Merge obiminion and obiconsensus

Former-commit-id: 49d65d671e9fe4454de60c20507c3d8df6e9c51c

cmd/obitools/obiconsensus/main.go

@@ -16,7 +16,6 @@ func main() {
 	optionParser := obioptions.GenerateOptionParser(obiconsensus.OptionSet)
 
 	_, args := optionParser(os.Args)
-	obiconvert.SetFullFileBatch()
 
 	fs, err := obiconvert.CLIReadBioSequences(args...)
 
@@ -25,8 +24,9 @@ func main() {
 		os.Exit(1)
 	}
 
-	consensus := obiconsensus.Consensus(fs)
+	cleaned := obiconsensus.CLIOBIMinion(fs)
-	obiconvert.CLIWriteBioSequences(consensus, true)
+
+	obiconvert.CLIWriteBioSequences(cleaned, true)
 
 	obiiter.WaitForLastPipe()
 

cmd/obitools/obiminion/main.go

@@ -1,33 +0,0 @@
-package main
-
-import (
-	"os"
-
-	log "github.com/sirupsen/logrus"
-
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiminion"
-
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
-)
-
-func main() {
-	optionParser := obioptions.GenerateOptionParser(obiminion.OptionSet)
-
-	_, args := optionParser(os.Args)
-
-	fs, err := obiconvert.CLIReadBioSequences(args...)
-
-	if err != nil {
-		log.Errorf("Cannot open file (%v)", err)
-		os.Exit(1)
-	}
-
-	cleaned := obiminion.CLIOBIMinion(fs)
-
-	obiconvert.CLIWriteBioSequences(cleaned, true)
-
-	obiiter.WaitForLastPipe()
-
-}

pkg/obikmer/debruijn.go

@@ -6,12 +6,11 @@ import (
 	"fmt"
 	"math"
 	"math/bits"
+	"os"
 	"slices"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
-	"github.com/daichi-m/go18ds/sets/linkedhashset"
-	"github.com/daichi-m/go18ds/stacks/arraystack"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -397,6 +396,10 @@ func (graph *DeBruijnGraph) append(sequence []byte, current uint64, weight int)
 	}
 }
 
+// Push appends a BioSequence to the DeBruijnGraph.
+//
+// Parameters:
+// - sequence: a pointer to a BioSequence containing the sequence to be added.
 func (graph *DeBruijnGraph) Push(sequence *obiseq.BioSequence) {
 	s := sequence.Sequence() // Get the sequence as a byte slice
 	w := sequence.Count()    // Get the weight of the sequence
@@ -493,45 +496,19 @@ func (graph *DeBruijnGraph) Gml() string {
 
 }
 
-// fonction tri_topologique(G, V):
+// WriteGml writes the DeBruijnGraph to a GML file.
-//     T <- une liste vide pour stocker l'ordre topologique
+//
-//     S <- une pile vide pour stocker les nœuds sans prédécesseurs
+// filename: the name of the file to write the GML representation to.
-//     pour chaque nœud v dans V:
+// error: an error if any occurs during the file creation or writing process.
-//         si Pred(v) est vide:
+func (graph *DeBruijnGraph) WriteGml(filename string) error {
-//             empiler S avec v
-//     tant que S n'est pas vide:
-//         nœud <- dépiler S
-//         ajouter nœud à T
-//         pour chaque successeur s de nœud:
-//             supprimer l'arc (nœud, s) de G
-//             si Pred(s) est vide:
-//                 empiler S avec s
-//     si G contient encore des arcs:
-//         renvoyer une erreur (le graphe contient au moins un cycle)
-//     sinon:
-//         renvoyer T (l'ordre topologique)
 
-// A topological sort of the graph.
+	f, err := os.Create(filename)
-func (g *DeBruijnGraph) PartialOrder() *linkedhashset.Set[uint64] {
+	if err != nil {
-	S := arraystack.New[uint64]()
+		return err
-	T := linkedhashset.New[uint64]()
-
-	for v := range g.graph {
-		if len(g.Previouses(v)) == 0 {
-			S.Push(v)
 	}
-	}
+	defer f.Close()
-
+	_, err = f.WriteString(graph.Gml())
-	for !S.Empty() {
+	return err
-		v, _ := S.Pop()
-		T.Add(v)
-		for _, w := range g.Nexts(v) {
-			if T.Contains(g.Previouses(w)...) {
-				S.Push(w)
-			}
-		}
-	}
-	return T
 }
 
