scout-browser 4.96.0__py3-none-any.whl → 4.97.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (85) hide show
  1. scout/adapter/mongo/case.py +51 -47
  2. scout/adapter/mongo/filter.py +28 -11
  3. scout/adapter/mongo/institute.py +2 -0
  4. scout/adapter/mongo/omics_variant.py +20 -5
  5. scout/adapter/mongo/query.py +104 -95
  6. scout/adapter/mongo/variant.py +0 -5
  7. scout/adapter/mongo/variant_loader.py +10 -12
  8. scout/build/individual.py +3 -11
  9. scout/commands/delete/delete_command.py +87 -49
  10. scout/commands/load/research.py +4 -4
  11. scout/commands/load/variants.py +25 -8
  12. scout/commands/setup/setup_scout.py +1 -1
  13. scout/commands/update/case.py +12 -0
  14. scout/commands/update/individual.py +1 -2
  15. scout/constants/__init__.py +7 -2
  16. scout/constants/file_types.py +68 -119
  17. scout/constants/filters.py +2 -1
  18. scout/constants/gene_tags.py +3 -3
  19. scout/constants/igv_tracks.py +7 -11
  20. scout/constants/query_terms.py +2 -2
  21. scout/demo/643594.config.yaml +6 -0
  22. scout/demo/643594.peddy.ped +1 -1
  23. scout/demo/643594.somalier.ancestry.tsv +4 -0
  24. scout/demo/643594.somalier.pairs.tsv +4 -0
  25. scout/demo/643594.somalier.samples.tsv +4 -0
  26. scout/demo/cancer.load_config.yaml +1 -0
  27. scout/demo/resources/__init__.py +1 -1
  28. scout/demo/resources/gnomad.v4.1.constraint_metrics_reduced.tsv +3755 -0
  29. scout/exceptions/database.py +1 -1
  30. scout/load/all.py +8 -16
  31. scout/models/case/case.py +1 -0
  32. scout/models/case/case_loading_models.py +12 -5
  33. scout/models/managed_variant.py +3 -3
  34. scout/models/omics_variant.py +3 -3
  35. scout/parse/case.py +112 -5
  36. scout/parse/pedqc.py +127 -0
  37. scout/parse/variant/frequency.py +9 -6
  38. scout/parse/variant/variant.py +71 -39
  39. scout/server/app.py +2 -0
  40. scout/server/blueprints/alignviewers/controllers.py +2 -0
  41. scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html +3 -0
  42. scout/server/blueprints/alignviewers/templates/alignviewers/utils.html +1 -1
  43. scout/server/blueprints/cases/controllers.py +23 -3
  44. scout/server/blueprints/cases/templates/cases/case.html +3 -0
  45. scout/server/blueprints/cases/templates/cases/chanjo2_form.html +2 -2
  46. scout/server/blueprints/cases/templates/cases/gene_panel.html +9 -3
  47. scout/server/blueprints/cases/templates/cases/individuals_table.html +4 -1
  48. scout/server/blueprints/cases/templates/cases/utils.html +23 -19
  49. scout/server/blueprints/cases/views.py +5 -9
  50. scout/server/blueprints/clinvar/controllers.py +11 -11
  51. scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +15 -7
  52. scout/server/blueprints/institutes/controllers.py +20 -1
  53. scout/server/blueprints/institutes/forms.py +5 -1
  54. scout/server/blueprints/institutes/templates/overview/institute_settings.html +7 -0
  55. scout/server/blueprints/institutes/templates/overview/utils.html +20 -1
  56. scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html +9 -2
  57. scout/server/blueprints/omics_variants/views.py +8 -10
  58. scout/server/blueprints/variant/controllers.py +30 -1
  59. scout/server/blueprints/variant/templates/variant/cancer-variant.html +19 -3
  60. scout/server/blueprints/variant/templates/variant/components.html +26 -9
  61. scout/server/blueprints/variant/templates/variant/variant.html +4 -2
  62. scout/server/blueprints/variant/utils.py +2 -0
  63. scout/server/blueprints/variants/controllers.py +29 -3
  64. scout/server/blueprints/variants/forms.py +37 -10
  65. scout/server/blueprints/variants/templates/variants/components.html +12 -10
  66. scout/server/blueprints/variants/templates/variants/utils.html +59 -36
  67. scout/server/blueprints/variants/views.py +45 -60
  68. scout/server/extensions/beacon_extension.py +1 -1
  69. scout/server/extensions/bionano_extension.py +5 -5
  70. scout/server/extensions/chanjo2_extension.py +40 -1
  71. scout/server/extensions/chanjo_extension.py +1 -1
  72. scout/server/extensions/matchmaker_extension.py +1 -1
  73. scout/server/static/bs_styles.css +2 -0
  74. scout/server/templates/layout.html +1 -0
  75. scout/server/utils.py +5 -0
  76. scout/utils/ensembl_biomart_clients.py +2 -11
  77. scout/utils/scout_requests.py +1 -1
  78. {scout_browser-4.96.0.dist-info → scout_browser-4.97.0.dist-info}/METADATA +1 -1
  79. {scout_browser-4.96.0.dist-info → scout_browser-4.97.0.dist-info}/RECORD +82 -80
  80. scout/demo/resources/gnomad.v4.0.constraint_metrics_reduced.tsv +0 -3755
  81. scout/parse/peddy.py +0 -149
  82. scout/utils/sort.py +0 -21
  83. {scout_browser-4.96.0.dist-info → scout_browser-4.97.0.dist-info}/WHEEL +0 -0
  84. {scout_browser-4.96.0.dist-info → scout_browser-4.97.0.dist-info}/entry_points.txt +0 -0
  85. {scout_browser-4.96.0.dist-info → scout_browser-4.97.0.dist-info}/licenses/LICENSE +0 -0

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