mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
114 lines
2.3 KiB
Go
114 lines
2.3 KiB
Go
package obiformats
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import (
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"bytes"
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"math"
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"strings"
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"unsafe"
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
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"github.com/goccy/go-json"
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)
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func _parse_json_header_(header string, annotations obiseq.Annotation) string {
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start := -1
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stop := -1
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level := 0
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lh := len(header)
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inquote := false
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for i := 0; (i < lh) && (stop < 0); i++ {
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// fmt.Printf("[%d,%d-%d] : %d (%c) (%d,%c)\n", i, start, stop, header[i], header[i], '{', '{')
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if level == 0 && header[i] == '{' && !inquote {
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start = i
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}
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// TODO: escaped double quotes are not considered
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if start > -1 && header[i] == '"' {
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inquote = !inquote
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}
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if header[i] == '{' && !inquote {
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level++
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}
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if header[i] == '}' && !inquote {
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level--
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}
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if start >= 0 && level == 0 {
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stop = i
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}
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}
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if start < 0 || stop < 0 {
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return header
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}
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stop++
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err := json.Unmarshal([]byte(header)[start:stop], &annotations)
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for k, v := range annotations {
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switch vt := v.(type) {
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case float64:
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if vt == math.Floor(vt) {
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annotations[k] = int(vt)
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}
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{
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annotations[k] = vt
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}
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}
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}
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if err != nil {
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log.Fatalf("annotation parsing error on %s : %v\n", header, err)
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}
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return strings.TrimSpace(header[stop:])
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}
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func ParseFastSeqJsonHeader(sequence *obiseq.BioSequence) {
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definition := sequence.Definition()
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sequence.SetDefinition("")
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definition_part := _parse_json_header_(
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definition,
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sequence.Annotations())
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if len(definition_part) > 0 {
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if sequence.HasDefinition() {
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definition_part = sequence.Definition() + " " + definition_part
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}
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sequence.SetDefinition(definition_part)
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}
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}
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func WriteFastSeqJsonHeader(buffer *bytes.Buffer, sequence *obiseq.BioSequence) {
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annotations := sequence.Annotations()
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if len(annotations) > 0 {
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err := obiutils.JsonMarshalByteBuffer(buffer, sequence.Annotations())
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if err != nil {
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log.Fatal(err)
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}
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}
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}
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func FormatFastSeqJsonHeader(sequence *obiseq.BioSequence) string {
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annotations := sequence.Annotations()
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buffer := bytes.Buffer{}
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if len(annotations) > 0 {
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obiutils.JsonMarshalByteBuffer(&buffer, sequence.Annotations())
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return unsafe.String(unsafe.SliceData(buffer.Bytes()), len(buffer.Bytes()))
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}
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return ""
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}
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