Adds the obimicrosat command

pkg/obitools/obimicrosat/microsat.go

@@ -0,0 +1,104 @@
+package obimicrosat
+
+import (
+	"fmt"
+	"sort"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"github.com/dlclark/regexp2"
+)
+
+func MakeMicrosatWorker(minLength, maxLength, minUnits int) obiseq.SeqWorker {
+
+	min_unit := func(microsat string) int {
+		for i := 1; i < len(microsat); i++ {
+			s1 := microsat[0 : len(microsat)-i]
+			s2 := microsat[i:]
+
+			if s1 == s2 {
+				return i
+			}
+		}
+
+		return 0
+	}
+
+	normalizedUnit := func(unit string) string {
+		all := make([]string, 0, len(unit)*2)
+
+		for i := 0; i < len(unit); i++ {
+			rotate := unit[i:] + unit[:i]
+			revcomp_rotate := obiseq.NewBioSequence("", []byte(rotate), "").ReverseComplement(true).String()
+			all = append(all, rotate, revcomp_rotate)
+		}
+
+		sort.Slice(all, func(i, j int) bool {
+			return all[i] < all[j]
+		})
+
+		return all[0]
+	}
+
+	build_regexp := func(minLength, maxLength, minUnits int) *regexp2.Regexp {
+		return regexp2.MustCompile(
+			fmt.Sprintf("([acgt]{%d,%d})\\1{%d,}",
+				minLength,
+				maxLength,
+				minUnits-1,
+			),
+			regexp2.RE2)
+	}
+
+	regexp := build_regexp(minLength, maxLength, minUnits)
+
+	w := func(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
+
+		match, _ := regexp.FindStringMatch(sequence.String())
+
+		if match == nil {
+			return obiseq.BioSequenceSlice{}, nil
+		}
+
+		unit_length := min_unit(match.String())
+
+		if unit_length < minLength {
+			return obiseq.BioSequenceSlice{}, nil
+		}
+
+		pattern := build_regexp(unit_length, unit_length, minUnits)
+
+		match, _ = pattern.FindStringMatch(sequence.String())
+
+		unit := match.String()[0:unit_length]
+
+		sequence.SetAttribute("microsat_unit_length", unit_length)
+		sequence.SetAttribute("microsat_unit_count", match.Length/unit_length)
+		sequence.SetAttribute("seq_length", sequence.Len())
+		sequence.SetAttribute("microsat", match.String())
+		sequence.SetAttribute("microsat_from", match.Index)
+		sequence.SetAttribute("microsat_to", match.Index+match.Length-1)
+
+		sequence.SetAttribute("microsat_unit", unit)
+		sequence.SetAttribute("microsat_unit_normalized", normalizedUnit(unit))
+
+		sequence.SetAttribute("microsat_left", sequence.String()[0:match.Index])
+		sequence.SetAttribute("microsat_right", sequence.String()[match.Index+match.Length:])
+
+		return obiseq.BioSequenceSlice{sequence}, nil
+	}
+
+	return obiseq.SeqWorker(w)
+}
+
+func CLIAnnotateMicrosat(iterator obiiter.IBioSequence) obiiter.IBioSequence {
+	var newIter obiiter.IBioSequence
+
+	worker := MakeMicrosatWorker(CLIMinUnitLength(), CLIMaxUnitLength(), CLIMinUnitCount())
+
+	newIter = iterator.MakeIWorker(worker, false, obioptions.CLIParallelWorkers())
+
+	return newIter.FilterEmpty()
+
+}

pkg/obitools/obimicrosat/options.go

@@ -0,0 +1,55 @@
+package obimicrosat
+
+import (
+	"fmt"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"github.com/DavidGamba/go-getoptions"
+)
+
+var _MinUnitLength = 1
+var _MaxUnitLength = 6
+var _MinUnitCount = 5
+
+// PCROptionSet defines every options related to a simulated PCR.
+//
+// The function adds to a CLI every options proposed to the user
+// to tune the parametters of the PCR simulation algorithm.
+//
+// # Parameters
+//
+// - option : is a pointer to a getoptions.GetOpt instance normaly
+// produced by the
+func MicroSatelliteOptionSet(options *getoptions.GetOpt) {
+	options.IntVar(&_MinUnitLength, "min-unit-length", _MinUnitLength,
+		options.Alias("m"),
+		options.Description("Minimum length of a microsatellite unit."))
+
+	options.IntVar(&_MaxUnitLength, "max-unit-length", _MaxUnitLength,
+		options.Alias("M"),
+		options.Description("Maximum length of a microsatellite unit."))
+
+	options.IntVar(&_MinUnitCount, "min-unit-count", _MinUnitCount,
+		options.Description("Minumum number of repeated units."))
+}
+
+func OptionSet(options *getoptions.GetOpt) {
+	obiconvert.OptionSet(options)
+	MicroSatelliteOptionSet(options)
+}
+
+func CLIMinUnitLength() int {
+	return _MinUnitLength
+}
+
+func CLIMaxUnitLength() int {
+	return _MaxUnitLength
+}
+
+func CLIMinUnitCount() int {
+	return _MinUnitCount
+}
+
+func CLIMicroSatRegex() string {
+	return fmt.Sprintf("([acgt]{%d,%d})\\1{%d}", _MinUnitLength, _MaxUnitLength, _MinUnitCount-1)
+}

pkg/obitools/obitag2/obitag.go

@@ -132,7 +132,7 @@ func FindClosests(sequence *obiseq.BioSequence,
 		lcs, alilength := -1, -1
 		switch maxe {
 		case 0:
-			if obiutils.UnsafeStringFreomBytes(sequence.Sequence()) == obiutils.UnsafeStringFreomBytes(references[order].Sequence()) {
+			if obiutils.UnsafeStringFromBytes(sequence.Sequence()) == obiutils.UnsafeStringFromBytes(references[order].Sequence()) {
 				score = 0
 				alilength = sequence.Len()
 				lcs = alilength
@@ -279,7 +279,7 @@ func Identify(sequence *obiseq.BioSequence,
 	var bestmatch string
 	var taxon *obitax.TaxNode
 
-	exacttaxon, ok := (*db.ExactTaxid)[obiutils.UnsafeStringFreomBytes(sequence.Sequence())]
+	exacttaxon, ok := (*db.ExactTaxid)[obiutils.UnsafeStringFromBytes(sequence.Sequence())]
 	if ok {
 		taxon = exacttaxon.Taxon
 		bestmatch = exacttaxon.Id
@@ -399,7 +399,7 @@ func CLIAssignTaxonomy(iterator obiiter.IBioSequence,
 
 		ft[len(ft)] = taxa[i]
 
-		seqstr := obiutils.UnsafeStringFreomBytes(seq.Sequence())
+		seqstr := obiutils.UnsafeStringFromBytes(seq.Sequence())
 		em, ok := exactmatch[seqstr]
 
 		if !ok {