├── .github └── workflows │ └── ci.yml ├── .gitignore ├── .gitlab-ci.yml ├── CHANGELOG.md ├── INSTALL.sh ├── LICENSE.txt ├── NOTICE.txt ├── README.md ├── docs ├── CHANGELOG.md ├── examples.md ├── extra.css ├── format.md ├── img │ └── favicon.ico ├── index.md ├── install.md ├── news.md ├── output.md ├── parameters.md └── walkthrough.md ├── documentation └── math │ ├── Mathematics.bib │ ├── Mathematics.pdf │ └── Mathematics.tex ├── galaxy └── neptune │ └── neptune.xml ├── mkdocs.yml ├── pyproject.toml ├── src └── neptune │ ├── AggregateKMers.py │ ├── ConsolidateSignatures.py │ ├── CountKMers.py │ ├── Database.py │ ├── Execution.py │ ├── ExtractSignatures.py │ ├── FilterSignatures.py │ ├── JobManager.py │ ├── JobManagerParallel.py │ ├── Neptune.py │ ├── PrepareKMers.py │ ├── Signature.py │ ├── Utility.py │ └── __init__.py ├── tests ├── TestingUtility.py ├── __init__.py ├── data │ ├── aggregate │ │ ├── .gitkeep │ │ ├── aggregate1.kmers │ │ ├── aggregate2.kmers │ │ ├── aggregate3.kmers │ │ └── aggregate4.kmers │ ├── ambiguous │ │ ├── exclusion.fasta │ │ └── inclusion.fasta │ ├── count │ │ ├── .gitkeep │ │ └── count1.fasta │ ├── database │ │ ├── long.database │ │ │ ├── LONG.nhr │ │ │ ├── LONG.nin │ │ │ └── LONG.nsq │ │ ├── long.query │ │ ├── missing.query │ │ └── multiple.fasta │ ├── example │ │ ├── exclusion │ │ │ ├── exclusion1.fasta │ │ │ ├── exclusion2.fasta │ │ │ └── exclusion3.fasta │ │ └── inclusion │ │ │ ├── inclusion1.fasta │ │ │ ├── inclusion2.fasta │ │ │ └── inclusion3.fasta │ ├── execution │ │ └── simple.fasta │ ├── extract │ │ ├── .gitkeep │ │ ├── alternative.fasta │ │ ├── random.fasta │ │ ├── random.kmers │ │ ├── simple.fasta │ │ └── simple.kmers │ ├── filter │ │ ├── .gitkeep │ │ ├── long.database │ │ │ ├── LONG.nhr │ │ │ ├── LONG.nin │ │ │ └── LONG.nsq │ │ ├── long.fasta │ │ ├── long.query │ │ ├── missing.query │ │ └── multiple.fasta │ ├── long.database │ │ ├── LONG.nhr │ │ ├── LONG.nin │ │ └── LONG.nsq │ ├── long.fasta │ ├── long.query │ ├── manager │ │ ├── .gitkeep │ │ ├── alternative.fasta │ │ └── simple.fasta │ ├── neptune │ │ ├── .gitkeep │ │ ├── alternative.fasta │ │ ├── large_exclusion │ │ │ ├── ex0.fasta │ │ │ ├── ex1.fasta │ │ │ ├── ex2.fasta │ │ │ ├── ex3.fasta │ │ │ ├── ex4.fasta │ │ │ ├── ex5.fasta │ │ │ ├── ex6.fasta │ │ │ ├── ex7.fasta │ │ │ ├── ex8.fasta │ │ │ └── ex9.fasta │ │ ├── large_inclusion │ │ │ ├── in0.fasta │ │ │ ├── in1.fasta │ │ │ ├── in2.fasta │ │ │ ├── in3.fasta │ │ │ ├── in4.fasta │ │ │ ├── in5.fasta │ │ │ ├── in6.fasta │ │ │ ├── in7.fasta │ │ │ ├── in8.fasta │ │ │ └── in9.fasta │ │ ├── n.fasta │ │ ├── simple.fasta │ │ ├── simple_exclusion │ │ │ ├── exclusion1.fasta │ │ │ └── exclusion2.fasta │ │ └── simple_inclusion │ │ │ ├── inclusion1.fasta │ │ │ └── inclusion2.fasta │ ├── random.fasta │ ├── random.kmers │ ├── signature │ │ └── multiple.fasta │ ├── simple.kmers │ ├── simple_exclusion │ │ ├── exclusion1.fasta │ │ └── exclusion2.fasta │ ├── simple_inclusion │ │ ├── inclusion1.fasta │ │ └── inclusion2.fasta │ └── utility │ │ └── .gitkeep ├── output │ ├── .gitkeep │ ├── aggregate │ │ └── .gitkeep │ ├── count │ │ └── .gitkeep │ ├── database │ │ └── .gitkeep │ ├── extract │ │ └── .gitkeep │ ├── filter │ │ └── .gitkeep │ ├── manager │ │ ├── .gitkeep │ │ └── log │ │ │ └── .gitkeep │ ├── neptune │ │ └── .gitkeep │ └── utility │ │ └── .gitkeep ├── test_aggregate.py ├── test_count.py ├── test_database.py ├── test_execution.py ├── test_extract.py ├── test_filter.py ├── test_job_manager.py ├── test_neptune.py ├── test_signature.py └── test_utility.py └── tox.ini /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/phac-nml/neptune/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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