Commit Graph

8 Commits

Author SHA1 Message Date
Eric Coissac 60b3753673 feat(obiconvert): add --raw-taxid option and refactor taxID formatting
- Add new `--tax-id` mode (`obiconvert --raw-taxid`) to output bare numeric taxIDs instead of full-format strings.
- Introduce `TaxNode.FullString()` to always return the complete "code:id [name]@rank" format, regardless of global `UseRawTaxids()` setting.
- Update `.String(taxonomyCode)` to respect the global flag, returning bare ID when `--raw-taxid` is active.
- Extract raw taxID from full-format strings in taxonomy methods when needed (e.g., fallback without loaded DB).
- Add comprehensive test suite covering:
a) `--raw-taxid` execution and idempotency
b) full-format taxID output with `--taxonomy`
c interaction of both flags
d format validation
- Add test data: new reference files `out_ecotag.fasta`, taxonomy.csv, and updated shell script.
2026-04-30 16:57:38 +02:00
Eric Coissac b18c9b7ac6 add the --raw-taxid option 2025-03-08 09:40:06 +01:00
Eric Coissac 5d0f996625 Patch a small bug on json write 2024-12-20 19:42:03 +01:00
Eric Coissac 3d06978808 a functional new version of obifind 2024-11-24 19:33:24 +01:00
Eric Coissac 36327c79c8 Changes to be committed:
modified:   .gitignore
	new file:   pkg/obitax/default_taxonomy.go
	modified:   pkg/obitax/taxon.go
	modified:   pkg/obitax/taxonnode.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonset.go
	modified:   pkg/obitax/taxonslice.go
	modified:   pkg/obitools/obifind/iterator.go
	modified:   pkg/obitools/obifind/options.go
2024-11-16 10:01:49 +01:00
Eric Coissac f5d79d0bc4 update api documentation 2024-11-16 05:59:41 +01:00
Eric Coissac 03f4e88a17 Fisrt functional version 2024-11-14 19:10:23 +01:00
Eric Coissac 9471fedfa1 Fisrt step in the obitax rewriting 2024-11-08 09:48:16 +01:00