Cleaning of obiminion

Former-commit-id: 75148afd70e5006cc6855bcddc86506b099761a1

pkg/obikmer/debruijn.go

@@ -9,6 +9,7 @@ import (
 	"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"
@@ -294,7 +295,7 @@ func (g *DeBruijnGraph) LongestPath(max_length int) []uint64 {
 	return path
 }
 
-func (g *DeBruijnGraph) LongestConsensus(id string, max_length int) (*obiseq.BioSequence, error) {
+func (g *DeBruijnGraph) LongestConsensus(id string) (*obiseq.BioSequence, error) {
 	//path := g.LongestPath(max_length)
 	path := g.HaviestPath()
 	s := g.DecodePath(path)
@@ -464,11 +465,12 @@ func (graph *DeBruijnGraph) Gml() string {
 
 	for idx := range graph.graph {
 		srcid := nodeidx[idx]
+		weight := graph.Weight(idx)
 		n := graph.Nexts(idx)
 		for _, dst := range n {
 			dstid := nodeidx[dst]
+			weight := obiutils.Min(graph.Weight(dst), weight)
 			label := decode[dst&3]
-			weight := graph.Weight(dst)
 			buffer.WriteString(
 				fmt.Sprintf(`edge [ source "%d"
 					target "%d" 

pkg/obitools/obiconsensus/obiconsensus.go

@@ -17,9 +17,7 @@ import (
 
 func BuildConsensus(seqs obiseq.BioSequenceSlice,
 	consensus_id string,
-	kmer_size int, quorum float64,
+	kmer_size int,
-	min_depth float64,
-	max_length int,
 	save_graph bool, dirname string) (*obiseq.BioSequence, error) {
 
 	if save_graph {
@@ -37,7 +35,7 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
 			}
 		}
 
-		fasta, err := os.Create(path.Join(dirname, fmt.Sprintf("%s.fasta", consensus_id)))
+		fasta, err := os.Create(path.Join(dirname, fmt.Sprintf("%s_consensus.fasta", consensus_id)))
 
 		if err == nil {
 			defer fasta.Close()
@@ -58,16 +56,7 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
 			longest[i] = slices.Max(sa.CommonSuffix())
 		}
 
-		// o := obiutils.Order(sort.IntSlice(longest))
-		// i := int(float64(len(seqs)) * quorum)
-
-		// if i >= len(o) {
-		// 	i = len(o) - 1
-		// }
-
 		kmer_size = slices.Max(longest) + 1
-
-		// kmer_size = longest[o[i]] + 1
 		log.Printf("estimated kmer size : %d", kmer_size)
 	}
 
@@ -90,7 +79,7 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
 	if save_graph {
 
 		file, err := os.Create(path.Join(dirname,
-			fmt.Sprintf("%s_raw_consensus.gml", consensus_id)))
+			fmt.Sprintf("%s_consensus.gml", consensus_id)))
 
 		if err != nil {
 			fmt.Println(err)
@@ -103,65 +92,7 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
 	log.Printf("Graph size : %d\n", graph.Len())
 	total_kmer := graph.Len()
 
-	// threshold := 0
+	seq, err := graph.LongestConsensus(consensus_id)
-
-	// switch {
-	// case min_depth < 0:
-	// 	spectrum := graph.WeightSpectrum()
-	// 	cum := make(map[int]int)
-
-	// 	spectrum[1] = 0
-	// 	for i := 2; i < len(spectrum); i++ {
-	// 		spectrum[i] += spectrum[i-1]
-	// 		cum[spectrum[i]]++
-	// 	}
-
-	// 	max := 0
-	// 	kmax := 0
-	// 	for k, obs := range cum {
-	// 		if obs > max {
-	// 			max = obs
-	// 			kmax = k
-	// 		}
-	// 	}
-
-	// 	for i, total := range spectrum {
-	// 		if total == kmax {
-	// 			threshold = i
-	// 			break
-	// 		}
-	// 	}
-	// 	threshold /= 2
-
-	// 	if threshold < 1 {
-	// 		threshold = 1
-	// 	}
-
-	// 	log.Info("Estimated kmer_min_occur = ", threshold)
-	// case min_depth >= 1:
-	// 	threshold = int(min_depth)
-	// default:
-	// 	threshold = int(float64(len(seqs)) * min_depth)
-	// }
-
-	// graph.FilterMinWeight(threshold)
-
-	// log.Printf("Graph size : %d\n", graph.Len())
-
-	// if save_graph {
-
-	// 	file, err := os.Create(path.Join(dirname,
-	// 		fmt.Sprintf("%s_consensus.gml", consensus_id)))
-
-	// 	if err != nil {
-	// 		fmt.Println(err)
-	// 	} else {
-	// 		file.WriteString(graph.Gml())
-	// 		file.Close()
-	// 	}
-	// }
-
-	seq, err := graph.LongestConsensus(consensus_id, max_length)
 
