Add a first version of obitag the successor of ecotag

cmd/obitools/obirefidx/main.go

@@ -0,0 +1,22 @@
+package main
+
+import (
+	"os"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obirefidx"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
+)
+
+func main() {
+	optionParser := obioptions.GenerateOptionParser(obirefidx.OptionSet)
+
+	_, args, _ := optionParser(os.Args)
+
+	fs, _ := obiconvert.ReadBioSequencesBatch(args...)
+	indexed := obirefidx.IndexReferenceDB(fs)
+
+	written, _ := obiconvert.WriteBioSequencesBatch(indexed, false)
+	written.Consume()
+}

cmd/obitools/obitag/main.go

@@ -0,0 +1,21 @@
+package main
+
+import (
+	"os"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obitag"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
+)
+
+func main() {
+	optionParser := obioptions.GenerateOptionParser(obitag.OptionSet)
+
+	_, args, _ := optionParser(os.Args)
+
+	fs, _ := obiconvert.ReadBioSequencesBatch(args...)
+	identified := obitag.AssignTaxonomy(fs)
+
+	obiconvert.WriteBioSequencesBatch(identified, true)
+}

pkg/goutils/goutils.go

@@ -4,6 +4,7 @@ import (
 	"bufio"
 	"bytes"
 	"encoding/json"
+	"fmt"
 	"io"
 	"os"
 	"reflect"
@@ -12,6 +13,15 @@ import (
 	"github.com/barkimedes/go-deepcopy"
 )
 
+// InterfaceToInt converts a interface{} to an integer value if possible.
+// If not a "NotAnInteger" error is returned via the err
+// return value and val is set to 0.
+func InterfaceToString(i interface{}) (val string, err error) {
+	err = nil
+	val = fmt.Sprintf("%V", i)
+	return
+}
+
 // NotAnInteger defines a new type of Error : "NotAnInteger"
 type NotAnInteger struct {
 	message string

pkg/goutils/minmax.go

@@ -0,0 +1,29 @@
+package goutils
+
+func MinInt(x, y int) int {
+	if x < y {
+		return x
+	}
+	return y
+}
+
+func MaxInt(x, y int) int {
+	if x < y {
+		return y
+	}
+	return x
+}
+
+func MinUInt16(x, y uint16) uint16 {
+	if x < y {
+		return x
+	}
+	return y
+}
+
+func MaxUInt16(x, y uint16) uint16 {
+	if x < y {
+		return y
+	}
+	return x
+}

pkg/goutils/ranks.go

@@ -0,0 +1,33 @@
+package goutils
+
+import "sort"
+
+// intRanker is a helper type for the rank function.
+type intRanker struct {
+	x []int // Data to be ranked.
+	r []int // A list of indexes into f that reflects rank order after sorting.
+}
+
+// ranker satisfies the sort.Interface without mutating the reference slice, f.
+func (r intRanker) Len() int           { return len(r.x) }
+func (r intRanker) Less(i, j int) bool { return r.x[r.r[i]] < r.x[r.r[j]] }
+func (r intRanker) Swap(i, j int)      { r.r[i], r.r[j] = r.r[j], r.r[i] }
+
+func IntOrder(data []int) []int {
+	if len(data) == 0 {
+		return nil
+	}
+
+	rk := intRanker{
+		x: data,
+		r: make([]int, len(data)),
+	}
+
+	for i := 0; i < len(data); i++ {
+		rk.r[i] = i
+	}
+
+	sort.Sort(rk)
+
+	return rk.r
+}

