loqusdb 2.7.23__tar.gz → 2.7.24__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 (96) hide show
  1. {loqusdb-2.7.23 → loqusdb-2.7.24}/PKG-INFO +1 -1
  2. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/__init__.py +1 -1
  3. loqusdb-2.7.24/loqusdb/resources/__init__.py +25 -0
  4. {loqusdb-2.7.23 → loqusdb-2.7.24}/pyproject.toml +1 -1
  5. loqusdb-2.7.23/loqusdb/resources/__init__.py +0 -24
  6. {loqusdb-2.7.23 → loqusdb-2.7.24}/LICENSE +0 -0
  7. {loqusdb-2.7.23 → loqusdb-2.7.24}/README.md +0 -0
  8. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/__main__.py +0 -0
  9. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/build_models/__init__.py +0 -0
  10. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/build_models/case.py +0 -0
  11. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/build_models/profile_variant.py +0 -0
  12. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/build_models/variant.py +0 -0
  13. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/__init__.py +0 -0
  14. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/annotate.py +0 -0
  15. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/cli.py +0 -0
  16. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/delete.py +0 -0
  17. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/export.py +0 -0
  18. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/identity.py +0 -0
  19. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/load.py +0 -0
  20. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/load_profile.py +0 -0
  21. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/migrate.py +0 -0
  22. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/restore.py +0 -0
  23. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/update.py +0 -0
  24. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/view.py +0 -0
  25. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/commands/wipe.py +0 -0
  26. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/constants/__init__.py +0 -0
  27. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/exceptions/__init__.py +0 -0
  28. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/exceptions/case.py +0 -0
  29. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/exceptions/profile.py +0 -0
  30. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/exceptions/vcf.py +0 -0
  31. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/log.py +0 -0
  32. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/models/__init__.py +0 -0
  33. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/models/case.py +0 -0
  34. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/models/identity.py +0 -0
  35. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/models/profile_variant.py +0 -0
  36. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/models/variant.py +0 -0
  37. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/plugins/__init__.py +0 -0
  38. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/plugins/mongo/__init__.py +0 -0
  39. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/plugins/mongo/adapter.py +0 -0
  40. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/plugins/mongo/case.py +0 -0
  41. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/plugins/mongo/profile_variant.py +0 -0
  42. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/plugins/mongo/structural_variant.py +0 -0
  43. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/plugins/mongo/variant.py +0 -0
  44. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/resources/loqusdb.20181005.gz +0 -0
  45. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/resources/maf_50_sites_GRCh37.vcf.gz +0 -0
  46. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/resources/maf_50_sites_GRCh38.vcf.gz +0 -0
  47. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/__init__.py +0 -0
  48. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/annotate.py +0 -0
  49. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/case.py +0 -0
  50. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/delete.py +0 -0
  51. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/load.py +0 -0
  52. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/migrate.py +0 -0
  53. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/profiling.py +0 -0
  54. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/update.py +0 -0
  55. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/variant.py +0 -0
  56. {loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/vcf.py +0 -0
  57. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/build_models/test_build_case.py +0 -0
  58. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/build_models/test_build_variant.py +0 -0
  59. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/build_models/test_is_greater.py +0 -0
  60. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/commands/test_export.py +0 -0
  61. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/commands/test_identity.py +0 -0
  62. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/commands/test_view.py +0 -0
  63. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/conftest.py +0 -0
  64. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/fixtures/643594.clinical.SV.vcf +0 -0
  65. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/fixtures/643594.clinical.vcf.gz +0 -0
  66. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/fixtures/double_variant.vcf +0 -0
  67. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/fixtures/funny_trio.ped +0 -0
  68. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/fixtures/profile_snv.vcf +0 -0
  69. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/fixtures/recessive_trio.ped +0 -0
  70. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/fixtures/test.SV.vcf +0 -0
  71. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/fixtures/test.vcf +0 -0
  72. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/fixtures/test.vcf.gz +0 -0
  73. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/fixtures/test.vcf.gz.tbi +0 -0
  74. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/fixtures/unsorted.vcf +0 -0
  75. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/functional/test_cli.py +0 -0
  76. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/plugins/mongo/test_case_operations.py +0 -0
  77. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/plugins/mongo/test_connect.py +0 -0
  78. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/plugins/mongo/test_flask_extension.py +0 -0
  79. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/plugins/mongo/test_get_sv.py +0 -0
  80. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/plugins/mongo/test_load_svs.py +0 -0
  81. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/plugins/mongo/test_variant_operations.py +0 -0
  82. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/utils/test_case.py +0 -0
  83. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/utils/test_delete.py +0 -0
  84. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/utils/test_delete_family.py +0 -0
  85. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/utils/test_delete_variant.py +0 -0
  86. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/utils/test_get_family.py +0 -0
  87. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/utils/test_load_database.py +0 -0
  88. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/utils/test_load_family.py +0 -0