 // Calculating the hamming distance between two k-mers.

pkg/obitools/obiconsensus/obiconsensus.go

@@ -5,14 +5,21 @@ import (
 	"os"
 	"path"
 	"slices"
+	"sync"
 
-	log "github.com/sirupsen/logrus"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
-
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obigraph"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obisuffix"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiannotate"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiuniq"
+	"github.com/schollz/progressbar/v3"
+	log "github.com/sirupsen/logrus"
 )
 
 func BuildConsensus(seqs obiseq.BioSequenceSlice,
@@ -111,12 +118,198 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
 	return seq, err
 }
 
-func Consensus(iterator obiiter.IBioSequence) obiiter.IBioSequence {
+// SampleWeight calculates the weight of a sample based on the statistics of a sequence.
+//
+// Parameters:
+// - seqs: a pointer to BioSequenceSlice representing the sequences (*BioSequenceSlice)
+// - sample: the sample for which the weight is calculated (string)
+// - sample_key: the key used to access the sample's statistics (string)
+// Return type: a function that takes an integer index and returns the weight of the sample at that index (func(int) int)
+func SampleWeight(seqs *obiseq.BioSequenceSlice, sample, sample_key string) func(int) float64 {
+
+	f := func(i int) float64 {
+
+		stats := (*seqs)[i].StatsOn(sample_key, "NA")
+
+		if value, ok := stats[sample]; ok {
+			return float64(value)
+		}
+
+		return 0
+	}
+
+	return f
+}
+
+// SeqBySamples sorts the sequences by samples.
+//
+// Parameters:
+// - seqs: a pointer to BioSequenceSlice representing the sequences (*BioSequenceSlice)
+// - sample_key: a string representing the sample key (string)
+//
+// Return type:
+// - map[string]BioSequenceSlice: a map indexed by sample names, each containing a slice of BioSequence objects (map[string]BioSequenceSlice)
+func SeqBySamples(seqs obiseq.BioSequenceSlice, sample_key string) map[string]*obiseq.BioSequenceSlice {
+
+	samples := make(map[string]*obiseq.BioSequenceSlice)
+
+	for _, s := range seqs {
+		if s.HasStatsOn(sample_key) {
+			stats := s.StatsOn(sample_key, "NA")
+			for k := range stats {
+				if seqset, ok := samples[k]; ok {
+					*seqset = append(*seqset, s)
+					samples[k] = seqset
+				} else {
+					samples[k] = &obiseq.BioSequenceSlice{s}
+				}
+			}
+		} else {
+			if k, ok := s.GetStringAttribute(sample_key); ok {
+				if seqset, ok := samples[k]; ok {
+					*seqset = append(*seqset, s)
+					samples[k] = seqset
+				} else {
+					samples[k] = &obiseq.BioSequenceSlice{s}
+				}
+			}
+		}
+	}
+
+	return samples
+
+}
+
+type Mutation struct {
+	Position int
+	SeqA     byte
+	SeqB     byte
+	Ratio    float64
+}
+
+func BuildDiffSeqGraph(name, name_key string,
+	seqs *obiseq.BioSequenceSlice,
+	distmax, nworkers int) *obigraph.Graph[*obiseq.BioSequence, Mutation] {
+	graph := obigraph.NewGraphBuffer[*obiseq.BioSequence, Mutation](name, (*[]*obiseq.BioSequence)(seqs))
+	iseq := make(chan int)
+	defer graph.Close()
+
+	ls := len(*seqs)
+
+	sw := SampleWeight(seqs, name, name_key)
+	graph.Graph.VertexWeight = sw
+
+	waiting := sync.WaitGroup{}
+	waiting.Add(nworkers)
+
+	bar := (*progressbar.ProgressBar)(nil)
+	if obiconvert.CLIProgressBar() {
+
+		pbopt := make([]progressbar.Option, 0, 5)
+		pbopt = append(pbopt,
+			progressbar.OptionSetWriter(os.Stderr),
