obitools/obitools4
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code refactoring. Prefix function name having behaviour depending on command line option by the prefix CLI

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This commit is contained in:
Eric Coissac
2023-02-23 23:32:59 +01:00
parent a0ab14c205
commit ebb05fcdf7
15 changed files with 39 additions and 21 deletions
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2
cmd/obitools/obiannotate/main.go
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@ -34,7 +34,7 @@ func main() {
_, args, _ := optionParser(os.Args)
sequences, _ := obiconvert.ReadBioSequences(args...)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
annotator := obiannotate.CLIAnnotationPipeline()
obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)

2
cmd/obitools/obiclean/main.go
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@ -15,7 +15,7 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...)
fs, _ := obiconvert.CLIReadBioSequences(args...)
cleaned := obiclean.IOBIClean(fs)

2
cmd/obitools/obicleandb/main.go
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@ -14,7 +14,7 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...)
fs, _ := obiconvert.CLIReadBioSequences(args...)
cleaned := obicleandb.ICleanDB(fs)

2
cmd/obitools/obicomplement/main.go
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@ -15,7 +15,7 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...)
fs, _ := obiconvert.CLIReadBioSequences(args...)
comp := fs.MakeIWorker(obiseq.ReverseComplementWorker(true))
obiconvert.CLIWriteBioSequences(comp, true)

2
cmd/obitools/obiconvert/main.go
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@ -14,7 +14,7 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...)
fs, _ := obiconvert.CLIReadBioSequences(args...)
obiconvert.CLIWriteBioSequences(fs, true)
obiiter.WaitForLastPipe()

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

17
cmd/obitools/obicsv/main.go Normal file
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@ -0,0 +1,17 @@
package main
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
)
func main() {
// optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet)
// _, args, _ := optionParser(os.Args)
// fs, _ := obiconvert.ReadBioSequences(args...)
// //obicsv.CLIWriteCSV(fs, true)
obiiter.WaitForLastPipe()
}

4
cmd/obitools/obidistribute/main.go
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@ -15,8 +15,8 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...)
fs, _ := obiconvert.CLIReadBioSequences(args...)
obidistribute.DistributeSequence(fs)
obiiter.WaitForLastPipe()

4
cmd/obitools/obigrep/main.go
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@ -34,8 +34,8 @@ func main() {
_, args, _ := optionParser(os.Args)
sequences, _ := obiconvert.ReadBioSequences(args...)
selected := obigrep.IFilterSequence(sequences)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
selected := obigrep.CLIFilterSequence(sequences)
obiconvert.CLIWriteBioSequences(selected, true)
obiiter.WaitForLastPipe()

2
cmd/obitools/obimultiplex/main.go
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@ -29,7 +29,7 @@ func main() {
_, args, _ := optionParser(os.Args)
sequences, _ := obiconvert.ReadBioSequences(args...)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
amplicons, _ := obimultiplex.IExtractBarcode(sequences)
obiconvert.CLIWriteBioSequences(amplicons, true)
amplicons.Wait()

13
cmd/obitools/obipairing/main.go
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@ -30,15 +30,16 @@ func main() {
optionParser := obioptions.GenerateOptionParser(obipairing.OptionSet)
optionParser(os.Args)
pairs, _ := obipairing.IBatchPairedSequence()
pairs, _ := obipairing.CLIPairedSequence()
paired := obipairing.IAssemblePESequencesBatch(pairs,
obipairing.GapPenality(),
obipairing.Delta(),
obipairing.MinOverlap(),
obipairing.MinIdentity(),
obipairing.WithStats(),
obipairing.CLIGapPenality(),
obipairing.CLIDelta(),
obipairing.CLIMinOverlap(),
obipairing.CLIMinIdentity(),
obipairing.CLIWithStats(),
obioptions.CLIParallelWorkers(),
)
obiconvert.CLIWriteBioSequences(paired, true)
obiiter.WaitForLastPipe()

2
cmd/obitools/obipcr/main.go
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@ -31,7 +31,7 @@ func main() {
_, args, _ := optionParser(os.Args)
sequences, _ := obiconvert.ReadBioSequences(args...)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
amplicons, _ := obipcr.PCR(sequences)
obiconvert.CLIWriteBioSequences(amplicons, true)
obiiter.WaitForLastPipe()

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

2
cmd/obitools/obitag/main.go
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@ -33,7 +33,7 @@ func main() {
_, args, _ := optionParser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...)
fs, _ := obiconvert.CLIReadBioSequences(args...)
identified := obitag.AssignTaxonomy(fs)
obiconvert.CLIWriteBioSequences(identified, true)

2
cmd/obitools/obiuniq/main.go
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@ -34,7 +34,7 @@ func main() {
_, args, _ := optionParser(os.Args)
sequences, _ := obiconvert.ReadBioSequences(args...)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
unique := obiuniq.Unique(sequences)
obiconvert.CLIWriteBioSequences(unique, true)