AdvancedAnalysisFileParser 0.1.1__tar.gz → 0.1.2__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 (66) hide show
  1. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Warnings/GenotypeWarning.py +5 -2
  2. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser.egg-info/PKG-INFO +1 -1
  3. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/PKG-INFO +1 -1
  4. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/pyproject.toml +1 -1
  5. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/AdvancedAnalysisConstants.py +0 -0
  6. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/AdvancedAnalysisParser.py +0 -0
  7. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Models/ConditionOperator.py +0 -0
  8. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Models/FieldCondition.py +0 -0
  9. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Models/FieldWarningConfig.py +0 -0
  10. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Models/JsonDict.py +0 -0
  11. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Models/SectionConfig.py +0 -0
  12. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Models/__init__.py +0 -0
  13. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Parsers/AdvancedAnalysisFileParserFactory.py +0 -0
  14. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Parsers/DragenTruSightOncology500TSVParser.py +0 -0
  15. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Parsers/IAdvancedAnalysisFileParser.py +0 -0
  16. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Parsers/JsonSectionParser.py +0 -0
  17. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Parsers/OneLineTsvParser.py +0 -0
  18. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Parsers/__init__.py +0 -0
  19. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/README.md +0 -0
  20. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/TruSightOncology500.CombinedVariantOutput.tsv +0 -0
  21. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/dragen424.targeted.json +0 -0
  22. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/dummy_gba_affected_nonrecomb_acn2.targeted.json +0 -0
  23. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/dummy_gba_carrier_one_recomb_only.targeted.json +0 -0
  24. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/dummy_gba_phase_unknown_one_recomb_plus_variant.targeted.json +0 -0
  25. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/dummy_warnset_1.targeted.json +0 -0
  26. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/dummy_warnset_2.targeted.json +0 -0
  27. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/dummy_warnset_3.targeted.json +0 -0
  28. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/gba.tsv +0 -0
  29. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/gba_carrier_1.json +0 -0
  30. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/gba_carrier_2.json +0 -0
  31. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/gba_multiple_phase_unknown_1.json +0 -0
  32. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/gba_multiple_phase_unknown_2.json +0 -0
  33. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/gba_positive_1.json +0 -0
  34. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/gba_positive_2.json +0 -0
  35. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/hba_carrier_1.json +0 -0
  36. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/hba_carrier_2.json +0 -0
  37. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/hba_carrier_3.json +0 -0
  38. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/hba_carrier_4.json +0 -0
  39. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/hba_hemoglobin_h_disease.json +0 -0
  40. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/hba_silent_carrier.json +0 -0
  41. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/smn.tsv +0 -0
  42. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/smn_carrier.json +0 -0
  43. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/smn_positive.json +0 -0
  44. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test/smn_silent_carrier_risk.json +0 -0
  45. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Test_AdvancedAnalysisParser.py +0 -0
  46. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Warnings/CarrierPositiveWarning.py +0 -0
  47. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Warnings/ConditionWarning.py +0 -0
  48. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Warnings/GbaWarning.py +0 -0
  49. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Warnings/IWarning.py +0 -0
  50. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Warnings/SmnWarning.py +0 -0
  51. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Warnings/WarningFactory.py +0 -0
  52. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Warnings/__init__.py +0 -0
  53. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/__init__.py +0 -0
  54. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/advConfig.json +0 -0
  55. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/dragen_500_tsv_config.json +0 -0
  56. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/gba_tsv_config.json +0 -0
  57. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/run_test_parser.py +0 -0
  58. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/smn_tsv_config.json +0 -0
  59. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser.egg-info/SOURCES.txt +0 -0
  60. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser.egg-info/dependency_links.txt +0 -0
  61. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser.egg-info/entry_points.txt +0 -0
  62. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser.egg-info/top_level.txt +0 -0
  63. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/LICENSE +0 -0
  64. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/MANIFEST.in +0 -0
  65. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/README.md +0 -0
  66. {advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/setup.cfg +0 -0
{advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser/Warnings/GenotypeWarning.py RENAMED
@@ -22,11 +22,14 @@ class GenotypeWarning(IWarning):
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  if all(isinstance(v, str) for v in mapping.values()):
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  # Old format: genotype→phenotype
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  if sample in mapping:
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- warning = f"Based on {name}, this sample is defined as <b>{mapping[sample]}</b>"
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+ phenotype = mapping[sample]
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+ if phenotype != "normal":
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+ warning = f"Based on {name}, this sample is defined as <b>{phenotype}</b>"
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  elif all(isinstance(v, list) for v in mapping.values()):
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  # New format: phenotype→[genotypes]
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  for phenotype, genotypes in mapping.items():
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  if sample in genotypes:
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- warning = f"Based on {name}, this sample is defined as <b>{phenotype}</b>"
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+ if phenotype != "normal":
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+ warning = f"Based on {name}, this sample is defined as <b>{phenotype}</b>"
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  break
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  return warning
{advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/AdvancedAnalysisFileParser.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: AdvancedAnalysisFileParser
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- Version: 0.1.1
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+ Version: 0.1.2
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  Summary: Parse Illumina-DRAGEN TSV/JSON outputs to unified geneyx JSON with warnings.
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  Author: Bar Cohen
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  Author-email: Bar Cohen <bar@geneyx.com>
{advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: AdvancedAnalysisFileParser
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- Version: 0.1.1
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+ Version: 0.1.2
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  Summary: Parse Illumina-DRAGEN TSV/JSON outputs to unified geneyx JSON with warnings.
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  Author: Bar Cohen
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  Author-email: Bar Cohen <bar@geneyx.com>
{advancedanalysisfileparser-0.1.1 → advancedanalysisfileparser-0.1.2}/pyproject.toml RENAMED
@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "AdvancedAnalysisFileParser"
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- version = "0.1.1"
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+ version = "0.1.2"
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  description = "Parse Illumina-DRAGEN TSV/JSON outputs to unified geneyx JSON with warnings."
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  authors = [
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  { name="Bar Cohen", email="bar@geneyx.com" }