Add some options to obiannotate

pkg/obitools/obiannotate/obiannotate.go

@@ -5,6 +5,7 @@ import (
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obicorazick"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obigrep"
@@ -65,6 +66,21 @@ func RenameAttributeWorker(toBeRenamed map[string]string) obiseq.SeqWorker {
 	return f
 }
 
+func EvalAttributeWorker(expression map[string]string) obiseq.SeqWorker {
+	var w obiseq.SeqWorker
+	w = nil
+
+	for a,e := range expression {
+		if w == nil {
+			w = obiseq.EditAttributeWorker(a,e)
+		} else {
+			w.ChainWorkers(obiseq.EditAttributeWorker(a,e))
+		}
+	}
+
+	return w
+}
+
 func AddTaxonAtRankWorker(taxonomy *obitax.Taxonomy, ranks ...string) obiseq.SeqWorker {
 	f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
 		for _, r := range ranks {
@@ -121,6 +137,11 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
 		annotator = annotator.ChainWorkers(w)
 	}
 
+	if CLIHasSetAttributeExpression() {
+		w := EvalAttributeWorker(CLISetAttributeExpression())
+		annotator = annotator.ChainWorkers(w)
+	}
+
 	if CLIHasAhoCorasick() {
 		patterns := CLIAhoCorazick()
 		log.Println("Matching : ", len(patterns), " patterns on sequences")
@@ -138,7 +159,7 @@ func CLIAnnotationPipeline() obiiter.Pipeable {
 	worker := CLIAnnotationWorker()
 
 	annotator := obiseq.SeqToSliceConditionalWorker(worker, predicate, true)
-	f := obiiter.SliceWorkerPipe(annotator)
+	f := obiiter.SliceWorkerPipe(annotator, obioptions.CLIParallelWorkers())
 
 	return f
 }

pkg/obitools/obiannotate/options.go

@@ -16,6 +16,7 @@ var _toBeRenamed = make(map[string]string, 0)
 var _toBeDeleted = make([]string, 0)
 var _keepOnly = make([]string, 0)
 var _taxonAtRank = make([]string, 0)
+var _evalAttribute = make(map[string]string, 0)
 var _tagList = ""
 var _clearAll = false
 var _setSeqLength = false
@@ -41,6 +42,12 @@ func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
 	// 	options.Description("Forces sequence record ids to be unique."),
 	// )
 
+	options.StringMapVar(&_evalAttribute, "set-tag", 1, 1,
+		options.Alias("S"),
+		options.ArgName("KEY=EXPRESSION"),
+		options.Description("Creates a new attribute named with a key <KEY> "+
+			"sets with a value computed from <EXPRESSION>."))
+
 	options.StringMapVar(&_toBeRenamed, "rename-tag", 1, 1,
 		options.Alias("R"),
 		options.ArgName("NEW_NAME=OLD_NAME"),
@@ -140,6 +147,17 @@ func CLIHasClearAllFlag() bool {
 	return _clearAll
 }
 
+func CLIHasSetAttributeExpression() bool {
+	return len(_evalAttribute) > 0
+}
+
+func CLISetAttributeExpression() map[string]string {
+	return _evalAttribute
+}
+
+
+
+
 func CLIHasAhoCorasick() bool {
 	_, err := os.Stat(_ahoCorazick)
 	return err == nil