mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-03-25 21:40:52 +00:00
56c1f4180c
This commit refactors the k-mer index management tools to use a unified subcommand structure with obik, adds support for per-set metadata and ID management, enhances the k-mer set group builder to support appending to existing groups, and improves command-line option handling with a new global options registration system. Key changes: - Introduce obik command with subcommands (index, ls, summary, cp, mv, rm, super, lowmask) - Add support for per-set metadata and ID management in kmer set groups - Implement ability to append to existing kmer index groups - Refactor option parsing to use a global options registration system - Add new commands for listing, copying, moving, and removing sets - Enhance low-complexity masking with new options and output formats - Improve kmer index summary with Jaccard distance matrix support - Remove deprecated obikindex and obisuperkmer commands - Update build process to use the new subcommand structure
97 lines
1.9 KiB
Go
97 lines
1.9 KiB
Go
package obik
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import (
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"context"
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"encoding/json"
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"fmt"
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"strings"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
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"github.com/DavidGamba/go-getoptions"
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"gopkg.in/yaml.v3"
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)
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type setEntry struct {
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Index int `json:"index" yaml:"index"`
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ID string `json:"id" yaml:"id"`
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Count uint64 `json:"count" yaml:"count"`
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}
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func runLs(ctx context.Context, opt *getoptions.GetOpt, args []string) error {
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if len(args) < 1 {
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return fmt.Errorf("usage: obik ls [options] <index_directory>")
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}
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ksg, err := obikmer.OpenKmerSetGroup(args[0])
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if err != nil {
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return fmt.Errorf("failed to open kmer index: %w", err)
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}
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// Determine which sets to show
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patterns := CLISetPatterns()
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var indices []int
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if len(patterns) > 0 {
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indices, err = ksg.MatchSetIDs(patterns)
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if err != nil {
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return err
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}
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} else {
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indices = make([]int, ksg.Size())
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for i := range indices {
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indices[i] = i
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}
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}
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entries := make([]setEntry, len(indices))
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for i, idx := range indices {
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entries[i] = setEntry{
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Index: idx,
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ID: ksg.SetIDOf(idx),
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Count: ksg.Len(idx),
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}
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}
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format := CLIOutFormat()
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switch format {
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case "json":
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return outputLsJSON(entries)
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case "yaml":
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return outputLsYAML(entries)
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case "csv":
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return outputLsCSV(entries)
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default:
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return outputLsCSV(entries)
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}
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}
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func outputLsCSV(entries []setEntry) error {
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fmt.Println("index,id,count")
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for _, e := range entries {
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// Escape commas in ID if needed
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id := e.ID
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if strings.ContainsAny(id, ",\"") {
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id = "\"" + strings.ReplaceAll(id, "\"", "\"\"") + "\""
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}
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fmt.Printf("%d,%s,%d\n", e.Index, id, e.Count)
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}
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return nil
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}
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func outputLsJSON(entries []setEntry) error {
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data, err := json.MarshalIndent(entries, "", " ")
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if err != nil {
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return err
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}
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fmt.Println(string(data))
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return nil
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}
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func outputLsYAML(entries []setEntry) error {
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data, err := yaml.Marshal(entries)
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if err != nil {
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return err
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}
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fmt.Print(string(data))
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return nil
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}
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