Add some options to obiannotate

pkg/obieval/language.go

@@ -1,13 +1,16 @@
 package obieval
 
 import (
+	"fmt"
+	"log"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"github.com/PaesslerAG/gval"
 )
 
 func maxIntVector(values []int) float64 {
 	m := values[0]
-	for _,v := range values {
+	for _, v := range values {
 		if v > m {
 			m = v
 		}
@@ -19,7 +22,7 @@ func maxIntVector(values []int) float64 {
 func maxIntMap(values map[string]int) float64 {
 	var m int
 	first := true
-	for _,v := range values {
+	for _, v := range values {
 		if first {
 			first = false
 			m = v
@@ -35,7 +38,7 @@ func maxIntMap(values  map[string]int) float64 {
 
 func minIntVector(values []int) float64 {
 	m := values[0]
-	for _,v := range values {
+	for _, v := range values {
 		if v < m {
 			m = v
 		}
@@ -47,7 +50,7 @@ func minIntVector(values []int) float64 {
 func minIntMap(values map[string]int) float64 {
 	var m int
 	first := true
-	for _,v := range values {
+	for _, v := range values {
 		if first {
 			first = false
 			m = v
@@ -61,10 +64,9 @@ func minIntMap(values  map[string]int) float64 {
 	return float64(m)
 }
 
-
 func maxFloatVector(values []float64) float64 {
 	m := values[0]
-	for _,v := range values {
+	for _, v := range values {
 		if v > m {
 			m = v
 		}
@@ -76,7 +78,7 @@ func maxFloatVector(values []float64) float64 {
 func maxFloatMap(values map[string]float64) float64 {
 	var m float64
 	first := true
-	for _,v := range values {
+	for _, v := range values {
 		if first {
 			first = false
 			m = v
@@ -92,7 +94,7 @@ func maxFloatMap(values  map[string]float64) float64 {
 
 func minFloatVector(values []float64) float64 {
 	m := values[0]
-	for _,v := range values {
+	for _, v := range values {
 		if v < m {
 			m = v
 		}
@@ -104,7 +106,7 @@ func minFloatVector(values []float64) float64 {
 func minFloatMap(values map[string]float64) float64 {
 	var m float64
 	first := true
-	for _,v := range values {
+	for _, v := range values {
 		if first {
 			first = false
 			m = v
@@ -139,6 +141,34 @@ var OBILang = gval.NewLanguage(
 	gval.Function("ismap", func(args ...interface{}) (interface{}, error) {
 		ismap := goutils.IsAMap(args[0])
 		return ismap, nil
+	}),
+	gval.Function("printf", func(args ...interface{}) (interface{}, error) {
+		text := fmt.Sprintf(args[0].(string), args[1:]...)
+		return text, nil
+	}),
+	gval.Function("int", func(args ...interface{}) (interface{}, error) {
+		val, err := goutils.InterfaceToInt(args[0])
+
+		if err != nil {
+			log.Fatalf("%v cannot be converted to an integer value", args[0])
+		}
+		return val, nil
+	}),
+	gval.Function("numeric", func(args ...interface{}) (interface{}, error) {
+		val, err := goutils.InterfaceToFloat64(args[0])
+
+		if err != nil {
+			log.Fatalf("%v cannot be converted to a numeric value", args[0])
+		}
+		return val, nil
+	}),
+	gval.Function("bool", func(args ...interface{}) (interface{}, error) {
+		val, err := goutils.InterfaceToBool(args[0])
+
+		if err != nil {
+			log.Fatalf("%v cannot be converted to a boolan value", args[0])
+		}
+		return val, nil
 	}))
 
 func Expression(expression string) (gval.Evaluable, error) {

pkg/obiiter/speed.go

@@ -1,12 +1,21 @@
 package obiiter
 
 import (
+	"fmt"
 	"os"
 
 	"github.com/schollz/progressbar/v3"
 )
 
 func (iterator IBioSequence) Speed(message ...string) IBioSequence {
+
+	// If the STDERR is redicted and doesn't end up to a terminal
+	// No progress bar is printed.
+	o, _ := os.Stderr.Stat()
+	if (o.Mode() & os.ModeCharDevice) != os.ModeCharDevice {
+		return iterator
+	}
+
 	newIter := MakeIBioSequence()
 
 	newIter.Add(1)
@@ -44,6 +53,7 @@ func (iterator IBioSequence) Speed(message ...string) IBioSequence {
 			bar.Add(l)
 		}
 
+		fmt.Fprintln(os.Stderr)
 		newIter.Done()
 	}()
 

pkg/obiseq/eval.go

@@ -0,0 +1,62 @@
+package obiseq
+
+import (
+	"context"
+	"fmt"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obieval"
+	log "github.com/sirupsen/logrus"
+)
+
+func Expression(expression string) func(*BioSequence) (interface{},error) {
+
+	exp, err := obieval.OBILang.NewEvaluable(expression)
+	if err != nil {
+		log.Fatalf("Error in the expression : %s", expression)
+	}
+
+	f := func(sequence *BioSequence) (interface{},error) {
+		return exp(context.Background(),
+			map[string]interface{}{
+				"annotations":     sequence.Annotations(),
+				"sequence":  sequence,
+			},
+		)
+	}
+
+	return f
+}
+
+func EditIdWorker(expression string) SeqWorker {
+	e := Expression(expression)
+	f := func(sequence *BioSequence) *BioSequence {
+		v,err := e(sequence)
+
+		if err != nil {
+			log.Fatalf("Expression '%s' cannot be evaluated on sequence %s",
+				expression,
+				sequence.Id())
+		}
+		sequence.SetId(fmt.Sprintf("%v",v))
+		return sequence
+	}
+
+	return f
+}
+
+func EditAttributeWorker(key string, expression string) SeqWorker {
+	e := Expression(expression)
+	f := func(sequence *BioSequence) *BioSequence {
+		v,err := e(sequence)
+
+		if err != nil {
+			log.Fatalf("Expression '%s' cannot be evaluated on sequence %s",
+				expression,
+				sequence.Id())
+		}
+		sequence.SetAttribute(key,v)
+		return sequence
+	}
+
+	return f
+}

pkg/obiseq/predicate.go

@@ -225,3 +225,4 @@ func ExpressionPredicat(expression string) SequencePredicate {
 
 	return f
 }
+

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