pyxetabase 3.1.0.dev0__py3-none-any.whl

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  1. pyopencga/__init__.py +0 -0
  2. pyopencga/commons.py +347 -0
  3. pyopencga/exceptions.py +8 -0
  4. pyopencga/opencga_client.py +334 -0
  5. pyopencga/opencga_config.py +160 -0
  6. pyopencga/rest_clients/__init__.py +0 -0
  7. pyopencga/rest_clients/_parent_rest_clients.py +110 -0
  8. pyopencga/rest_clients/admin_client.py +173 -0
  9. pyopencga/rest_clients/alignment_client.py +373 -0
  10. pyopencga/rest_clients/clinical_analysis_client.py +1279 -0
  11. pyopencga/rest_clients/cohort_client.py +338 -0
  12. pyopencga/rest_clients/disease_panel_client.py +352 -0
  13. pyopencga/rest_clients/family_client.py +355 -0
  14. pyopencga/rest_clients/file_client.py +698 -0
  15. pyopencga/rest_clients/ga4gh_client.py +86 -0
  16. pyopencga/rest_clients/individual_client.py +435 -0
  17. pyopencga/rest_clients/job_client.py +415 -0
  18. pyopencga/rest_clients/meta_client.py +83 -0
  19. pyopencga/rest_clients/organization_client.py +206 -0
  20. pyopencga/rest_clients/project_client.py +128 -0
  21. pyopencga/rest_clients/sample_client.py +446 -0
  22. pyopencga/rest_clients/study_client.py +433 -0
  23. pyopencga/rest_clients/user_client.py +192 -0
  24. pyopencga/rest_clients/variant_client.py +1378 -0
  25. pyopencga/rest_clients/variant_operation_client.py +719 -0
  26. pyopencga/rest_clients/workflow_client.py +263 -0
  27. pyopencga/rest_response.py +220 -0
  28. pyopencga/retry.py +57 -0
  29. pyxetabase/__init__.py +0 -0
  30. pyxetabase/commons.py +347 -0
  31. pyxetabase/exceptions.py +8 -0
  32. pyxetabase/opencga_client.py +344 -0
  33. pyxetabase/opencga_config.py +160 -0
  34. pyxetabase/rest_clients/__init__.py +0 -0
  35. pyxetabase/rest_clients/_parent_rest_clients.py +110 -0
  36. pyxetabase/rest_clients/admin_client.py +173 -0
  37. pyxetabase/rest_clients/alignment_client.py +373 -0
  38. pyxetabase/rest_clients/clinical_analysis_client.py +1273 -0
  39. pyxetabase/rest_clients/cohort_client.py +338 -0
  40. pyxetabase/rest_clients/cvdb_client.py +2258 -0
  41. pyxetabase/rest_clients/disease_panel_client.py +352 -0
  42. pyxetabase/rest_clients/family_client.py +355 -0
  43. pyxetabase/rest_clients/federation_client.py +133 -0
  44. pyxetabase/rest_clients/file_client.py +698 -0
  45. pyxetabase/rest_clients/ga4gh_client.py +86 -0
  46. pyxetabase/rest_clients/individual_client.py +435 -0
  47. pyxetabase/rest_clients/job_client.py +415 -0
  48. pyxetabase/rest_clients/meta_client.py +83 -0
  49. pyxetabase/rest_clients/organization_client.py +206 -0
  50. pyxetabase/rest_clients/project_client.py +128 -0
  51. pyxetabase/rest_clients/sample_client.py +446 -0
  52. pyxetabase/rest_clients/study_client.py +433 -0
  53. pyxetabase/rest_clients/user_client.py +212 -0
  54. pyxetabase/rest_clients/variant_client.py +1378 -0
  55. pyxetabase/rest_clients/variant_operation_client.py +719 -0
  56. pyxetabase/rest_clients/workflow_client.py +263 -0
  57. pyxetabase/rest_response.py +220 -0
  58. pyxetabase/retry.py +57 -0
  59. pyxetabase-3.1.0.dev0.dist-info/METADATA +159 -0
  60. pyxetabase-3.1.0.dev0.dist-info/RECORD +63 -0
  61. pyxetabase-3.1.0.dev0.dist-info/WHEEL +5 -0
  62. pyxetabase-3.1.0.dev0.dist-info/licenses/LICENSE +202 -0
  63. pyxetabase-3.1.0.dev0.dist-info/top_level.txt +1 -0
@@ -0,0 +1,2258 @@
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+ """
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+ WARNING: AUTOGENERATED CODE
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+
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+ This code was generated by a tool.
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+
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+ Manual changes to this file may cause unexpected behavior in your application.
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+ Manual changes to this file will be overwritten if the code is regenerated.
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+ """
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+
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+ from pyxetabase.rest_clients._parent_rest_clients import _ParentRestClient
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+
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+
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+ class CVDB(_ParentRestClient):
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+ """
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+ This class contains methods for the 'Analysis - CVDB' webservices
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+ PATH: /{apiVersion}/analysis/cvdb
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+ """
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+
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+ def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
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+ super(CVDB, self).__init__(configuration, token, login_handler, *args, **kwargs)
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+
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+ def aggregate_analysis(self, **options):
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+ """
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+ Calculate and fetch clinical analysis aggregation stats.
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+ PATH: /{apiVersion}/analysis/cvdb/analysis/aggregate
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+
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+ :param str project: Project ID.
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+ :param str study: Study ID (or list of study IDs separated by commas).
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+ :param str ca_id: Clinical analysis ID (or list of IDs separated by
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+ commas).
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+ :param str ca_description: Clinical analysis description (word or list
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+ of words contained in the text, if the words are separated by a
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+ comma an OR will be applied; if the words are separated by a
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+ semicolon, an AND will be applied).
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+ :param str ca_type: Clinical analysis type (or list of types separated
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+ by commas).
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+ :param str ca_disorder_id: Clinical analysis disorder ID (or list of
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+ IDs separated by commas).
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+ :param str ca_filename: Clinical analysis filename (or list of
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+ filenames separated by commas).
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+ :param str ca_proband_id: Clinical analysis proband ID (or list of IDs
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+ separated by commas).
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+ :param str ca_proband_disorder_id: Clinical analysis proband disorder
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+ ID (or list of disorder IDs separated by commas).
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+ :param str ca_proband_phenotype_name: Clinical analysis proband
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+ phenotype name (or list of phenotype names separated by commas).
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+ :param str ca_family_id: Clinical analysis family ID (or list of IDs
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+ separated by commas).
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+ :param str ca_family_phenotype_name: Clinical analysis family
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+ phenotype names (or list of names separated by commas).
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+ :param str ca_family_member_id: Clinical analysis family member ID (or
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+ list of IDs separated by commas).
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+ :param str ca_report: Clinical analysis report text (word or list of
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+ words contained in the text, if the words are separated by a comma
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+ an OR will be applied; if the words are separated by a semicolon,
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+ an AND will be applied).
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+ :param str ca_status: Clinical analysis status (or list of status
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+ separated by commas).
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+ :param bool ca_locked: Clinical analysis locked (true or false).
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+ :param str ci_id: Clinical interpretation ID (or list of IDs separated
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+ by commas).
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+ :param bool ci_primary: Clinical interpretation primary (true or
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+ false).
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+ :param str ci_description: Clinical interpretation description (word
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+ or list of words contained in the text, if the words are separated
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+ by a comma an OR will be applied; if the words are separated by a
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+ semicolon, an AND will be applied).
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+ :param str ci_panel_id: Clinical interpretation panel ID or name (or
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+ list of IDs or names separated by commas).
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+ :param str ci_analyst_id: Clinical interpretation analyst ID (or list
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+ of IDs separated by commas).
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+ :param str ci_analyst_name: Clinical interpretation analyst name (or
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+ list of names separated by commas).