pkg/obialign/fulllcs.go

@@ -0,0 +1,118 @@
+package obialign
+
+import (
+	"log"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+)
+
+type FullLCSMatrix struct {
+	matrix []int16 // Score matrix
+	lenght []int16 // Alignment length matrix
+	ll     int     // Length of the longest sequence
+	l      int     // Length of the shortest sequence
+}
+
+func NewFullLCSMatrix(matrix *FullLCSMatrix, L, l int) *FullLCSMatrix {
+	if matrix == nil {
+		matrix = &FullLCSMatrix{}
+	}
+
+	if l > L {
+		log.Panicf("L (%d) must be greater or equal to l (%d)", L, l)
+	}
+
+	needed := (L) * (l)
+
+	if needed > matrix.Cap() {
+		matrix.matrix = make([]int16, needed)
+		matrix.lenght = make([]int16, needed)
+	}
+
+	matrix.matrix = matrix.matrix[:needed]
+	matrix.lenght = matrix.lenght[:needed]
+
+	matrix.ll = L
+	matrix.l = l
+
+	return matrix
+}
+
+func (matrix *FullLCSMatrix) Cap() int {
+	return cap(matrix.matrix)
+}
+
+func (matrix *FullLCSMatrix) Length() int {
+	return len(matrix.matrix)
+}
+
+func (matrix *FullLCSMatrix) Get(i, j int) (int16, int16) {
+	if i == 0 {
+		return 0, int16(j)
+	}
+	if j == 0 {
+		return 0, int16(i)
+	}
+
+	pos := (i-1)*matrix.ll + j - 1
+	return matrix.matrix[pos], matrix.lenght[pos]
+}
+
+func (matrix *FullLCSMatrix) Set(i, j int, score, length int16) {
+	if i > 0 && j > 0 {
+		pos := (i-1)*matrix.ll + j - 1
+		matrix.matrix[pos] = score
+		matrix.lenght[pos] = length
+	}
+}
+
+// Computes the LCS between two DNA sequences and the length of the
+// corresponding alignment
+func FullLCSScore(seqA, seqB *obiseq.BioSequence,
+	matrix *FullLCSMatrix) (int, int) {
+
+	if seqA.Length() == 0 {
+		log.Fatal("Sequence A has a length of 0")
+	}
+
+	if seqB.Length() == 0 {
+		log.Fatal("Sequence B has a length of 0")
+	}
+	// swapped := false
+
+	if seqA.Length() < seqB.Length() {
+		seqA, seqB = seqB, seqA
+		// swapped = true
+	}
+
+	la := seqA.Length()
+	lb := seqB.Length()
+	sa := seqA.Sequence()
+	sb := seqB.Sequence()
+
+	matrix = NewFullLCSMatrix(matrix, la, lb)
+
+	for i := 1; i <= matrix.l; i++ {
+		for j := 1; j <= matrix.ll; j++ {
+			sd, ld := matrix.Get(i-1, j-1)
+
+			if sb[i-1] == sa[j-1] {
+				sd++
+			}
+			sup, lup := matrix.Get(i-1, j)
+			sleft, lleft := matrix.Get(i, j-1)
+			switch {
+			case sd >= sup && sd >= sleft:
+				matrix.Set(i, j, sd, ld+1)
+			case sup >= sleft && sup >= sd:
+				matrix.Set(i, j, sup, lup+1)
+			default:
+				matrix.Set(i, j, sleft, lleft+1)
+			}
+		}
+	}
+
+	s, l := matrix.Get(lb, la)
+
+	return int(s), int(l)
+}

pkg/obialign/lcs.go

@@ -96,8 +96,18 @@ func (matrix *LCSMatrix) Set(i, j int, score, length int16) {
 	}
 }
 
+// Computes the LCS between two DNA sequences and the length of the
+// corresponding alignment
 func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
 	matrix *LCSMatrix) (int, int) {
+	
+	if seqA.Length() == 0 {
+		log.Fatal("Sequence A has a length of 0")
+	}
+
+	if seqB.Length() == 0 {
+		log.Fatal("Sequence B has a length of 0")
+	}
 	// swapped := false
 
 	if seqA.Length() < seqB.Length() {
@@ -105,18 +115,39 @@ func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
 		// swapped = true
 	}
 
+
+
 	if (seqA.Length() - seqB.Length()) > maxError {
 		return -1, -1
 	}
 
-	matrix = NewLCSMatrix(matrix, seqA.Length(), seqB.Length(), maxError)
+	la := seqA.Length()
+	lb := seqB.Length()
+	sa := seqA.Sequence()
+	sb := seqB.Sequence()
+
+	matrix = NewLCSMatrix(matrix, la, lb, maxError)
 
 	for i := 1; i <= matrix.l; i++ {
 		ij := max(1, i-matrix.extra)
 		sj := min(i+matrix.delta+matrix.extra, matrix.ll)
 		for j := ij; j <= sj; j++ {
 			sd, ld := matrix.Get(i-1, j-1)
-			if seqB.Sequence()[i-1] == seqA.Sequence()[j-1] {
+			if i > lb {
+				log.Println("Error on seq B ", 1, matrix.l)
+				log.Println(i)
+				log.Println(seqB.Length(), "/", lb)
+				log.Println(string(sa))
+				log.Fatalln(string(sb))
+			}
+			if j > la {
+				log.Println("Error on seq A ", ij, sj)
+				log.Println(j)
+				log.Println(seqA.Length(), "/", la)
+				log.Println(string(sa))
+				log.Fatalln(string(sb))
+			}
+			if sb[i-1] == sa[j-1] {
 				sd++
 			}
 			sup, lup := matrix.Get(i-1, j)
@@ -132,11 +163,13 @@ func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
 		}
 	}
 
