7384895578
Writing now uses named MLST profile
automlst.engine/pipeline/head This commit looks good
automlst.engine/pipeline/tag This commit looks good
2025-02-18 16:03:17 +00:00
5a03c7e8d8
Multiple string profiling now respects grouped queries (for non-WGS)
automlst.engine/pipeline/head This commit looks good
2025-02-18 15:34:18 +00:00
ddf9cde175
Added a license text to pyproject.toml
2025-02-14 20:47:06 +00:00
2e8cdd8da9
Updated URL links
automlst.engine/pipeline/head This commit looks good
2025-02-14 20:37:13 +00:00
d0318536b2
Changed FASTA reading to group based on file for merging partial targets
2025-02-14 14:35:53 +00:00
765cf9d418
Merge branch 'features/improved-oop-architecture' into features/non-exact-notation
2025-02-12 17:53:25 +00:00
348c3d00b4
Updated README.md to be more clear
2025-02-12 17:52:53 +00:00
1c3f7f9ed8
Removed test for instantiating local MLST profiler
2025-02-12 17:46:55 +00:00
e4ddaf2e8c
Changed to a MLST typable sequence for pubMLST tests
2025-02-12 17:43:26 +00:00
73aade2bde
Merge branch 'features/improved-oop-architecture' into features/non-exact-notation
2025-02-12 17:07:51 +00:00
af8590baa7
Removed import of deleted feature
2025-02-12 17:07:10 +00:00
36bca1b70d
Merge branch 'features/improved-oop-architecture' into features/non-exact-notation
2025-02-12 17:02:22 +00:00
09a693b696
Removed features being worked on in separate branch
2025-02-12 17:02:00 +00:00
f76bf86ef6
Fixed bad profile for H. influenzae non-exact test case
2025-02-12 16:59:50 +00:00
a60daf3ee2
Updated H. influenzae database API url
2025-02-12 16:39:13 +00:00
fbfd993269
Copied tests over from CSV tests and updated to reflect current code base
2025-02-12 16:36:59 +00:00
ba606c35a9
conversion of collection of alleles to map now produces results with tuples instead of lists
2025-02-12 16:36:31 +00:00
4183840ba0
Added notation to indicate inexact matching in CSV
2025-02-12 15:59:19 +00:00
7fb3eab5b6
Added pubMLST test case to bigsdb tests and updated to reflect codebase changes
2025-02-12 15:53:14 +00:00
175a51f968
Replaced local profiler with a not implemented exception
2025-02-12 15:52:48 +00:00
897f7ee922
Merge branch 'develop' into features/local-typing
automlst.engine/pipeline/head Something is wrong with the build of this commit
2025-02-12 15:01:12 +00:00
bfc286e6b0
Updated test cases to reflect changes in codebase
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MLSTProfile will always return a value, even if there were no exact matches.
Removed a test case specifically testing for stopping on failure, which is a removed feature.
2025-02-12 14:57:51 +00:00
a88225fcff
Added check to wrap string into list to prevent decomposing string for querying
2025-02-12 14:46:29 +00:00
c18d817cd9
Added test to verify that CSV target columns are ordered
2025-02-12 14:38:12 +00:00
f462e6d5e0
Moved "LazyPersistentCachedBIGSdbMLSTProfiler" to separate branch and deleted from current branch
2025-02-11 19:24:23 +00:00
e568e9fb2c
Adapted latest merged reading codebase to current codebase
2025-02-11 19:13:29 +00:00
4b9eb8674d
Merge branch 'develop' into features/local-typing
2025-02-11 17:55:34 +00:00
f75707e4fe
CSV output column order is now predictable (sorted)
2025-02-11 17:54:48 +00:00
b4845fab34
Added automatic handling of strings instead of arrays of sequences to typing
2025-02-06 21:15:50 +00:00
fe999f1cab
Added a unit test for multithreaded alignments
2025-02-06 18:01:50 +00:00
85946eb110
Fixed match metric difference between remote and local
2025-02-06 17:12:31 +00:00
a27e09da31
Added code to retrieve sequences and annotations from NCBI GenBank
2025-02-06 17:11:20 +00:00
ba2b688e89
Removed sorting as it seems unecessary
2025-02-05 22:06:50 +00:00
49f31b7943
Async aligner work tracking issue fixed
2025-02-05 21:47:51 +00:00
1c6e1cfb35
Fixed issue with hashing a ndarray by using tuple.
2025-02-05 20:43:53 +00:00
fb99526162
Updated iteration on asynchronous aligner
2025-02-05 17:17:37 +00:00
ff8a1aff08
Implemented annotated local typing method without testing
2025-02-04 16:19:00 +00:00
341ca933a3
Fixed typo in CI script
2025-01-29 17:00:25 +00:00
3e3898334f
Began implementing LazyPersistentCachedBIGSdbMLSTProfiler
2025-01-27 22:03:49 +00:00
ba1f0aa318
Fixed potential memory leak
2025-01-27 22:02:52 +00:00
6d0157581f
Removed conda environment step for now
2025-01-24 21:43:55 +00:00
4bcbfa0c6a
Began adding conda steps for automatic PRs to Bioconda
2025-01-24 19:33:27 +00:00
ca0f9673b0
Upgraded Python version requirement due to use of f-strings
2025-01-24 17:00:57 +00:00
5048fa8057
Deleted uneeded file
2025-01-23 19:23:56 +00:00
39125c848e
Added a wildcard patch specifier for aiohttp
2025-01-23 19:23:42 +00:00
744a6c2009
Pinned key dependency versions
2025-01-23 17:57:07 +00:00
1773bb9dcb
Updated naming (again).
2025-01-22 21:05:19 +00:00
1372141b57
Fixed typo in Jenkinsfile
2025-01-22 20:30:55 +00:00
677c5e1aa8
Revert "Reapply "Began preparing for conda deployment""
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This reverts commit ade2f3b84572b4356d404da2dbcd1d7266f10205.
2025-01-22 18:29:37 +00:00
53e74af20a
Refactoring project name to autoBIGSst.engine
2025-01-22 18:24:04 +00:00