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+ :param str ci_analyst_email: Clinical interpretation analyst e-mail
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+ (or list of e-mails separated by commas).
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+ :param str ci_analyst_assigned_by: Clinical interpretation analyst
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+ assignee name (or list of names separated by commas).
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+ :param str ci_analyst_date: Clinical interpretation analyst date (or
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+ list of dates separated by commas), with format YYYYMMDDhhmmss,
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+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
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+ 20231001000000-20231101000000.
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+ :param str ci_method_name: Clinical interpretation method name (or
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+ list of names separated by commas).
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+ :param str ci_method_version: Clinical interpretation method version
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+ (or list of versions separated by commas).
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+ :param str ci_method_commit: Clinical interpretation method commit (or
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+ list of commits separated by commas).
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+ :param str ci_method_dependencies: Clinical interpretation method
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+ dependencies (word or list of words contained in the text, if the
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+ words are separated by a comma an OR will be applied; if the words
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+ are separated by a semicolon, an AND will be applied).
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+ :param str ci_comments: Clinical interpretation comment text (word or
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+ list of words contained in the text, if the words are separated by
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+ a comma an OR will be applied; if the words are separated by a
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+ semicolon, an AND will be applied).
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+ :param bool ci_locked: Clinical interpretation locked (true or false).
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+ :param str ci_status_id: Clinical interpretation status ID (or list of
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+ IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
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+ CLOSED.
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+ :param str ci_status_name: Clinical interpretation status name (or
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+ list of names separated by commas).
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+ :param str ci_status_description: Clinical interpretation status
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+ description (word or list of words contained in the text, if the
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+ words are separated by a comma an OR will be applied; if the words
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+ are separated by a semicolon, an AND will be applied).
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+ :param str ci_status_date: Clinical interpretation status date (or
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+ list of dates separated by commas), with format YYYYMMDDhhmmss,
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+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
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+ 20231001000000-20231101000000.
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+ :param str ci_creation_date: Clinical interpretation creation date (or
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+ list of dates separated by commas), with format YYYYMMDDhhmmss,
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+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
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+ 20231001000000-20231101000000.
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+ :param str ci_modification_date: Clinical interpretation modification
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+ date (or list of dates separated by commas), with format
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+ YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
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+ start_date-end_date, e.g.: 20231001000000-20231101000000.
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+ :param int ci_version: Clinical interpretation version number (or list
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+ of versions separated by commas).
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+ :param str cv_id: Clinical variant ID (or list of IDs separated by
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+ commas).
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+ :param str cv_variant_id: Variant ID (or list of IDs separated by
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+ commas).
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+ :param bool cv_primary_finding: Clinical variant is a primary finding
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+ (true or false).
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+ :param bool cv_primary_interpretation: Clinical variant belongs to the
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+ primary interpretation (true or false).
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+ :param str cv_comments: Clinical variant comment text (word or list of
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+ words contained in the text, if the words are separated by a comma
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+ an OR will be applied; if the words are separated by a semicolon,
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+ an AND will be applied).
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+ :param str cv_discussion_author: Clinical variant discussion author
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+ (or list of authors separated by commas).
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+ :param str cv_discussion_date: Clinical variant discussion date (or
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+ list of dates separated by commas), with format YYYYMMDDhhmmss,
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+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
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+ 20231001000000-20231101000000.
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+ :param str cv_discussion_text: Clinical variant discussion text (word
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+ or list of words contained in the text, if the words are separated
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+ by a comma an OR will be applied; if the words are separated by a
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+ semicolon, an AND will be applied).
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+ :param str cv_confidence_value: Clinical variant confidence value (or
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+ list of values separated by commas).
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+ :param str cv_confidence_author: Clinical variant confidence author
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+ (or list of authors separated by commas).
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+ :param str cv_confidence_date: Clinical variant confidence date (or
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+ list of dates separated by commas), with format YYYYMMDDhhmmss,
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+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
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+ 20231001000000-20231101000000.
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+ :param str cv_tag: Clinical variant tag (or list of tags separated by
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+ commas).
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+ :param str cv_status: Clinical variant status (or list of status
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+ separated by commas).
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+ :param str cv_region: Variant region (or list of regions, these can be
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+ just a single chromosome name or regions in the format
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+ chr:start-end, e.g.: 2,3:100000-200000).
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+ :param str cv_biotype: Variant biotype, e.g. protein_coding (or list
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+ of biotypes separated by commas).
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+ :param str cv_ct: Variant SO consequence type (or list of SOs
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+ separated by commas), e.g. missense_variant,stop_lost or
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+ SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
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+ 'protein_altering'.
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+ :param str cv_transcript_flag: Variant transcript flag (or list of
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+ flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
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+ Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
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+ :param str cv_gene: Variant gene (or list genes separated by commas),
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+ most gene IDs are accepted (HGNC, Ensembl gene, ...).
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+ :param str cv_xref: Variant external reference (or list of references
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+ separated by commas), these can be genes, proteins or variants.
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+ Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
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+ Cosmic, ...
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+ :param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
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+ (or list of roles separated by commas).
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+ :param str cv_type: Variant type or list of types, accepted values are
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+ SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
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+ COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
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+ TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
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+ :param str cv_protein_substitution: Variant protein substitution score
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+ (or list of scores separated by commas), include SIFT and PolyPhen.
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+ You can query using the score {protein_score}[<|>|<=|>=]{number} or
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+ the description {protein_score}[~=|=]{description} e.g.
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+ polyphen>0.1,sift=tolerant.
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+ :param str cv_conservation: Variant conservation score (or list of
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+ scores separated by commas) with the format
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+ {conservation_score}[<|>|<=|>=]{number} e.g.
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+ phastCons>0.5,phylop<0.1,gerp>0.1.
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+ :param str cv_functional_score: Variant functional score (or list of
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+ scores separated by commas) with the format
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+ {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
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+ cadd_raw<=0.3.
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+ :param str cv_population_frequency_alt: Variant alternate population
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+ frequency (or list of frequencies separated by commas), with the
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+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
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+ 1000G:ALL<0.01.
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+ :param str cv_population_frequency_maf: Variant population minor
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+ allele frequency (or list of frequencies separated by commas), with
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+ the format {study}:{population}[<|>|<=|>=]{number}. e.g.
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+ 1000G:ALL<0.01.
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+ :param str cv_population_frequency_ref: Variant reference population
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+ frequency (or list of frequences separated by commas), with the
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+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
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+ 1000G:ALL<0.01.
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+ :param str cv_cohort_stats_alt: Variant alternate allele frequency (or
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+ list of frequencies separated by commas), with the format
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+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
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+ :param str cv_cohort_stats_maf: Variant minor allele frequency (or
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+ list of frequencies separated by commas), with the format
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+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
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+ :param str cv_cohort_stats_ref: Variant reference allele frequency (or
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+ list of frequencies separated by commas), with the foramt
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+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
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+ :param str cv_cohort_stats_pass: Variant filter PASS frequency (or
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+ list of frequencies separated by commas), with the format
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+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
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+ :param str cv_score: Variant score (or list of scores separated by
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+ commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
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+ :param str cv_annot_go_genes: Variant gene GO (or list of GOs
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+ separated by commas).
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+ :param str cv_annot_expression_genes: Variant gene expression (or list
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+ of expressions separated by commas).
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+ :param str cv_gene_trait_id: Variant gene trait association ID (or
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+ list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
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+ 'OMIM:269600'.
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+ :param str cv_trait: Variant Trait (or list of traits separated by
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+ commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
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+ descriptions,...
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+ :param str cv_protein_keyword: Uniprot protein variant annotation
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+ keyword (or list of keywords separated by commas).
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+ :param str cve_variant_id: Variant ID (or list of IDs separated by
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+ commas).
