AdvancedAnalysisFileParser 0.1.0__py3-none-any.whl

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Files changed (60) hide show
  1. AdvancedAnalysisFileParser/AdvancedAnalysisConstants.py +9 -0
  2. AdvancedAnalysisFileParser/AdvancedAnalysisParser.py +129 -0
  3. AdvancedAnalysisFileParser/Models/ConditionOperator.py +9 -0
  4. AdvancedAnalysisFileParser/Models/FieldCondition.py +29 -0
  5. AdvancedAnalysisFileParser/Models/FieldWarningConfig.py +4 -0
  6. AdvancedAnalysisFileParser/Models/JsonDict.py +2 -0
  7. AdvancedAnalysisFileParser/Models/SectionConfig.py +8 -0
  8. AdvancedAnalysisFileParser/Models/__init__.py +13 -0
  9. AdvancedAnalysisFileParser/Parsers/AdvancedAnalysisFileParserFactory.py +36 -0
  10. AdvancedAnalysisFileParser/Parsers/DragenTruSightOncology500TSVParser.py +102 -0
  11. AdvancedAnalysisFileParser/Parsers/IAdvancedAnalysisFileParser.py +86 -0
  12. AdvancedAnalysisFileParser/Parsers/JsonSectionParser.py +39 -0
  13. AdvancedAnalysisFileParser/Parsers/OneLineTsvParser.py +26 -0
  14. AdvancedAnalysisFileParser/Parsers/__init__.py +7 -0
  15. AdvancedAnalysisFileParser/README.md +570 -0
  16. AdvancedAnalysisFileParser/Test/TruSightOncology500.CombinedVariantOutput.tsv +1586 -0
  17. AdvancedAnalysisFileParser/Test/dragen424.targeted.json +202 -0
  18. AdvancedAnalysisFileParser/Test/dummy_gba_affected_nonrecomb_acn2.targeted.json +21 -0
  19. AdvancedAnalysisFileParser/Test/dummy_gba_carrier_one_recomb_only.targeted.json +14 -0
  20. AdvancedAnalysisFileParser/Test/dummy_gba_phase_unknown_one_recomb_plus_variant.targeted.json +21 -0
  21. AdvancedAnalysisFileParser/Test/dummy_warnset_1.targeted.json +132 -0
  22. AdvancedAnalysisFileParser/Test/dummy_warnset_2.targeted.json +145 -0
  23. AdvancedAnalysisFileParser/Test/dummy_warnset_3.targeted.json +146 -0
  24. AdvancedAnalysisFileParser/Test/gba.tsv +2 -0
  25. AdvancedAnalysisFileParser/Test/gba_carrier_1.json +96 -0
  26. AdvancedAnalysisFileParser/Test/gba_carrier_2.json +101 -0
  27. AdvancedAnalysisFileParser/Test/gba_multiple_phase_unknown_1.json +101 -0
  28. AdvancedAnalysisFileParser/Test/gba_multiple_phase_unknown_2.json +105 -0
  29. AdvancedAnalysisFileParser/Test/gba_positive_1.json +96 -0
  30. AdvancedAnalysisFileParser/Test/gba_positive_2.json +101 -0
  31. AdvancedAnalysisFileParser/Test/hba_carrier_1.json +96 -0
  32. AdvancedAnalysisFileParser/Test/hba_carrier_2.json +96 -0
  33. AdvancedAnalysisFileParser/Test/hba_carrier_3.json +96 -0
  34. AdvancedAnalysisFileParser/Test/hba_carrier_4.json +96 -0
  35. AdvancedAnalysisFileParser/Test/hba_hemoglobin_h_disease.json +96 -0
  36. AdvancedAnalysisFileParser/Test/hba_silent_carrier.json +96 -0
  37. AdvancedAnalysisFileParser/Test/smn.tsv +2 -0
  38. AdvancedAnalysisFileParser/Test/smn_carrier.json +96 -0
  39. AdvancedAnalysisFileParser/Test/smn_positive.json +96 -0
  40. AdvancedAnalysisFileParser/Test/smn_silent_carrier_risk.json +101 -0
  41. AdvancedAnalysisFileParser/Test_AdvancedAnalysisParser.py +342 -0
  42. AdvancedAnalysisFileParser/Warnings/CarrierPositiveWarning.py +18 -0
  43. AdvancedAnalysisFileParser/Warnings/ConditionWarning.py +20 -0
  44. AdvancedAnalysisFileParser/Warnings/GbaWarning.py +50 -0
  45. AdvancedAnalysisFileParser/Warnings/GenotypeWarning.py +22 -0
  46. AdvancedAnalysisFileParser/Warnings/IWarning.py +7 -0
  47. AdvancedAnalysisFileParser/Warnings/SmnWarning.py +29 -0
  48. AdvancedAnalysisFileParser/Warnings/WarningFactory.py +31 -0
  49. AdvancedAnalysisFileParser/Warnings/__init__.py +7 -0
  50. AdvancedAnalysisFileParser/__init__.py +18 -0
  51. AdvancedAnalysisFileParser/advConfig.json +96 -0
  52. AdvancedAnalysisFileParser/dragen_500_tsv_config.json +53 -0
  53. AdvancedAnalysisFileParser/gba_tsv_config.json +23 -0
  54. AdvancedAnalysisFileParser/run_test_parser.py +29 -0
  55. AdvancedAnalysisFileParser/smn_tsv_config.json +23 -0
  56. advancedanalysisfileparser-0.1.0.dist-info/METADATA +152 -0
  57. advancedanalysisfileparser-0.1.0.dist-info/RECORD +60 -0
  58. advancedanalysisfileparser-0.1.0.dist-info/WHEEL +5 -0
  59. advancedanalysisfileparser-0.1.0.dist-info/licenses/LICENSE +9 -0
  60. advancedanalysisfileparser-0.1.0.dist-info/top_level.txt +1 -0
AdvancedAnalysisFileParser/Test/gba_carrier_1.json ADDED
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+ "genotype": "aa/aa",
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+ "genotypeQuality": 56,
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+ "genotypeFilter": "PASS",
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+ "variants": []
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+ "smn": {
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+ "totalCopyNumberFloat": "3.56",
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+ "variants": []
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+ }
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+ }
AdvancedAnalysisFileParser/Test/gba_carrier_2.json ADDED
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+ "sampleId": "22WVHMLT4_5_270UDI-idt-UMI",
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+ "genomeBuild": "hg38",
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+ "phenotypeDatabaseSources": [
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+ ],
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+ "cyp2b6": {
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+ "genotype": "*1/*29",
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+ "genotypeFilter": "PASS",
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+ "phenotypeDatabaseAnnotation": "Intermediate Metabolizer"
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+ },
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+ "lpa": {
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+ "refMarkerAlleleCopyNumber": null,
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+ "altMarkerAlleleCopyNumber": null,
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+ "phenotypeDatabaseAnnotation": "Intermediate Metabolizer",
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+ "variants": [