+			progressbar.OptionSetWidth(15),
+			progressbar.OptionShowIts(),
+			progressbar.OptionSetPredictTime(true),
+			progressbar.OptionSetDescription(fmt.Sprintf("[Build graph] on %s", name)),
+		)
+
+		bar = progressbar.NewOptions(len(*seqs), pbopt...)
+	}
+
+	computeEdges := func() {
+		defer waiting.Done()
+		for i := range iseq {
+			s1 := (*seqs)[i]
+			for j := i + 1; j < ls; j++ {
+				s2 := (*seqs)[j]
+				ratio := sw(i) / sw(j)
+				ok, pos, a1, a2 := obialign.D1Or0(s1, s2)
+				if ok >= 0 {
+					graph.AddEdge(i, j, &Mutation{pos, a1, a2, ratio})
+				} else if distmax > 1 {
+					lcs, lali := obialign.FastLCSScore(s1, s2, distmax, nil)
+					dist := lali - lcs
+					if lcs > 0 && dist <= distmax {
+						// log.Infof("Seq %s and %s: LCSScore: %d, dist: %d\n", s1.Id(), s2.Id(), lcs, dist)
+						graph.AddEdge(i, j, &Mutation{pos, a1, a2, ratio})
+					}
+				}
+			}
+
+			if bar != nil {
+				bar.Add(1)
+			}
+		}
+	}
+
+	for i := 0; i < nworkers; i++ {
+		go computeEdges()
+	}
+
+	for i := 0; i < ls; i++ {
+		iseq <- i
+	}
+	close(iseq)
+
+	waiting.Wait()
+	return graph.Graph
+}
+
+func MinionDenoise(graph *obigraph.Graph[*obiseq.BioSequence, Mutation],
+	sample_key string, kmer_size int) obiseq.BioSequenceSlice {
+	denoised := obiseq.MakeBioSequenceSlice(len(*graph.Vertices))
+
+	for i, v := range *graph.Vertices {
+		var err error
+		var clean *obiseq.BioSequence
+		degree := graph.Degree(i)
+		if degree > 4 {
+			pack := obiseq.MakeBioSequenceSlice(degree + 1)
+			for k, j := range graph.Neighbors(i) {
+				pack[k] = (*graph.Vertices)[j]
+			}
+			pack[degree] = v
+			clean, err = BuildConsensus(pack,
+				fmt.Sprintf("%s_consensus", v.Id()),
+				kmer_size,
+				CLISaveGraphToFiles(), CLIGraphFilesDirectory())
+
+			if err != nil {
+				log.Warning(err)
+				clean = (*graph.Vertices)[i]
+				clean.SetAttribute("obiminion_consensus", false)
+			} else {
+				clean.SetAttribute("obiminion_consensus", true)
+			}
+			pack.Recycle(false)
+		} else {
+			clean = obiseq.NewBioSequence(v.Id(), v.Sequence(), v.Definition())
+			clean.SetAttribute("obiminion_consensus", false)
+		}
+
+		clean.SetCount(int(graph.VertexWeight(i)))
+		clean.SetAttribute(sample_key, graph.Name)
+
+		denoised[i] = clean
+	}
+
+	return denoised
+}
+func CLIOBIMinion(itertator obiiter.IBioSequence) obiiter.IBioSequence {
+	dirname := CLIGraphFilesDirectory()
 	newIter := obiiter.MakeIBioSequence()
-	size := 10
+
+	db := itertator.Load()
+
+	log.Infof("Sequence dataset of %d sequeences loaded\n", len(db))
+
+	samples := SeqBySamples(db, CLISampleAttribute())
+	db.Recycle(false)
+
+	log.Infof("Dataset composed of %d samples\n", len(samples))
 
 	if CLISaveGraphToFiles() {
-		dirname := CLIGraphFilesDirectory()
 		if stat, err := os.Stat(dirname); err != nil || !stat.IsDir() {
 			// path does not exist or is not directory
 			os.RemoveAll(dirname)
@@ -128,52 +321,60 @@ func Consensus(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 		}
 	}
 
+	bar := (*progressbar.ProgressBar)(nil)
+	if obiconvert.CLIProgressBar() {
+
+		pbopt := make([]progressbar.Option, 0, 5)
+		pbopt = append(pbopt,
+			progressbar.OptionSetWriter(os.Stderr),
+			progressbar.OptionSetWidth(15),
+			progressbar.OptionShowIts(),
+			progressbar.OptionSetPredictTime(true),
+			progressbar.OptionSetDescription("[Filter graph on abundance ratio]"),
+		)
+
+		bar = progressbar.NewOptions(len(samples), pbopt...)
+	}
+
 	newIter.Add(1)
 