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+ :param bool cve_primary_finding: Clinical variant evidence belongs to
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+ a primary finding (true or false).
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+ :param bool cve_primary_interpretation: Clinical variant evidence
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+ belongs to the primary interpretation (true or false).
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+ :param str cve_phenotype_name: Clinical variant evidence phenotype
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+ name (or names separated by commas).
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+ :param str cve_gene_name: Clinical variant evidence gene name (or
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+ names separated by commas).
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+ :param str cve_transcript_id: Clinical variant evidence transcript ID
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+ (or IDs separated by commas).
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+ :param str cve_so_term_name: Clinical variant evidence sequence
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+ ontology name (or names separated by commas).
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+ :param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
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+ separated by commas).
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+ :param str cve_panel_id: Clinical variant evidence panel ID (or IDs
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+ separated by commas).
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+ :param str cve_moi: Clinical variant evidence mode of inheritance (or
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+ list of modes of inheritance separated by commas), valid values:
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+ AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
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+ X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
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+ MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
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+ :param str cve_penetrance: Clinical variant evidence penetrance (or
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+ list of penetrance values separated by commas), valid values:
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+ COMPLETE, INCOMPLETE, UNKNOWN.
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+ :param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
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+ separated by commas).
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+ :param str cve_tier: Clinical variant evidence tier (or list of tier
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+ values separated by commas).
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+ :param str cve_clinical_significance: Clinical variant evidence
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+ clinical significance (or list of clinical significances separated
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+ by commas).
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+ :param str cve_drug_response: Clinical variant evidence drug response
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+ (or list of drug responses separated by commas).
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+ :param str cve_trait_association: Clinical variant evidence trait
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+ association (or list of traits separated by commas).
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+ :param str cve_functional_effect: Clinical variant evidence functional
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+ effect (or list of functional effects separated by commas).
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+ :param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
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+ (or list of tumorigenesis values separated by commas).
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+ :param str cve_other_classification: Clinical variant evidence
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+ other-classification (or list of other classification values
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+ separated by commas).
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+ :param str cve_role_in_cancer: Clinical variant evidence role in
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+ cancer (or roles in cancer separated by commas).
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+ :param str cve_review_acmg: Clinical variant evidence review ACMG (or
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+ ACGMs separated by commas).
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+ :param str cve_review_tier: Clinical variant evidence review tier (or
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+ list of tier values separated by commas).
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+ :param str cve_review_clinical_significance: Clinical variant evidence
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+ review clinical significance (or list of clinical significances
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+ separated by commas).
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+ :param str cve_review_text: Clinical variant evidence review text
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+ (word or list of words contained in the text, if the words are
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+ separated by a comma an OR will be applied; if the words are
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+ separated by a semicolon, an AND will be applied).
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+ :param str field: List of facet fields separated by semicolons, e.g.:
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+ type;disorderId. For nested faceted fields use >>, e.g.:
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+ type>>disorderId. Accepted values: studyId, type, disorderId,
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+ fileNames, probandId, probandDisorderIds, probandPhenotypeNames,
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+ familyId, familyPhenotypeNames, familyMemberIds, panelIds, status.
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+ """
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+
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+ return self._get(category='analysis', resource='aggregate', subcategory='cvdb/analysis', **options)
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+
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+ def query_analysis(self, **options):
296
+ """
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+ Filter and fetch clinical analyses from CVDB.
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+ PATH: /{apiVersion}/analysis/cvdb/analysis/query
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+
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+ :param str project: Project ID.
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+ :param str study: Study ID (or list of study IDs separated by commas).
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+ :param str include: Fields included in the response, whole JSON path
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+ must be provided.
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+ :param str exclude: Fields excluded in the response, whole JSON path
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+ must be provided.
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+ :param int limit: Number of results to be returned.
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+ :param int skip: Number of results to skip.
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+ :param str ca_id: Clinical analysis ID (or list of IDs separated by
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+ commas).
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+ :param str ca_description: Clinical analysis description (word or list
311
+ of words contained in the text, if the words are separated by a
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+ comma an OR will be applied; if the words are separated by a
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+ semicolon, an AND will be applied).
314
+ :param str ca_type: Clinical analysis type (or list of types separated
315
+ by commas).
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+ :param str ca_disorder_id: Clinical analysis disorder ID (or list of
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+ IDs separated by commas).
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+ :param str ca_filename: Clinical analysis filename (or list of
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+ filenames separated by commas).
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+ :param str ca_proband_id: Clinical analysis proband ID (or list of IDs
321
+ separated by commas).
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+ :param str ca_proband_disorder_id: Clinical analysis proband disorder
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+ ID (or list of disorder IDs separated by commas).
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+ :param str ca_proband_phenotype_name: Clinical analysis proband
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+ phenotype name (or list of phenotype names separated by commas).
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+ :param str ca_family_id: Clinical analysis family ID (or list of IDs
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+ separated by commas).
328
+ :param str ca_family_phenotype_name: Clinical analysis family
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+ phenotype names (or list of names separated by commas).
330
+ :param str ca_family_member_id: Clinical analysis family member ID (or
331
+ list of IDs separated by commas).
332
+ :param str ca_report: Clinical analysis report text (word or list of
333
+ words contained in the text, if the words are separated by a comma
334
+ an OR will be applied; if the words are separated by a semicolon,
335
+ an AND will be applied).
336
+ :param str ca_status: Clinical analysis status (or list of status
337
+ separated by commas).
338
+ :param bool ca_locked: Clinical analysis locked (true or false).
339
+ :param str ci_id: Clinical interpretation ID (or list of IDs separated
340
+ by commas).
341
+ :param bool ci_primary: Clinical interpretation primary (true or
342
+ false).
343
+ :param str ci_description: Clinical interpretation description (word
344
+ or list of words contained in the text, if the words are separated
345
+ by a comma an OR will be applied; if the words are separated by a
346
+ semicolon, an AND will be applied).
347
+ :param str ci_panel_id: Clinical interpretation panel ID or name (or
348
+ list of IDs or names separated by commas).
349
+ :param str ci_analyst_id: Clinical interpretation analyst ID (or list
350
+ of IDs separated by commas).
351
+ :param str ci_analyst_name: Clinical interpretation analyst name (or
352
+ list of names separated by commas).
353
+ :param str ci_analyst_email: Clinical interpretation analyst e-mail
354
+ (or list of e-mails separated by commas).
355
+ :param str ci_analyst_assigned_by: Clinical interpretation analyst
356
+ assignee name (or list of names separated by commas).
357
+ :param str ci_analyst_date: Clinical interpretation analyst date (or
358
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
359
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
360
+ 20231001000000-20231101000000.
361
+ :param str ci_method_name: Clinical interpretation method name (or
362
+ list of names separated by commas).
363
+ :param str ci_method_version: Clinical interpretation method version
364
+ (or list of versions separated by commas).
365
+ :param str ci_method_commit: Clinical interpretation method commit (or
366
+ list of commits separated by commas).
367
+ :param str ci_method_dependencies: Clinical interpretation method
368
+ dependencies (word or list of words contained in the text, if the
369
+ words are separated by a comma an OR will be applied; if the words
370
+ are separated by a semicolon, an AND will be applied).
371
+ :param str ci_comments: Clinical interpretation comment text (word or
372
+ list of words contained in the text, if the words are separated by
373
+ a comma an OR will be applied; if the words are separated by a
374
+ semicolon, an AND will be applied).
375
+ :param bool ci_locked: Clinical interpretation locked (true or false).
376
+ :param str ci_status_id: Clinical interpretation status ID (or list of
377
+ IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
378
+ CLOSED.
379
+ :param str ci_status_name: Clinical interpretation status name (or
380
+ list of names separated by commas).
