several small changes

Former-commit-id: c1cdb95885e44fd6ee7d1c963860d7ab41230c96

pkg/obitools/obiannotate/obiannotate.go

@@ -81,6 +81,7 @@ func EvalAttributeWorker(expression map[string]string) obiseq.SeqWorker {
 	return w
 }
 
+
 func AddTaxonAtRankWorker(taxonomy *obitax.Taxonomy, ranks ...string) obiseq.SeqWorker {
 	f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
 		for _, r := range ranks {
@@ -111,6 +112,11 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
 		annotator = annotator.ChainWorkers(w)
 	}
 
+	if CLIHasSetId() {
+		w := obiseq.EditIdWorker(CLSetIdExpression())
+		annotator = annotator.ChainWorkers(w)
+	}
+
 	if CLIHasAttibuteToDelete() {
 		w := DeleteAttributesWorker(CLIAttibuteToDelete())
 		annotator = annotator.ChainWorkers(w)

pkg/obitools/obiannotate/options.go

@@ -24,6 +24,7 @@ var _uniqueID = false
 var _ahoCorazick = ""
 var _lcaSlot = ""
 var _lcaError = 0.0
+var _setId = ""
 
 func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
 	// options.BoolVar(&_addRank, "seq-rank", _addRank,
@@ -47,6 +48,10 @@ func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
 			"a new slot named <SLOT_NAME> is added with the taxid of the lowest common ancester corresponding "+
 			"to the current annotation."))
 
+	options.StringVar(&_setId, "set-identifier", _setId,
+		options.ArgName("EXPRESSION"),
+		options.Description("An expression used to assigned the new id of the sequence"))
+
 	options.Float64Var(&_lcaError, "lca-error", _lcaError,
 		options.ArgName("#.###"),
 		options.Description("Error rate tolerated on the taxonomical discription during the lowest common "+
@@ -123,6 +128,15 @@ func OptionSet(options *getoptions.GetOpt) {
 // --uniq-id
 // Forces sequence record ids to be unique.
 
+func CLIHasSetId() bool {
+	return _setId != ""
+}
+
+func CLSetIdExpression() string {
+	return _setId 
+}
+
+
 func CLIHasAttributeToBeRenamed() bool {
 	return len(_toBeRenamed) > 0
 }

pkg/obitools/obifind/options.go

@@ -36,13 +36,6 @@ func LoadTaxonomyOptionSet(options *getoptions.GetOpt, required, alternatiive bo
 			options.Alias("a"),
 			options.Description("Enable the search on all alternative names and not only scientific names."))
 	}
-	options.BoolVar(&__rank_list__, "rank-list", false,
-		options.Alias("l"),
-		options.Description("List every taxonomic rank available in the taxonomy."))
-
-	options.IntSliceVar(&__taxonomical_restriction__, "restrict-to-taxon", 1, 1,
-		options.Alias("r"),
-		options.Description("Restrict output to some subclades."))
 }
 
 func FilterTaxonomyOptionSet(options *getoptions.GetOpt) {