phc-ingestion 0.10.13__tar.gz → 0.10.14__tar.gz

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  1. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/PKG-INFO +1 -1
  2. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nebula/manifest_assembler.py +3 -3
  3. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/pyproject.toml +1 -1
  4. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/PYPI.md +0 -0
  5. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/__init__.py +0 -0
  6. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/__init__.py +0 -0
  7. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/process.py +0 -0
  8. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/__init__.py +0 -0
  9. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/cnv.py +0 -0
  10. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/detect_genome_ref.py +0 -0
  11. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/hla.py +0 -0
  12. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/ihc.py +0 -0
  13. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/interpretation.py +0 -0
  14. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/json.py +0 -0
  15. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/metadata.py +0 -0
  16. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/specimen_details.py +0 -0
  17. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/structural.py +0 -0
  18. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/tests.py +0 -0
  19. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/tmb.py +0 -0
  20. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/tsv.py +0 -0
  21. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/caris/util/vcf.py +0 -0
  22. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/foundation/__init__.py +0 -0
  23. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/foundation/process.py +0 -0
  24. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/foundation/util/__init__.py +0 -0
  25. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/foundation/util/cnv.py +0 -0
  26. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/foundation/util/fnv.py +0 -0
  27. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/foundation/util/ga4gh.py +0 -0
  28. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/foundation/util/interpretation.py +0 -0
  29. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/foundation/util/vcf_etl.py +0 -0
  30. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/generic/__init__.py +0 -0
  31. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/generic/process.py +0 -0
  32. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/generic/utils.py +0 -0
  33. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nebula/__init__.py +0 -0
  34. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nebula/constants.py +0 -0
  35. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nebula/process.py +0 -0
  36. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/__init__.py +0 -0
  37. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/process.py +0 -0
  38. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/util/alteration_table.py +0 -0
  39. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/util/interpretation.py +0 -0
  40. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/util/manifest_helpers.py +0 -0
  41. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/util/nextgen_specific_genes.py +0 -0
  42. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/util/pre_filter_somatic_vcf.py +0 -0
  43. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/util/process_cnv.py +0 -0
  44. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/util/process_manifest.py +0 -0
  45. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/util/process_structural.py +0 -0
  46. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/util/process_vcf.py +0 -0
  47. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nextgen/util/types.py +0 -0
  48. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/resources/GRCh37_map.csv.gz +0 -0
  49. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/resources/GRCh38_map.csv.gz +0 -0
  50. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/shared_util/__init__.py +0 -0
  51. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/shared_util/coords_to_genes.py +0 -0
  52. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/shared_util/ga4gh.py +0 -0
  53. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/shared_util/gene_to_coords.py +0 -0
  54. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/shared_util/lambda_client.py +0 -0
  55. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/shared_util/open_maybe_gzipped.py +0 -0
  56. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/shared_util/tar.py +0 -0
  57. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/shared_util/types.py +0 -0
  58. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/vcf_standardization/Variant.py +0 -0
  59. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/vcf_standardization/__init__.py +0 -0
  60. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/vcf_standardization/standardize.py +0 -0
  61. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/vcf_standardization/util/__init__.py +0 -0
  62. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/vcf_standardization/util/af_helpers.py +0 -0
  63. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/vcf_standardization/util/dp_helpers.py +0 -0
  64. {phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/vcf_standardization/util/read_write.py +0 -0
{phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: phc-ingestion
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- Version: 0.10.13
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+ Version: 0.10.14
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  Summary: Functions for LifeOmic PHC genomic ingestions
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  License: MIT
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  Author-email: LifeOmic Development <development@lifeomic.com>
{phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/ingestion/nebula/manifest_assembler.py RENAMED
@@ -154,7 +154,7 @@ class ManifestAssembler:
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  except Exception as e:
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  return None
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- def __extract_report_date(self) -> dict[str, str]:
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+ def __extract_collection_date(self) -> dict[str, str]:
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  in_file = self.vcf_file_path
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  with gzip.open(in_file, "rt") if in_file.endswith(".gz") else open(in_file, "r") as f:
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  headers = read_headers(f)
@@ -173,7 +173,7 @@ class ManifestAssembler:
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  report_date = epoch_time or date_string
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  if report_date:
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  return {
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- "reportDate": report_date.astimezone(tz=timezone.utc)
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+ "collDate": report_date.astimezone(tz=timezone.utc)
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  .isoformat(timespec="milliseconds")
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  .replace("+00:00", "Z")
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  }
@@ -204,7 +204,7 @@ class ManifestAssembler:
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  return {
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  "name": "Nebula",
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  "indexedDate": datetime.now().strftime("%Y-%m-%d"),
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- **self.__extract_report_date(),
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+ **self.__extract_collection_date(),
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  "reference": "GRCh38",
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  "patientId": patient.get("id"),
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  "mrn": self.__extract_elation_mrn(patient),
{phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "phc-ingestion"
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- version = "0.10.13"
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+ version = "0.10.14"
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  description = "Functions for LifeOmic PHC genomic ingestions"
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  authors = [
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  { name = "LifeOmic Development", email = "development@lifeomic.com" },
{phc-ingestion-0.10.13 → phc-ingestion-0.10.14}/PYPI.md RENAMED
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