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Refactoring related to iterators

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This commit is contained in:
Eric Coissac
2022-11-16 17:13:03 +01:00
parent 6f853da9df
commit 09fc426b67
29 changed files with 95 additions and 93 deletions
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4
cmd/obitools/obiclean/main.go
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@ -14,9 +14,9 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequencesBatch(args...)
fs, _ := obiconvert.ReadBioSequences(args...)
cleaned := obiclean.IOBIClean(fs)
obiconvert.WriteBioSequencesBatch(cleaned, true)
obiconvert.WriteBioSequences(cleaned, true)
}

4
cmd/obitools/obicomplement/main.go
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@ -14,8 +14,8 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequencesBatch(args...)
fs, _ := obiconvert.ReadBioSequences(args...)
comp := fs.MakeIWorker(obiiter.ReverseComplementWorker(true))
obiconvert.WriteBioSequencesBatch(comp, true)
obiconvert.WriteBioSequences(comp, true)
}

4
cmd/obitools/obiconvert/main.go
View File

@ -13,6 +13,6 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequencesBatch(args...)
obiconvert.WriteBioSequencesBatch(fs, true)
fs, _ := obiconvert.ReadBioSequences(args...)
obiconvert.WriteBioSequences(fs, true)
}

2
cmd/obitools/obicount/main.go
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@ -33,7 +33,7 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequencesBatch(args...)
fs, _ := obiconvert.ReadBioSequences(args...)
nvariant, nread, nsymbol := fs.Count(true)
if obicount.CLIIsPrintingVariantCount() {

2
cmd/obitools/obidistribute/main.go
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@ -14,6 +14,6 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequencesBatch(args...)
fs, _ := obiconvert.ReadBioSequences(args...)
obidistribute.DistributeSequence(fs)
}

4
cmd/obitools/obigrep/main.go
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@ -36,7 +36,7 @@ func main() {
_, args, _ := optionParser(os.Args)
sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
sequences, _ := obiconvert.ReadBioSequences(args...)
selected := obigrep.IFilterSequence(sequences)
obiconvert.WriteBioSequencesBatch(selected, true)
obiconvert.WriteBioSequences(selected, true)
}

9
cmd/obitools/obimultiplex/main.go
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@ -1,10 +1,11 @@
package main
import (
log "github.com/sirupsen/logrus"
"os"
"runtime/pprof"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimultiplex"
@ -30,8 +31,8 @@ func main() {
_, args, _ := optionParser(os.Args)
sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
amplicons, _ := obimultiplex.IExtractBarcodeBatches(sequences)
obiconvert.WriteBioSequencesBatch(amplicons, true)
sequences, _ := obiconvert.ReadBioSequences(args...)
amplicons, _ := obimultiplex.IExtractBarcode(sequences)
obiconvert.WriteBioSequences(amplicons, true)
amplicons.Wait()
}

5
cmd/obitools/obipairing/main.go
View File

@ -1,10 +1,11 @@
package main
import (
log "github.com/sirupsen/logrus"
"os"
"runtime/trace"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing"
@ -40,5 +41,5 @@ func main() {
obipairing.WithStats(),
obioptions.CLIParallelWorkers(),
)
obiconvert.WriteBioSequencesBatch(paired, true)
obiconvert.WriteBioSequences(paired, true)
}

4
cmd/obitools/obipcr/main.go
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@ -33,7 +33,7 @@ func main() {
_, args, _ := optionParser(os.Args)
sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
sequences, _ := obiconvert.ReadBioSequences(args...)
amplicons, _ := obipcr.PCR(sequences)
obiconvert.WriteBioSequencesBatch(amplicons, true)
obiconvert.WriteBioSequences(amplicons, true)
}

4
cmd/obitools/obirefidx/main.go
View File

@ -14,9 +14,9 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequencesBatch(args...)
fs, _ := obiconvert.ReadBioSequences(args...)
indexed := obirefidx.IndexReferenceDB(fs)
written, _ := obiconvert.WriteBioSequencesBatch(indexed, false)
written, _ := obiconvert.WriteBioSequences(indexed, false)
written.Consume()
}

4
cmd/obitools/obitag/main.go
View File

@ -33,8 +33,8 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequencesBatch(args...)
fs, _ := obiconvert.ReadBioSequences(args...)
identified := obitag.AssignTaxonomy(fs)
obiconvert.WriteBioSequencesBatch(identified, true)
obiconvert.WriteBioSequences(identified, true)
}

4
cmd/obitools/obiuniq/main.go
View File

@ -36,7 +36,7 @@ func main() {
_, args, _ := optionParser(os.Args)
sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
sequences, _ := obiconvert.ReadBioSequences(args...)
unique := obiuniq.Unique(sequences)
obiconvert.WriteBioSequencesBatch(unique, true)
obiconvert.WriteBioSequences(unique, true)
}