mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
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
Normal file
@ -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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@ -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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|
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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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|
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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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|
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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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|
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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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|
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return nil
|
||||
}
|
||||
|
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// Match finds the best matching demultiplex for a given sequence.
|
||||
//
|
||||
// Parameters:
|
||||
//
|
||||
// marker - a pointer to a Marker struct that contains the forward and reverse primers.
|
||||
// sequence - a pointer to a BioSequence struct that represents the input sequence.
|
||||
//
|
||||
// Returns:
|
||||
//
|
||||
// A pointer to a DemultiplexMatch struct that contains the best matching demultiplex.
|
||||
func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
|
||||
aseq, _ := obiapat.MakeApatSequence(sequence, false)
|
||||
|
||||
start, end, nerr, matched := marker.forward.BestMatch(aseq, marker.taglength, -1)
|
||||
|
||||
if matched {
|
||||
if start < 0 {
|
||||
start = 0
|
||||
}
|
||||
|
||||
if end > sequence.Len() {
|
||||
end = sequence.Len()
|
||||
}
|
||||
|
||||
sseq := sequence.String()
|
||||
direct := sseq[start:end]
|
||||
tagstart := max(start-marker.taglength, 0)
|
||||
ftag := strings.ToLower(sseq[tagstart:start])
|
||||
|
||||
m := DemultiplexMatch{
|
||||
ForwardMatch: direct,
|
||||
ForwardTag: ftag,
|
||||
BarcodeStart: end,
|
||||
ForwardMismatches: nerr,
|
||||
IsDirect: true,
|
||||
Error: nil,
|
||||
}
|
||||
|
||||
start, end, nerr, matched = marker.creverse.BestMatch(aseq, start, -1)
|
||||
|
||||
if matched {
|
||||
|
||||
// extracting primer matches
|
||||
reverse, _ := sequence.Subsequence(start, end, false)
|
||||
defer reverse.Recycle()
|
||||
reverse = reverse.ReverseComplement(true)
|
||||
endtag := min(end+marker.taglength, sequence.Len())
|
||||
rtag, err := sequence.Subsequence(end, endtag, false)
|
||||
defer rtag.Recycle()
|
||||
srtag := ""
|
||||
|
||||
if err != nil {
|
||||
rtag = nil
|
||||
} else {
|
||||
rtag.ReverseComplement(true)
|
||||
srtag = strings.ToLower(rtag.String())
|
||||
}
|
||||
|
||||
m.ReverseMatch = strings.ToLower(reverse.String())
|
||||
m.ReverseMismatches = nerr
|
||||
m.BarcodeEnd = start
|
||||
m.ReverseTag = srtag
|
||||
|
||||
sample, ok := marker.samples[TagPair{ftag, srtag}]
|
||||
|
||||
if ok {
|
||||
m.Pcr = sample
|
||||
}
|
||||
|
||||
return &m
|
||||
|
||||
}
|
||||
|
||||
m.Error = fmt.Errorf("cannot locates reverse priming site")
|
||||
|
||||
return &m
|
||||
}
|
||||
|
||||
//
|
||||
// At this point the forward primer didn't match.
|
||||
// We try now with the reverse primer
|
||||
//
|
||||
|
||||
start, end, nerr, matched = marker.reverse.BestMatch(aseq, marker.taglength, -1)
|
||||
|
||||
if matched {
|
||||
if start < 0 {
|
||||
start = 0
|
||||
}
|
||||
|
||||
if end > sequence.Len() {
|
||||
end = sequence.Len()
|
||||
}
|
||||
|
||||
sseq := sequence.String()
|
||||
|
||||
reverse := strings.ToLower(sseq[start:end])
|
||||
tagstart := max(start-marker.taglength, 0)
|
||||
rtag := strings.ToLower(sseq[tagstart:start])
|
||||
|
||||
m := DemultiplexMatch{
|
||||
ReverseMatch: reverse,
|
||||
ReverseTag: rtag,
|
||||
BarcodeStart: end,
|
||||
ReverseMismatches: nerr,
|
||||
IsDirect: false,
|
||||
Error: nil,
|
||||
}
|
||||
|
||||
start, end, nerr, matched = marker.cforward.BestMatch(aseq, end, -1)
|
||||
|
||||
if matched {
|
||||
|
||||
direct, _ := sequence.Subsequence(start, end, false)
|
||||
defer direct.Recycle()
|
||||
direct = direct.ReverseComplement(true)
|
||||
|
||||
endtag := min(end+marker.taglength, sequence.Len())
|
||||
ftag, err := sequence.Subsequence(end, endtag, false)
|
||||
defer ftag.Recycle()
|
||||
sftag := ""
|
||||
if err != nil {
|
||||
ftag = nil
|
||||
|
||||
} else {
|
||||
ftag = ftag.ReverseComplement(true)
|
||||
sftag = strings.ToLower(ftag.String())
|
||||
}
|
||||
|
||||
m.ForwardMatch = direct.String()
|
||||
m.ForwardTag = sftag
|
||||
m.ForwardMismatches = nerr
|
||||
m.BarcodeEnd = start
|
||||
|
||||
sample, ok := marker.samples[TagPair{sftag, rtag}]
|
||||
|
||||
if ok {
|
||||
m.Pcr = sample
|
||||
}
|
||||
|
||||
return &m
|
||||
}
|
||||
|
||||
m.Error = fmt.Errorf("cannot locates forward priming site")
|
||||
|
||||
return &m
|
||||
}
|
||||
|
||||
return nil
|
||||
}
|
||||
|
||||
// ExtractBarcode extracts the barcode from the given biosequence.
