├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ ├── cd-pypi.yml │ ├── ci-lint.yml │ ├── ci-package.yml │ └── ci-test.yml ├── .gitignore ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTION.md ├── LICENSE ├── README.md ├── bin └── tadrep ├── environment.yml ├── images └── tadrep.png ├── pytest.ini ├── setup.py ├── tadrep ├── __init__.py ├── blast.py ├── characterize.py ├── cluster.py ├── config.py ├── database │ ├── __init__.py │ ├── main.py │ ├── plsdb.py │ └── refseq.py ├── detect.py ├── extract.py ├── io.py ├── main.py ├── plasmids.py ├── setup.py ├── utils.py └── visualize.py └── test ├── __init__.py ├── conftest.py ├── data ├── blastn.tsv ├── db.json ├── draft.fna ├── inc-types.fasta └── plasmids.fna ├── test_args.py ├── test_blast.py ├── test_plasmids.py └── test_tadrep.py /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- 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