Eric Coissac
d735ac6188
feat: add JSON input support for biological sequences
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Introduce a streaming JSON parser that decodes biological sequences using `goccy/go-json` with configurable batching to minimize memory overhead. Extend the CLI, file suffix filters, and MIME type detection to automatically recognize and route JSON inputs. Refactor header parsing into a centralized switch-case handler for improved maintainability.
2026-07-03 10:16:55 +02:00
Eric Coissac
cef29005a5
debug url reading
2025-11-18 15:30:20 +01:00
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
8448783499
Make sequence files recognized as a taxonomy
2025-03-14 14:22:22 +01:00
Eric Coissac
0339e4dffa
Patch size limite of the filetype guesser
2025-03-08 07:34:02 +01:00
Eric Coissac
4774438644
Changes to be committed:
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modified: pkg/obiformats/universal_read.go
modified: pkg/obioptions/version.go
modified: pkg/obiseq/taxonomy_methods.go
2025-02-12 08:40:38 +01:00
Eric Coissac
3137c1f841
Adds the ability to read gzip-tar file for the taxonomy dump
2025-01-24 11:47:59 +01:00
Eric Coissac
05bf2bfd6c
Add option related to agrep match on obigrep and obiannotate
2024-09-09 16:52:13 +02:00
Eric Coissac
65ae82622e
correction of several small bugs
2024-09-03 06:08:07 -03:00
Eric Coissac
1b1cd41fd3
Add some code refactoring from the blackboard branch
2024-08-02 12:35:46 +02:00
Eric Coissac
bd855c4965
Adds CSV as an input format
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Former-commit-id: a365bb6947064adc2709d66df05fa54c6fe47fad
2024-07-03 21:04:27 +02:00
Eric Coissac
1b43fa4247
First complete version of obimultiplex2
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Former-commit-id: 170593bd597c7914d3f1fd3d2b865186d7f11966
2024-06-06 23:11:13 +02:00
coissac
8d77cc4133
Change path of the obitools pkg
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Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
2023-11-29 12:14:37 +01:00
coissac
6a6a6f6f2c
Correctly handle empty files
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Former-commit-id: d166aa352ce4bf32739ddc2f7d1c9967918822fd
2023-10-16 15:34:06 +02:00
coissac
e8c55a2b6b
optimize sequence readers and patch a bug in the format guesser
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Former-commit-id: 9dce1e96c57ae9a88c26fac5c8e1bdcdc2c0c7a5
2023-10-13 21:52:57 +02:00
coissac
5c30ec354f
Go implementation of fasta and fastq parser
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Former-commit-id: 3f4fd355c169afbef2d5fef1f5e407aabb71d031
2023-09-03 19:16:37 +02:00
coissac
62b57f4ede
A go implementation of the fasta reader
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Former-commit-id: 603592c4761fb0722e9e0501d78de1bd3ba238fa
2023-09-01 09:30:12 +02:00
coissac
3f8c0d6a2f
Replace MakeBioSequence call by NewBioSequence call,
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Implements a new file format guesser
Adds some more API doc
Former-commit-id: 9837bf1c28beca6ddb599b367f93548950ba83c1
2023-08-30 19:59:46 +02:00
coissac
2a11adb346
Add some doc and switch to the parallel gzip library
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Former-commit-id: 2c1187001f989ba3de5895f516d4c8b54d52a4c4
2023-08-25 14:36:38 +02:00
coissac
a33e471b39
First attempt for obiconsensus... The graph traversing algorithm is too simple
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Former-commit-id: 0456e6c7fd55d6d0fcf9856c40386b976b912cba
2023-03-27 19:51:10 +07:00
coissac
b3922c3896
Produce less weird crash on non existing files
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Former-commit-id: 74bb27bd53c685be530632994bd2ba24c1f362e1
2023-03-07 17:34:25 +07:00
coissac
d04eb915b3
adds a directory option to obidistribute
2023-02-17 22:52:53 +01:00
coissac
f97f92df72
rename the iterator class
2023-01-22 22:04:17 +01:00
coissac
09fc426b67
Refactoring related to iterators
2022-11-16 17:13:03 +01:00
coissac
6f853da9df
Remove single sequence ierators. Only batch iterators persist
2022-11-16 10:58:59 +01:00
coissac
5a81525e46
Adds a genbank parser
2022-08-23 11:04:57 +02:00
coissac
abcf02e488
Start to use leveled log
2022-02-24 12:14:52 +01:00
coissac
eaf65fbcce
Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools
2022-02-24 07:08:40 +01:00
coissac
2e7c1834b0
Big change iin the data model, and a first version of obiuniq
2022-02-21 19:00:23 +01:00
coissac
3586ecc483
second version of obidistribute and a first buggy version of obiuniq
2022-02-15 00:47:02 +01:00
coissac
b9b9c0f179
Patch module name from oa2 to obitools
2022-01-13 23:43:01 +01:00
coissac
f53bf1b804
First commit
2022-01-13 23:27:39 +01:00
Eric Coissac
coissac