-	s, l := matrix.Get(seqB.Length(), seqA.Length())
+	s, l := matrix.Get(lb, la)
 
 	if (l - s) > int16(maxError) {
+		// log.Println(l,s,l-s,maxError)
 		return -1, -1
 	}
 
 	return int(s), int(l)
 }
+

pkg/obiiter/batchiterator.go

@@ -465,6 +465,14 @@ func (iterator IBioSequenceBatch) Recycle() {
 	log.Debugf("End of the recycling of %d Bioseq objects", recycled)
 }
 
+func (iterator IBioSequenceBatch) Consume() {
+	for iterator.Next() {
+		batch := iterator.Get()
+		batch.Recycle()
+	}
+}
+
+
 func (iterator IBioSequenceBatch) Count(recycle bool) (int, int, int) {
 	variants := 0
 	reads := 0

pkg/obiiter/sequence_workers.go

@@ -0,0 +1,17 @@
+package obiiter
+
+// func MakeSetAttributeWorker(rank string) obiiter.SeqWorker {
+
+// 	if !goutils.Contains(taxonomy.RankList(), rank) {
+// 		log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
+// 			rank,
+// 			taxonomy.RankList())
+// 	}
+
+// 	w := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
+// 		taxonomy.SetTaxonAtRank(sequence, rank)
+// 		return sequence
+// 	}
+
+// 	return w
+// }

pkg/obikmer/counting.go

@@ -0,0 +1,76 @@
+package obikmer
+
+import (
+	"math"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+)
+
+type Table4mer [256]uint16
+
+func Count4Mer(seq *obiseq.BioSequence, buffer *[]byte, counts *Table4mer) *Table4mer {
+
+	iternal_buffer := Encode4mer(seq, buffer)
+
+	if counts == nil {
+		var w Table4mer
+		counts = &w
+	}
+
+	// Every cells of the counter is set to zero
+	for i := 0; i < 256; i++ {
+		(*counts)[i] = 0
+	}
+
+	for _, code := range iternal_buffer {
+		(*counts)[code]++
+	}
+	return counts
+}
+
+func Common4Mer(count1, count2 *Table4mer) int {
+	sum := 0
+	for i := 0; i < 256; i++ {
+		sum += int(goutils.MinUInt16((*count1)[i], (*count2)[i]))
+	}
+	return sum
+}
+
+func Sum4Mer(count *Table4mer) int {
+	sum := 0
+	for i := 0; i < 256; i++ {
+		sum += int((*count)[i])
+	}
+	return sum
+}
+
+func LCS4MerBounds(count1, count2 *Table4mer) (int, int) {
+	s1 := Sum4Mer(count1)
+	s2 := Sum4Mer(count2)
+	smin := goutils.MinInt(s1, s2)
+
+	cw := Common4Mer(count1, count2)
+
+	lcsMax := smin + 3 - int(math.Ceil(float64(smin-cw)/4.0))
+	lcsMin := cw
+
+	if cw > 0 {
+		lcsMin += 3
+	}
+
+	return lcsMin, lcsMax
+}
+
+func Error4MerBounds(count1, count2 *Table4mer) (int, int) {
+	s1 := Sum4Mer(count1)
+	s2 := Sum4Mer(count2)
+	smax := goutils.MaxInt(s1, s2)
+
+	cw := Common4Mer(count1, count2)
+
+	errorMax := smax - cw + 2* int(math.Floor(float64(cw+5)/8.0))
+	errorMin := int(math.Ceil(float64(errorMax) / 4.0))
+
+	return errorMin, errorMax
+}

pkg/obikmer/encodefourmer.go

@@ -21,7 +21,7 @@ var __single_base_code__ = []byte{0,
 }
 
 // Encode4mer transforms an obiseq.BioSequence into a sequence
-// of kmer of length 4. Each letter of the sequence noot belonging
+// of kmer of length 4. Each letter of the sequence not belonging
 // A, C, G, T, U are considered as a A. The kmer is encoded as a byte
 // value ranging from 0 to 255. Each nucleotite is represented by
 // two bits. The values 0, 1, 2, 3 correspond respectively to A, C, G,
@@ -65,15 +65,24 @@ func Encode4mer(seq *obiseq.BioSequence, buffer *[]byte) []byte {
 	return *buffer
 }
 
