Adds Aho-Corasick matching to obiannotate

pkg/obicorazick/worker.go

@@ -0,0 +1,45 @@
+package obicorazick
+
+import (
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"github.com/rrethy/ahocorasick"
+)
+
+func AhoCorazickWorker(slot string, patterns []string) obiseq.SeqWorker {
+
+	matcher := ahocorasick.CompileStrings(patterns)
+	
+	fslot := slot + "_Fwd"
+	rslot := slot + "_Rev"
+
+	f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
+		matchesF := len(matcher.FindAllByteSlice(s.Sequence()))
+		matchesR := len(matcher.FindAllByteSlice(s.ReverseComplement(false).Sequence()))
+
+		log.Debugln("Macthes = ",matchesF,matchesR)
+		matches := matchesF + matchesR
+		if matches > 0 {
+			s.SetAttribute(slot, matches)
+			s.SetAttribute(fslot, matchesF)
+			s.SetAttribute(rslot, matchesR)
+		}
+
+		return s
+	}
+
+	return f
+}
+
+func AhoCorazickPredicate(minMatches int, patterns []string) obiseq.SequencePredicate {
+
+	matcher := ahocorasick.CompileStrings(patterns)
+
+	f := func(s *obiseq.BioSequence) bool {
+		matches := matcher.FindAllByteSlice(s.Sequence())
+		return len(matches) >= minMatches
+	}
+
+	return f
+}