  89. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/utils/test_load_variants.py +0 -0
  90. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/utils/test_migrate.py +0 -0
  91. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/utils/test_profiling.py +0 -0
  92. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/vcf_tools/test_check_par.py +0 -0
  93. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/vcf_tools/test_check_vcf.py +0 -0
  94. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/vcf_tools/test_format_sv_variant.py +0 -0
  95. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/vcf_tools/test_format_variant.py +0 -0
  96. {loqusdb-2.7.23 → loqusdb-2.7.24}/tests/vcf_tools/test_vcf.py +0 -0
{loqusdb-2.7.23 → loqusdb-2.7.24}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: loqusdb
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- Version: 2.7.23
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+ Version: 2.7.24
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  Summary: A simple observation count database
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  License: MIT
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  Author: Mans Magnuson
{loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/__init__.py RENAMED
@@ -4,7 +4,7 @@ from pymongo import ASCENDING, IndexModel
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  logger = logging.getLogger(__name__)
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- __version__ = "2.7.23"
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+ __version__ = "2.7.24"
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  INDEXES = {
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  "variant": [
loqusdb-2.7.24/loqusdb/resources/__init__.py ADDED
@@ -0,0 +1,25 @@
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+ from importlib.resources import files, as_file
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+
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+ from loqusdb.constants import GRCH37, GRCH38
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+
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+ ###### Files ######
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+
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+ # Background data
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+ PATH_NAME = "loqusdb.resources"
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+
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+ backround_svs = "loqusdb.20181005.gz"
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+ maf_50_grch37 = "maf_50_sites_GRCh37.vcf.gz"
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+ maf_50_grch38 = "maf_50_sites_GRCh38.vcf.gz"
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+
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+ ### Profile SNPs for Grch37 and 38
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+
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+ ###### Paths ######
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+
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+ # Backround data path
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+
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+ background_path = str(files(PATH_NAME).joinpath(backround_svs))
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+
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+ maf_grch37_path = str(files(PATH_NAME).joinpath(maf_50_grch37))
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+ maf_grch38_path = str(files(PATH_NAME).joinpath(maf_50_grch38))
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+
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+ MAF_PATH = {GRCH37: maf_grch37_path, GRCH38: maf_grch38_path}
{loqusdb-2.7.23 → loqusdb-2.7.24}/pyproject.toml RENAMED
@@ -6,7 +6,7 @@ authors = [{name="Mans Magnuson", email="monsunas@gmail.com"}, {name="Adam Rosen
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  maintainers = [ {name="Clinical Genomics Bioinformatics Team"}, {name="Clinical Genomics System Development Team"}, {name="Clinical Genomics Scout Team"}]
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  license = "MIT"
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  readme = "README.md"
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- version = "2.7.23"
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+ version = "2.7.24"
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  [tool.poetry]
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  include = [
loqusdb-2.7.23/loqusdb/resources/__init__.py DELETED
@@ -1,24 +0,0 @@
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- import pkg_resources
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-
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- from loqusdb.constants import GRCH37, GRCH38
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-
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- ###### Files ######
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-
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- # Background data
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-
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- backround_svs = "resources/loqusdb.20181005.gz"
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- maf_50_grch37 = "resources/maf_50_sites_GRCh37.vcf.gz"
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- maf_50_grch38 = "resources/maf_50_sites_GRCh38.vcf.gz"
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-
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- ### Profile SNPs for Grch37 and 38
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-
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- ###### Paths ######
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-
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- # Backround data path
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-
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- background_path = pkg_resources.resource_filename("loqusdb", backround_svs)
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-
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- maf_grch37_path = pkg_resources.resource_filename("loqusdb", maf_50_grch37)
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- maf_grch38_path = pkg_resources.resource_filename("loqusdb", maf_50_grch38)
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-
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- MAF_PATH = {GRCH37: maf_grch37_path, GRCH38: maf_grch38_path}
{loqusdb-2.7.23 → loqusdb-2.7.24}/LICENSE RENAMED
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{loqusdb-2.7.23 → loqusdb-2.7.24}/README.md RENAMED
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{loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/__main__.py RENAMED
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{loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/log.py RENAMED
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{loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/case.py RENAMED
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{loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/load.py RENAMED
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{loqusdb-2.7.23 → loqusdb-2.7.24}/loqusdb/utils/vcf.py RENAMED
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{loqusdb-2.7.23 → loqusdb-2.7.24}/tests/conftest.py RENAMED
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