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https://github.com/metabarcoding/obitools4.git
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46 lines
1.0 KiB
Go
46 lines
1.0 KiB
Go
package obicorazick
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import (
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
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"github.com/rrethy/ahocorasick"
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)
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func AhoCorazickWorker(slot string, patterns []string) obiseq.SeqWorker {
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matcher := ahocorasick.CompileStrings(patterns)
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fslot := slot + "_Fwd"
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rslot := slot + "_Rev"
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f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
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matchesF := len(matcher.FindAllByteSlice(s.Sequence()))
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matchesR := len(matcher.FindAllByteSlice(s.ReverseComplement(false).Sequence()))
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log.Debugln("Macthes = ",matchesF,matchesR)
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matches := matchesF + matchesR
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if matches > 0 {
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s.SetAttribute(slot, matches)
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s.SetAttribute(fslot, matchesF)
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s.SetAttribute(rslot, matchesR)
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}
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return s
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}
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return f
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}
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func AhoCorazickPredicate(minMatches int, patterns []string) obiseq.SequencePredicate {
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matcher := ahocorasick.CompileStrings(patterns)
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f := func(s *obiseq.BioSequence) bool {
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matches := matcher.FindAllByteSlice(s.Sequence())
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return len(matches) >= minMatches
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}
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return f
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}
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