381
+ :param str ci_status_description: Clinical interpretation status
382
+ description (word or list of words contained in the text, if the
383
+ words are separated by a comma an OR will be applied; if the words
384
+ are separated by a semicolon, an AND will be applied).
385
+ :param str ci_status_date: Clinical interpretation status date (or
386
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
387
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
388
+ 20231001000000-20231101000000.
389
+ :param str ci_creation_date: Clinical interpretation creation date (or
390
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
391
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
392
+ 20231001000000-20231101000000.
393
+ :param str ci_modification_date: Clinical interpretation modification
394
+ date (or list of dates separated by commas), with format
395
+ YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
396
+ start_date-end_date, e.g.: 20231001000000-20231101000000.
397
+ :param int ci_version: Clinical interpretation version number (or list
398
+ of versions separated by commas).
399
+ :param str cv_id: Clinical variant ID (or list of IDs separated by
400
+ commas).
401
+ :param str cv_variant_id: Variant ID (or list of IDs separated by
402
+ commas).
403
+ :param bool cv_primary_finding: Clinical variant is a primary finding
404
+ (true or false).
405
+ :param bool cv_primary_interpretation: Clinical variant belongs to the
406
+ primary interpretation (true or false).
407
+ :param str cv_comments: Clinical variant comment text (word or list of
408
+ words contained in the text, if the words are separated by a comma
409
+ an OR will be applied; if the words are separated by a semicolon,
410
+ an AND will be applied).
411
+ :param str cv_discussion_author: Clinical variant discussion author
412
+ (or list of authors separated by commas).
413
+ :param str cv_discussion_date: Clinical variant discussion date (or
414
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
415
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
416
+ 20231001000000-20231101000000.
417
+ :param str cv_discussion_text: Clinical variant discussion text (word
418
+ or list of words contained in the text, if the words are separated
419
+ by a comma an OR will be applied; if the words are separated by a
420
+ semicolon, an AND will be applied).
421
+ :param str cv_confidence_value: Clinical variant confidence value (or
422
+ list of values separated by commas).
423
+ :param str cv_confidence_author: Clinical variant confidence author
424
+ (or list of authors separated by commas).
425
+ :param str cv_confidence_date: Clinical variant confidence date (or
426
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
427
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
428
+ 20231001000000-20231101000000.
429
+ :param str cv_tag: Clinical variant tag (or list of tags separated by
430
+ commas).
431
+ :param str cv_status: Clinical variant status (or list of status
432
+ separated by commas).
433
+ :param str cv_region: Variant region (or list of regions, these can be
434
+ just a single chromosome name or regions in the format
435
+ chr:start-end, e.g.: 2,3:100000-200000).
436
+ :param str cv_biotype: Variant biotype, e.g. protein_coding (or list
437
+ of biotypes separated by commas).
438
+ :param str cv_ct: Variant SO consequence type (or list of SOs
439
+ separated by commas), e.g. missense_variant,stop_lost or
440
+ SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
441
+ 'protein_altering'.
442
+ :param str cv_transcript_flag: Variant transcript flag (or list of
443
+ flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
444
+ Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
445
+ :param str cv_gene: Variant gene (or list genes separated by commas),
446
+ most gene IDs are accepted (HGNC, Ensembl gene, ...).
447
+ :param str cv_xref: Variant external reference (or list of references
448
+ separated by commas), these can be genes, proteins or variants.
449
+ Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
450
+ Cosmic, ...
451
+ :param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
452
+ (or list of roles separated by commas).
453
+ :param str cv_type: Variant type or list of types, accepted values are
454
+ SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
455
+ COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
456
+ TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
457
+ :param str cv_protein_substitution: Variant protein substitution score
458
+ (or list of scores separated by commas), include SIFT and PolyPhen.
459
+ You can query using the score {protein_score}[<|>|<=|>=]{number} or
460
+ the description {protein_score}[~=|=]{description} e.g.
461
+ polyphen>0.1,sift=tolerant.
462
+ :param str cv_conservation: Variant conservation score (or list of
463
+ scores separated by commas) with the format
464
+ {conservation_score}[<|>|<=|>=]{number} e.g.
465
+ phastCons>0.5,phylop<0.1,gerp>0.1.
466
+ :param str cv_functional_score: Variant functional score (or list of
467
+ scores separated by commas) with the format
468
+ {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
469
+ cadd_raw<=0.3.
470
+ :param str cv_population_frequency_alt: Variant alternate population
471
+ frequency (or list of frequencies separated by commas), with the
472
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
473
+ 1000G:ALL<0.01.
474
+ :param str cv_population_frequency_maf: Variant population minor
475
+ allele frequency (or list of frequencies separated by commas), with
476
+ the format {study}:{population}[<|>|<=|>=]{number}. e.g.
477
+ 1000G:ALL<0.01.
478
+ :param str cv_population_frequency_ref: Variant reference population
479
+ frequency (or list of frequences separated by commas), with the
480
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
481
+ 1000G:ALL<0.01.
482
+ :param str cv_cohort_stats_alt: Variant alternate allele frequency (or
483
+ list of frequencies separated by commas), with the format
484
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
485
+ :param str cv_cohort_stats_maf: Variant minor allele frequency (or
486
+ list of frequencies separated by commas), with the format
487
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
488
+ :param str cv_cohort_stats_ref: Variant reference allele frequency (or
489
+ list of frequencies separated by commas), with the foramt
490
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
491
+ :param str cv_cohort_stats_pass: Variant filter PASS frequency (or
492
+ list of frequencies separated by commas), with the format
493
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
494
+ :param str cv_score: Variant score (or list of scores separated by
495
+ commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
496
+ :param str cv_annot_go_genes: Variant gene GO (or list of GOs
497
+ separated by commas).
498
+ :param str cv_annot_expression_genes: Variant gene expression (or list
499
+ of expressions separated by commas).
500
+ :param str cv_gene_trait_id: Variant gene trait association ID (or
501
+ list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
502
+ 'OMIM:269600'.
503
+ :param str cv_trait: Variant Trait (or list of traits separated by
504
+ commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
505
+ descriptions,...
506
+ :param str cv_protein_keyword: Uniprot protein variant annotation
507
+ keyword (or list of keywords separated by commas).
508
+ :param str cve_variant_id: Variant ID (or list of IDs separated by
509
+ commas).
510
+ :param bool cve_primary_finding: Clinical variant evidence belongs to
511
+ a primary finding (true or false).
512
+ :param bool cve_primary_interpretation: Clinical variant evidence
513
+ belongs to the primary interpretation (true or false).
514
+ :param str cve_phenotype_name: Clinical variant evidence phenotype
515
+ name (or names separated by commas).
516
+ :param str cve_gene_name: Clinical variant evidence gene name (or
517
+ names separated by commas).
518
+ :param str cve_transcript_id: Clinical variant evidence transcript ID
519
+ (or IDs separated by commas).
520
+ :param str cve_so_term_name: Clinical variant evidence sequence
521
+ ontology name (or names separated by commas).
522
+ :param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
523
+ separated by commas).
524
+ :param str cve_panel_id: Clinical variant evidence panel ID (or IDs
525
+ separated by commas).
526
+ :param str cve_moi: Clinical variant evidence mode of inheritance (or
527
+ list of modes of inheritance separated by commas), valid values:
528
+ AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
529
+ X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
530
+ MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
531
+ :param str cve_penetrance: Clinical variant evidence penetrance (or
532
+ list of penetrance values separated by commas), valid values:
533
+ COMPLETE, INCOMPLETE, UNKNOWN.
534
+ :param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
535
+ separated by commas).
536
+ :param str cve_tier: Clinical variant evidence tier (or list of tier
537
+ values separated by commas).
