mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
135 lines
2.9 KiB
Go
135 lines
2.9 KiB
Go
package obingslibrary
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import (
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"fmt"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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)
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type PrimerPair struct {
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Forward string
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Reverse string
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}
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type TagPair struct {
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Forward string
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Reverse string
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}
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type PCR struct {
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Experiment string
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Sample string
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Partial bool
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Annotations obiseq.Annotation
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}
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type NGSLibrary struct {
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Matching string
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Primers map[string]PrimerPair
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Markers map[PrimerPair]*Marker
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}
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func MakeNGSLibrary() NGSLibrary {
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return NGSLibrary{
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Primers: make(map[string]PrimerPair, 10),
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Markers: make(map[PrimerPair]*Marker, 10),
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}
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}
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func (library *NGSLibrary) GetMarker(forward, reverse string) (*Marker, bool) {
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pair := PrimerPair{forward, reverse}
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marker, ok := (library.Markers)[pair]
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if ok {
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return marker, true
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}
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m := Marker{
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Forward_tag_length: 0,
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Reverse_tag_length: 0,
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Forward_spacer: 0,
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Reverse_spacer: 0,
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Forward_tag_delimiter: 0,
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Reverse_tag_delimiter: 0,
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samples: make(map[TagPair]*PCR, 1000),
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}
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(library.Markers)[pair] = &m
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return &m, false
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}
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func (library *NGSLibrary) SetForwardTagSpacer(spacer int) {
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for _, marker := range library.Markers {
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marker.SetForwardTagSpacer(spacer)
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}
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}
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func (library *NGSLibrary) SetReverseTagSpacer(spacer int) {
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for _, marker := range library.Markers {
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marker.SetReverseTagSpacer(spacer)
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}
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}
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func (library *NGSLibrary) SetTagSpacer(spacer int) {
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library.SetForwardTagSpacer(spacer)
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library.SetReverseTagSpacer(spacer)
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}
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func (library *NGSLibrary) SetTagSpacerFor(primer string, spacer int) {
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primers, ok := library.Primers[primer]
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if ok {
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marker, ok := library.Markers[primers]
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if ok {
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if primer == primers.Forward {
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marker.SetForwardTagSpacer(spacer)
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} else {
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marker.SetReverseTagSpacer(spacer)
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}
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}
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}
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}
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func (library *NGSLibrary) SetForwardTagDelimiter(delim byte) {
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for _, marker := range library.Markers {
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marker.SetForwardTagDelimiter(delim)
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}
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}
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func (library *NGSLibrary) SetReverseTagDelimiter(delim byte) {
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for _, marker := range library.Markers {
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marker.SetReverseTagDelimiter(delim)
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}
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}
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func (library *NGSLibrary) SetTagDelimiter(delim byte) {
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library.SetForwardTagDelimiter(delim)
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library.SetReverseTagDelimiter(delim)
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}
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func (library *NGSLibrary) CheckTagLength() {
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for _, marker := range library.Markers {
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marker.CheckTagLength()
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}
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}
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func (library *NGSLibrary) CheckPrimerUnicity() error {
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for primers := range library.Markers {
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if _, ok := library.Primers[primers.Forward]; ok {
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return fmt.Errorf("forward primer %s is used more than once", primers.Forward)
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}
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if _, ok := library.Primers[primers.Reverse]; ok {
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return fmt.Errorf("reverse primer %s is used more than once", primers.Reverse)
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}
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if primers.Forward == primers.Reverse {
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return fmt.Errorf("forward and reverse primers are the same : %s", primers.Forward)
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}
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library.Primers[primers.Forward] = primers
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library.Primers[primers.Reverse] = primers
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}
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return nil
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}
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