ribometric 1.5.0__tar.gz

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Files changed (64) hide show
  1. ribometric-1.5.0/AUTHORS.rst +13 -0
  2. ribometric-1.5.0/CHANGELOG.md +722 -0
  3. ribometric-1.5.0/CITATION.cff +24 -0
  4. ribometric-1.5.0/CONTRIBUTING.rst +94 -0
  5. ribometric-1.5.0/LICENSE +22 -0
  6. ribometric-1.5.0/MANIFEST.in +29 -0
  7. ribometric-1.5.0/PKG-INFO +333 -0
  8. ribometric-1.5.0/README.rst +261 -0
  9. ribometric-1.5.0/RiboMetric/RiboMetric.py +634 -0
  10. ribometric-1.5.0/RiboMetric/__init__.py +5 -0
  11. ribometric-1.5.0/RiboMetric/arg_parser.py +434 -0
  12. ribometric-1.5.0/RiboMetric/bam_processing.py +853 -0
  13. ribometric-1.5.0/RiboMetric/cli.py +46 -0
  14. ribometric-1.5.0/RiboMetric/config.yml +360 -0
  15. ribometric-1.5.0/RiboMetric/evaluate.py +139 -0
  16. ribometric-1.5.0/RiboMetric/file_parser.py +610 -0
  17. ribometric-1.5.0/RiboMetric/file_splitting.py +255 -0
  18. ribometric-1.5.0/RiboMetric/html_report.py +478 -0
  19. ribometric-1.5.0/RiboMetric/metrics.py +1147 -0
  20. ribometric-1.5.0/RiboMetric/modules.py +1729 -0
  21. ribometric-1.5.0/RiboMetric/plots.py +1310 -0
  22. ribometric-1.5.0/RiboMetric/qc.py +1244 -0
  23. ribometric-1.5.0/RiboMetric/registry.py +461 -0
  24. ribometric-1.5.0/RiboMetric/results_output.py +923 -0
  25. ribometric-1.5.0/RiboMetric/rust.py +524 -0
  26. ribometric-1.5.0/RiboMetric/scoring.py +377 -0
  27. ribometric-1.5.0/RiboMetric/templates/RiboMetric_favicon.png +0 -0
  28. ribometric-1.5.0/RiboMetric/templates/RiboMetric_logo.png +0 -0
  29. ribometric-1.5.0/RiboMetric/templates/__init__.py +1 -0
  30. ribometric-1.5.0/RiboMetric/templates/base.html +412 -0
  31. ribometric-1.5.0/RiboMetric/tui.py +572 -0
  32. ribometric-1.5.0/docs/AUDIT_NOTES.md +201 -0
  33. ribometric-1.5.0/docs/METRICS.md +144 -0
  34. ribometric-1.5.0/docs/METRICS_DESIGN.md +653 -0
  35. ribometric-1.5.0/docs/METRIC_CONTRACT.md +660 -0
  36. ribometric-1.5.0/docs/METRIC_NAMING.md +210 -0
  37. ribometric-1.5.0/docs/Makefile +20 -0
  38. ribometric-1.5.0/docs/PRODUCTIONISATION.md +305 -0
  39. ribometric-1.5.0/docs/RELEASE.md +137 -0
  40. ribometric-1.5.0/docs/REPORTING_GUIDE.md +469 -0
  41. ribometric-1.5.0/docs/SCORING_PHASE1_TASKS.md +137 -0
  42. ribometric-1.5.0/docs/TESTING.md +297 -0
  43. ribometric-1.5.0/docs/V1.2_REPORT_AND_PREPRINT_PLAN.md +224 -0
  44. ribometric-1.5.0/docs/authors.rst +1 -0
  45. ribometric-1.5.0/docs/conf.py +225 -0
  46. ribometric-1.5.0/docs/contributing.rst +1 -0
  47. ribometric-1.5.0/docs/functions.rst +215 -0
  48. ribometric-1.5.0/docs/history.md +10 -0
  49. ribometric-1.5.0/docs/index.rst +28 -0
  50. ribometric-1.5.0/docs/installation.rst +73 -0
  51. ribometric-1.5.0/docs/make.bat +36 -0
  52. ribometric-1.5.0/docs/readme.rst +1 -0
  53. ribometric-1.5.0/docs/results.rst +77 -0
  54. ribometric-1.5.0/docs/usage.rst +145 -0
  55. ribometric-1.5.0/pyproject.toml +25 -0
  56. ribometric-1.5.0/ribometric.egg-info/PKG-INFO +333 -0
  57. ribometric-1.5.0/ribometric.egg-info/SOURCES.txt +62 -0
  58. ribometric-1.5.0/ribometric.egg-info/dependency_links.txt +1 -0
  59. ribometric-1.5.0/ribometric.egg-info/entry_points.txt +3 -0
  60. ribometric-1.5.0/ribometric.egg-info/not-zip-safe +1 -0
  61. ribometric-1.5.0/ribometric.egg-info/requires.txt +40 -0
  62. ribometric-1.5.0/ribometric.egg-info/top_level.txt +1 -0
  63. ribometric-1.5.0/setup.cfg +4 -0
  64. ribometric-1.5.0/setup.py +118 -0
ribometric-1.5.0/AUTHORS.rst ADDED
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+ =======
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+ Credits
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+ =======
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+
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+ Development Lead
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+ ----------------
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+
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+ * Jack Tierney <jackcurragh@gmail.com>
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+
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+ Contributors
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+ ------------
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+
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+ None yet. Why not be the first?