Eric Coissac
6ee8750635
Replace SplitInTwo with LeftSplitInTwo/RightSplitInTwo for precise splitting
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Replace SplitInTwo calls with LeftSplitInTwo or RightSplitInTwo depending on the intended split direction. In fastseq_json_header.go, extract rank from suffix without splitting; in biosequenceslice.go and taxid.go, use LeftSplitInTwo to split from the left; add RightSplitInTwo utility function for splitting from the right.
2026-03-12 18:41:28 +01:00
Eric Coissac
cef29005a5
debug url reading
2025-11-18 15:30:20 +01:00
Eric Coissac
2d7dc7d09d
debug taxonomy core dump
2025-11-05 19:01:15 +01:00
Eric Coissac
43b285587e
Debug on taxonomy extraction and CSV conversion
2025-07-07 15:29:40 +02:00
Eric Coissac
7b23985693
Add _ to allowed in taxid
2025-06-06 14:37:57 +02:00
Eric Coissac
6cb7a5a352
Changes to be committed:
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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
03b5ce9397
Patch a bug in obitag when some reference sequences have taxid absent from the taxonomy
2025-03-27 16:45:02 +01:00
Eric Coissac
5a3705b6bb
Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.
2025-03-25 16:44:46 +01:00
Eric Coissac
8448783499
Make sequence files recognized as a taxonomy
2025-03-14 14:22:22 +01:00
Eric Coissac
b18c9b7ac6
add the --raw-taxid option
2025-03-08 09:40:06 +01:00
Eric Coissac
6a8061cc4f
Add managment of the taxonomy alias politic
2025-02-10 14:05:47 +01:00
Eric Coissac
e2563cd8df
Patch a bug in registering merged taxa
2025-02-10 11:42:46 +01:00
Eric Coissac
773e54965d
Patch a bug on compressed output
2025-02-05 14:18:24 +01:00
Eric Coissac
c10df073a7
Changes to be committed:
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modified: pkg/obioptions/version.go
modified: pkg/obitax/iterator.go
2025-02-01 12:06:19 +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
2452aef7a9
patch multiple -Z options
2025-01-29 21:35:28 +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
c50a0f409d
break the import cyccle
2025-01-27 17:23:07 +01:00
Eric Coissac
7c4042df6b
introduce obidefault
2025-01-27 17:12:45 +01:00
Eric Coissac
9acb4a85a8
Refactoring of the default values
2025-01-24 18:09:59 +01:00
Eric Coissac
5d0f996625
Patch a small bug on json write
2024-12-20 19:42:03 +01:00
Eric Coissac
abfa8f357a
patch a bug in Taxid parsing
2024-12-19 13:54:23 +01:00
Eric Coissac
795df34d1a
Changes to be committed:
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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
00b0edc15a
refactoring of the file chunck writing
2024-11-29 18:15:03 +01:00
Eric Coissac
69ef1758a2
obicsv debug
2024-11-24 23:38:49 +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:
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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
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Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
2024-07-25 18:09:03 -04:00
Eric Coissac
54a138196c
Patch a bug in fasta and fastq reading
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Former-commit-id: bcaa264b4c4a7c67617eb909b199176bf09913db
2024-06-21 14:28:57 +02:00
Eric Coissac
b428c48353
Obitag, allow for reference sequences with bad taxid, which are discarded with the emission of a warning
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Former-commit-id: a8781da1afa86de9c34b008959f0705ae69fc64f
2024-03-18 19:11:41 +01:00
0f3871d203
Change the API of workers
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Former-commit-id: 9b07306edd8cf28266f86f95823948fa99d39ea9
2024-03-02 16:03:46 -04:00
4a0b20484f
Add the --taxonomic-path option to obiannotate
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Former-commit-id: 385309a1c4bc5ed33aeaafc63eedb9fc552f78a6
2024-02-27 20:10:26 +01:00
23758b00f6
Patch a bug in the embl reader and adds some doc
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Former-commit-id: 9b5f75fb14bcc3043da1647055279987a295d271
2024-01-31 15:43:02 +01:00
b9a7961c91
Add more error checks on taxonomy reading
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Former-commit-id: 30c848d8e61214afcc7d92f0d3a3f5a1474fc720
2023-12-14 08:09:06 +01:00
8d77cc4133
Change path of the obitools pkg
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Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
2023-11-29 12:14:37 +01:00
18d3eec24a
Change the annotation locker to a pointer to mutex to avoid coying mutex
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Former-commit-id: d179d8753b593183312bd11184e5d8ebb301138a
2023-08-27 16:00:35 +02:00
7b7128196a
small refactoring including doc
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Former-commit-id: 6d6b527d89d77aa571831f7500f841840e280536
2023-08-27 15:52:28 +02:00
60c187404d
Restore old obisort and add LCA functionnality to obiannotate.
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Former-commit-id: aecaacc9dae49f74bd888a8eb8140822d31a42a6
2023-05-02 10:43:22 +02:00
d5e84ec676
rename goutils to obiutils
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Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
2023-03-24 10:25:12 +07:00
ed87f821eb
adds the _taxid suffix to the rank taxid attributes.
2023-02-16 16:13:55 +01:00
5639a09fb9
Add the --with-taxon-at-rank option code to obiannotate
2023-02-02 16:36:32 +01:00
2d375df94f
move the worker class to the obiseq package
2023-01-22 22:39:13 +01:00
29563aa94e
Rename the Length methods Len to follow GO standart
2022-11-17 11:09:58 +01:00
8aa323dad5
Add a first version of obitag the successor of ecotag
2022-10-26 13:16:56 +02:00
6b8f4490cf
Change obiclean algorithm for a better evaluation of ratio
2022-08-31 20:38:03 +02:00
abaede48b5
Refactoring of some code
2022-08-23 11:07:39 +02:00
011898bd9d
A first version of obigrep. Normally fully functionnal, but not fully tested
2022-02-25 07:29:52 +01:00