+	go func() {
+		sample_order := 0
+		for sample, seqs := range samples {
+			graph := BuildDiffSeqGraph(sample,
+				CLISampleAttribute(),
+				seqs,
+				CLIDistStepMax(),
+				obioptions.CLIParallelWorkers())
+			if bar != nil {
+				bar.Add(1)
+			}
+
+			if CLISaveGraphToFiles() {
+				graph.WriteGmlFile(fmt.Sprintf("%s/%s.gml",
+					CLIGraphFilesDirectory(),
+					sample),
+					false, 1, 0, 3)
+			}
+
+			denoised := MinionDenoise(graph,
+				CLISampleAttribute(),
+				CLIKmerSize())
+
+			newIter.Push(obiiter.MakeBioSequenceBatch(sample_order, denoised))
+
+			sample_order++
+		}
+
+		newIter.Done()
+	}()
+
 	go func() {
 		newIter.WaitAndClose()
 	}()
 
-	go func() {
+	obiuniq.AddStatsOn(CLISampleAttribute())
-		order := 0
+	obiuniq.SetUniqueInMemory(false)
-		iterator = iterator.SortBatches()
+	obiuniq.SetNoSingleton(CLINoSingleton())
-		buffer := obiseq.MakeBioSequenceSlice()
+	return obiuniq.CLIUnique(newIter).Pipe(obiiter.WorkerPipe(obiannotate.AddSeqLengthWorker(), false))
-
-		for iterator.Next() {
-			seqs := iterator.Get()
-
-			sequences := seqs.Slice()
-
-			id := sequences[0].Source()
-			if id == "" {
-				id = sequences[0].Id()
-			}
-			consensus, err := BuildConsensus(sequences,
-				id,
-				CLIKmerSize(),
-				CLISaveGraphToFiles(),
-				CLIGraphFilesDirectory(),
-			)
-
-			if err == nil {
-				buffer = append(buffer, consensus)
-			}
-
-			if len(buffer) == size {
-				newIter.Push(obiiter.MakeBioSequenceBatch(order, buffer))
-				order++
-				buffer = obiseq.MakeBioSequenceSlice()
-			}
-			seqs.Recycle(true)
-		}
-
-		if len(buffer) > 0 {
-			newIter.Push(obiiter.MakeBioSequenceBatch(order, buffer))
-		}
-
-		newIter.Done()
-
-	}()
-
-	return newIter
 }

pkg/obitools/obiconsensus/options.go

@@ -5,29 +5,90 @@ import (
 	"github.com/DavidGamba/go-getoptions"
 )
 
-var _saveGraph = "__@@NOSAVE@@__"
+var _distStepMax = 1
+var _sampleAttribute = "sample"
+
+var _ratioMax = 1.0
+
+var _clusterMode = false
+var _onlyHead = false
+
 var _kmerSize = -1
 
-func ObiconsensusOptionSet(options *getoptions.GetOpt) {
+var _NoSingleton = false
+
+var _saveGraph = "__@@NOSAVE@@__"
+var _saveRatio = "__@@NOSAVE@@__"
+
+// ObiminionOptionSet sets the options for obiminion.
+//
+// options: The options for configuring obiminion.
+func ObiminionOptionSet(options *getoptions.GetOpt) {
+	options.StringVar(&_sampleAttribute, "sample", _sampleAttribute,
+		options.Alias("s"),
+		options.Description("Attribute containing sample descriptions (default %s)."))
+
+	options.IntVar(&_distStepMax, "distance", _distStepMax,
+		options.Alias("d"),
+		options.Description("Maximum numbers of differences between two variant sequences (default: %d)."))
 
 	options.StringVar(&_saveGraph, "save-graph", _saveGraph,
-		options.Description("Creates a directory containing the set of De Bruijn graphs used by "+
+		options.Description("Creates a directory containing the set of DAG used by the obiclean clustering algorithm. "+
-			"the obiconsensus algorithm. "+
 			"The graph files follow the graphml format."),
 	)
 