 	sumCount := 0
 
@@ -173,7 +104,6 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
 		seq.SetCount(sumCount)
 		seq.SetAttribute("seq_length", seq.Len())
 		seq.SetAttribute("kmer_size", kmer_size)
-		//seq.SetAttribute("kmer_min_occur", threshold)
 		seq.SetAttribute("kmer_max_occur", graph.MaxWeight())
 		seq.SetAttribute("filtered_graph_size", graph.Len())
 		seq.SetAttribute("full_graph_size", total_kmer)
@@ -181,52 +111,6 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
 	return seq, err
 }
 
-// func BuildConsensusWithTimeout(seqs obiseq.BioSequenceSlice,
-// 	kmer_size int, quorum float64,
-// 	min_depth float64,
-// 	save_graph bool, dirname string, timeout time.Duration) (*obiseq.BioSequence, error) {
-
-// 	ctx, cancel := context.WithTimeout(context.Background(), timeout)
-// 	defer cancel()
-
-// 	consensus := func() *obiseq.BioSequence {
-// 		cons, err := BuildConsensus(seqs, kmer_size, quorum, min_depth, save_graph, dirname,)
-// 		if err != nil {
-// 			cons = nil
-// 		}
-
-// 		return cons
-// 	}
-
-// 	computation := func() <-chan *obiseq.BioSequence {
-// 		result := make(chan *obiseq.BioSequence)
-
-// 		go func() {
-// 			select {
-// 			case <-ctx.Done():
-// 				result <- nil
-// 			default:
-// 				result <- consensus()
-
-// 			}
-// 		}()
-
-// 		return result
-// 	}
-
-// 	calcResult := computation()
-
-// 	select {
-// 	case result := <-calcResult:
-// 		if result == nil {
-// 			return nil, fmt.Errorf("cannot compute consensus")
-// 		}
-// 		return result, nil
-// 	case <-ctx.Done():
-// 		return nil, fmt.Errorf("compute consensus timeout, exiting")
-// 	}
-// }
-
 func Consensus(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	newIter := obiiter.MakeIBioSequence()
 	size := 10
@@ -266,9 +150,7 @@ func Consensus(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 			}
 			consensus, err := BuildConsensus(sequences,
 				id,
-				CLIKmerSize(), CLIThreshold(),
+				CLIKmerSize(),
-				CLIKmerDepth(),
-				CLIMaxConsensusLength(),
 				CLISaveGraphToFiles(),
 				CLIGraphFilesDirectory(),
 			)

pkg/obitools/obiconsensus/options.go

@@ -7,9 +7,6 @@ import (
 
 var _saveGraph = "__@@NOSAVE@@__"
 var _kmerSize = -1
-var _threshold = 0.99
-var _mindepth = -1.0
-var _consensus_max_length = -1
 
 func ObiconsensusOptionSet(options *getoptions.GetOpt) {
 
@@ -25,26 +22,6 @@ func ObiconsensusOptionSet(options *getoptions.GetOpt) {
 			"Default value = -1, which means that the kmer size is estimated from the data"),
 	)
 
-	options.Float64Var(&_threshold, "threshold", _threshold,
-		options.ArgName("RATIO"),
-		options.Description("A threshold between O and 1 used to determine the optimal "+
-			"kmer size"),
-	)
-
-	options.Float64Var(&_mindepth, "min-depth", _mindepth,
-		options.ArgName("DEPTH"),
-		options.Description("if DEPTH is between 0 and 1, it corresponds to fraction of the "+
-			"reads in which a kmer must occurs to be conserved in the graph. If DEPTH is greater "+
-			"than 1, indicate the minimum count of occurrence for a kmer to be kept. "+
-			"Default value = -1, which means that the DEPTH is estimated from the data"),
-	)
-
-	options.IntVar(&_consensus_max_length, "consensus-max-length", _consensus_max_length,
-		options.ArgName("LENGTH"),
-		options.Description("Maximum length of the consensus sequence. "+
-			"Default value = -1, which means that no limit is applied"),
-	)	
-
 }
 
 func OptionSet(options *getoptions.GetOpt) {
@@ -66,15 +43,3 @@ func CLIGraphFilesDirectory() string {
 func CLIKmerSize() int {
 	return _kmerSize
 }
-
-func CLIKmerDepth() float64 {
-	return _mindepth
-}
-
-func CLIThreshold() float64 {
-	return _threshold
-}
-
-func CLIMaxConsensusLength() int {
-	return _consensus_max_length
-}