+// Index4mer returns an index where the occurrence position of every fourmer is
+// stored. The index is returned as an array of slices of integer.  The first
+// dimention corresponds to the code of the 4mer, the second
 func Index4mer(seq *obiseq.BioSequence, index *[][]int, buffer *[]byte) [][]int {
 
 	iternal_buffer := Encode4mer(seq, buffer)
 
 	if index == nil || cap(*index) < 256 {
+		// A new index is created
 		i := make([][]int, 256)
-		index = &i
+		if index == nil {
+			index = &i
+		} else {
+			*index = i
+		}
 	}
 
+	// Every cells of the index is emptied
 	for i := 0; i < 256; i++ {
 		(*index)[i] = (*index)[i][:0]
 	}
@@ -85,6 +94,9 @@ func Index4mer(seq *obiseq.BioSequence, index *[][]int, buffer *[]byte) [][]int
 	return *index
 }
 
+// FastShiftFourMer runs a Fast algorithm (similar to the one used in FASTA) to compare two sequences.
+// The returned values are two integer values. The shift between both the sequences and the count of
+// matching 4mer when this shift is applied between both the sequences.
 func FastShiftFourMer(index [][]int, seq *obiseq.BioSequence, buffer *[]byte) (int, int) {
 
 	iternal_buffer := Encode4mer(seq, buffer)
@@ -115,3 +127,4 @@ func FastShiftFourMer(index [][]int, seq *obiseq.BioSequence, buffer *[]byte) (i
 
 	return maxshift, maxcount
 }
+

pkg/obiseq/biosequence.go

@@ -13,6 +13,7 @@ package obiseq
 import (
 	"crypto/md5"
 	"fmt"
+	"strconv"
 	"sync/atomic"
 
 	log "github.com/sirupsen/logrus"
@@ -298,6 +299,49 @@ func (s *BioSequence) Taxid() int {
 	return taxid
 }
 
+func (s *BioSequence) EcotagRefIndex() map[int]string {
+
+	var val map[int]string
+
+	i, ok := s.GetAttribute("ecotag_ref_index")
+
+	if !ok {
+		return nil
+	}
+
+	switch i := i.(type) {
+	case map[int]string:
+		val = i
+	case map[string]interface{}:
+		val = make(map[int]string, len(i))
+		for k, v := range i {
+			score, err := strconv.Atoi(k)
+			if err != nil {
+				log.Panicln(err)
+			}
+
+			val[score], err = goutils.InterfaceToString(v)
+			if err != nil {
+				log.Panicln(err)
+			}
+		}
+	case map[string]string:
+		val = make(map[int]string, len(i))
+		for k, v := range i {
+			score, err := strconv.Atoi(k)
+			if err != nil {
+				log.Panicln(err)
+			}
+			val[score] = v
+
+		}
+	default:
+		log.Panicln("value of attribute ecotag_ref_index cannot be casted to a map[int]string")
+	}
+
+	return val
+}
+
 func (s *BioSequence) SetTaxid(taxid int) {
 	annot := s.Annotations()
 	annot["taxid"] = taxid

pkg/obitax/lca.go

@@ -0,0 +1,25 @@
+package obitax
+
+func (t1 *TaxNode) LCA(t2 *TaxNode) (*TaxNode, error) {
+	p1, err1 := t1.Path()
+
+	if err1 != nil {
+		return nil, err1
+	}
+
+	p2, err2 := t2.Path()
+
+	if err2 != nil {
+		return nil, err2
+	}
+
+	i1 := len(*p1) - 1
+	i2 := len(*p2) - 1
+
+	for i1 >= 0 && i2 >= 0 && (*p1)[i1].taxid == (*p2)[i2].taxid {
+		i1--
+		i2--
+	}
+
+	return (*p1)[i1+1], nil
+}

