mirror of
https://github.com/metabarcoding/obitools4.git
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Plenty of small bugs
Former-commit-id: 42c7fab7d65906c80ab4cd32da6867ff21842ea8
This commit is contained in:
Eric Coissac
@ -7,7 +7,6 @@ import (
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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)
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@ -28,7 +27,7 @@ type DemultiplexMatch struct {
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}
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func (library *NGSLibrary) Compile(maxError int, allowsIndel bool) error {
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for primers, marker := range *library {
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for primers, marker := range library.Markers {
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err := marker.Compile(primers.Forward,
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primers.Reverse,
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maxError, allowsIndel)
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@ -40,7 +39,7 @@ func (library *NGSLibrary) Compile(maxError int, allowsIndel bool) error {
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}
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func (library *NGSLibrary) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
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for primers, marker := range *library {
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for primers, marker := range library.Markers {
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m := marker.Match(sequence)
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if m != nil {
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m.ForwardPrimer = strings.ToLower(primers.Forward)
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@ -57,203 +56,6 @@ func (library *NGSLibrary) ExtractBarcode(sequence *obiseq.BioSequence, inplace
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return match.ExtractBarcode(sequence, inplace)
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}
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func (marker *Marker) Compile(forward, reverse string, maxError int, allowsIndel bool) error {
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var err error
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marker.forward, err = obiapat.MakeApatPattern(forward, maxError, allowsIndel)
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if err != nil {
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return err
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}
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marker.reverse, err = obiapat.MakeApatPattern(reverse, maxError, allowsIndel)
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if err != nil {
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return err
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}
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marker.cforward, err = marker.forward.ReverseComplement()
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if err != nil {
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return err
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}
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marker.creverse, err = marker.reverse.ReverseComplement()
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if err != nil {
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return err
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}
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marker.taglength = 0
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for tags := range marker.samples {
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lf := len(tags.Forward)
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lr := len(tags.Reverse)
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l := lf
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if lf == 0 {
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l = lr
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}
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if lr != 0 && l != lr {
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return fmt.Errorf("forward tag (%s) and reverse tag (%s) do not have the same length",
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tags.Forward, tags.Reverse)
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}
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if marker.taglength != 0 && l != marker.taglength {
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return fmt.Errorf("tag pair (%s,%s) is not compatible with a tag length of %d",
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tags.Forward, tags.Reverse, marker.taglength)
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} else {
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marker.taglength = l
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}
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}
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return nil
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}
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// Match finds the best matching demultiplex for a given sequence.
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//
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// Parameters:
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//
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// marker - a pointer to a Marker struct that contains the forward and reverse primers.
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// sequence - a pointer to a BioSequence struct that represents the input sequence.
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//
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// Returns:
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//
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// A pointer to a DemultiplexMatch struct that contains the best matching demultiplex.
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func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
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aseq, _ := obiapat.MakeApatSequence(sequence, false)
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start, end, nerr, matched := marker.forward.BestMatch(aseq, marker.taglength, -1)
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if matched {
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if start < 0 {
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start = 0
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}
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if end > sequence.Len() {
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end = sequence.Len()
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}
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sseq := sequence.String()
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direct := sseq[start:end]
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tagstart := max(start-marker.taglength, 0)
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ftag := strings.ToLower(sseq[tagstart:start])
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m := DemultiplexMatch{
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ForwardMatch: direct,
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ForwardTag: ftag,
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BarcodeStart: end,
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ForwardMismatches: nerr,
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IsDirect: true,
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Error: nil,
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}
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start, end, nerr, matched = marker.creverse.BestMatch(aseq, start, -1)
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if matched {
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// extracting primer matches
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reverse, _ := sequence.Subsequence(start, end, false)
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defer reverse.Recycle()
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reverse = reverse.ReverseComplement(true)
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endtag := min(end+marker.taglength, sequence.Len())
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rtag, err := sequence.Subsequence(end, endtag, false)
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defer rtag.Recycle()
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srtag := ""
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if err != nil {
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rtag = nil
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} else {
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rtag.ReverseComplement(true)
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srtag = strings.ToLower(rtag.String())
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}
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m.ReverseMatch = strings.ToLower(reverse.String())
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m.ReverseMismatches = nerr
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m.BarcodeEnd = start
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m.ReverseTag = srtag
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sample, ok := marker.samples[TagPair{ftag, srtag}]
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if ok {
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m.Pcr = sample
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}
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return &m
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}
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m.Error = fmt.Errorf("cannot locates reverse priming site")
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return &m
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}
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//
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// At this point the forward primer didn't match.
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// We try now with the reverse primer
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//
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start, end, nerr, matched = marker.reverse.BestMatch(aseq, marker.taglength, -1)
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if matched {
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if start < 0 {
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start = 0
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}
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if end > sequence.Len() {
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end = sequence.Len()
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}
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sseq := sequence.String()
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reverse := strings.ToLower(sseq[start:end])
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tagstart := max(start-marker.taglength, 0)
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rtag := strings.ToLower(sseq[tagstart:start])
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m := DemultiplexMatch{
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ReverseMatch: reverse,
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ReverseTag: rtag,
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BarcodeStart: end,
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ReverseMismatches: nerr,
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IsDirect: false,
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Error: nil,
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}
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start, end, nerr, matched = marker.cforward.BestMatch(aseq, end, -1)
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if matched {
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direct, _ := sequence.Subsequence(start, end, false)
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defer direct.Recycle()
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direct = direct.ReverseComplement(true)
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endtag := min(end+marker.taglength, sequence.Len())
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ftag, err := sequence.Subsequence(end, endtag, false)
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defer ftag.Recycle()
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sftag := ""
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if err != nil {
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ftag = nil
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} else {
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ftag = ftag.ReverseComplement(true)
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sftag = strings.ToLower(ftag.String())
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}
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m.ForwardMatch = direct.String()
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m.ForwardTag = sftag
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m.ForwardMismatches = nerr
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m.BarcodeEnd = start
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sample, ok := marker.samples[TagPair{sftag, rtag}]
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if ok {
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m.Pcr = sample
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}
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return &m
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}
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m.Error = fmt.Errorf("cannot locates forward priming site")
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return &m
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}
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return nil
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}
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// ExtractBarcode extracts the barcode from the given biosequence.
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//
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// Parameters:
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