phc-ingestion 0.10.15__tar.gz → 0.10.16__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 (64) hide show
  1. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/PKG-INFO +1 -1
  2. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/foundation/util/vcf_etl.py +3 -0
  3. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/pyproject.toml +1 -1
  4. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/PYPI.md +0 -0
  5. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/__init__.py +0 -0
  6. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/__init__.py +0 -0
  7. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/process.py +0 -0
  8. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/__init__.py +0 -0
  9. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/cnv.py +0 -0
  10. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/detect_genome_ref.py +0 -0
  11. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/hla.py +0 -0
  12. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/ihc.py +0 -0
  13. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/interpretation.py +0 -0
  14. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/json.py +0 -0
  15. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/metadata.py +0 -0
  16. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/specimen_details.py +0 -0
  17. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/structural.py +0 -0
  18. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/tests.py +0 -0
  19. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/tmb.py +0 -0
  20. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/tsv.py +0 -0
  21. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/caris/util/vcf.py +0 -0
  22. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/foundation/__init__.py +0 -0
  23. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/foundation/process.py +0 -0
  24. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/foundation/util/__init__.py +0 -0
  25. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/foundation/util/cnv.py +0 -0
  26. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/foundation/util/fnv.py +0 -0
  27. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/foundation/util/ga4gh.py +0 -0
  28. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/foundation/util/interpretation.py +0 -0
  29. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/generic/__init__.py +0 -0
  30. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/generic/process.py +0 -0
  31. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/generic/utils.py +0 -0
  32. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nebula/__init__.py +0 -0
  33. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nebula/constants.py +0 -0
  34. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nebula/manifest_assembler.py +0 -0
  35. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nebula/process.py +0 -0
  36. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/__init__.py +0 -0
  37. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/process.py +0 -0
  38. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/util/alteration_table.py +0 -0
  39. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/util/interpretation.py +0 -0
  40. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/util/manifest_helpers.py +0 -0
  41. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/util/nextgen_specific_genes.py +0 -0
  42. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/util/pre_filter_somatic_vcf.py +0 -0
  43. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/util/process_cnv.py +0 -0
  44. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/util/process_manifest.py +0 -0
  45. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/util/process_structural.py +0 -0
  46. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/util/process_vcf.py +0 -0
  47. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/nextgen/util/types.py +0 -0
  48. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/resources/GRCh37_map.csv.gz +0 -0
  49. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/resources/GRCh38_map.csv.gz +0 -0
  50. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/shared_util/__init__.py +0 -0
  51. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/shared_util/coords_to_genes.py +0 -0
  52. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/shared_util/ga4gh.py +0 -0
  53. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/shared_util/gene_to_coords.py +0 -0
  54. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/shared_util/lambda_client.py +0 -0
  55. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/shared_util/open_maybe_gzipped.py +0 -0
  56. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/shared_util/tar.py +0 -0
  57. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/shared_util/types.py +0 -0
  58. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/vcf_standardization/Variant.py +0 -0
  59. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/vcf_standardization/__init__.py +0 -0
  60. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/vcf_standardization/standardize.py +0 -0
  61. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/vcf_standardization/util/__init__.py +0 -0
  62. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/vcf_standardization/util/af_helpers.py +0 -0
  63. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/vcf_standardization/util/dp_helpers.py +0 -0
  64. {phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/vcf_standardization/util/read_write.py +0 -0
{phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: phc-ingestion
3
- Version: 0.10.15
3
+ Version: 0.10.16
4
4
  Summary: Functions for LifeOmic PHC genomic ingestions
5
5
  License: MIT
6
6
  Author-email: LifeOmic Development <development@lifeomic.com>
{phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/ingestion/foundation/util/vcf_etl.py RENAMED
@@ -55,6 +55,9 @@ def get_xml_short_vars(xml_file: str, log):
55
55
  xml_short_vars = xml_dict["rr:ResultsReport"]["rr:ResultsPayload"]["variant-report"][
56
56
  "short-variants"
57
57
  ]["short-variant"]
58
+ except KeyError as e:
59
+ log.info(f"Missing key in XML structure for short variants: {str(e)}")
60
+ return vendsig_dict
58
61
  except TypeError:
59
62
  log.info("No short variants found in xml")
60
63
  return vendsig_dict
{phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "phc-ingestion"
3
- version = "0.10.15"
3
+ version = "0.10.16"
4
4
  description = "Functions for LifeOmic PHC genomic ingestions"
5
5
  authors = [
6
6
  { name = "LifeOmic Development", email = "development@lifeomic.com" },
{phc-ingestion-0.10.15 → phc-ingestion-0.10.16}/PYPI.md RENAMED
File without changes