first trial of obilandmark

Former-commit-id: 00a50bdbf407b03dfdc385a848a536559f5966a5

pkg/obitools/obilandmark/obilandmark.go

@@ -0,0 +1,139 @@
+package obilandmark
+
+import (
+	"math"
+	"os"
+	"sort"
+	"sync"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
+	"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/obistats"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
+	"github.com/schollz/progressbar/v3"
+	log "github.com/sirupsen/logrus"
+)
+
+func MapOnLandmarkSequences(library obiseq.BioSequenceSlice, landmark_idx []int, sizes ...int) obiutils.Matrix[float64] {
+	nworkers := obioptions.CLIParallelWorkers()
+
+	if len(sizes) > 0 {
+		nworkers = sizes[0]
+	}
+
+	library_size := len(library)
+	n_landmark := len(landmark_idx)
+	todo := make(chan int, 0)
+
+	seqworld := obiutils.Make2DArray[float64](library_size, n_landmark)
+
+	pbopt := make([]progressbar.Option, 0, 5)
+	pbopt = append(pbopt,
+		progressbar.OptionSetWriter(os.Stderr),
+		progressbar.OptionSetWidth(15),
+		progressbar.OptionShowCount(),
+		progressbar.OptionShowIts(),
+		progressbar.OptionSetDescription("[Sequence mapping]"),
+	)
+
+	bar := progressbar.NewOptions(library_size, pbopt...)
+
+	waiting := sync.WaitGroup{}
+	waiting.Add(nworkers)
+
+	compute_coordinates := func() {
+		buffer := make([]uint64, 1000)
+		for i := range todo {
+			seq := library[i]
+			coord := seqworld[i]
+			for j := 0; j < n_landmark; j++ {
+				landmark := library[landmark_idx[j]]
+				match, lalign := obialign.FastLCSScore(landmark, seq, -1, &buffer)
+				coord[j] = float64(lalign - match)
+			}
+			bar.Add(1)
+		}
+		waiting.Done()
+	}
+
+	for i := 0; i < nworkers; i++ {
+		go compute_coordinates()
+	}
+
+	for i := 0; i < library_size; i++ {
+		todo <- i
+	}
+
+	close(todo)
+
+	waiting.Wait()
+
+	return seqworld
+}
+
+func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSequence {
+
+	library := iterator.Load()
+
+	library_size := len(library)
+	n_landmark := NCenter()
+
+	landmark_idx := obistats.SampleIntWithoutReplacemant(n_landmark, library_size)
+	log.Infof("Library contains %d sequence", len(library))
+
+	var seqworld obiutils.Matrix[float64]
+
+	for loop := 0; loop < 5; loop++ {
+		sort.IntSlice(landmark_idx).Sort()
+		log.Infof("Selected indices : %v", landmark_idx)
+
+		seqworld = MapOnLandmarkSequences(library, landmark_idx)
+		initialCenters := obiutils.Make2DArray[float64](n_landmark, n_landmark)
+		for i, seq_idx := range landmark_idx {
+			initialCenters[i] = seqworld[seq_idx]
+		}
+
+		// classes, centers := obistats.Kmeans(&seqworld, n_landmark, &initialCenters)
+		_, centers, inertia, converged := obistats.Kmeans(&seqworld, n_landmark, 0.001, &initialCenters)
+
+		dist_centers := 0.0
+		for i := 0; i < n_landmark; i++ {
+			for j := 0; j < n_landmark; j++ {
+				dist_centers += math.Pow((*centers)[i][j]-initialCenters[i][j], 2)
+			}
+		}
+
+		landmark_idx = obistats.KmeansBestRepresentative(&seqworld, centers)
+		log.Infof("Inertia: %f, Dist centers: %f, converged: %t", inertia, dist_centers, converged)
+
+	}
+
+	sort.IntSlice(landmark_idx).Sort()
+
+	log.Infof("Selected indices : %v", landmark_idx)
+	seqworld = MapOnLandmarkSequences(library, landmark_idx)
+
+	seq_landmark := make(map[int]int, n_landmark)
+	for i, val := range landmark_idx {
+		seq_landmark[val] = i
+	}
+
+	initialCenters := obiutils.Make2DArray[float64](n_landmark, n_landmark)
+	for i, seq_idx := range landmark_idx {
+		initialCenters[i] = seqworld[seq_idx]
+	}
+
+	classes := obistats.AssignToClass(&seqworld, &initialCenters)
+	for i, seq := range library {
+		seq.SetAttribute("landmark_coord", seqworld[i])
+		seq.SetAttribute("landmark_class", classes[i])
+		if i, ok := seq_landmark[i]; ok {
+			seq.SetAttribute("landmark_id", i)
+		}
+	}
+
+	return obiiter.IBatchOver(library, obioptions.CLIBatchSize())
+
+}

pkg/obitools/obilandmark/options.go

@@ -0,0 +1,29 @@
+package obilandmark
+
+import (
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"github.com/DavidGamba/go-getoptions"
+)
+
+var _nCenter = 200
+
+// ObilandmarkOptionSet sets the options for Obilandmark.
+//
+// options: a pointer to the getoptions.GetOpt struct.
+// Return type: none.
+func ObilandmarkOptionSet(options *getoptions.GetOpt) {
+
+	options.IntVar(&_nCenter, "center", _nCenter,
+		options.Alias("n"),
+		options.Description("Maximum numbers of differences between two variant sequences (default: %d)."))
+}
+
+func OptionSet(options *getoptions.GetOpt) {
+	obiconvert.InputOptionSet(options)
+	obiconvert.OutputOptionSet(options)
+	ObilandmarkOptionSet(options)
+}
+
+func NCenter() int {
+	return _nCenter
+}