Merge branch 'master' into taxonomy

pkg/obilua/lua.go

@@ -4,6 +4,7 @@ import (
 	"bytes"
 	"fmt"
 	"os"
+	"reflect"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
@@ -119,11 +120,17 @@ func LuaWorker(proto *lua.FunctionProto) obiseq.SeqWorker {
 				case *obiseq.BioSequenceSlice:
 					return *val, err
 				default:
-					return nil, fmt.Errorf("worker function doesn't return the correct type %T", val)
+					r := reflect.TypeOf(val)
+					return nil, fmt.Errorf("worker function doesn't return the correct type %s", r)
 				}
 			}
 
-			return nil, fmt.Errorf("worker function doesn't return the correct type")
+			// If worker retuns nothing then it is considered as nil biosequence
+			if _, ok = lreponse.(*lua.LNilType); ok {
+				return nil, nil
+			}
+
+			return nil, fmt.Errorf("worker function doesn't return the correct type %T", lreponse)
 		}
 
 		return f

pkg/obilua/lua_push_interface.go

@@ -46,6 +46,8 @@ func pushInterfaceToLua(L *lua.LState, val interface{}) {
 		pushSliceNumericToLua(L, v)
 	case []bool:
 		pushSliceBoolToLua(L, v)
+	case []interface{}:
+		pushSliceInterfaceToLua(L, v)
 	case nil:
 		L.Push(lua.LNil)
 	case *sync.Mutex:
@@ -78,6 +80,29 @@ func pushMapStringInterfaceToLua(L *lua.LState, m map[string]interface{}) {
 	L.Push(luaTable)
 }
 
+func pushSliceInterfaceToLua(L *lua.LState, s []interface{}) {
+	// Create a new Lua table
+	luaTable := L.NewTable()
+	// Iterate over the Go map and set the key-value pairs in the Lua table
+	for _, value := range s {
+		switch v := value.(type) {
+		case int:
+			luaTable.Append(lua.LNumber(v))
+		case float64:
+			luaTable.Append(lua.LNumber(v))
+		case bool:
+			luaTable.Append(lua.LBool(v))
+		case string:
+			luaTable.Append(lua.LString(v))
+		default:
+			log.Fatalf("Doesn't deal with slice containing value %v of type %T", v, v)
+		}
+	}
+
+	// Push the Lua table onto the stack
+	L.Push(luaTable)
+}
+
 // pushMapStringIntToLua creates a new Lua table and iterates over the Go map to set key-value pairs in the Lua table. It then pushes the Lua table onto the stack.
 //
 // L *lua.LState - the Lua state

pkg/obilua/obiseq.go

@@ -47,18 +47,21 @@ func newObiSeq(luaState *lua.LState) int {
 }
 
 var bioSequenceMethods = map[string]lua.LGFunction{
-	"id":            bioSequenceGetSetId,
-	"sequence":      bioSequenceGetSetSequence,
-	"qualities":     bioSequenceGetSetQualities,
-	"definition":    bioSequenceGetSetDefinition,
-	"count":         bioSequenceGetSetCount,
-	"taxid":         bioSequenceGetSetTaxid,
-	"attribute":     bioSequenceGetSetAttribute,
-	"len":           bioSequenceGetLength,
-	"has_sequence":  bioSequenceHasSequence,
-	"has_qualities": bioSequenceHasQualities,
-	"source":        bioSequenceGetSource,
-	"md5":           bioSequenceGetMD5,
+	"id":                 bioSequenceGetSetId,
+	"sequence":           bioSequenceGetSetSequence,
+	"qualities":          bioSequenceGetSetQualities,
+	"definition":         bioSequenceGetSetDefinition,
+	"count":              bioSequenceGetSetCount,
+	"taxid":              bioSequenceGetSetTaxid,
+	"attribute":          bioSequenceGetSetAttribute,
+	"len":                bioSequenceGetLength,
+	"has_sequence":       bioSequenceHasSequence,
+	"has_qualities":      bioSequenceHasQualities,
+	"source":             bioSequenceGetSource,
+	"md5":                bioSequenceGetMD5,
+	"md5_string":         bioSequenceGetMD5String,
+	"subsequence":        bioSequenceGetSubsequence,
+	"reverse_complement": bioSequenceGetRevcomp,
 }
 
 // checkBioSequence checks if the first argument in the Lua stack is a *obiseq.BioSequence.
@@ -224,3 +227,30 @@ func bioSequenceGetMD5(luaState *lua.LState) int {
 	luaState.Push(rt)
 	return 1
 }
+
+func bioSequenceGetMD5String(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	md5 := s.MD5String()
+	luaState.Push(lua.LString(md5))
+	return 1
+}
+
+func bioSequenceGetSubsequence(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	start := luaState.CheckInt(2)
+	end := luaState.CheckInt(3)
+	subseq, err := s.Subsequence(start, end, false)
+	if err != nil {
+		luaState.RaiseError("%s : Error on subseq: %v", s.Id(), err)
+		return 0
+	}
+	luaState.Push(obiseq2Lua(luaState, subseq))
+	return 1
+}
+
+func bioSequenceGetRevcomp(luaState *lua.LState) int {
+	s := checkBioSequence(luaState)
+	revcomp := s.ReverseComplement(false)
+	luaState.Push(obiseq2Lua(luaState, revcomp))
+	return 1
+}