16 Commits

Author	SHA1	Message	Date
Eric Coissac	6cb7a5a352	Changes to be committed: ... modified: cmd/obitools/obitag/main.go modified: cmd/obitools/obitaxonomy/main.go modified: pkg/obiformats/csvtaxdump_read.go modified: pkg/obiformats/ecopcr_read.go modified: pkg/obiformats/ncbitaxdump_read.go modified: pkg/obiformats/ncbitaxdump_readtar.go modified: pkg/obiformats/newick_write.go modified: pkg/obiformats/options.go modified: pkg/obiformats/taxonomy_read.go modified: pkg/obiformats/universal_read.go modified: pkg/obiiter/extract_taxonomy.go modified: pkg/obioptions/options.go modified: pkg/obioptions/version.go new file: pkg/obiphylo/tree.go modified: pkg/obiseq/biosequenceslice.go modified: pkg/obiseq/taxonomy_methods.go modified: pkg/obitax/taxonomy.go modified: pkg/obitax/taxonset.go modified: pkg/obitools/obiconvert/sequence_reader.go modified: pkg/obitools/obitag/obitag.go modified: pkg/obitools/obitaxonomy/obitaxonomy.go modified: pkg/obitools/obitaxonomy/options.go deleted: sample/.DS_Store	2025-06-04 09:48:10 +02:00
Eric Coissac	6a8061cc4f	Add managment of the taxonomy alias politic	2025-02-10 14:05:47 +01:00
Eric Coissac	0df082da06	Adds possibility to extract a taxonomy from taxonomic path included in sequence files	2025-01-30 11:18:21 +01:00
Eric Coissac	00f2dc2697	Rename obifind obitaxonomy and introduce the new CSV format for taxonomy.	2025-01-29 10:45:26 +01:00
Eric Coissac	795df34d1a	Changes to be committed: ... modified: cmd/obitools/obitag/main.go modified: cmd/obitools/obitag2/main.go modified: go.mod modified: go.sum modified: pkg/obiformats/ncbitaxdump/read.go modified: pkg/obioptions/version.go modified: pkg/obiseq/attributes.go modified: pkg/obiseq/taxonomy_lca.go modified: pkg/obiseq/taxonomy_methods.go modified: pkg/obiseq/taxonomy_predicate.go modified: pkg/obitax/inner.go modified: pkg/obitax/lca.go new file: pkg/obitax/taxid.go modified: pkg/obitax/taxon.go modified: pkg/obitax/taxonomy.go modified: pkg/obitax/taxonslice.go modified: pkg/obitools/obicleandb/obicleandb.go modified: pkg/obitools/obigrep/options.go modified: pkg/obitools/obilandmark/obilandmark.go modified: pkg/obitools/obilandmark/options.go modified: pkg/obitools/obirefidx/famlilyindexing.go modified: pkg/obitools/obirefidx/geomindexing.go modified: pkg/obitools/obirefidx/obirefidx.go modified: pkg/obitools/obirefidx/options.go modified: pkg/obitools/obitag/obigeomtag.go modified: pkg/obitools/obitag/obitag.go modified: pkg/obitools/obitag/options.go modified: pkg/obiutils/strings.go	2024-12-19 13:36:59 +01:00
Eric Coissac	69ef1758a2	obicsv debug	2024-11-24 23:38:49 +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
Eric Coissac	67665a6b40	Xprize update ... Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7	2024-07-25 18:09:03 -04:00
Eric Coissac	29563aa94e	Rename the Length methods Len to follow GO standart	2022-11-17 11:09:58 +01:00
Eric Coissac	abaede48b5	Refactoring of some code	2022-08-23 11:07:39 +02:00
Eric Coissac	abcf02e488	Start to use leveled log	2022-02-24 12:14:52 +01:00
Eric Coissac	ff40222902	Code reefactoring	2022-01-14 16:10:19 +01:00
Eric Coissac	f53bf1b804	First commit	2022-01-13 23:27:39 +01:00