538
+ :param str cve_clinical_significance: Clinical variant evidence
539
+ clinical significance (or list of clinical significances separated
540
+ by commas).
541
+ :param str cve_drug_response: Clinical variant evidence drug response
542
+ (or list of drug responses separated by commas).
543
+ :param str cve_trait_association: Clinical variant evidence trait
544
+ association (or list of traits separated by commas).
545
+ :param str cve_functional_effect: Clinical variant evidence functional
546
+ effect (or list of functional effects separated by commas).
547
+ :param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
548
+ (or list of tumorigenesis values separated by commas).
549
+ :param str cve_other_classification: Clinical variant evidence
550
+ other-classification (or list of other classification values
551
+ separated by commas).
552
+ :param str cve_role_in_cancer: Clinical variant evidence role in
553
+ cancer (or roles in cancer separated by commas).
554
+ :param str cve_review_acmg: Clinical variant evidence review ACMG (or
555
+ ACGMs separated by commas).
556
+ :param str cve_review_tier: Clinical variant evidence review tier (or
557
+ list of tier values separated by commas).
558
+ :param str cve_review_clinical_significance: Clinical variant evidence
559
+ review clinical significance (or list of clinical significances
560
+ separated by commas).
561
+ :param str cve_review_text: Clinical variant evidence review text
562
+ (word or list of words contained in the text, if the words are
563
+ separated by a comma an OR will be applied; if the words are
564
+ separated by a semicolon, an AND will be applied).
565
+ """
566
+
567
+ return self._get(category='analysis', resource='query', subcategory='cvdb/analysis', **options)
568
+
569
+ def aggregate_evidence(self, **options):
570
+ """
571
+ Calculate and fetch clinical variant evidence aggregation stats.
572
+ PATH: /{apiVersion}/analysis/cvdb/evidence/aggregate
573
+
574
+ :param str project: Project ID.
575
+ :param str study: Study ID (or list of study IDs separated by commas).
576
+ :param str ca_id: Clinical analysis ID (or list of IDs separated by
577
+ commas).
578
+ :param str ca_description: Clinical analysis description (word or list
579
+ of words contained in the text, if the words are separated by a
580
+ comma an OR will be applied; if the words are separated by a
581
+ semicolon, an AND will be applied).
582
+ :param str ca_type: Clinical analysis type (or list of types separated
583
+ by commas).
584
+ :param str ca_disorder_id: Clinical analysis disorder ID (or list of
585
+ IDs separated by commas).
586
+ :param str ca_filename: Clinical analysis filename (or list of
587
+ filenames separated by commas).
588
+ :param str ca_proband_id: Clinical analysis proband ID (or list of IDs
589
+ separated by commas).
590
+ :param str ca_proband_disorder_id: Clinical analysis proband disorder
591
+ ID (or list of disorder IDs separated by commas).
592
+ :param str ca_proband_phenotype_name: Clinical analysis proband
593
+ phenotype name (or list of phenotype names separated by commas).
594
+ :param str ca_family_id: Clinical analysis family ID (or list of IDs
595
+ separated by commas).
596
+ :param str ca_family_phenotype_name: Clinical analysis family
597
+ phenotype names (or list of names separated by commas).
598
+ :param str ca_family_member_id: Clinical analysis family member ID (or
599
+ list of IDs separated by commas).
600
+ :param str ca_report: Clinical analysis report text (word or list of
601
+ words contained in the text, if the words are separated by a comma
602
+ an OR will be applied; if the words are separated by a semicolon,
603
+ an AND will be applied).
604
+ :param str ca_status: Clinical analysis status (or list of status
605
+ separated by commas).
606
+ :param bool ca_locked: Clinical analysis locked (true or false).
607
+ :param str ci_id: Clinical interpretation ID (or list of IDs separated
608
+ by commas).
609
+ :param bool ci_primary: Clinical interpretation primary (true or
610
+ false).
611
+ :param str ci_description: Clinical interpretation description (word
612
+ or list of words contained in the text, if the words are separated
613
+ by a comma an OR will be applied; if the words are separated by a
614
+ semicolon, an AND will be applied).
615
+ :param str ci_panel_id: Clinical interpretation panel ID or name (or
616
+ list of IDs or names separated by commas).
617
+ :param str ci_analyst_id: Clinical interpretation analyst ID (or list
618
+ of IDs separated by commas).
619
+ :param str ci_analyst_name: Clinical interpretation analyst name (or
620
+ list of names separated by commas).
621
+ :param str ci_analyst_email: Clinical interpretation analyst e-mail
622
+ (or list of e-mails separated by commas).
623
+ :param str ci_analyst_assigned_by: Clinical interpretation analyst
624
+ assignee name (or list of names separated by commas).
625
+ :param str ci_analyst_date: Clinical interpretation analyst date (or
626
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
627
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
628
+ 20231001000000-20231101000000.
629
+ :param str ci_method_name: Clinical interpretation method name (or
630
+ list of names separated by commas).
631
+ :param str ci_method_version: Clinical interpretation method version
632
+ (or list of versions separated by commas).
633
+ :param str ci_method_commit: Clinical interpretation method commit (or
634
+ list of commits separated by commas).
635
+ :param str ci_method_dependencies: Clinical interpretation method
636
+ dependencies (word or list of words contained in the text, if the
637
+ words are separated by a comma an OR will be applied; if the words
638
+ are separated by a semicolon, an AND will be applied).
639
+ :param str ci_comments: Clinical interpretation comment text (word or
640
+ list of words contained in the text, if the words are separated by
641
+ a comma an OR will be applied; if the words are separated by a
642
+ semicolon, an AND will be applied).
643
+ :param bool ci_locked: Clinical interpretation locked (true or false).
644
+ :param str ci_status_id: Clinical interpretation status ID (or list of
645
+ IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
646
+ CLOSED.
647
+ :param str ci_status_name: Clinical interpretation status name (or
648
+ list of names separated by commas).
649
+ :param str ci_status_description: Clinical interpretation status
650
+ description (word or list of words contained in the text, if the
651
+ words are separated by a comma an OR will be applied; if the words
652
+ are separated by a semicolon, an AND will be applied).
653
+ :param str ci_status_date: Clinical interpretation status date (or
654
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
655
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
656
+ 20231001000000-20231101000000.
657
+ :param str ci_creation_date: Clinical interpretation creation date (or
658
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
659
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
660
+ 20231001000000-20231101000000.
661
+ :param str ci_modification_date: Clinical interpretation modification
662
+ date (or list of dates separated by commas), with format
663
+ YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
664
+ start_date-end_date, e.g.: 20231001000000-20231101000000.
665
+ :param int ci_version: Clinical interpretation version number (or list
666
+ of versions separated by commas).
667
+ :param str cv_id: Clinical variant ID (or list of IDs separated by
668
+ commas).
669
+ :param str cv_variant_id: Variant ID (or list of IDs separated by
670
+ commas).
671
+ :param bool cv_primary_finding: Clinical variant is a primary finding
672
+ (true or false).
673
+ :param bool cv_primary_interpretation: Clinical variant belongs to the
674
+ primary interpretation (true or false).
675
+ :param str cv_comments: Clinical variant comment text (word or list of
676
+ words contained in the text, if the words are separated by a comma
677
+ an OR will be applied; if the words are separated by a semicolon,
678
+ an AND will be applied).
679
+ :param str cv_discussion_author: Clinical variant discussion author
680
+ (or list of authors separated by commas).
681
+ :param str cv_discussion_date: Clinical variant discussion date (or
682
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
683
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
684
+ 20231001000000-20231101000000.
685
+ :param str cv_discussion_text: Clinical variant discussion text (word
686
+ or list of words contained in the text, if the words are separated
687
+ by a comma an OR will be applied; if the words are separated by a
688
+ semicolon, an AND will be applied).