pkg/obitools/obiminion/obiminion.go

@@ -157,7 +157,7 @@ func BuildDiffSeqGraph(name, name_key string,
 }
 
 func MinionDenoise(graph *obigraph.Graph[*obiseq.BioSequence, Mutation],
-	sample_key string, kmer_size int, max_length int, threshold float64, depth float64) obiseq.BioSequenceSlice {
+	sample_key string, kmer_size int) obiseq.BioSequenceSlice {
 	denoised := obiseq.MakeBioSequenceSlice(len(*graph.Vertices))
 
 	for i, v := range *graph.Vertices {
@@ -173,8 +173,6 @@ func MinionDenoise(graph *obigraph.Graph[*obiseq.BioSequence, Mutation],
 			clean, err = obiconsensus.BuildConsensus(pack,
 				fmt.Sprintf("%s_consensus", v.Id()),
 				kmer_size,
-				threshold,
-				depth, max_length,
 				CLISaveGraphToFiles(), CLIGraphFilesDirectory())
 
 			if err != nil {
@@ -209,11 +207,6 @@ func CLIOBIMinion(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 	samples := SeqBySamples(db, CLISampleAttribute())
 	db.Recycle(false)
 
-	log.Infof("Dataset composed of %d samples\n", len(samples))
-	if CLIMaxConsensusLength() > 0 {
-		log.Infof("Maximum consensus length: %d\n", CLIMaxConsensusLength())
-	}
-
 	log.Infof("Dataset composed of %d samples\n", len(samples))
 
 	if CLISaveGraphToFiles() {
@@ -266,10 +259,7 @@ func CLIOBIMinion(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 
 			denoised := MinionDenoise(graph,
 				CLISampleAttribute(),
-				CLIKmerSize(),
+				CLIKmerSize())
-				CLIMaxConsensusLength(),
-				CLIThreshold(),
-				CLIKmerDepth())
 
 			newIter.Push(obiiter.MakeBioSequenceBatch(sample_order, denoised))
 

pkg/obitools/obiminion/options.go

@@ -9,16 +9,11 @@ var _distStepMax = 1
 var _sampleAttribute = "sample"
 
 var _ratioMax = 1.0
-var _minEvalRate = 1000
 
 var _clusterMode = false
 var _onlyHead = false
 
 var _kmerSize = -1
-var _threshold = 1.0
-var _mindepth = -1.0
-
-var _consensus_max_length = 1000
 
 var _NoSingleton = false
 
@@ -37,9 +32,6 @@ func ObiminionOptionSet(options *getoptions.GetOpt) {
 		options.Alias("d"),
 		options.Description("Maximum numbers of differences between two variant sequences (default: %d)."))
 
-	options.IntVar(&_minEvalRate, "min-eval-rate", _minEvalRate,
-		options.Description("Minimum abundance of a sequence to be used to evaluate mutation rate."))
-
 	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."),
@@ -55,30 +47,9 @@ func ObiminionOptionSet(options *getoptions.GetOpt) {
 			"Default value = -1, which means that the kmer size is estimated from the data"),
 	)
 
-	options.Float64Var(&_threshold, "threshold", _threshold,
-		options.ArgName("RATIO"),
-		options.Description("A threshold between O and 1 used to determine the optimal "+
-			"kmer size"),
-	)
-
-	options.Float64Var(&_mindepth, "min-depth", _mindepth,
-		options.ArgName("DEPTH"),
-		options.Description("if DEPTH is between 0 and 1, it corresponds to fraction of the "+
-			"reads in which a kmer must occurs to be conserved in the graph. If DEPTH is greater "+
-			"than 1, indicate the minimum count of occurrence for a kmer to be kept. "+
-			"Default value = -1, which means that the DEPTH is estimated from the data"),
-	)
-
-	options.IntVar(&_consensus_max_length, "consensus-max-length", _consensus_max_length,
-		options.ArgName("LENGTH"),
-		options.Description("Maximum length of the consensus sequence. "+
-			"Default value = -1, which means that no limit is applied"),
-	)
-
 	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.
@@ -111,12 +82,6 @@ func CLISampleAttribute() string {
 	return _sampleAttribute
 }
 
-// > The function `CLIMinCountToEvalMutationRate()` returns the minimum number of reads that must be
-// observed before the mutation rate can be evaluated
-func CLIMinCountToEvalMutationRate() int {
-	return _minEvalRate
-}
-
 func ClusterMode() bool {
 	return _clusterMode
 }
@@ -158,18 +123,6 @@ func CLIKmerSize() int {
 	return _kmerSize
 }
 
-func CLIKmerDepth() float64 {
-	return _mindepth
-}
-
-func CLIThreshold() float64 {
-	return _threshold
-}
-
-func CLIMaxConsensusLength() int {
-	return _consensus_max_length
-}
-
 // CLINoSingleton returns a boolean value indicating whether or not singleton sequences should be discarded.
 //
 // No parameters.