obitools/obitools4
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Changes to be committed:

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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
This commit is contained in:
Eric Coissac
2025-02-02 16:52:52 +01:00
parent c10df073a7
commit b9bee5f426
8 changed files with 446 additions and 1 deletions
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100
pkg/obilua/obiseqslice.go
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@@ -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
}