689
+ :param str cv_confidence_value: Clinical variant confidence value (or
690
+ list of values separated by commas).
691
+ :param str cv_confidence_author: Clinical variant confidence author
692
+ (or list of authors separated by commas).
693
+ :param str cv_confidence_date: Clinical variant confidence date (or
694
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
695
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
696
+ 20231001000000-20231101000000.
697
+ :param str cv_tag: Clinical variant tag (or list of tags separated by
698
+ commas).
699
+ :param str cv_status: Clinical variant status (or list of status
700
+ separated by commas).
701
+ :param str cv_region: Variant region (or list of regions, these can be
702
+ just a single chromosome name or regions in the format
703
+ chr:start-end, e.g.: 2,3:100000-200000).
704
+ :param str cv_biotype: Variant biotype, e.g. protein_coding (or list
705
+ of biotypes separated by commas).
706
+ :param str cv_ct: Variant SO consequence type (or list of SOs
707
+ separated by commas), e.g. missense_variant,stop_lost or
708
+ SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
709
+ 'protein_altering'.
710
+ :param str cv_transcript_flag: Variant transcript flag (or list of
711
+ flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
712
+ Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
713
+ :param str cv_gene: Variant gene (or list genes separated by commas),
714
+ most gene IDs are accepted (HGNC, Ensembl gene, ...).
715
+ :param str cv_xref: Variant external reference (or list of references
716
+ separated by commas), these can be genes, proteins or variants.
717
+ Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
718
+ Cosmic, ...
719
+ :param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
720
+ (or list of roles separated by commas).
721
+ :param str cv_type: Variant type or list of types, accepted values are
722
+ SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
723
+ COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
724
+ TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
725
+ :param str cv_protein_substitution: Variant protein substitution score
726
+ (or list of scores separated by commas), include SIFT and PolyPhen.
727
+ You can query using the score {protein_score}[<|>|<=|>=]{number} or
728
+ the description {protein_score}[~=|=]{description} e.g.
729
+ polyphen>0.1,sift=tolerant.
730
+ :param str cv_conservation: Variant conservation score (or list of
731
+ scores separated by commas) with the format
732
+ {conservation_score}[<|>|<=|>=]{number} e.g.
733
+ phastCons>0.5,phylop<0.1,gerp>0.1.
734
+ :param str cv_functional_score: Variant functional score (or list of
735
+ scores separated by commas) with the format
736
+ {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
737
+ cadd_raw<=0.3.
738
+ :param str cv_population_frequency_alt: Variant alternate population
739
+ frequency (or list of frequencies separated by commas), with the
740
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
741
+ 1000G:ALL<0.01.
742
+ :param str cv_population_frequency_maf: Variant population minor
743
+ allele frequency (or list of frequencies separated by commas), with
744
+ the format {study}:{population}[<|>|<=|>=]{number}. e.g.
745
+ 1000G:ALL<0.01.
746
+ :param str cv_population_frequency_ref: Variant reference population
747
+ frequency (or list of frequences separated by commas), with the
748
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
749
+ 1000G:ALL<0.01.
750
+ :param str cv_cohort_stats_alt: Variant alternate allele frequency (or
751
+ list of frequencies separated by commas), with the format
752
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
753
+ :param str cv_cohort_stats_maf: Variant minor allele frequency (or
754
+ list of frequencies separated by commas), with the format
755
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
756
+ :param str cv_cohort_stats_ref: Variant reference allele frequency (or
757
+ list of frequencies separated by commas), with the foramt
758
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
759
+ :param str cv_cohort_stats_pass: Variant filter PASS frequency (or
760
+ list of frequencies separated by commas), with the format
761
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
762
+ :param str cv_score: Variant score (or list of scores separated by
763
+ commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
764
+ :param str cv_annot_go_genes: Variant gene GO (or list of GOs
765
+ separated by commas).
766
+ :param str cv_annot_expression_genes: Variant gene expression (or list
767
+ of expressions separated by commas).
768
+ :param str cv_gene_trait_id: Variant gene trait association ID (or
769
+ list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
770
+ 'OMIM:269600'.
771
+ :param str cv_trait: Variant Trait (or list of traits separated by
772
+ commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
773
+ descriptions,...
774
+ :param str cv_protein_keyword: Uniprot protein variant annotation
775
+ keyword (or list of keywords separated by commas).
776
+ :param str cve_variant_id: Variant ID (or list of IDs separated by
777
+ commas).
778
+ :param bool cve_primary_finding: Clinical variant evidence belongs to
779
+ a primary finding (true or false).
780
+ :param bool cve_primary_interpretation: Clinical variant evidence
781
+ belongs to the primary interpretation (true or false).
782
+ :param str cve_phenotype_name: Clinical variant evidence phenotype
783
+ name (or names separated by commas).
784
+ :param str cve_gene_name: Clinical variant evidence gene name (or
785
+ names separated by commas).
786
+ :param str cve_transcript_id: Clinical variant evidence transcript ID
787
+ (or IDs separated by commas).
788
+ :param str cve_so_term_name: Clinical variant evidence sequence
789
+ ontology name (or names separated by commas).
790
+ :param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
791
+ separated by commas).
792
+ :param str cve_panel_id: Clinical variant evidence panel ID (or IDs
793
+ separated by commas).
794
+ :param str cve_moi: Clinical variant evidence mode of inheritance (or
795
+ list of modes of inheritance separated by commas), valid values:
796
+ AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
797
+ X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
798
+ MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
799
+ :param str cve_penetrance: Clinical variant evidence penetrance (or
800
+ list of penetrance values separated by commas), valid values:
801
+ COMPLETE, INCOMPLETE, UNKNOWN.
802
+ :param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
803
+ separated by commas).
804
+ :param str cve_tier: Clinical variant evidence tier (or list of tier
805
+ values separated by commas).
806
+ :param str cve_clinical_significance: Clinical variant evidence
807
+ clinical significance (or list of clinical significances separated
808
+ by commas).
809
+ :param str cve_drug_response: Clinical variant evidence drug response
810
+ (or list of drug responses separated by commas).
811
+ :param str cve_trait_association: Clinical variant evidence trait
812
+ association (or list of traits separated by commas).
813
+ :param str cve_functional_effect: Clinical variant evidence functional
814
+ effect (or list of functional effects separated by commas).
815
+ :param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
816
+ (or list of tumorigenesis values separated by commas).
817
+ :param str cve_other_classification: Clinical variant evidence
818
+ other-classification (or list of other classification values
819
+ separated by commas).
820
+ :param str cve_role_in_cancer: Clinical variant evidence role in
821
+ cancer (or roles in cancer separated by commas).
822
+ :param str cve_review_acmg: Clinical variant evidence review ACMG (or
823
+ ACGMs separated by commas).
824
+ :param str cve_review_tier: Clinical variant evidence review tier (or
825
+ list of tier values separated by commas).
826
+ :param str cve_review_clinical_significance: Clinical variant evidence
827
+ review clinical significance (or list of clinical significances
828
+ separated by commas).
829
+ :param str cve_review_text: Clinical variant evidence review text
830
+ (word or list of words contained in the text, if the words are
831
+ separated by a comma an OR will be applied; if the words are
832
+ separated by a semicolon, an AND will be applied).
833
+ :param str field: List of facet fields separated by semicolons, e.g.:
834
+ geneName;tier. For nested faceted fields use >>, e.g.:
835
+ geneName>>tier. Accepted values: caId, ciId, cvId, variantId,
836
+ studyId, phenotypeNames, geneName, transcriptId, soTermNames,
837
+ xrefIds, panelId, mois, penetrance, acmgs, tier,
838
+ clinicalSignificance, drugResponse, traitAssociation,
839
+ functionalEffect, tumorigenesis, otherClassifications,
840
+ rolesInCancer, reviewAcmgs, reviewTier, reviewClinicalSignificance.