+	options.StringVar(&_saveRatio, "save-ratio", _saveRatio,
+		options.Description("Creates a file containing the set of abundance ratio on the graph edge. "+
+			"The ratio file follows the csv format."),
+	)
 	options.IntVar(&_kmerSize, "kmer-size", _kmerSize,
 		options.ArgName("SIZE"),
 		options.Description("The size of the kmer used to build the consensus. "+
 			"Default value = -1, which means that the kmer size is estimated from the data"),
 	)
 
+	options.BoolVar(&_NoSingleton, "no-singleton", _NoSingleton,
+		options.Description("If set, sequences occurring a single time in the data set are discarded."))
+
 }
 
+// OptionSet sets up the options for the obiminion package.
+//
+// It takes a pointer to a getoptions.GetOpt object as a parameter.
+// It does not return any value.
 func OptionSet(options *getoptions.GetOpt) {
 	obiconvert.InputOptionSet(options)
 	obiconvert.OutputOptionSet(options)
-	ObiconsensusOptionSet(options)
+	ObiminionOptionSet(options)
+}
+
+// CLIDistStepMax returns the maximum distance between two sequences.
+//
+// The value of the distance is set by the user with the `-d` flag.
+//
+// No parameters.
+// Returns an integer.
+func CLIDistStepMax() int {
+	return _distStepMax
+}
+
+// CLISampleAttribute returns the name of the attribute used to store sample name.
+//
+// The value of the sample attribute is set by the user with the `-s` flag.
+//
+// No parameters.
+// Returns a string.
+func CLISampleAttribute() string {
+	return _sampleAttribute
+}
+
+func ClusterMode() bool {
+	return _clusterMode
+}
+
+// `OnlyHead()` returns a boolean value that indicates whether the `-h` flag was passed to the program
+func OnlyHead() bool {
+	return _onlyHead
 }
 
 // Returns true it the obliclean graphs must be saved
@@ -40,6 +101,32 @@ func CLIGraphFilesDirectory() string {
 	return _saveGraph
 }
 
+// Returns true it the table of ratio must be saved
+func IsSaveRatioTable() bool {
+	return _saveRatio != "__@@NOSAVE@@__"
+}
+
+// It returns the filename of the file that stores the ratio table
+func RatioTableFilename() string {
+	return _saveRatio
+}
+
+// CLIKmerSize returns the value of the kmer size to use for building the consensus.
+//
+// The value of the kmer size is set by the user with the `-k` flag.
+// The value -1 means that the kmer size is estimated as the minimum value that
+// insure that no kmer are present more than one time in a sequence.
+//
+// No parameters.
+// Returns an integer value.
 func CLIKmerSize() int {
 	return _kmerSize
 }
+
+// CLINoSingleton returns a boolean value indicating whether or not singleton sequences should be discarded.
+//
+// No parameters.
+// Returns a boolean value indicating whether or not singleton sequences should be discarded.
+func CLINoSingleton() bool {
+	return _NoSingleton
+}

