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/dragen424.targeted.json ADDED
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+ {
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+ "dragenVersion": "05.121.676.4.2.4a",
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+ "sample": "SRR12898317_",
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+ "pharmcatMetabolismStatusResourceUrl": "https://github.com/PharmGKB/PharmCAT/blob/aeecfe5f787e95dfb31ede62884e287affef45b3/src/main/resources/org/pharmgkb/pharmcat/definition/gene_phenotypes.json",
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+ "cyp2d6": {
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+ "genotype": "None",
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+ "genotypeFilter": "No_call",
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+ "pharmcatDescription": null,
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+ "pharmcatMetabolismStatus": null
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+ },
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+ "cyp2b6": {
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+ "genotype": "*1/*1",
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+ "genotypeFilter": "PASS",
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+ "pharmcatDescription": "null",
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+ "pharmcatMetabolismStatus": "Normal Metabolizer"
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+ },
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+ "cyp21a2": {
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+ "totalCopyNumber": 4,
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+ "deletionBreakpointInGene": null,
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+ "recombinantHaplotypes": [
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+ "",
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+ ""
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+ ],
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+ "variants": []
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+ },
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+ "lpa": {
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+ "kiv2CopyNumber": 36.90938336204826,
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+ "refMarkerAlleleCopyNumber": 22.284910709161213,
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+ "altMarkerAlleleCopyNumber": 14.624472652887047,
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+ "type": "Heterozygous markers call",
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+ "variants": [
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+ {
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+ "hgvs": "LPA:4925G>A",
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+ }
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+ ]
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+ },
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+ "hba": {
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+ "genotype": "aa/aa",
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+ "genotypeFilter": "PASS",
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+ "genotypeQual": 85.0,
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+ "minPValue": 0.0731288557825458,
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+ "variants": [
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+ "rh": {
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+ "totalCopyNumber": 4,
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+ "rhdCopyNumber": 2,
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+ "rhceCopyNumber": 2,
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+ "variants": [
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+ "hgvs": "NC_000001.11g.25405596_25409676con25283766_25287797",
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+ "altCopyNumber": 0,
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+ "altCopyNumberQuality": 0.0
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+ }
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+ ]
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+ },
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+ "smn": {
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+ "smn1CopyNumber": 2,
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+ "smn2CopyNumber": 2,
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+ "smn2Delta78CopyNumber": 0,
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+ "totalCopyNumberFloat": "4.01",
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+ "fullLengthCopyNumberFloat": "4.14",
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+ "variants": [
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+ {
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+ "hgvs": "NM_000344.4:c.*3+80T>G",
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+ "qual": 0.0,
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+ "altCopyNumber": 0,
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+ "altCopyNumberQuality": 150.0
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+ }
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+ ]
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+ },
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+ "gba": {
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+ "totalCopyNumber": 4,
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+ "deletionBreakpointInGene": null,
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+ "recombinantHaplotypes": [
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+ "",
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+ ""
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+ ],
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+ "variants": [
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+ "NM_000157.4:c.754T>A",
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+ "NM_000157.4:c.580A>T"
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+ ]
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+ }
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+ }
AdvancedAnalysisFileParser/Test/dummy_gba_affected_nonrecomb_acn2.targeted.json ADDED
@@ -0,0 +1,21 @@
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+ {
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+ "softwareVersion": "dragen v05.121.779.4.4.4",
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+ "sampleId": "DUMMY_GBA_AFFECTED_NONRECOMB_HOM",
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+ "genomeBuild": "hg38",
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+ "gba": {
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+ "totalCopyNumber": 4,
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+ "deletionBreakpointInGene": null,
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+ "recombinantHaplotypes": [
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+ "",
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+ ""
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+ ],
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+ "variants": [
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+ {
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+ "alleleId": "GBA:p.N370S",
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+ "alleleCopyNumber": 2,
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+ "genotypeQuality": 99,
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+ "filter": "PASS"
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+ }
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+ ]
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+ }
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+ }
AdvancedAnalysisFileParser/Test/dummy_gba_carrier_one_recomb_only.targeted.json ADDED
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+ {
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+ "softwareVersion": "dragen v05.121.779.4.4.4",
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+ "sampleId": "DUMMY_GBA_CARRIER_RECOMB_ONLY",
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+ "genomeBuild": "hg38",
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+ "gba": {
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+ "totalCopyNumber": 4,
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+ "deletionBreakpointInGene": null,
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+ "recombinantHaplotypes": [
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+ "",