pkg/obitools/obirefidx/obirefidx.go

@@ -0,0 +1,167 @@
+package obirefidx
+
+import (
+	"fmt"
+	"log"
+	"os"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
+	"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/obifind"
+	"github.com/schollz/progressbar/v3"
+)
+
+func IndexSequence(seqidx int,
+	references obiseq.BioSequenceSlice,
+	refcounts []*obikmer.Table4mer,
+	taxo *obitax.Taxonomy) map[int]string {
+
+	sequence := references[seqidx]
+	matrix := obialign.NewFullLCSMatrix(nil,
+		sequence.Length(),
+		sequence.Length())
+
+	score := make([]int, len(references))
+	for i, ref := range references {
+		// maxe := goutils.MaxInt(sequence.Length(), ref.Length())
+		// mine := 0
+		// if refcounts != nil {
+		// 	mine, maxe = obikmer.Error4MerBounds(refcounts[seqidx], refcounts[i])
+		// }
+
+		
+		lcs, alilength := obialign.FullLCSScore(sequence, ref, matrix)
+
+		// if lcs < 0 {
+		// 	log.Print("Max error wrongly estimated", mine, maxe)
+		// 	log.Println(string(sequence.Sequence()))
+		// 	log.Fatalln(string(ref.Sequence()))
+
+		// 	maxe := goutils.MaxInt(sequence.Length(), ref.Length())
+		// 	lcs, alilength = obialign.LCSScore(sequence, ref, matrix)
+		// }
+		score[i] = alilength - lcs
+	}
+
+	o := goutils.IntOrder(score)
+
+	current_taxid, err := taxo.Taxon(references[o[0]].Taxid())
+	current_score := score[o[0]]
+	current_idx := o[0]
+
+	if err != nil {
+		log.Panicln(err)
+	}
+
+	ecotag_index := make(map[int]string)
+
+	for _, idx := range o {
+		new_taxid, err := taxo.Taxon(references[idx].Taxid())
+		if err != nil {
+			log.Panicln(err)
+		}
+
+		new_taxid, err = current_taxid.LCA(new_taxid)
+		if err != nil {
+			log.Panicln(err)
+		}
+
+		new_score := score[idx]
+
+		if current_taxid.Taxid() != new_taxid.Taxid() {
+
+			if new_score > current_score {
+				ecotag_index[score[current_idx]] = fmt.Sprintf(
+					"%d@%s@%s",
+					current_taxid.Taxid(),
+					current_taxid.ScientificName(),
+					current_taxid.Rank())
+				current_score = new_score
+			}
+
+			current_taxid = new_taxid
+			current_idx = idx
+		}
+	}
+
+	ecotag_index[score[current_idx]] = fmt.Sprintf(
+		"%d@%s@%s",
+		current_taxid.Taxid(),
+		current_taxid.ScientificName(),
+		current_taxid.Rank())
+
+	sequence.SetAttribute("ecotag_ref_index", ecotag_index)
+
+	return ecotag_index
+}
+
+func IndexReferenceDB(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
+
+	references := iterator.Load()
+	refcounts := make(
+		[]*obikmer.Table4mer,
+		len(references))
+
+	buffer := make([]byte, 0, 1000)
+
+	for i, seq := range references {
+		refcounts[i] = obikmer.Count4Mer(seq, &buffer, nil)
+	}
+
+	taxo, error := obifind.CLILoadSelectedTaxonomy()
+	if error != nil {
+		log.Panicln(error)
+	}
+
+	pbopt := make([]progressbar.Option, 0, 5)
+	pbopt = append(pbopt,
+		progressbar.OptionSetWriter(os.Stderr),
+		progressbar.OptionSetWidth(15),
+		progressbar.OptionShowCount(),
+		progressbar.OptionShowIts(),
+		progressbar.OptionSetDescription("[Sequence Processing]"),
+	)
+
+	bar := progressbar.NewOptions(len(references), pbopt...)
+
+	limits := make(chan [2]int)
+	indexed := obiiter.MakeIBioSequenceBatch()
+	go func() {
+		for i := 0; i < len(references); i += 10 {
+			limits <- [2]int{i, goutils.MinInt(i+10, len(references))}
+		}
+		close(limits)
+	}()
+
+	f := func() {
+		for l := range limits {
+			sl := obiseq.MakeBioSequenceSlice()
+			for i := l[0]; i < l[1]; i++ {
+				IndexSequence(i, references, refcounts, taxo)
+				sl = append(sl, references[i])
+			}
+			indexed.Push(obiiter.MakeBioSequenceBatch(l[0]/10, sl))
+			bar.Add(len(sl))
+		}
+
+		indexed.Done()
+	}
+
+	nworkers := obioptions.CLIParallelWorkers()
+	indexed.Add(nworkers)
+
+	go func() {
+		indexed.WaitAndClose()
+	}()
+
+	for w := 0; w < nworkers; w++ {
+		go f()
+	}
+
+	return indexed.Rebatch(1000)
+}