|
||||
//
|
||||
// Parameters:
|
||||
|
||||
186
pkg/obingslibrary/multimatch.go
Normal file
186
pkg/obingslibrary/multimatch.go
Normal file
@ -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)
|
||||
}
|
||||
@ -1,7 +1,8 @@
|
||||
package obingslibrary
|
||||
|
||||
import (
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
|
||||
"fmt"
|
||||
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
|
||||
)
|
||||
|
||||
@ -22,44 +23,112 @@ type PCR struct {
|
||||
Annotations obiseq.Annotation
|
||||
}
|
||||
|
||||
type Marker struct {
|
||||
forward obiapat.ApatPattern
|
||||
cforward obiapat.ApatPattern
|
||||
reverse obiapat.ApatPattern
|
||||
creverse obiapat.ApatPattern
|
||||
taglength int
|
||||
samples map[TagPair]*PCR
|
||||
type NGSLibrary struct {
|
||||
Matching string
|
||||
Primers map[string]PrimerPair
|
||||
Markers map[PrimerPair]*Marker
|
||||
}
|
||||
type NGSLibrary map[PrimerPair]*Marker
|
||||
|
||||
func MakeNGSLibrary() NGSLibrary {
|
||||
return make(NGSLibrary, 10)
|
||||
return NGSLibrary{
|
||||
Primers: make(map[string]PrimerPair, 10),
|
||||
Markers: make(map[PrimerPair]*Marker, 10),
|
||||
}
|
||||
}
|
||||
|
||||
func (library *NGSLibrary) GetMarker(forward, reverse string) (*Marker, bool) {
|
||||
pair := PrimerPair{forward, reverse}
|
||||
marker, ok := (*library)[pair]
|
||||
marker, ok := (library.Markers)[pair]
|
||||
|
||||
if ok {
|
||||
return marker, true
|
||||
}
|
||||
|
||||
m := Marker{samples: make(map[TagPair]*PCR, 1000)}
|
||||
(*library)[pair] = &m
|
||||
m := Marker{
|
||||
Forward_tag_length: 0,
|
||||
Reverse_tag_length: 0,
|
||||
Forward_spacer: 0,
|
||||
Reverse_spacer: 0,
|
||||
Forward_tag_delimiter: 0,
|
||||
Reverse_tag_delimiter: 0,
|
||||
samples: make(map[TagPair]*PCR, 1000),
|
||||
}
|
||||
|
||||
(library.Markers)[pair] = &m
|
||||
|
||||
return &m, false
|
||||
}
|
||||
|
||||
func (marker *Marker) GetPCR(forward, reverse string) (*PCR, bool) {
|
||||
pair := TagPair{forward, reverse}
|
||||
pcr, ok := marker.samples[pair]
|
||||
func (library *NGSLibrary) SetForwardTagSpacer(spacer int) {
|
||||
for _, marker := range library.Markers {
|
||||
marker.SetForwardTagSpacer(spacer)
|
||||
}
|
||||
}
|
||||
|
||||
func (library *NGSLibrary) SetReverseTagSpacer(spacer int) {
|
||||
for _, marker := range library.Markers {
|
||||
marker.SetReverseTagSpacer(spacer)
|
||||
}
|
||||
}
|
||||
|
||||
func (library *NGSLibrary) SetTagSpacer(spacer int) {
|
||||
library.SetForwardTagSpacer(spacer)
|
||||
library.SetReverseTagSpacer(spacer)
|
||||
}
|
||||
|
||||
func (library *NGSLibrary) SetTagSpacerFor(primer string, spacer int) {
|
||||
primers, ok := library.Primers[primer]
|
||||
|
||||
if ok {
|
||||
return pcr, ok
|
||||
marker, ok := library.Markers[primers]
|
||||
|
||||
if ok {
|
||||
