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
281
pkg/obingslibrary/marker.go
Normal file
281
pkg/obingslibrary/marker.go
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@@ -0,0 +1,281 @@
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package obingslibrary
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import (
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"fmt"
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"strings"
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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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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
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)
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type Marker struct {
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forward obiapat.ApatPattern
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cforward obiapat.ApatPattern
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reverse obiapat.ApatPattern
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creverse obiapat.ApatPattern
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Forward_tag_length int
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Reverse_tag_length int
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Forward_spacer int
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Reverse_spacer int
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Forward_tag_delimiter byte
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Reverse_tag_delimiter byte
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samples map[TagPair]*PCR
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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.CheckTagLength()
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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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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.Forward_tag_length, -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.Forward_tag_length, 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.Reverse_tag_length, 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.Reverse_tag_length, -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.Reverse_tag_length, 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.Forward_tag_length, 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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func (marker *Marker) GetPCR(forward, reverse string) (*PCR, bool) {
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pair := TagPair{forward, reverse}
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pcr, ok := marker.samples[pair]
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if ok {
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return pcr, ok
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}
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ipcr := PCR{}
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marker.samples[pair] = &ipcr
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return &ipcr, false
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}
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func (marker *Marker) CheckTagLength() error {
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forward_length := make(map[int]int)
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reverse_length := make(map[int]int)
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marker.Forward_tag_length = -1
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marker.Reverse_tag_length = -1
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for tags := range marker.samples {
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forward_length[len(tags.Forward)]++
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reverse_length[len(tags.Reverse)]++
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}
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maxfl, _ := obiutils.MaxMap(forward_length)
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if len(forward_length) > 1 {
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others := make([]int, 0)
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for k := range forward_length {
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if k != maxfl {
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others = append(others, k)
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}
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}
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return fmt.Errorf("forward tag length %d is not the same for all the PCRs : %v\n", maxfl, others)
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}
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maxrl, _ := obiutils.MaxMap(reverse_length)
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if len(reverse_length) > 1 {
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others := make([]int, 0)
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for k := range reverse_length {
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if k != maxrl {
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others = append(others, k)
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}
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}
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return fmt.Errorf("reverse tag length %d is not the same for all the PCRs : %v\n", maxrl, others)
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}
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marker.Forward_tag_length = maxfl
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marker.Reverse_tag_length = maxrl
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return nil
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}
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func (marker *Marker) SetForwardTagSpacer(spacer int) {
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marker.Forward_spacer = spacer
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}
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func (marker *Marker) SetReverseTagSpacer(spacer int) {
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marker.Reverse_spacer = spacer
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}
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func (marker *Marker) SetTagSpacer(spacer int) {
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marker.SetForwardTagSpacer(spacer)
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marker.SetReverseTagSpacer(spacer)
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}
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func (marker *Marker) SetForwardTagDelimiter(delim byte) {
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marker.Forward_tag_delimiter = delim
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}
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func (marker *Marker) SetReverseTagDelimiter(delim byte) {
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marker.Reverse_tag_delimiter = delim
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}
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func (marker *Marker) SetTagDelimiter(delim byte) {
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marker.SetForwardTagDelimiter(delim)
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marker.SetReverseTagDelimiter(delim)
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}
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