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81 lines
2.1 KiB
Go
81 lines
2.1 KiB
Go
// obicount function utility package.
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//
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// The obitols/obicount package contains every
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// functions specificaly required by the obicount utility.
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package obimatrix
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import (
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicsv"
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"github.com/DavidGamba/go-getoptions"
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)
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var __threeColumns__ = false
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var __transpose__ = true
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var __mapAttribute__ = "merged_sample"
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var __valueName__ = "count"
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var __sampleName__ = "sample"
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var __MapNAValue__ = "0"
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var __AllowEmpty__ = false
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func MatrixOptionSet(options *getoptions.GetOpt) {
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options.BoolVar(&__threeColumns__, "three-columns", false,
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options.Description("Printouts the matrix in tree column format."))
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options.BoolVar(&__transpose__, "transpose", __transpose__,
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options.Description("Printouts the transposed matrix."))
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options.StringVar(&__mapAttribute__, "map", __mapAttribute__,
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options.Description("Which attribute is usd to produce th matrix."))
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options.StringVar(&__valueName__, "value-name", __valueName__,
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options.Description("Name of the coulumn containing the values in the three column format."))
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options.StringVar(&__sampleName__, "sample-name", __sampleName__,
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options.Description("Name of the coulumn containing the sample names in the three column format."))
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options.StringVar(&__MapNAValue__, "map-na-value", __MapNAValue__,
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options.Description("Value used when the map attribute is not defined for a sequence."))
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options.BoolVar(&__AllowEmpty__, "allow-empty", __AllowEmpty__,
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options.Description("Allow sequences with empty map"))
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}
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func OptionSet(options *getoptions.GetOpt) {
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MatrixOptionSet(options)
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obicsv.CSVOptionSet(options)
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obiconvert.InputOptionSet(options)
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}
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func CLIOutFormat() string {
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if __threeColumns__ {
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return "three-columns"
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}
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return "matrix"
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}
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func CLIValueName() string {
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return __valueName__
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}
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func CLISampleName() string {
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return __sampleName__
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}
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func CLIMapNaValue() string {
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return __MapNAValue__
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}
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func CLIMapAttribute() string {
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return __mapAttribute__
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}
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func CLITranspose() bool {
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return __transpose__
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}
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func CLIStrict() bool {
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return !__AllowEmpty__
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}
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