pkg/obitools/obirefidx/options.go

@@ -0,0 +1,14 @@
+package obirefidx
+
+import (
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
+	"github.com/DavidGamba/go-getoptions"
+)
+
+// OptionSet adds to the basic option set every options declared for
+// the obiuniq command
+func OptionSet(options *getoptions.GetOpt) {
+	obiconvert.OptionSet(options)
+	obifind.LoadTaxonomyOptionSet(options, true, false)
+}

pkg/obitools/obitag/obitag.go

@@ -0,0 +1,204 @@
+package obitag
+
+import (
+	"fmt"
+	"log"
+	"strconv"
+	"strings"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
+	"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/obifind"
+)
+
+func IndexSequence(seqidx int,
+	references obiseq.BioSequenceSlice,
+	refcounts []*obikmer.Table4mer,
+	taxo *obitax.Taxonomy) map[int]string {
+
+	sequence := references[seqidx]
+	matrix := obialign.NewLCSMatrix(nil,
+		sequence.Length(),
+		sequence.Length(),
+		sequence.Length())
+
+	score := make([]int, len(references))
+	for i, ref := range references {
+		maxe := goutils.MaxInt(sequence.Length(), ref.Length())
+		mine := 0
+		if refcounts != nil {
+			mine, maxe = obikmer.Error4MerBounds(refcounts[seqidx], refcounts[i])
+		}
+		lcs, alilength := obialign.LCSScore(sequence, ref, (maxe+1)*2, matrix)
+
+		if lcs < 0 {
+			log.Print("Max error wrongly estimated", mine, maxe)
+			log.Println(string(sequence.Sequence()))
+			log.Fatalln(string(ref.Sequence()))
+
+			maxe := goutils.MaxInt(sequence.Length(), ref.Length())
+			lcs, alilength = obialign.LCSScore(sequence, ref, maxe, matrix)
+		}
+		score[i] = alilength - lcs
+	}
+
+	o := goutils.IntOrder(score)
+
+	current_taxid, err := taxo.Taxon(references[o[0]].Taxid())
+	current_score := score[o[0]]
+	current_idx := o[0]
+
+	if err != nil {
+		log.Panicln(err)
+	}
+
+	ecotag_index := make(map[int]string)
+
+	for _, idx := range o {
+		new_taxid, err := taxo.Taxon(references[idx].Taxid())
+		if err != nil {
+			log.Panicln(err)
+		}
+
+		new_taxid, err = current_taxid.LCA(new_taxid)
+		if err != nil {
+			log.Panicln(err)
+		}
+
+		new_score := score[idx]
+
+		if current_taxid.Taxid() != new_taxid.Taxid() {
+
+			if new_score > current_score {
+				ecotag_index[score[current_idx]] = fmt.Sprintf(
+					"%d@%s@%s",
+					current_taxid.Taxid(),
+					current_taxid.ScientificName(),
+					current_taxid.Rank())
+				current_score = new_score
+			}
+
+			current_taxid = new_taxid
+			current_idx = idx
+		}
+	}
+
+	ecotag_index[score[current_idx]] = fmt.Sprintf(
+		"%d@%s@%s",
+		current_taxid.Taxid(),
+		current_taxid.ScientificName(),
+		current_taxid.Rank())
+
+	sequence.SetAttribute("ecotag_ref_index", ecotag_index)
+
+	return ecotag_index
+}
+
+func FindClosest(sequence *obiseq.BioSequence,
+	references obiseq.BioSequenceSlice) (*obiseq.BioSequence, int, float64, int) {
+
+	matrix := obialign.NewLCSMatrix(nil,
+		sequence.Length(),
+		sequence.Length(),
+		sequence.Length())
+
+	maxe := goutils.MaxInt(sequence.Length(), references[0].Length())
+	best := references[0]
+	bestidx := 0
+	bestId := 0.0
+
+	for i, ref := range references {
+		lcs, alilength := obialign.LCSScore(sequence, ref, maxe, matrix)
+		if lcs == -1 {
