Refactoring codes for removing buffer size options. An some other changes...

Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce

pkg/obitools/obicsv/obicsv.go

@@ -0,0 +1,61 @@
+package obicsv
+
+import (
+	"log"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+)
+
+func CLIWriteCSV(iterator obiiter.IBioSequence,
+	terminalAction bool, filenames ...string) (obiiter.IBioSequence, error) {
+
+	if obiconvert.CLIProgressBar() {
+		iterator = iterator.Speed()
+	}
+
+	var newIter obiiter.IBioSequence
+
+	opts := make([]obiformats.WithOption, 0, 10)
+
+	nworkers := obioptions.CLIParallelWorkers() / 4
+	if nworkers < 2 {
+		nworkers = 2
+	}
+
+	opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
+	opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
+
+	opts = append(opts, obiformats.OptionsQualityShift(obiconvert.CLIOutputQualityShift()))
+	opts = append(opts, obiformats.OptionsCompressed(obiconvert.CLICompressed()))
+
+	opts = append(opts, obiformats.CSVId(CLIPrintId()),
+		obiformats.CSVCount(CLIPrintCount()),
+		obiformats.CSVTaxon(CLIPrintTaxon()),
+		obiformats.CSVDefinition(CLIPrintDefinition()),
+		obiformats.CSVKeys(CLIToBeKeptAttributes()),
+	)
+
+	var err error
+
+	if len(filenames) == 0 {
+		newIter, err = obiformats.WriteCSVToStdout(iterator, opts...)
+	} else {
+		newIter, err = obiformats.WriteCSVToFile(iterator, filenames[0], opts...)
+	}
+
+	if err != nil {
+		log.Fatalf("Write file error: %v", err)
+		return obiiter.NilIBioSequence, err
+	}
+
+	if terminalAction {
+		newIter.Recycle()
+		return obiiter.NilIBioSequence, nil
+	}
+
+	return newIter, nil
+
+}

pkg/obitools/obicsv/options.go

@@ -0,0 +1,126 @@
+package obicsv
+
+import (
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"github.com/DavidGamba/go-getoptions"
+)
+
+var _outputIds = true
+var _outputCount = false
+var _outputTaxon = false
+var _outputSequence = true
+var _outputQuality = true
+var _outputDefinition = false
+var _obipairing = false
+var _autoColumns = false
+var _keepOnly = make([]string, 0)
+var _naValue = "NA"
+
+var _softAttributes = map[string][]string{
+	"obipairing": {"mode", "seq_a_single", "seq_b_single",
+		"ali_dir", "score", "score_norm",
+		"seq_ab_match", "pairing_mismatches",
+	},
+}
+
+func CSVOptionSet(options *getoptions.GetOpt) {
+	options.BoolVar(&_outputIds, "ids", _outputIds,
+		options.Alias("i"),
+		options.Description("Prints sequence ids in the ouput."))
+
+	options.BoolVar(&_outputSequence, "sequence", _outputSequence,
+		options.Alias("s"),
+		options.Description("Prints sequence itself in the output."))
+
+	options.BoolVar(&_outputQuality, "quality", _outputQuality,
+		options.Alias("q"),
+		options.Description("Prints sequence quality in the output."))
+
+	options.BoolVar(&_outputDefinition, "definition", _outputDefinition,
+		options.Alias("d"),
+		options.Description("Prints sequence definition in the output."))
+
+	options.BoolVar(&_autoColumns, "auto", _autoColumns,
+		options.Description("Based on the first sequences, propose a list of attibutes to print"))
+
+	options.BoolVar(&_outputCount, "count", _outputCount,
+		options.Description("Prints the count attribute in the output"))
+
+	options.BoolVar(&_outputTaxon, "taxon", _outputTaxon,
+		options.Description("Prints the NCBI taxid and its related scientific name"))
+
+	options.BoolVar(&_obipairing, "obipairing", _obipairing,
+		options.Description("Prints the attributes added by obipairing"))
+
+	options.StringSliceVar(&_keepOnly, "keep", 1, 1,
+		options.Alias("k"),
+		options.ArgName("KEY"),
+		options.Description("Keeps only attribute with key <KEY>. Several -k options can be combined."))
+
+	options.StringVar(&_naValue, "na-value", _naValue,
+		options.ArgName("NAVALUE"),
+		options.Description("A string representing non available values in the CSV file."))
+}
+
+func OptionSet(options *getoptions.GetOpt) {
+	obiconvert.OutputModeOptionSet(options)
+	CSVOptionSet(options)
+}
+
+func CLIPrintId() bool {
+	return _outputIds
+}
+
+func CLIPrintSequence() bool {
+	return _outputSequence
+}
+
+func CLIPrintCount() bool {
+	return _outputCount
+}
+func CLIPrintTaxon() bool {
+	return _outputTaxon
+}
+func CLIPrintQuality() bool {
+	return _outputQuality
+}
+
+func CLIPrintDefinition() bool {
+	return _outputDefinition
+}
+
+func CLIAutoColumns() bool {
+	return _autoColumns
+}
+
+func CLIHasToBeKeptAttributes() bool {
+	return len(_keepOnly) > 0
+}
+
+func CLIToBeKeptAttributes() []string {
+	if _obipairing {
+		_keepOnly = append(_keepOnly, _softAttributes["obipairing"]...)
+	}
+
+	if i := goutils.LookFor(_keepOnly, "count"); i >= 0 {
+		_keepOnly = goutils.RemoveIndex(_keepOnly, i)
+		_outputCount = true
+	}
+
+	if i := goutils.LookFor(_keepOnly, "taxid"); i >= 0 {
+		_keepOnly = goutils.RemoveIndex(_keepOnly, i)
+		_outputTaxon = true
+	}
+
+	if i := goutils.LookFor(_keepOnly, "scientific_name"); i >= 0 {
+		_keepOnly = goutils.RemoveIndex(_keepOnly, i)
+		_outputTaxon = true
+	}
+
+	return _keepOnly
+}
+
+func CLINAValue() string {
+	return _naValue
+}