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Normalise the managment of speed measure

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This commit is contained in:
Eric Coissac
2023-02-16 13:31:49 +01:00
parent f56363a100
commit 6e36b22040
17 changed files with 48 additions and 17 deletions
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2
cmd/obitools/obiannotate/main.go
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@ -36,7 +36,7 @@ func main() {
sequences, _ := obiconvert.ReadBioSequences(args...)
annotator := obiannotate.CLIAnnotationPipeline()
obiconvert.WriteBioSequences(sequences.Pipe(annotator).Speed(), true)
obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)
obiiter.WaitForLastPipe()

2
cmd/obitools/obiclean/main.go
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@ -19,7 +19,7 @@ func main() {
cleaned := obiclean.IOBIClean(fs)
obiconvert.WriteBioSequences(cleaned, true)
obiconvert.CLIWriteBioSequences(cleaned, true)
obiiter.WaitForLastPipe()

22
cmd/obitools/obicleandb/main.go Normal file
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@ -0,0 +1,22 @@
package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obicleandb"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)
func main() {
optionParser := obioptions.GenerateOptionParser(obicleandb.OptionSet)
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...)
cleaned := obicleandb.ICleanDB(fs)
obiconvert.CLIWriteBioSequences(cleaned, true)
}

2
cmd/obitools/obicomplement/main.go
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@ -18,7 +18,7 @@ func main() {
fs, _ := obiconvert.ReadBioSequences(args...)
comp := fs.MakeIWorker(obiseq.ReverseComplementWorker(true))
obiconvert.WriteBioSequences(comp, true)
obiconvert.CLIWriteBioSequences(comp, true)
obiiter.WaitForLastPipe()

2
cmd/obitools/obiconvert/main.go
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@ -15,7 +15,7 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...)
obiconvert.WriteBioSequences(fs, true)
obiconvert.CLIWriteBioSequences(fs, true)
obiiter.WaitForLastPipe()

2
cmd/obitools/obigrep/main.go
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@ -36,7 +36,7 @@ func main() {
sequences, _ := obiconvert.ReadBioSequences(args...)
selected := obigrep.IFilterSequence(sequences)
obiconvert.WriteBioSequences(selected, true)
obiconvert.CLIWriteBioSequences(selected, true)
obiiter.WaitForLastPipe()
}

2
cmd/obitools/obimultiplex/main.go
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@ -31,7 +31,7 @@ func main() {
sequences, _ := obiconvert.ReadBioSequences(args...)
amplicons, _ := obimultiplex.IExtractBarcode(sequences)
obiconvert.WriteBioSequences(amplicons, true)
obiconvert.CLIWriteBioSequences(amplicons, true)
amplicons.Wait()
obiiter.WaitForLastPipe()

2
cmd/obitools/obipairing/main.go
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@ -39,7 +39,7 @@ func main() {
obipairing.WithStats(),
obioptions.CLIParallelWorkers(),
)
obiconvert.WriteBioSequences(paired, true)
obiconvert.CLIWriteBioSequences(paired, true)
obiiter.WaitForLastPipe()
}

2
cmd/obitools/obipcr/main.go
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@ -33,7 +33,7 @@ func main() {
sequences, _ := obiconvert.ReadBioSequences(args...)
amplicons, _ := obipcr.PCR(sequences)
obiconvert.WriteBioSequences(amplicons, true)
obiconvert.CLIWriteBioSequences(amplicons, true)
obiiter.WaitForLastPipe()
}

2
cmd/obitools/obirefidx/main.go
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@ -18,7 +18,7 @@ func main() {
fs, _ := obiconvert.ReadBioSequences(args...)
indexed := obirefidx.IndexReferenceDB(fs)
obiconvert.WriteBioSequences(indexed, true)
obiconvert.CLIWriteBioSequences(indexed, true)
obiiter.WaitForLastPipe()
}

2
cmd/obitools/obitag/main.go
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@ -36,7 +36,7 @@ func main() {
fs, _ := obiconvert.ReadBioSequences(args...)
identified := obitag.AssignTaxonomy(fs)
obiconvert.WriteBioSequences(identified, true)
obiconvert.CLIWriteBioSequences(identified, true)
obiiter.WaitForLastPipe()
fmt.Println("")

2
cmd/obitools/obiuniq/main.go
View File

@ -36,7 +36,7 @@ func main() {
sequences, _ := obiconvert.ReadBioSequences(args...)
unique := obiuniq.Unique(sequences)
obiconvert.WriteBioSequences(unique, true)
obiconvert.CLIWriteBioSequences(unique, true)
obiiter.WaitForLastPipe()

10
pkg/obitools/obiconvert/options.go
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@ -24,6 +24,8 @@ var __output_fastjson_format__ = false
var __output_fastobi_format__ = false
var __output_solexa_quality__ = false
var __no_progress_bar__ = false
func InputOptionSet(options *getoptions.GetOpt) {
// options.IntVar(&__skipped_entries__, "skip", __skipped_entries__,
// options.Description("The N first sequence records of the file are discarded from the analysis and not reported to the output file."))
@ -67,8 +69,8 @@ func OutputOptionSet(options *getoptions.GetOpt) {
options.Alias("O"),
options.Description("output FASTA/FASTQ title line annotations follow OBI format."))
options.BoolVar(&__output_solexa_quality__, "solexa-output", false,
options.Description("Encodes quality string according to the Solexa specification."))
options.BoolVar(&__no_progress_bar__, "no-progressbar", false,
options.Description("Disable the progress bar printing"))
}
func OptionSet(options *getoptions.GetOpt) {
@ -154,3 +156,7 @@ func CLIOutputQualityShift() int {
return 33
}
}
func CLIProgressBar() bool {
return !__no_progress_bar__
}

5
pkg/obitools/obiconvert/sequence_writer.go
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@ -8,9 +8,12 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)
func WriteBioSequences(iterator obiiter.IBioSequence,
func CLIWriteBioSequences(iterator obiiter.IBioSequence,
terminalAction bool, filenames ...string) (obiiter.IBioSequence, error) {
if CLIProgressBar() {
iterator = iterator.Speed()
}
var newIter obiiter.IBioSequence
opts := make([]obiformats.WithOption, 0, 10)

2
pkg/obitools/obigrep/grep.go
View File

@ -22,7 +22,7 @@ func IFilterSequence(iterator obiiter.IBioSequence) obiiter.IBioSequence {
obioptions.CLIBatchSize())
go func() {
_, err := obiconvert.WriteBioSequences(discarded,
_, err := obiconvert.CLIWriteBioSequences(discarded,
true,
CLIDiscardedFileName())

2
pkg/obitools/obimultiplex/demultiplex.go
View File

@ -44,7 +44,7 @@ func IExtractBarcode(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error
obioptions.CLIBatchSize())
go func() {
_, err := obiconvert.WriteBioSequences(unidentified,
_, err := obiconvert.CLIWriteBioSequences(unidentified,
true,
CLIUnidentifiedFileName())

2
pkg/obitools/obitag/obitag.go
View File

@ -192,5 +192,5 @@ func AssignTaxonomy(iterator obiiter.IBioSequence) obiiter.IBioSequence {
worker := IdentifySeqWorker(references, refcounts, taxo, CLIRunExact())
return iterator.Rebatch(17).MakeIWorker(worker, obioptions.CLIParallelWorkers(), 0).Speed("Annotated sequences").Rebatch(1000)
return iterator.Rebatch(17).MakeIWorker(worker, obioptions.CLIParallelWorkers(), 0).Rebatch(1000)
}