Plenty of small bugs

Former-commit-id: 42c7fab7d65906c80ab4cd32da6867ff21842ea8
2025-12-08 16:50:27 +00:00 · 2024-06-04 16:49:12 +02:00
parent e843d2aa5c
commit 65f5109957
15 changed files with 894 additions and 264 deletions
--- a/pkg/obingslibrary/multimatch.go
+++ b/pkg/obingslibrary/multimatch.go
@@ -0,0 +1,186 @@
+package obingslibrary
+
+import (
+	"sort"
+
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+)
+
+type PrimerMatch struct {
+	Begin      int
+	End        int
+	Mismatches int
+	Marker     int
+	Forward    bool
+}
+
+type TagMatcher func(
+	sequence *obiseq.BioSequence,
+	begin, end int, forward bool) (TagPair, error)
+
+// func (library *NGSLibrary) MakeTagMatcherFixedLength() TagMatcher {
+// 	return func(sequence *obiseq.BioSequence, begin, end int, forward bool) (TagPair, error) {
+// 		fb := 0
+// 		fe := 0
+// 		if forward {
+// 			fb = begin - library.Forward_spacer - library.Forward_tag_length
+// 		} else {
+// 			fb = begin - library.Reverse_spacer - library.Reverse_tag_length
+// 		}
+
+// 		if fb < 0 {
+// 			return TagPair{}, fmt.Errorf("begin too small")
+// 		}
+// 		if forward {
+// 			fe = end + library.Reverse_tag_length + library.Reverse_spacer
+// 		} else {
+// 			fe = end + library.Forward_tag_length + library.Forward_spacer
+// 		}
+
+// 		if fe > len(sequence.String()) {
+// 			return TagPair{}, fmt.Errorf("end too large")
+// 		}
+
+// 		ftag := sequence.String()[fb:begin]
+// 		rtag, err := sequence.Subsequence(end, fe, true)
+
+// 		if err != nil {
+// 			return TagPair{}, fmt.Errorf("error in subsequence : %v", err)
+// 		}
+
+// 		return TagPair{Forward: ftag, Reverse: rtag.String()}, nil
+// 	}
+
+// }
+
+func (library *NGSLibrary) ExtractMultiBarcode(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
+	i := 1
+	markers := make([]*Marker, len(library.Markers)+1)
+	primerseqs := make([]PrimerPair, len(library.Markers)+1)
+	matches := make([]PrimerMatch, 0, len(library.Markers)+1)
+	aseq, err := obiapat.MakeApatSequence(sequence, false)
+
+	if err != nil {
+		log.Fatalf("error in building apat sequence : %v\n", err)
+	}
+
+	for primers, marker := range library.Markers {
+		markers[i] = marker
+		primerseqs[i] = primers
+		locs := marker.forward.AllMatches(aseq, 0, -1)
+		if len(locs) > 0 {
+			for _, loc := range locs {
+				matches = append(matches, PrimerMatch{
+					Begin:      loc[0],
+					End:        loc[1],
+					Mismatches: loc[2],
+					Marker:     i,
+					Forward:    true,
+				})
+
+			}
+
+			locs = marker.creverse.AllMatches(aseq, locs[0][0]+1, -1)
+
+			if len(locs) > 0 {
+				for _, loc := range locs {
+					matches = append(matches, PrimerMatch{
+						Begin:      loc[0],
+						End:        loc[1],
+						Mismatches: loc[2],
+						Marker:     -i,
+						Forward:    true,
+					})
+				}
+			}
+		}
+
+		locs = marker.reverse.AllMatches(aseq, 0, -1)
+		if len(locs) > 0 {
+			for _, loc := range locs {
+				matches = append(matches, PrimerMatch{
+					Begin:      loc[0],
+					End:        loc[1],
+					Mismatches: loc[2],
+					Marker:     i,
+					Forward:    false,
+				})
+			}
+
+			locs = marker.cforward.AllMatches(aseq, locs[0][0]+1, -1)
+
+			if len(locs) > 0 {
+				for _, loc := range locs {
+					matches = append(matches, PrimerMatch{
+						Begin:      loc[0],
+						End:        loc[1],
+						Mismatches: loc[2],
+						Marker:     -i,
+						Forward:    false,
+					})
+				}
+			}
+		}
+		i++
+	}
+
+	if len(matches) > 0 {
+		sort.Slice(matches, func(i, j int) bool {
+			return matches[i].Begin < matches[j].Begin
+		})
+
+		state := 0
+		var from PrimerMatch
+		q := 0
+		for _, match := range matches {
+
+			switch state {
+			case 0:
+				if match.Marker > 0 {
+					from = match
+					state = 1
+				}
+
+			case 1:
+				if match.Marker == -from.Marker && match.Forward == from.Forward {
+					q++
+					log.Infof("%d -- %s [%s:%s] %s : %d -> %d mismatches : %d:%d",
+						q,
+						sequence.Id(),
+						primerseqs[from.Marker].Forward,
+						primerseqs[from.Marker].Reverse,
+						map[bool]string{true: "forward", false: "reverse"}[from.Forward],
+						from.End,
+						match.Begin-1,
+						from.Mismatches,
+						match.Mismatches,
+					)
+					state = 0
+				} else if match.Marker > 0 {
+					log.Warnf("Marker mismatch : %d %d", match.Marker, from.Marker)
+					from = match
+				} else {
+					log.Warnf("Marker mismatch : %d %d", match.Marker, from.Marker)
+					state = 0
+				}
+			}
+		}
+	}
+
+	return nil, nil
+}
+
+func (library *NGSLibrary) ExtractMultiBarcodeSliceWorker(options ...WithOption) obiseq.SeqSliceWorker {
+	opt := MakeOptions(options)
+
+	library.Compile(opt.AllowedMismatch(), opt.AllowsIndel())
+
+	worker := func(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
+		return library.ExtractMultiBarcode(sequence)
+	}
+
+	return obiseq.SeqToSliceWorker(worker, true)
+}