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+ "alleleId": "g.42126938C>T",
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+ "alleleCopyNumber": 2,
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+ "gba": {
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+ "hba": {
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+ "genotype": "aa/aa",
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+ "totalCopyNumberFloat": "3.56",
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+ "variants": []
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+ }
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+ }
AdvancedAnalysisFileParser/Test/gba_multiple_phase_unknown_1.json ADDED
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+ {
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+ "softwareVersion": "dragen v05.121.779.4.4.4",
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+ "sampleId": "22WVHMLT4_5_270UDI-idt-UMI",
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+ "genomeBuild": "hg38",
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+ "phenotypeDatabaseSources": [
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+ "PharmCAT Phenotypes Version: Snapshot-2022.09.15"
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+ ],
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+ "cyp2b6": {
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+ "genotype": "*1/*29",
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+ "genotypeFilter": "PASS",
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+ "phenotypeDatabaseAnnotation": "Intermediate Metabolizer"
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+ },
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+ "lpa": {
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+ "kiv2CopyNumber": 39.45213332616308,
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+ "refMarkerAlleleCopyNumber": null,
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+ "altMarkerAlleleCopyNumber": null,
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+ "type": "Homozygous REF markers call",
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+ "variants": [
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+ "altCopyNumber": 0,
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+ "cyp21a2": {
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+ "recombinantHaplotypes": [
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+ "variants": []
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+ "cyp2d6": {
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+ "phenotypeDatabaseAnnotation": "Intermediate Metabolizer",
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+ "variants": [
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+ "gba": {
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+ }
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AdvancedAnalysisFileParser/Test/gba_multiple_phase_unknown_2.json ADDED
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+ "genomeBuild": "hg38",
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+ "phenotypeDatabaseSources": [
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+ "PharmCAT Phenotypes Version: Snapshot-2022.09.15"
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+ ],
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+ "cyp2b6": {
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AdvancedAnalysisFileParser/Test/gba_positive_1.json ADDED
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+ "cyp21a2": {
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+ "recombinantHaplotypes": [
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+ "variants": []
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+ },
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+ "cyp2d6": {
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+ "genotype": "*1/*5",
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+ "genotypeFilter": "PASS",
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+ "genotypeQuality": 150,
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+ "phenotypeDatabaseAnnotation": "Intermediate Metabolizer",
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+ "variants": [
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+ {
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+ "alleleId": "g.42126938C>T",
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+ "alleleCopyNumber": 2,
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+ "genotypeQuality": 21,
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+ "filter": "PASS"
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+ }
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+ ]
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+ },
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+ "gba": {
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+ "deletionBreakpointInGene": null,
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+ "rec2"
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+ ],
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+ "hba": {
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+ "variants": []
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+ "smn": {
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+ "variants": []
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+ }
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+ }
AdvancedAnalysisFileParser/Test/gba_positive_2.json ADDED
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+ {
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+ "softwareVersion": "dragen v05.121.779.4.4.4",
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+ "sampleId": "22WVHMLT4_5_270UDI-idt-UMI",
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+ "genomeBuild": "hg38",
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+ "phenotypeDatabaseSources": [
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+ "PharmCAT Phenotypes Version: Snapshot-2022.09.15"
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@@ -0,0 +1,96 @@
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