Sarand v2: Redevelopment and simplification - #8

Merged

fmaguire merged 50 commits into

Jun 22, 2026

Commits on Jun 15, 2026

Fix setup.py
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ab2e6c4
Move to more modern pyproject.toml
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1890cf5
Add pyrodigal dependency to replace rgi and bakta
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d31fdca
Update version and add more explanation to arg help
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816401a
Remove old extract code
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6011b61
Remove PDB, unused imports, and dead code
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6af1c06
Fix regex syntaxwarnings
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024398f

Commits on Jun 16, 2026

Remove graphaligner optional dependency
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177a9e3
Move visualisation code out of sarand proper into a standalone script
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99752ed
Remove bakta and RGI from annotation and just run pyrodigal
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e39d088
Remove awkward conda run environments now dependencies are simpler
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08d0aaa
Update tets
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10c6ebd
Major code refactor and reorganisation into more logical flow
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e27af1a
Remove direct calling
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928096a
Move to pathlib
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135b783
Fix CD-HIT paralellisation for big jobs - have multiprocessing pool handle parallelisation
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328fd50
Call blastn with num_threads
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455f75b
Replace inefficient graph pickling per AMR task
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85180bf
try out freezing and forking the graph context to prevent copying per worker - protect with COW
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7f3641b
Add NCBI database and CARD downloader
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d9b9b2a
Partial clean up of options
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b9c70eb
Properly run and check cd-hit as external dep
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6b54c55
Replace AMR specific language and separate ID/Coverage
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b629386
Rename output folders
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8083415
De-AMR target_finding
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482c755
Review and check bandage searching
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5a3ea7b
Fix alignment folders
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8c55217
Concatenate and retain bandage results
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1263e2c
Do AMR specific extract_targets
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3a761d5
Reduce redundancy in extract_neighborhood and strip redundancy
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c914f7c
Tidy output format
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e7d7a1b
Return ORF calling results for final neighborhoods
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5250257
Tidy up coverage filtering further
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59e78ef
Update readme
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a5c4ae0
Remove unused code; unusued imports; and add docstrings
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da3eb0f
update README
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fe9a67e
Remove commented out code
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5dfc985
Update dependencies
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c286de2

Commits on Jun 22, 2026

Fix length help
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5287073
Fix readme
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8a3624d
Update test, readme, and install
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34838cf
Tidy up parallelisation code
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9274652
Update unit and integration tests
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731e13b
Fix tests
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7bafd39
Move extract prints to log
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05db31f
Fix debugging output
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3f6197e
Update output paths for debugging
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5a414ab
Fix output format and gfapy bug
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e1db037
Replace blastn dedup with minimap2 and reduce redundant cd-hit calls
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a9fa6b7
Push updated Dockerfile
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7d03180