if primer == primers.Forward {
|
||||
marker.SetForwardTagSpacer(spacer)
|
||||
} else {
|
||||
marker.SetReverseTagSpacer(spacer)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
ipcr := PCR{}
|
||||
marker.samples[pair] = &ipcr
|
||||
|
||||
return &ipcr, false
|
||||
}
|
||||
|
||||
func (library *NGSLibrary) SetForwardTagDelimiter(delim byte) {
|
||||
for _, marker := range library.Markers {
|
||||
marker.SetForwardTagDelimiter(delim)
|
||||
}
|
||||
}
|
||||
|
||||
func (library *NGSLibrary) SetReverseTagDelimiter(delim byte) {
|
||||
for _, marker := range library.Markers {
|
||||
marker.SetReverseTagDelimiter(delim)
|
||||
}
|
||||
}
|
||||
|
||||
func (library *NGSLibrary) SetTagDelimiter(delim byte) {
|
||||
library.SetForwardTagDelimiter(delim)
|
||||
library.SetReverseTagDelimiter(delim)
|
||||
}
|
||||
|
||||
func (library *NGSLibrary) CheckTagLength() {
|
||||
|
||||
for _, marker := range library.Markers {
|
||||
marker.CheckTagLength()
|
||||
}
|
||||
}
|
||||
|
||||
func (library *NGSLibrary) CheckPrimerUnicity() error {
|
||||
for primers := range library.Markers {
|
||||
if _, ok := library.Primers[primers.Forward]; ok {
|
||||
return fmt.Errorf("forward primer %s is used more than once", primers.Forward)
|
||||
}
|
||||
if _, ok := library.Primers[primers.Reverse]; ok {
|
||||
return fmt.Errorf("reverse primer %s is used more than once", primers.Reverse)
|
||||
}
|
||||
if primers.Forward == primers.Reverse {
|
||||
return fmt.Errorf("forward and reverse primers are the same : %s", primers.Forward)
|
||||
}
|
||||
library.Primers[primers.Forward] = primers
|
||||
library.Primers[primers.Reverse] = primers
|
||||
}
|
||||
return nil
|
||||
}
|
||||
|
||||
@ -139,7 +139,7 @@ func MakeOptions(setters []WithOption) Options {
|
||||
return opt
|
||||
}
|
||||
|
||||
func _ExtractBarcodeSlice(ngslibrary NGSLibrary,
|
||||
func _ExtractBarcodeSlice(ngslibrary *NGSLibrary,
|
||||
sequences obiseq.BioSequenceSlice,
|
||||
options Options) obiseq.BioSequenceSlice {
|
||||
newSlice := make(obiseq.BioSequenceSlice, 0, len(sequences))
|
||||
@ -154,7 +154,7 @@ func _ExtractBarcodeSlice(ngslibrary NGSLibrary,
|
||||
return newSlice
|
||||
}
|
||||
|
||||
func ExtractBarcodeSlice(ngslibrary NGSLibrary,
|
||||
func ExtractBarcodeSlice(ngslibrary *NGSLibrary,
|
||||
sequences obiseq.BioSequenceSlice,
|
||||
options ...WithOption) obiseq.BioSequenceSlice {
|
||||
|
||||
@ -165,7 +165,7 @@ func ExtractBarcodeSlice(ngslibrary NGSLibrary,
|
||||
return _ExtractBarcodeSlice(ngslibrary, sequences, opt)
|
||||
}
|
||||
|
||||
func ExtractBarcodeSliceWorker(ngslibrary NGSLibrary,
|
||||
func ExtractBarcodeSliceWorker(ngslibrary *NGSLibrary,
|
||||
options ...WithOption) obiseq.SeqSliceWorker {
|
||||
|
||||
opt := MakeOptions(options)
|
||||
|
||||
Reference in New Issue
Block a user