
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}
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sequence := obiseq.NewBioSequence(seqid, seq, definition)
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luaState.Push(obiseq2Lua(luaState, sequence))
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return 1
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}
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var bioSequenceMethods = map[string]lua.LGFunction{
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"id": bioSequenceGetSetId,
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"sequence": bioSequenceGetSetSequence,
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"qualities": bioSequenceGetSetQualities,
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"definition": bioSequenceGetSetDefinition,
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"count": bioSequenceGetSetCount,
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"taxid": bioSequenceGetSetTaxid,
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"taxon": bioSequenceGetSetTaxon,
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"attribute": bioSequenceGetSetAttribute,
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"len": bioSequenceGetLength,
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"has_sequence": bioSequenceHasSequence,
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"has_qualities": bioSequenceHasQualities,
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"source": bioSequenceGetSource,
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"md5": bioSequenceGetMD5,
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"md5_string": bioSequenceGetMD5String,
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"subsequence": bioSequenceGetSubsequence,
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"reverse_complement": bioSequenceGetRevcomp,
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"fasta": bioSequenceGetFasta,
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"fastq": bioSequenceGetFastq,
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"string": bioSequenceAsString,
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}
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// checkBioSequence checks if the first argument in the Lua stack is a *obiseq.BioSequence.
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//
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// This function accepts a pointer to the Lua state and attempts to retrieve a userdata
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// that holds a pointer to a BioSequence. If the conversion is successful, it returns
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// the *BioSequence. If the conversion fails, it raises a Lua argument error.
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// Returns a pointer to obiseq.BioSequence or nil if the argument is not of the expected type.
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func checkBioSequence(L *lua.LState) *obiseq.BioSequence {
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ud := L.CheckUserData(1)
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if v, ok := ud.Value.(*obiseq.BioSequence); ok {
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return v
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}
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L.ArgError(1, "obiseq.BioSequence expected")
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return nil
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}
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// bioSequenceGetSetId gets the ID of a biosequence or sets a new ID if provided.
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//
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// This function expects a *lua.LState pointer as its only parameter.
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// If a second argument is provided, it sets the new ID for the biosequence.
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// It returns 0 if a new ID is set, or 1 after pushing the current ID onto the stack.
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func bioSequenceGetSetId(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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if luaState.GetTop() == 2 {
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s.SetId(luaState.CheckString(2))
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return 0
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}
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luaState.Push(lua.LString(s.Id()))
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return 1
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}
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func bioSequenceGetSetSequence(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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if luaState.GetTop() == 2 {
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s.SetSequence([]byte(luaState.CheckString(2)))
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return 0
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}
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luaState.Push(lua.LString(s.String()))
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return 1
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}
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func bioSequenceGetSetQualities(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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if luaState.GetTop() == 2 {
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ud := luaState.CheckAny(2)
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//
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// Perhaps the code needs some type checking on ud.Value
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// It's a first test
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//
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if v, ok := ud.(*lua.LTable); ok {
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s.SetQualities(Table2ByteSlice(luaState, v))
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return 0
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}
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}
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value := []byte(s.Qualities())
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pushInterfaceToLua(luaState, value)
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return 1
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}
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func bioSequenceGetSetDefinition(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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if luaState.GetTop() == 2 {
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s.SetDefinition(luaState.CheckString(2))
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return 0
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}
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luaState.Push(lua.LString(s.Definition()))
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return 1
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}
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func bioSequenceGetSetCount(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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if luaState.GetTop() == 2 {
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s.SetCount(luaState.CheckInt(2))
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return 0
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}
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luaState.Push(lua.LNumber(s.Count()))
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return 1
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}
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func bioSequenceGetSetTaxid(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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if luaState.GetTop() == 2 {
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s.SetTaxid(luaState.CheckString(2))
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return 0
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}
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luaState.Push(lua.LString(s.Taxid()))
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return 1
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}
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func bioSequenceGetSetAttribute(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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attName := luaState.CheckString(2)
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if luaState.GetTop() == 3 {
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ud := luaState.CheckAny(3)
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//
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// Perhaps the code needs some type checking on ud.Value
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// It's a first test
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//
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if v, ok := ud.(*lua.LTable); ok {
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s.SetAttribute(attName, Table2Interface(luaState, v))
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} else {
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s.SetAttribute(attName, ud)
