AdvancedAnalysisFileParser 0.1.2__tar.gz → 0.1.3__tar.gz

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 (87) hide show
  1. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/HG002.paraphase.json +128289 -0
  2. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Parsers/AdvancedAnalysisFileParserFactory.py +6 -1
  3. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Parsers/JsonSectionParser.py +125 -0
  4. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/README.md +1 -1
  5. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/HG002.paraphase.json +128289 -0
  6. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_display_f8.json +9 -0
  7. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_display_gba.json +10 -0
  8. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_display_hba.json +9 -0
  9. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_display_ncf1.json +10 -0
  10. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_display_pms2.json +10 -0
  11. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_display_rccx.json +11 -0
  12. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_display_smn.json +12 -0
  13. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_display_strc.json +10 -0
  14. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_hba_carrier_aaa_reversed.json +10 -0
  15. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_hba_carrier_reversed.json +10 -0
  16. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_hba_commutative.json +10 -0
  17. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_hba_positive_h_disease.json +10 -0
  18. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_hba_positive_h_disease_reversed.json +10 -0
  19. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_smn_positive.json +10 -0
  20. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/paraphase_smn_silent_carrier.json +17 -0
  21. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Test_AdvancedAnalysisParser.py +265 -17
  22. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Warnings/GenotypeWarning.py +56 -0
  23. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Warnings/SmnWarning.py +87 -0
  24. advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/pacbio_paraphase_config.json +131 -0
  25. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/run_test_parser.py +2 -2
  26. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser.egg-info/PKG-INFO +2 -2
  27. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser.egg-info/SOURCES.txt +34 -16
  28. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/PKG-INFO +2 -2
  29. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/README.md +1 -1
  30. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/pyproject.toml +1 -1
  31. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/setup.cfg +2 -2
  32. advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Parsers/JsonSectionParser.py +0 -39
  33. advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Warnings/GenotypeWarning.py +0 -35
  34. advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Warnings/SmnWarning.py +0 -39
  35. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/AdvancedAnalysisConstants.py +0 -0
  36. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/AdvancedAnalysisParser.py +0 -0
  37. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Models/ConditionOperator.py +0 -0
  38. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Models/FieldCondition.py +0 -0
  39. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Models/FieldWarningConfig.py +0 -0
  40. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Models/JsonDict.py +0 -0
  41. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Models/SectionConfig.py +0 -0
  42. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Models/__init__.py +0 -0
  43. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Parsers/DragenTruSightOncology500TSVParser.py +0 -0
  44. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Parsers/IAdvancedAnalysisFileParser.py +0 -0
  45. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Parsers/OneLineTsvParser.py +0 -0
  46. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Parsers/__init__.py +0 -0
  47. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Test/TruSightOncology500.CombinedVariantOutput.tsv +0 -0
  48. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Test/dragen424.targeted.json +0 -0
  49. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Test/dummy_gba_affected_nonrecomb_acn2.targeted.json +0 -0
  50. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Test/dummy_gba_carrier_one_recomb_only.targeted.json +0 -0
  51. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Test/dummy_gba_phase_unknown_one_recomb_plus_variant.targeted.json +0 -0
  52. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Test/dummy_warnset_1.targeted.json +0 -0
  53. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Test/dummy_warnset_2.targeted.json +0 -0
  54. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Test/dummy_warnset_3.targeted.json +0 -0
  55. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Test/gba.tsv +0 -0
  56. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/gba_carrier_1.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/gba_carrier_1.targeted.json +0 -0
  57. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/gba_carrier_2.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/gba_carrier_2.targeted.json +0 -0
  58. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/gba_multiple_phase_unknown_1.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/gba_multiple_phase_unknown_1.targeted.json +0 -0
  59. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/gba_multiple_phase_unknown_2.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/gba_multiple_phase_unknown_2.targeted.json +0 -0
  60. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/gba_positive_1.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/gba_positive_1.targeted.json +0 -0
  61. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/gba_positive_2.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/gba_positive_2.targeted.json +0 -0
  62. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/hba_carrier_1.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/hba_carrier_1.targeted.json +0 -0
  63. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/hba_carrier_2.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/hba_carrier_2.targeted.json +0 -0
  64. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/hba_carrier_3.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/hba_carrier_3.targeted.json +0 -0
  65. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/hba_carrier_4.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/hba_carrier_4.targeted.json +0 -0
  66. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/hba_hemoglobin_h_disease.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/hba_hemoglobin_h_disease.targeted.json +0 -0
  67. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/hba_silent_carrier.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/hba_silent_carrier.targeted.json +0 -0
  68. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Test/smn.tsv +0 -0
  69. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/smn_carrier.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/smn_carrier.targeted.json +0 -0
  70. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/smn_positive.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/smn_positive.targeted.json +0 -0
  71. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/Test/smn_silent_carrier_risk.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/Test/smn_silent_carrier_risk.targeted.json +0 -0
  72. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Warnings/CarrierPositiveWarning.py +0 -0
  73. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Warnings/ConditionWarning.py +0 -0
  74. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Warnings/GbaWarning.py +0 -0
  75. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Warnings/IWarning.py +0 -0
  76. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Warnings/WarningFactory.py +0 -0
  77. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/Warnings/__init__.py +0 -0
  78. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/__init__.py +0 -0
  79. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/dragen_500_tsv_config.json +0 -0
  80. /advancedanalysisfileparser-0.1.2/AdvancedAnalysisFileParser/advConfig.json → /advancedanalysisfileparser-0.1.3/AdvancedAnalysisFileParser/dragen_targeted_config.json +0 -0
  81. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/gba_tsv_config.json +0 -0
  82. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser/smn_tsv_config.json +0 -0
  83. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser.egg-info/dependency_links.txt +0 -0
  84. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser.egg-info/entry_points.txt +0 -0
  85. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/AdvancedAnalysisFileParser.egg-info/top_level.txt +0 -0
  86. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/LICENSE +0 -0
  87. {advancedanalysisfileparser-0.1.2 → advancedanalysisfileparser-0.1.3}/MANIFEST.in +0 -0

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