+			// That aligment is worst than maxe, go to the next sequence
+			continue
+		}
+
+		score := alilength - lcs
+		if score < maxe {
+			best = references[i]
+			bestidx = i
+			maxe = score
+			bestId = float64(lcs) / float64(alilength)
+			// log.Println(best.Id(), maxe, bestId)
+		}
+
+		if maxe == 0 {
+			// We have found identity no need to continue to search
+			break
+		}
+	}
+	return best, maxe, bestId, bestidx
+}
+
+func Identify(sequence *obiseq.BioSequence,
+	references obiseq.BioSequenceSlice,
+	refcounts []*obikmer.Table4mer,
+	taxo *obitax.Taxonomy) *obiseq.BioSequence {
+	best, differences, identity, seqidx := FindClosest(sequence, references)
+
+	idx := best.EcotagRefIndex()
+	if idx == nil {
+		idx = IndexSequence(seqidx, references, refcounts, taxo)
+	}
+
+	d := differences
+	identification, ok := idx[d]
+	for !ok && d >= 0 {
+		identification, ok = idx[d]
+		d--
+	}
+
+	parts := strings.Split(identification, "@")
+	taxid, err := strconv.Atoi(parts[0])
+
+	if err != nil {
+		log.Panicln("Cannot extract taxid from :", identification)
+	}
+
+	sequence.SetTaxid(taxid)
+	sequence.SetAttribute("scientific_name", parts[1])
+	sequence.SetAttribute("ecotag_rank", parts[2])
+	sequence.SetAttribute("ecotag_id", identity)
+	sequence.SetAttribute("ecotag_difference", differences)
+	sequence.SetAttribute("ecotag_match", best.Id())
+
+	return sequence
+}
+
+func IdentifySeqWorker(references obiseq.BioSequenceSlice,
+	refcounts []*obikmer.Table4mer,
+	taxo *obitax.Taxonomy) obiiter.SeqWorker {
+	return func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
+		return Identify(sequence, references, refcounts, taxo)
+	}
+}
+
+func AssignTaxonomy(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
+
+	references := CLIRefDB()
+	refcounts := make(
+		[]*obikmer.Table4mer,
+		len(references))
+
+	buffer := make([]byte, 0, 1000)
+
+	for i, seq := range references {
+		refcounts[i] = obikmer.Count4Mer(seq, &buffer, nil)
+	}
+
+	taxo, error := obifind.CLILoadSelectedTaxonomy()
+
+	if error != nil {
+		log.Panicln(error)
+	}
+
+	worker := IdentifySeqWorker(references, refcounts, taxo)
+
+	return iterator.Rebatch(10).MakeIWorker(worker, obioptions.CLIParallelWorkers(), 0).Rebatch(1000)
+}

pkg/obitools/obitag/options.go

@@ -0,0 +1,45 @@
+package obitag
+
+import (
+	"log"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
+	"github.com/DavidGamba/go-getoptions"
+)
+
+var _RefDB = ""
+
+func TagOptionSet(options *getoptions.GetOpt) {
+	options.StringVar(&_RefDB, "reference-db",_RefDB,
+		options.Alias("R"),
+		options.Required(),
+		options.ArgName("FILENAME"),
+		options.Description("The name of the file containing the reference DB"))
+
+
+}
+
+// OptionSet adds to the basic option set every options declared for
+// the obiuniq command
+func OptionSet(options *getoptions.GetOpt) {
+	obiconvert.OptionSet(options)
+	obifind.LoadTaxonomyOptionSet(options,true,false)
+	TagOptionSet(options)
+}
+
+func CLIRefDBName() string {
+	return _RefDB
+}
+
+func CLIRefDB() obiseq.BioSequenceSlice {
+	refdb,err := obiformats.ReadSequencesBatchFromFile(_RefDB)
+
+	if err != nil {
+		log.Panicf("Cannot open the reference library file : %s\n",_RefDB)
+	}
+
+	return refdb.Load()
+}