pkg/obitools/obiminion/obiminion.go

@@ -1,280 +0,0 @@
-package obiminion
-
-import (
-	"fmt"
-	"os"
-	"sync"
-
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obigraph"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiannotate"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconsensus"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiuniq"
-	"github.com/schollz/progressbar/v3"
-	log "github.com/sirupsen/logrus"
-)
-
-// SampleWeight calculates the weight of a sample based on the statistics of a sequence.
-//
-// Parameters:
-// - seqs: a pointer to BioSequenceSlice representing the sequences (*BioSequenceSlice)
-// - sample: the sample for which the weight is calculated (string)
-// - sample_key: the key used to access the sample's statistics (string)
-// Return type: a function that takes an integer index and returns the weight of the sample at that index (func(int) int)
-func SampleWeight(seqs *obiseq.BioSequenceSlice, sample, sample_key string) func(int) float64 {
-
-	f := func(i int) float64 {
-
-		stats := (*seqs)[i].StatsOn(sample_key, "NA")
-
-		if value, ok := stats[sample]; ok {
-			return float64(value)
-		}
-
-		return 0
-	}
-
-	return f
-}
-
-// SeqBySamples sorts the sequences by samples.
-//
-// Parameters:
-// - seqs: a pointer to BioSequenceSlice representing the sequences (*BioSequenceSlice)
-// - sample_key: a string representing the sample key (string)
-//
-// Return type:
-// - map[string]BioSequenceSlice: a map indexed by sample names, each containing a slice of BioSequence objects (map[string]BioSequenceSlice)
-func SeqBySamples(seqs obiseq.BioSequenceSlice, sample_key string) map[string]*obiseq.BioSequenceSlice {
-
-	samples := make(map[string]*obiseq.BioSequenceSlice)
-
-	for _, s := range seqs {
-		if s.HasStatsOn(sample_key) {
-			stats := s.StatsOn(sample_key, "NA")
-			for k := range stats {
-				if seqset, ok := samples[k]; ok {
-					*seqset = append(*seqset, s)
-					samples[k] = seqset
-				} else {
-					samples[k] = &obiseq.BioSequenceSlice{s}
-				}
-			}
-		} else {
-			if k, ok := s.GetStringAttribute(sample_key); ok {
-				if seqset, ok := samples[k]; ok {
-					*seqset = append(*seqset, s)
-					samples[k] = seqset
-				} else {
-					samples[k] = &obiseq.BioSequenceSlice{s}
-				}
-			}
-		}
-	}
-
-	return samples
-
-}
-
-type Mutation struct {
-	Position int
-	SeqA     byte
-	SeqB     byte
-	Ratio    float64
-}
-
-func BuildDiffSeqGraph(name, name_key string,
-	seqs *obiseq.BioSequenceSlice,
-	distmax, nworkers int) *obigraph.Graph[*obiseq.BioSequence, Mutation] {
-	graph := obigraph.NewGraphBuffer[*obiseq.BioSequence, Mutation](name, (*[]*obiseq.BioSequence)(seqs))
-	iseq := make(chan int)
-	defer graph.Close()
-
-	ls := len(*seqs)
-
-	sw := SampleWeight(seqs, name, name_key)
-	graph.Graph.VertexWeight = sw
-
-	waiting := sync.WaitGroup{}
-	waiting.Add(nworkers)
-
-	bar := (*progressbar.ProgressBar)(nil)
-	if obiconvert.CLIProgressBar() {
-
-		pbopt := make([]progressbar.Option, 0, 5)
-		pbopt = append(pbopt,
-			progressbar.OptionSetWriter(os.Stderr),
-			progressbar.OptionSetWidth(15),
-			progressbar.OptionShowIts(),
-			progressbar.OptionSetPredictTime(true),
-			progressbar.OptionSetDescription(fmt.Sprintf("[Build graph] on %s", name)),
-		)
-
-		bar = progressbar.NewOptions(len(*seqs), pbopt...)
-	}
-
-	computeEdges := func() {
-		defer waiting.Done()
-		for i := range iseq {
-			s1 := (*seqs)[i]
-			for j := i + 1; j < ls; j++ {
-				s2 := (*seqs)[j]
-				ratio := sw(i) / sw(j)
-				ok, pos, a1, a2 := obialign.D1Or0(s1, s2)
-				if ok >= 0 {
-					graph.AddEdge(i, j, &Mutation{pos, a1, a2, ratio})
-				} else if distmax > 1 {
-					lcs, lali := obialign.FastLCSScore(s1, s2, distmax, nil)
