From ebb05fcdf7c32b57bea5a1247c2175084bba4b97 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Thu, 23 Feb 2023 23:32:59 +0100 Subject: [PATCH] code refactoring. Prefix function name having behaviour depending on command line option by the prefix `CLI` --- cmd/obitools/obiannotate/main.go | 2 +- cmd/obitools/obiclean/main.go | 2 +- cmd/obitools/obicleandb/main.go | 2 +- cmd/obitools/obicomplement/main.go | 2 +- cmd/obitools/obiconvert/main.go | 2 +- cmd/obitools/obicount/main.go | 2 +- cmd/obitools/obicsv/main.go | 17 +++++++++++++++++ cmd/obitools/obidistribute/main.go | 4 ++-- cmd/obitools/obigrep/main.go | 4 ++-- cmd/obitools/obimultiplex/main.go | 2 +- cmd/obitools/obipairing/main.go | 13 +++++++------ cmd/obitools/obipcr/main.go | 2 +- cmd/obitools/obirefidx/main.go | 2 +- cmd/obitools/obitag/main.go | 2 +- cmd/obitools/obiuniq/main.go | 2 +- 15 files changed, 39 insertions(+), 21 deletions(-) create mode 100644 cmd/obitools/obicsv/main.go diff --git a/cmd/obitools/obiannotate/main.go b/cmd/obitools/obiannotate/main.go index fc19cfd..ed45267 100644 --- a/cmd/obitools/obiannotate/main.go +++ b/cmd/obitools/obiannotate/main.go @@ -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) diff --git a/cmd/obitools/obiclean/main.go b/cmd/obitools/obiclean/main.go index 1f345e5..4216e4e 100644 --- a/cmd/obitools/obiclean/main.go +++ b/cmd/obitools/obiclean/main.go @@ -15,7 +15,7 @@ func main() { _, args, _ := optionParser(os.Args) - fs, _ := obiconvert.ReadBioSequences(args...) + fs, _ := obiconvert.CLIReadBioSequences(args...) cleaned := obiclean.IOBIClean(fs) diff --git a/cmd/obitools/obicleandb/main.go b/cmd/obitools/obicleandb/main.go index f117283..c69d0ef 100644 --- a/cmd/obitools/obicleandb/main.go +++ b/cmd/obitools/obicleandb/main.go @@ -14,7 +14,7 @@ func main() { _, args, _ := optionParser(os.Args) - fs, _ := obiconvert.ReadBioSequences(args...) + fs, _ := obiconvert.CLIReadBioSequences(args...) cleaned := obicleandb.ICleanDB(fs) diff --git a/cmd/obitools/obicomplement/main.go b/cmd/obitools/obicomplement/main.go index 75fc860..476f66b 100644 --- a/cmd/obitools/obicomplement/main.go +++ b/cmd/obitools/obicomplement/main.go @@ -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) diff --git a/cmd/obitools/obiconvert/main.go b/cmd/obitools/obiconvert/main.go index 39d245f..f53ea58 100644 --- a/cmd/obitools/obiconvert/main.go +++ b/cmd/obitools/obiconvert/main.go @@ -14,7 +14,7 @@ func main() { _, args, _ := optionParser(os.Args) - fs, _ := obiconvert.ReadBioSequences(args...) + fs, _ := obiconvert.CLIReadBioSequences(args...) obiconvert.CLIWriteBioSequences(fs, true) obiiter.WaitForLastPipe() diff --git a/cmd/obitools/obicount/main.go b/cmd/obitools/obicount/main.go index 3801f27..c5e1981 100644 --- a/cmd/obitools/obicount/main.go +++ b/cmd/obitools/obicount/main.go @@ -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() { diff --git a/cmd/obitools/obicsv/main.go b/cmd/obitools/obicsv/main.go new file mode 100644 index 0000000..f05a730 --- /dev/null +++ b/cmd/obitools/obicsv/main.go @@ -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() + +} diff --git a/cmd/obitools/obidistribute/main.go b/cmd/obitools/obidistribute/main.go index 80e47ae..2f2e980 100644 --- a/cmd/obitools/obidistribute/main.go +++ b/cmd/obitools/obidistribute/main.go @@ -15,8 +15,8 @@ func main() { _, args, _ := optionParser(os.Args) - fs, _ := obiconvert.ReadBioSequences(args...) - + fs, _ := obiconvert.CLIReadBioSequences(args...) + obidistribute.DistributeSequence(fs) obiiter.WaitForLastPipe() diff --git a/cmd/obitools/obigrep/main.go b/cmd/obitools/obigrep/main.go index 29eab13..4a56310 100644 --- a/cmd/obitools/obigrep/main.go +++ b/cmd/obitools/obigrep/main.go @@ -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() diff --git a/cmd/obitools/obimultiplex/main.go b/cmd/obitools/obimultiplex/main.go index bf56cda..0e6d7f1 100644 --- a/cmd/obitools/obimultiplex/main.go +++ b/cmd/obitools/obimultiplex/main.go @@ -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() diff --git a/cmd/obitools/obipairing/main.go b/cmd/obitools/obipairing/main.go index f4d30c2..23277b6 100644 --- a/cmd/obitools/obipairing/main.go +++ b/cmd/obitools/obipairing/main.go @@ -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() diff --git a/cmd/obitools/obipcr/main.go b/cmd/obitools/obipcr/main.go index 8c65239..8e67528 100644 --- a/cmd/obitools/obipcr/main.go +++ b/cmd/obitools/obipcr/main.go @@ -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() diff --git a/cmd/obitools/obirefidx/main.go b/cmd/obitools/obirefidx/main.go index 9cde304..a6b3988 100644 --- a/cmd/obitools/obirefidx/main.go +++ b/cmd/obitools/obirefidx/main.go @@ -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) diff --git a/cmd/obitools/obitag/main.go b/cmd/obitools/obitag/main.go index d62b650..4011caf 100644 --- a/cmd/obitools/obitag/main.go +++ b/cmd/obitools/obitag/main.go @@ -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) diff --git a/cmd/obitools/obiuniq/main.go b/cmd/obitools/obiuniq/main.go index 12cf69b..e9ef08d 100644 --- a/cmd/obitools/obiuniq/main.go +++ b/cmd/obitools/obiuniq/main.go @@ -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)