mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
Add a new command obitagpcr able to tag reads according to their corresponding pcr samples
Former-commit-id: 1f34bf0a27d55afc3556efd64f6ccee6d2329aff
This commit is contained in:
55
cmd/obitools/obitagpcr/main.go
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55
cmd/obitools/obitagpcr/main.go
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package main
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import (
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"os"
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obitagpcr"
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)
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func main() {
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// go tool pprof -http=":8000" ./obipairing ./cpu.pprof
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// f, err := os.Create("cpu.pprof")
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// if err != nil {
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// log.Fatal(err)
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// }
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// pprof.StartCPUProfile(f)
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// defer pprof.StopCPUProfile()
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// go tool trace cpu.trace
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// ftrace, err := os.Create("cpu.trace")
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// if err != nil {
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// log.Fatal(err)
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// }
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// trace.Start(ftrace)
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// defer trace.Stop()
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obioptions.SetWorkerPerCore(1)
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optionParser := obioptions.GenerateOptionParser(obitagpcr.OptionSet)
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optionParser(os.Args)
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pairs, err := obipairing.CLIPairedSequence()
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if err != nil {
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log.Errorf("Cannot open file (%v)", err)
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os.Exit(1)
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}
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paired := obitagpcr.IPCRTagPESequencesBatch(pairs,
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obipairing.CLIGapPenality(),
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obipairing.CLIDelta(),
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obipairing.CLIMinOverlap(),
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obipairing.CLIMinIdentity(),
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obipairing.CLIWithStats())
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obiconvert.CLIWriteBioSequences(paired, true)
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obiiter.WaitForLastPipe()
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}
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28
pkg/obitools/obitagpcr/options.go
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28
pkg/obitools/obitagpcr/options.go
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package obitagpcr
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import (
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimultiplex"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing"
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"github.com/DavidGamba/go-getoptions"
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)
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var _reorientate = false
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func TagPCROptionSet(options *getoptions.GetOpt) {
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options.BoolVar(&_reorientate, "reference-db", _reorientate,
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options.Description("Reverse complemente reads if needed to store all the sequences in "+
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"the same orientation respectively to forward and reverse primers"))
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}
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// OptionSet adds to the basic option set every options declared for
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// the obiuniq command
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func OptionSet(options *getoptions.GetOpt) {
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obipairing.OptionSet(options)
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obimultiplex.MultiplexOptionSet(options)
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TagPCROptionSet(options)
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}
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func CLIReorientate() bool {
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return _reorientate
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}
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190
pkg/obitools/obitagpcr/pcrtag.go
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190
pkg/obitools/obitagpcr/pcrtag.go
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package obitagpcr
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import (
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimultiplex"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing"
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)
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func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
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gap float64, delta, minOverlap int,
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minIdentity float64,
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withStats bool) obiiter.IBioSequence {
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if !iterator.IsPaired() {
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log.Fatalln("Sequence data must be paired")
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}
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nworkers := obioptions.CLIParallelWorkers()
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ngsfilter, err := obimultiplex.CLINGSFIlter()
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if err != nil {
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log.Fatalf("%v", err)
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}
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ngsfilter.Compile(obimultiplex.CLIAllowedMismatch(),
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obimultiplex.CLIAllowsIndel())
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newIter := obiiter.MakeIBioSequence()
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newIter.MarkAsPaired()
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newIter.Add(nworkers)
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go func() {
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newIter.WaitAndClose()
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log.Printf("End of the sequence PCR Taging")
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}()
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f := func(iterator obiiter.IBioSequence, wid int) {
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arena := obialign.MakePEAlignArena(150, 150)
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var err error
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for iterator.Next() {
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batch := iterator.Get()
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for i, A := range batch.Slice() {
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B := A.PairedWith()
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consensus := obipairing.AssemblePESequences(
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A.Copy(), B.ReverseComplement(false),
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gap, delta, minOverlap, minIdentity, withStats, true, arena,
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)
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consensus, err = ngsfilter.ExtractBarcode(consensus, true)
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// log.Println("@@ ",wid," Error : ",err)
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// log.Println("@@ ",wid," SEQA : ",*A)
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// log.Println("@@ ",wid," SEQB : ",*B)