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+ "RecombinantHaplotype_B"
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+ ],
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+ "variants": []
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+ }
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+ }
AdvancedAnalysisFileParser/Test/dummy_gba_phase_unknown_one_recomb_plus_variant.targeted.json ADDED
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+ {
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+ "softwareVersion": "dragen v05.121.779.4.4.4",
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+ "sampleId": "DUMMY_GBA_PHASE_UNKNOWN_RECOMB_PLUS_VARIANT",
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+ "genomeBuild": "hg38",
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+ "gba": {
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+ "totalCopyNumber": 4,
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+ "deletionBreakpointInGene": null,
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+ "recombinantHaplotypes": [
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+ "RecombinantHaplotype_A",
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+ ""
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+ ],
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+ "variants": [
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+ {
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+ "alleleId": "GBA:p.L444P",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 99,
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+ "filter": "PASS"
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+ }
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+ ]
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+ }
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+ }
AdvancedAnalysisFileParser/Test/dummy_warnset_1.targeted.json ADDED
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+ {
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+ "softwareVersion": "dragen v05.121.779.4.4.4",
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+ "sampleId": "DUMMY_HBA_HbH_SMN_AFFECTED_GBA_AFFECTED",
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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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+ "altMarkerAlleleCopyNumber": 19.377495799427994,
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+ "type": "Heterozygous markers call",
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+ "variants": [
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+ "cyp21a2": {
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+ "variants": []
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+ "cyp2d6": {
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+ "genotype": "*2/*4",
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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": 1,
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+ "genotypeQuality": 24,
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+ {
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+ "alleleId": "g.42126611C>G",
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+ "alleleCopyNumber": 2,
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+ "alleleId": "g.42127941G>A",
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+ "alleleId": "g.42128945C>T",
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+ "alleleCopyNumber": 1,
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+ "alleleId": "g.42129809T>C",
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+ "alleleId": "g.42129819G>T",
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+ "alleleCopyNumber": 1,
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+ "gba": {
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+ "RecombinantHaplotype_B"
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+ "genotypeQuality": 99,
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+ }
AdvancedAnalysisFileParser/Test/dummy_warnset_2.targeted.json ADDED
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+ {
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+ "softwareVersion": "dragen v05.121.779.4.4.4",
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+ "sampleId": "DUMMY_HBA_CARRIER_SMN_CARRIER_GBA_PHASE_UNKNOWN",
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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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+ "refMarkerAlleleCopyNumber": 11.704790391977719,
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+ "altMarkerAlleleCopyNumber": 19.377495799427994,
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+ "type": "Heterozygous markers call",
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+ "variants": [
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+ "hgvs": "LPA:4925G>A",
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+ "hgvs": "LPA:4733G>A",
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+ "variants": [
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+ "hgvs": "NC_000001.11g.25405596_25409676con25283766_25287797",
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+ "qual": 0.0,
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+ "altCopyNumber": 0,
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+ "altCopyNumberQuality": 0.0
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+ }
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+ ]
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+ },
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+ "cyp21a2": {
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+ "totalCopyNumber": 4,
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+ "deletionBreakpointInGene": null,
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+ "recombinantHaplotypes": [
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+ "",
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+ ""
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+ ],
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+ "variants": []
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+ },
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+ "cyp2d6": {
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+ "totalCopyNumber": 4,
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+ "genotype": "*2/*4",
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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": 1,
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+ "genotypeQuality": 24,
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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleId": "g.42126611C>G",
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+ "alleleCopyNumber": 2,
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+ "genotypeQuality": 87,
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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleId": "g.42127941G>A",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 150,
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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleId": "g.42128945C>T",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 150,
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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleId": "g.42129809T>C",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 150,
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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleId": "g.42129819G>T",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 150,
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+ },
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+ "alleleId": "g.42130692G>A",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 150,
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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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+ "totalCopyNumber": 4,
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+ "deletionBreakpointInGene": null,
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+ "recombinantHaplotypes": [
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+ "",
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+ ""
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+ ],
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+ "variants": [
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+ "alleleId": "GBA:p.N370S",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 99,