841
+ """
842
+
843
+ return self._get(category='analysis', resource='aggregate', subcategory='cvdb/evidence', **options)
844
+
845
+ def query_evidence(self, **options):
846
+ """
847
+ Filter and fetch clinical variant evidences from CVDB.
848
+ PATH: /{apiVersion}/analysis/cvdb/evidence/query
849
+
850
+ :param str project: Project ID.
851
+ :param str study: Study ID (or list of study IDs separated by commas).
852
+ :param str include: Fields included in the response, whole JSON path
853
+ must be provided.
854
+ :param str exclude: Fields excluded in the response, whole JSON path
855
+ must be provided.
856
+ :param int limit: Number of results to be returned.
857
+ :param int skip: Number of results to skip.
858
+ :param str ca_id: Clinical analysis ID (or list of IDs separated by
859
+ commas).
860
+ :param str ca_description: Clinical analysis description (word or list
861
+ of words contained in the text, if the words are separated by a
862
+ comma an OR will be applied; if the words are separated by a
863
+ semicolon, an AND will be applied).
864
+ :param str ca_type: Clinical analysis type (or list of types separated
865
+ by commas).
866
+ :param str ca_disorder_id: Clinical analysis disorder ID (or list of
867
+ IDs separated by commas).
868
+ :param str ca_filename: Clinical analysis filename (or list of
869
+ filenames separated by commas).
870
+ :param str ca_proband_id: Clinical analysis proband ID (or list of IDs
871
+ separated by commas).
872
+ :param str ca_proband_disorder_id: Clinical analysis proband disorder
873
+ ID (or list of disorder IDs separated by commas).
874
+ :param str ca_proband_phenotype_name: Clinical analysis proband
875
+ phenotype name (or list of phenotype names separated by commas).
876
+ :param str ca_family_id: Clinical analysis family ID (or list of IDs
877
+ separated by commas).
878
+ :param str ca_family_phenotype_name: Clinical analysis family
879
+ phenotype names (or list of names separated by commas).
880
+ :param str ca_family_member_id: Clinical analysis family member ID (or
881
+ list of IDs separated by commas).
882
+ :param str ca_report: Clinical analysis report text (word or list of
883
+ words contained in the text, if the words are separated by a comma
884
+ an OR will be applied; if the words are separated by a semicolon,
885
+ an AND will be applied).
886
+ :param str ca_status: Clinical analysis status (or list of status
887
+ separated by commas).
888
+ :param bool ca_locked: Clinical analysis locked (true or false).
889
+ :param str ci_id: Clinical interpretation ID (or list of IDs separated
890
+ by commas).
891
+ :param bool ci_primary: Clinical interpretation primary (true or
892
+ false).
893
+ :param str ci_description: Clinical interpretation description (word
894
+ or list of words contained in the text, if the words are separated
895
+ by a comma an OR will be applied; if the words are separated by a
896
+ semicolon, an AND will be applied).
897
+ :param str ci_panel_id: Clinical interpretation panel ID or name (or
898
+ list of IDs or names separated by commas).
899
+ :param str ci_analyst_id: Clinical interpretation analyst ID (or list
900
+ of IDs separated by commas).
901
+ :param str ci_analyst_name: Clinical interpretation analyst name (or
902
+ list of names separated by commas).
903
+ :param str ci_analyst_email: Clinical interpretation analyst e-mail
904
+ (or list of e-mails separated by commas).
905
+ :param str ci_analyst_assigned_by: Clinical interpretation analyst
906
+ assignee name (or list of names separated by commas).
907
+ :param str ci_analyst_date: Clinical interpretation analyst date (or
908
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
909
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
910
+ 20231001000000-20231101000000.
911
+ :param str ci_method_name: Clinical interpretation method name (or
912
+ list of names separated by commas).
913
+ :param str ci_method_version: Clinical interpretation method version
914
+ (or list of versions separated by commas).
915
+ :param str ci_method_commit: Clinical interpretation method commit (or
916
+ list of commits separated by commas).
917
+ :param str ci_method_dependencies: Clinical interpretation method
918
+ dependencies (word or list of words contained in the text, if the
919
+ words are separated by a comma an OR will be applied; if the words
920
+ are separated by a semicolon, an AND will be applied).
921
+ :param str ci_comments: Clinical interpretation comment text (word or
922
+ list of words contained in the text, if the words are separated by
923
+ a comma an OR will be applied; if the words are separated by a
924
+ semicolon, an AND will be applied).
925
+ :param bool ci_locked: Clinical interpretation locked (true or false).
926
+ :param str ci_status_id: Clinical interpretation status ID (or list of
927
+ IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
928
+ CLOSED.
929
+ :param str ci_status_name: Clinical interpretation status name (or
930
+ list of names separated by commas).
931
+ :param str ci_status_description: Clinical interpretation status
932
+ description (word or list of words contained in the text, if the
933
+ words are separated by a comma an OR will be applied; if the words
934
+ are separated by a semicolon, an AND will be applied).
935
+ :param str ci_status_date: Clinical interpretation status date (or
936
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
937
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
938
+ 20231001000000-20231101000000.
939
+ :param str ci_creation_date: Clinical interpretation creation date (or
940
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
941
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
942
+ 20231001000000-20231101000000.
943
+ :param str ci_modification_date: Clinical interpretation modification
944
+ date (or list of dates separated by commas), with format
945
+ YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
946
+ start_date-end_date, e.g.: 20231001000000-20231101000000.
947
+ :param int ci_version: Clinical interpretation version number (or list
948
+ of versions separated by commas).
949
+ :param str cv_id: Clinical variant ID (or list of IDs separated by
950
+ commas).
951
+ :param str cv_variant_id: Variant ID (or list of IDs separated by
952
+ commas).
953
+ :param bool cv_primary_finding: Clinical variant is a primary finding
954
+ (true or false).
955
+ :param bool cv_primary_interpretation: Clinical variant belongs to the
956
+ primary interpretation (true or false).
957
+ :param str cv_comments: Clinical variant comment text (word or list of
958
+ words contained in the text, if the words are separated by a comma
959
+ an OR will be applied; if the words are separated by a semicolon,
960
+ an AND will be applied).
961
+ :param str cv_discussion_author: Clinical variant discussion author
962
+ (or list of authors separated by commas).
963
+ :param str cv_discussion_date: Clinical variant discussion date (or
964
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
965
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
966
+ 20231001000000-20231101000000.
967
+ :param str cv_discussion_text: Clinical variant discussion text (word
968
+ or list of words contained in the text, if the words are separated
969
+ by a comma an OR will be applied; if the words are separated by a
970
+ semicolon, an AND will be applied).
971
+ :param str cv_confidence_value: Clinical variant confidence value (or
972
+ list of values separated by commas).
973
+ :param str cv_confidence_author: Clinical variant confidence author
974
+ (or list of authors separated by commas).
975
+ :param str cv_confidence_date: Clinical variant confidence date (or
976
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
977
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
978
+ 20231001000000-20231101000000.
979
+ :param str cv_tag: Clinical variant tag (or list of tags separated by
980
+ commas).
981
+ :param str cv_status: Clinical variant status (or list of status
982
+ separated by commas).
983
+ :param str cv_region: Variant region (or list of regions, these can be
984
+ just a single chromosome name or regions in the format
985
+ chr:start-end, e.g.: 2,3:100000-200000).
986
+ :param str cv_biotype: Variant biotype, e.g. protein_coding (or list
987
+ of biotypes separated by commas).
988
+ :param str cv_ct: Variant SO consequence type (or list of SOs
989
+ separated by commas), e.g. missense_variant,stop_lost or
990
+ SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
991
+ 'protein_altering'.