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// log.Println("@@ ",wid," consensus : ",*consensus)
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if err == nil {
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annot := consensus.Annotations()
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direction := annot["direction"].(string)
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forward_match := annot["forward_match"].(string)
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forward_mismatches := annot["forward_mismatches"].(int)
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forward_tag := annot["forward_tag"].(string)
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reverse_match := annot["reverse_match"].(string)
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reverse_mismatches := annot["reverse_mismatches"].(int)
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reverse_tag := annot["reverse_tag"].(string)
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sample := annot["sample"].(string)
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experiment := annot["experiment"].(string)
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aanot := A.Annotations()
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aanot["direction"] = direction
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aanot["forward_match"] = forward_match
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aanot["forward_mismatches"] = forward_mismatches
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aanot["forward_tag"] = forward_tag
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aanot["reverse_match"] = reverse_match
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aanot["reverse_mismatches"] = reverse_mismatches
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aanot["reverse_tag"] = reverse_tag
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aanot["sample"] = sample
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aanot["experiment"] = experiment
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banot := B.Annotations()
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banot["direction"] = direction
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banot["forward_match"] = forward_match
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banot["forward_mismatches"] = forward_mismatches
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banot["forward_tag"] = forward_tag
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banot["reverse_match"] = reverse_match
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banot["reverse_mismatches"] = reverse_mismatches
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banot["reverse_tag"] = reverse_tag
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banot["sample"] = sample
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banot["experiment"] = experiment
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if CLIReorientate() && direction == "reverse" {
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B.ReverseComplement(true)
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A.ReverseComplement(true)
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B.PairTo(A)
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batch.Slice()[i] = B
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}
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} else {
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demultiplex_error := consensus.Annotations()["demultiplex_error"]
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if demultiplex_error!=nil {
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A.Annotations()["demultiplex_error"] = demultiplex_error.(string)
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B.Annotations()["demultiplex_error"] = demultiplex_error.(string)
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} else {
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log.Panicln("@@ ",wid,"Error : ",err,*consensus)
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}
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}
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}
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newIter.Push(batch)
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}
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newIter.Done()
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}
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log.Printf("Start of the sequence Pairing using %d workers\n", nworkers)
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for i := 1; i < nworkers; i++ {
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go f(iterator.Split(), i)
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}
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go f(iterator, 0)
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iout := newIter
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if !obimultiplex.CLIConservedErrors() {
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log.Println("Discards unassigned sequences")
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iout = iout.Rebatch(obioptions.CLIBatchSize())
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}
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var unidentified obiiter.IBioSequence
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if obimultiplex.CLIUnidentifiedFileName() != "" {
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log.Printf("Unassigned sequences saved in file: %s\n", obimultiplex.CLIUnidentifiedFileName())
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unidentified, iout = iout.DivideOn(obiseq.HasAttribute("demultiplex_error"),
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obioptions.CLIBatchSize())
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go func() {
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_, err := obiconvert.CLIWriteBioSequences(unidentified,
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true,
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obimultiplex.CLIUnidentifiedFileName())
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if err != nil {
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log.Fatalf("%v", err)
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}
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}()
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}
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log.Printf("Sequence demultiplexing using %d workers\n", nworkers)
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return iout
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}
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// if match.IsDirect {
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// annot["direction"] = "direct"
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// } else {
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// annot["direction"] = "reverse"
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// }
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// if match.ForwardMatch != "" {
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// annot["forward_match"] = match.ForwardMatch
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// annot["forward_mismatches"] = match.ForwardMismatches
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// annot["forward_tag"] = match.ForwardTag
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// }
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// if match.ReverseMatch != "" {
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// annot["reverse_match"] = match.ReverseMatch
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// annot["reverse_mismatches"] = match.ReverseMismatches
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// annot["reverse_tag"] = match.ReverseTag
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// }
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// if match.Error == nil {
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// if match.Pcr != nil {
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// annot["sample"] = match.Pcr.Sample
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// annot["experiment"] = match.Pcr.Experiment
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// for k, val := range match.Pcr.Annotations {
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// annot[k] = val
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// }
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// } else {
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// annot["demultiplex_error"]
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