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obimultiplex saves unassigned sequence

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This commit is contained in:
Eric Coissac
2022-02-01 23:25:19 +01:00
parent e9cdfd7e03
commit 98a4363d22
6 changed files with 189 additions and 0 deletions
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19
pkg/obitools/obimultiplex/demultiplex.go
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@@ -6,6 +6,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obingslibrary"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
)
func IExtractBarcodeBatches(iterator obiseq.IBioSequenceBatch) (obiseq.IBioSequenceBatch, error) {
@@ -31,9 +32,27 @@ func IExtractBarcodeBatches(iterator obiseq.IBioSequenceBatch) (obiseq.IBioSeque
newIter := iterator.MakeISliceWorker(worker)
if !CLIConservedErrors() {
log.Println("Discards unassigned sequences")
newIter = newIter.Rebatch(obioptions.CLIBatchSize())
}
var unidentified obiseq.IBioSequenceBatch
if CLIUnidentifiedFileName() != "" {
log.Printf("Unassigned sequences saved in file: %s\n", CLIUnidentifiedFileName())
unidentified, newIter = newIter.DivideOn(obiseq.HasAttribute("demultiplex_error"),
obioptions.CLIBatchSize())
go func() {
_, err := obiconvert.WriteBioSequencesBatch(unidentified,
true,
CLIUnidentifiedFileName())
if err != nil {
log.Fatalf("%v", err)
}
}()
}
log.Printf("Sequence demultiplexing using %d workers\n", obioptions.CLIParallelWorkers())
return newIter, nil