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}
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return 0
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}
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value, ok := s.GetAttribute(attName)
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if !ok {
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luaState.Push(lua.LNil)
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} else {
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pushInterfaceToLua(luaState, value)
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}
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return 1
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}
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func bioSequenceGetLength(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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luaState.Push(lua.LNumber(s.Len()))
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return 1
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}
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func bioSequenceHasSequence(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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luaState.Push(lua.LBool(s.HasSequence()))
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return 1
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}
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func bioSequenceHasQualities(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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luaState.Push(lua.LBool(s.HasQualities()))
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return 1
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}
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func bioSequenceGetSource(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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if s.HasSource() {
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luaState.Push(lua.LString(s.Source()))
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} else {
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luaState.Push(lua.LNil)
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}
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return 1
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}
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func bioSequenceGetMD5(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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md5 := s.MD5()
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rt := luaState.NewTable()
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for i := 0; i < 16; i++ {
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rt.Append(lua.LNumber(md5[i]))
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}
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luaState.Push(rt)
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return 1
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}
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func bioSequenceGetMD5String(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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md5 := s.MD5String()
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luaState.Push(lua.LString(md5))
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return 1
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}
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func bioSequenceGetSubsequence(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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start := luaState.CheckInt(2)
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end := luaState.CheckInt(3)
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subseq, err := s.Subsequence(start, end, false)
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if err != nil {
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luaState.RaiseError("%s : Error on subseq: %v", s.Id(), err)
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return 0
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}
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luaState.Push(obiseq2Lua(luaState, subseq))
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return 1
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}
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func bioSequenceGetRevcomp(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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revcomp := s.ReverseComplement(false)
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luaState.Push(obiseq2Lua(luaState, revcomp))
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return 1
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}
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func bioSequenceGetSetTaxon(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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if luaState.GetTop() > 1 {
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taxon := checkTaxon(luaState, 2)
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s.SetTaxon(taxon)
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return 0
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}
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taxon := s.Taxon(obitax.DefaultTaxonomy())
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luaState.Push(taxon2Lua(luaState, taxon))
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return 1
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}
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func bioSequenceGetFasta(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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formater := obiformats.FormatFastSeqJsonHeader
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if luaState.GetTop() > 1 {
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format := luaState.CheckString(2)
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switch format {
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case "json":
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formater = obiformats.FormatFastSeqJsonHeader
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case "obi":
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formater = obiformats.FormatFastSeqOBIHeader
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}
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}
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txt := obiformats.FormatFasta(s, formater)
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luaState.Push(lua.LString(txt))
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return 1
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}
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func bioSequenceGetFastq(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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formater := obiformats.FormatFastSeqJsonHeader
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if luaState.GetTop() > 1 {
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format := luaState.CheckString(2)
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switch format {
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case "json":
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formater = obiformats.FormatFastSeqJsonHeader
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case "obi":
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formater = obiformats.FormatFastSeqOBIHeader
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}
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}
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txt := obiformats.FormatFastq(s, formater)
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luaState.Push(lua.LString(txt))
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return 1
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}
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func bioSequenceAsString(luaState *lua.LState) int {
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s := checkBioSequence(luaState)
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formater := obiformats.FormatFastSeqJsonHeader
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format := obiformats.FormatFasta
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if s.HasQualities() {
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format = obiformats.FormatFastq
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}
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if luaState.GetTop() > 1 {
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format := luaState.CheckString(2)
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switch format {
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case "json":
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formater = obiformats.FormatFastSeqJsonHeader
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case "obi":
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formater = obiformats.FormatFastSeqOBIHeader
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}
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}
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txt := format(s, formater)
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luaState.Push(lua.LString(txt))
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return 1
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}
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