-					dist := lali - lcs
-					if lcs > 0 && dist <= distmax {
-						// log.Infof("Seq %s and %s: LCSScore: %d, dist: %d\n", s1.Id(), s2.Id(), lcs, dist)
-						graph.AddEdge(i, j, &Mutation{pos, a1, a2, ratio})
-					}
-				}
-			}
-
-			if bar != nil {
-				bar.Add(1)
-			}
-		}
-	}
-
-	for i := 0; i < nworkers; i++ {
-		go computeEdges()
-	}
-
-	for i := 0; i < ls; i++ {
-		iseq <- i
-	}
-	close(iseq)
-
-	waiting.Wait()
-	return graph.Graph
-}
-
-func MinionDenoise(graph *obigraph.Graph[*obiseq.BioSequence, Mutation],
-	sample_key string, kmer_size int) obiseq.BioSequenceSlice {
-	denoised := obiseq.MakeBioSequenceSlice(len(*graph.Vertices))
-
-	for i, v := range *graph.Vertices {
-		var err error
-		var clean *obiseq.BioSequence
-		degree := graph.Degree(i)
-		if degree > 4 {
-			pack := obiseq.MakeBioSequenceSlice(degree + 1)
-			for k,j := range graph.Neighbors(i) {
-				pack[k] = (*graph.Vertices)[j]
-			}
-			pack[degree] = v
-			clean, err = obiconsensus.BuildConsensus(pack,
-				fmt.Sprintf("%s_consensus", v.Id()),
-				kmer_size,
-				CLISaveGraphToFiles(), CLIGraphFilesDirectory())
-
-			if err != nil {
-				log.Warning(err)
-				clean = (*graph.Vertices)[i]
-				clean.SetAttribute("obiminion_consensus", false)
-			} else {
-				clean.SetAttribute("obiminion_consensus", true)
-			}
-			pack.Recycle(false)
-		} else {
-			clean = obiseq.NewBioSequence(v.Id(), v.Sequence(), v.Definition())
-			clean.SetAttribute("obiminion_consensus", false)
-		}
-
-		clean.SetCount(int(graph.VertexWeight(i)))
-		clean.SetAttribute(sample_key, graph.Name)
-
-		denoised[i] = clean
-	}
-
-	return denoised
-}
-func CLIOBIMinion(itertator obiiter.IBioSequence) obiiter.IBioSequence {
-	dirname := CLIGraphFilesDirectory()
-	newIter := obiiter.MakeIBioSequence()
-
-	db := itertator.Load()
-
-	log.Infof("Sequence dataset of %d sequeences loaded\n", len(db))
-
-	samples := SeqBySamples(db, CLISampleAttribute())
-	db.Recycle(false)
-
-	log.Infof("Dataset composed of %d samples\n", len(samples))
-
-	if CLISaveGraphToFiles() {
-		if stat, err := os.Stat(dirname); err != nil || !stat.IsDir() {
-			// path does not exist or is not directory
-			os.RemoveAll(dirname)
-			err := os.Mkdir(dirname, 0755)
-
-			if err != nil {
-				log.Panicf("Cannot create directory %s for saving graphs", dirname)
-			}
-		}
-	}
-
-	bar := (*progressbar.ProgressBar)(nil)
-	if obiconvert.CLIProgressBar() {
-
-		pbopt := make([]progressbar.Option, 0, 5)
-		pbopt = append(pbopt,
-			progressbar.OptionSetWriter(os.Stderr),
-			progressbar.OptionSetWidth(15),
-			progressbar.OptionShowIts(),
-			progressbar.OptionSetPredictTime(true),
-			progressbar.OptionSetDescription("[Filter graph on abundance ratio]"),
-		)
-
-		bar = progressbar.NewOptions(len(samples), pbopt...)
-	}
-
-	newIter.Add(1)
-
-	go func() {
-		sample_order := 0
-		for sample, seqs := range samples {
-			graph := BuildDiffSeqGraph(sample,
-				CLISampleAttribute(),
-				seqs,
-				CLIDistStepMax(),
-				obioptions.CLIParallelWorkers())
-			if bar != nil {
-				bar.Add(1)
-			}
-
-			if CLISaveGraphToFiles() {
-				graph.WriteGmlFile(fmt.Sprintf("%s/%s.gml",
-					CLIGraphFilesDirectory(),
-					sample),
-					false, 1, 0, 3)
-			}
-
-			denoised := MinionDenoise(graph,
-				CLISampleAttribute(),
-				CLIKmerSize())
-
-			newIter.Push(obiiter.MakeBioSequenceBatch(sample_order, denoised))
-
-			sample_order++
-		}
-
-		newIter.Done()
-	}()
-
-	go func() {
-		newIter.WaitAndClose()
-	}()
-
-	obiuniq.AddStatsOn(CLISampleAttribute())
-	obiuniq.SetUniqueInMemory(false)
-	obiuniq.SetNoSingleton(CLINoSingleton())
-	return obiuniq.CLIUnique(newIter).Pipe(obiiter.WorkerPipe(obiannotate.AddSeqLengthWorker(), false))
-}