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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleId": "GBA:p.L444P",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 99,
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+ "filter": "PASS"
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+ }
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+ ]
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+ },
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+ "hba": {
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+ "totalCopyNumber": 2,
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+ "genotype": "-a20.5/-a3.7",
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+ "genotypeQuality": 99,
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+ "genotypeFilter": "PASS",
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+ "variants": []
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+ },
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+ "smn": {
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+ "fullLengthCopyNumber": 3,
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+ "totalCopyNumber": 3,
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+ "smn1CopyNumber": 1,
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+ "smn2CopyNumber": 2,
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+ "smn2Delta78CopyNumber": 0,
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+ "fullLengthCopyNumberFloat": "3.00",
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+ "totalCopyNumberFloat": "3.00",
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+ "variants": []
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+ }
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+ }
AdvancedAnalysisFileParser/Test/dummy_warnset_3.targeted.json ADDED
@@ -0,0 +1,146 @@
1
+ {
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+ "softwareVersion": "dragen v05.121.779.4.4.4",
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+ "sampleId": "DUMMY_HBA_SILENT_SMN_2PLUS0_RISK_GBA_CARRIER",
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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": 31.08228619140571,
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+ "refMarkerAlleleCopyNumber": 11.704790391977719,
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+ "altMarkerAlleleCopyNumber": 19.377495799427994,
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+ "type": "Heterozygous markers call",
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+ "variants": [
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+ "hgvs": "LPA:4925G>A",
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+ "altCopyNumberQuality": 150.0
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+ },
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+ {
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+ "hgvs": "LPA:4733G>A",
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+ "altCopyNumber": 0,
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+ "altCopyNumberQuality": 150.0
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+ }
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+ ]
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+ },
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+ "rhdCopyNumber": 0,
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+ "rhceCopyNumber": 2,
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+ "variants": [
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+ {
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+ "hgvs": "NC_000001.11g.25405596_25409676con25283766_25287797",
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+ "altCopyNumber": 0,
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+ "altCopyNumberQuality": 0.0
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+ }
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+ ]
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+ "deletionBreakpointInGene": null,
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+ "recombinantHaplotypes": [
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+ "",
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+ ""
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+ ],
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+ "variants": []
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+ },
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+ "cyp2d6": {
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+ "totalCopyNumber": 4,
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+ "genotype": "*2/*4",
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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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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleId": "g.42126611C>G",
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+ "genotypeQuality": 87,
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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 150,
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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleId": "g.42128945C>T",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 150,
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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleId": "g.42129809T>C",
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+ "genotypeQuality": 150,
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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleId": "g.42129819G>T",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 150,
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+ "filter": "PASS"
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+ },
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+ {
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+ "alleleId": "g.42130692G>A",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 150,
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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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+ "totalCopyNumber": 4,
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+ "deletionBreakpointInGene": null,
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+ "recombinantHaplotypes": [
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+ "",
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+ ""
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+ ],
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+ "variants": [
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+ {
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+ "alleleId": "GBA:p.N370S",
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+ "alleleCopyNumber": 1,
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+ "genotypeQuality": 99,
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+ "filter": "PASS"
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+ }
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+ ]
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+ },
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+ "hba": {
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+ "totalCopyNumber": 3,
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+ "genotype": "-a20.5/aa",
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+ "genotypeQuality": 99,
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+ "genotypeFilter": "PASS",
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+ "variants": []
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+ "smn1CopyNumber": 2,
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+ "fullLengthCopyNumberFloat": "4.00",
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+ "totalCopyNumberFloat": "4.00",
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+ "variants": [
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+ "genotypeQuality": 99,
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+ "filter": "PASS"
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+ }
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+ ]
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+ }
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+ }
AdvancedAnalysisFileParser/Test/gba.tsv ADDED
@@ -0,0 +1,2 @@
1
+ #Sample is_biallelic is_carrier total_CN deletion_breakpoint_in_GBA_gene recombinant_variants other_variants
2
+ SRR12898317_ True True 4 None NM_000157.4:c.754T>A,NM_000157.4:c.580A>T