gff3-validator 0.1.0__py3-none-any.whl

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Files changed (24) hide show
  1. gff3_validator/__init__.py +25 -0
  2. gff3_validator/__main__.py +5 -0
  3. gff3_validator/catalogue.yaml +1537 -0
  4. gff3_validator/checks/__init__.py +1 -0
  5. gff3_validator/checks/attributes.py +262 -0
  6. gff3_validator/checks/biology.py +517 -0
  7. gff3_validator/checks/directives.py +170 -0
  8. gff3_validator/checks/structure.py +436 -0
  9. gff3_validator/checks/syntax.py +204 -0
  10. gff3_validator/cli.py +84 -0
  11. gff3_validator/codons.py +182 -0
  12. gff3_validator/engine.py +316 -0
  13. gff3_validator/findings.py +32 -0
  14. gff3_validator/genome.py +284 -0
  15. gff3_validator/header.py +33 -0
  16. gff3_validator/reader.py +72 -0
  17. gff3_validator/report.py +385 -0
  18. gff3_validator/rules.py +147 -0
  19. gff3_validator/web.py +106 -0
  20. gff3_validator-0.1.0.dist-info/METADATA +331 -0
  21. gff3_validator-0.1.0.dist-info/RECORD +24 -0
  22. gff3_validator-0.1.0.dist-info/WHEEL +4 -0
  23. gff3_validator-0.1.0.dist-info/entry_points.txt +3 -0
  24. gff3_validator-0.1.0.dist-info/licenses/LICENSE +21 -0
gff3_validator/__init__.py ADDED
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+ """gff3-validator: validate GFF3 files against GFF3 1.26 and the Sequence Ontology.
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+
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+ Pre-release. Only the rules marked ``implemented`` in the catalogue are checked.
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+ """
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+
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+ __version__ = "0.1.0"
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+
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+ from gff3_validator.engine import Report, Validator, validate # noqa: E402
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+ from gff3_validator.findings import Finding # noqa: E402
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+ from gff3_validator.genome import GenomeError # noqa: E402
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+ from gff3_validator.reader import InputError # noqa: E402
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+ from gff3_validator.rules import Catalogue, Rule, load_catalogue # noqa: E402
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+
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+ __all__ = [
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+ "Catalogue",
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+ "Finding",
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+ "GenomeError",
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+ "InputError",
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+ "Report",
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+ "Rule",
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+ "Validator",
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+ "__version__",
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+ "load_catalogue",
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+ "validate",
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+ ]
gff3_validator/__main__.py ADDED
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+ import sys
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+
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+ from gff3_validator.cli import main
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+
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+ sys.exit(main())