pkg/obitools/obiminion/options.go

@@ -1,132 +0,0 @@
-package obiminion
-
-import (
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
-	"github.com/DavidGamba/go-getoptions"
-)
-
-var _distStepMax = 1
-var _sampleAttribute = "sample"
-
-var _ratioMax = 1.0
-
-var _clusterMode = false
-var _onlyHead = false
-
-var _kmerSize = -1
-
-var _NoSingleton = false
-
-var _saveGraph = "__@@NOSAVE@@__"
-var _saveRatio = "__@@NOSAVE@@__"
-
-// ObiminionOptionSet sets the options for obiminion.
-//
-// options: The options for configuring obiminion.
-func ObiminionOptionSet(options *getoptions.GetOpt) {
-	options.StringVar(&_sampleAttribute, "sample", _sampleAttribute,
-		options.Alias("s"),
-		options.Description("Attribute containing sample descriptions (default %s)."))
-
-	options.IntVar(&_distStepMax, "distance", _distStepMax,
-		options.Alias("d"),
-		options.Description("Maximum numbers of differences between two variant sequences (default: %d)."))
-
-	options.StringVar(&_saveGraph, "save-graph", _saveGraph,
-		options.Description("Creates a directory containing the set of DAG used by the obiclean clustering algorithm. "+
-			"The graph files follow the graphml format."),
-	)
-
-	options.StringVar(&_saveRatio, "save-ratio", _saveRatio,
-		options.Description("Creates a file containing the set of abundance ratio on the graph edge. "+
-			"The ratio file follows the csv format."),
-	)
-	options.IntVar(&_kmerSize, "kmer-size", _kmerSize,
-		options.ArgName("SIZE"),
-		options.Description("The size of the kmer used to build the consensus. "+
-			"Default value = -1, which means that the kmer size is estimated from the data"),
-	)
-
-	options.BoolVar(&_NoSingleton, "no-singleton", _NoSingleton,
-		options.Description("If set, sequences occurring a single time in the data set are discarded."))
-
-}
-
-// OptionSet sets up the options for the obiminion package.
-//
-// It takes a pointer to a getoptions.GetOpt object as a parameter.
-// It does not return any value.
-func OptionSet(options *getoptions.GetOpt) {
-	obiconvert.InputOptionSet(options)
-	obiconvert.OutputOptionSet(options)
-	ObiminionOptionSet(options)
-}
-
-// CLIDistStepMax returns the maximum distance between two sequences.
-//
-// The value of the distance is set by the user with the `-d` flag.
-//
-// No parameters.
-// Returns an integer.
-func CLIDistStepMax() int {
-	return _distStepMax
-}
-
-// CLISampleAttribute returns the name of the attribute used to store sample name.
-//
-// The value of the sample attribute is set by the user with the `-s` flag.
-//
-// No parameters.
-// Returns a string.
-func CLISampleAttribute() string {
-	return _sampleAttribute
-}
-
-func ClusterMode() bool {
-	return _clusterMode
-}
-
-// `OnlyHead()` returns a boolean value that indicates whether the `-h` flag was passed to the program
-func OnlyHead() bool {
-	return _onlyHead
-}
-
-// Returns true it the obliclean graphs must be saved
-func CLISaveGraphToFiles() bool {
-	return _saveGraph != "__@@NOSAVE@@__"
-}
-
-// It returns the directory where the graph files are saved
-func CLIGraphFilesDirectory() string {
-	return _saveGraph
-}
-
-// Returns true it the table of ratio must be saved
-func IsSaveRatioTable() bool {
-	return _saveRatio != "__@@NOSAVE@@__"
-}
-
-// It returns the filename of the file that stores the ratio table
-func RatioTableFilename() string {
-	return _saveRatio
-}
-
-// CLIKmerSize returns the value of the kmer size to use for building the consensus.
-//
-// The value of the kmer size is set by the user with the `-k` flag.
-// The value -1 means that the kmer size is estimated as the minimum value that
-// insure that no kmer are present more than one time in a sequence.
-//
-// No parameters.
-// Returns an integer value.
-func CLIKmerSize() int {
-	return _kmerSize
-}
-
-// CLINoSingleton returns a boolean value indicating whether or not singleton sequences should be discarded.
-//
-// No parameters.
-// Returns a boolean value indicating whether or not singleton sequences should be discarded.
-func CLINoSingleton() bool {
-	return _NoSingleton
-}