992
+ :param str cv_transcript_flag: Variant transcript flag (or list of
993
+ flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
994
+ Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
995
+ :param str cv_gene: Variant gene (or list genes separated by commas),
996
+ most gene IDs are accepted (HGNC, Ensembl gene, ...).
997
+ :param str cv_xref: Variant external reference (or list of references
998
+ separated by commas), these can be genes, proteins or variants.
999
+ Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
1000
+ Cosmic, ...
1001
+ :param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
1002
+ (or list of roles separated by commas).
1003
+ :param str cv_type: Variant type or list of types, accepted values are
1004
+ SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
1005
+ COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
1006
+ TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
1007
+ :param str cv_protein_substitution: Variant protein substitution score
1008
+ (or list of scores separated by commas), include SIFT and PolyPhen.
1009
+ You can query using the score {protein_score}[<|>|<=|>=]{number} or
1010
+ the description {protein_score}[~=|=]{description} e.g.
1011
+ polyphen>0.1,sift=tolerant.
1012
+ :param str cv_conservation: Variant conservation score (or list of
1013
+ scores separated by commas) with the format
1014
+ {conservation_score}[<|>|<=|>=]{number} e.g.
1015
+ phastCons>0.5,phylop<0.1,gerp>0.1.
1016
+ :param str cv_functional_score: Variant functional score (or list of
1017
+ scores separated by commas) with the format
1018
+ {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
1019
+ cadd_raw<=0.3.
1020
+ :param str cv_population_frequency_alt: Variant alternate population
1021
+ frequency (or list of frequencies separated by commas), with the
1022
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
1023
+ 1000G:ALL<0.01.
1024
+ :param str cv_population_frequency_maf: Variant population minor
1025
+ allele frequency (or list of frequencies separated by commas), with
1026
+ the format {study}:{population}[<|>|<=|>=]{number}. e.g.
1027
+ 1000G:ALL<0.01.
1028
+ :param str cv_population_frequency_ref: Variant reference population
1029
+ frequency (or list of frequences separated by commas), with the
1030
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
1031
+ 1000G:ALL<0.01.
1032
+ :param str cv_cohort_stats_alt: Variant alternate allele frequency (or
1033
+ list of frequencies separated by commas), with the format
1034
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1035
+ :param str cv_cohort_stats_maf: Variant minor allele frequency (or
1036
+ list of frequencies separated by commas), with the format
1037
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1038
+ :param str cv_cohort_stats_ref: Variant reference allele frequency (or
1039
+ list of frequencies separated by commas), with the foramt
1040
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1041
+ :param str cv_cohort_stats_pass: Variant filter PASS frequency (or
1042
+ list of frequencies separated by commas), with the format
1043
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
1044
+ :param str cv_score: Variant score (or list of scores separated by
1045
+ commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
1046
+ :param str cv_annot_go_genes: Variant gene GO (or list of GOs
1047
+ separated by commas).
1048
+ :param str cv_annot_expression_genes: Variant gene expression (or list
1049
+ of expressions separated by commas).
1050
+ :param str cv_gene_trait_id: Variant gene trait association ID (or
1051
+ list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
1052
+ 'OMIM:269600'.
1053
+ :param str cv_trait: Variant Trait (or list of traits separated by
1054
+ commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
1055
+ descriptions,...
1056
+ :param str cv_protein_keyword: Uniprot protein variant annotation
1057
+ keyword (or list of keywords separated by commas).
1058
+ :param str cve_variant_id: Variant ID (or list of IDs separated by
1059
+ commas).
1060
+ :param bool cve_primary_finding: Clinical variant evidence belongs to
1061
+ a primary finding (true or false).
1062
+ :param bool cve_primary_interpretation: Clinical variant evidence
1063
+ belongs to the primary interpretation (true or false).
1064
+ :param str cve_phenotype_name: Clinical variant evidence phenotype
1065
+ name (or names separated by commas).
1066
+ :param str cve_gene_name: Clinical variant evidence gene name (or
1067
+ names separated by commas).
1068
+ :param str cve_transcript_id: Clinical variant evidence transcript ID
1069
+ (or IDs separated by commas).
1070
+ :param str cve_so_term_name: Clinical variant evidence sequence
1071
+ ontology name (or names separated by commas).
1072
+ :param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
1073
+ separated by commas).
1074
+ :param str cve_panel_id: Clinical variant evidence panel ID (or IDs
1075
+ separated by commas).
1076
+ :param str cve_moi: Clinical variant evidence mode of inheritance (or
1077
+ list of modes of inheritance separated by commas), valid values:
1078
+ AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
1079
+ X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
1080
+ MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
1081
+ :param str cve_penetrance: Clinical variant evidence penetrance (or
1082
+ list of penetrance values separated by commas), valid values:
1083
+ COMPLETE, INCOMPLETE, UNKNOWN.
1084
+ :param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
1085
+ separated by commas).
1086
+ :param str cve_tier: Clinical variant evidence tier (or list of tier
1087
+ values separated by commas).
1088
+ :param str cve_clinical_significance: Clinical variant evidence
1089
+ clinical significance (or list of clinical significances separated
1090
+ by commas).
1091
+ :param str cve_drug_response: Clinical variant evidence drug response
1092
+ (or list of drug responses separated by commas).
1093
+ :param str cve_trait_association: Clinical variant evidence trait
1094
+ association (or list of traits separated by commas).
1095
+ :param str cve_functional_effect: Clinical variant evidence functional
1096
+ effect (or list of functional effects separated by commas).
1097
+ :param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
1098
+ (or list of tumorigenesis values separated by commas).
1099
+ :param str cve_other_classification: Clinical variant evidence
1100
+ other-classification (or list of other classification values
1101
+ separated by commas).
1102
+ :param str cve_role_in_cancer: Clinical variant evidence role in
1103
+ cancer (or roles in cancer separated by commas).
1104
+ :param str cve_review_acmg: Clinical variant evidence review ACMG (or
1105
+ ACGMs separated by commas).
1106
+ :param str cve_review_tier: Clinical variant evidence review tier (or
1107
+ list of tier values separated by commas).
1108
+ :param str cve_review_clinical_significance: Clinical variant evidence
1109
+ review clinical significance (or list of clinical significances
1110
+ separated by commas).
1111
+ :param str cve_review_text: Clinical variant evidence review text
1112
+ (word or list of words contained in the text, if the words are
1113
+ separated by a comma an OR will be applied; if the words are
1114
+ separated by a semicolon, an AND will be applied).
1115
+ """
1116
+
1117
+ return self._get(category='analysis', resource='query', subcategory='cvdb/evidence', **options)
1118
+
1119
+ def run_index(self, data=None, **options):
1120
+ """
1121
+ Index clinical analyses of a OpenCGA project, a study or a list of
1122
+ clinical analyses into CVDB.
1123
+ PATH: /{apiVersion}/analysis/cvdb/index/run
1124
+
1125
+ :param dict data: Parameters: Index clinical analyses of a OpenCGA
1126
+ project, a study or a list of clinical analyses into CVDB.
1127
+ (REQUIRED)
1128
+ :param str study: Study [[organization@]project:]study where study and
1129
+ project can be either the ID or UUID.
1130
+ :param str job_id: Job ID. It must be a unique string within the
1131
+ study. An ID will be autogenerated automatically if not provided.
1132
+ :param str job_description: Job description.
1133
+ :param str job_depends_on: Comma separated list of existing job IDs
1134
+ the job will depend on.
1135
+ :param str job_tags: Job tags.
1136
+ :param str job_scheduled_start_time: Time when the job is scheduled to
1137
+ start.
1138
+ :param str job_priority: Priority of the job.
1139
+ :param bool job_dry_run: Flag indicating that the job will be executed
1140
+ in dry-run mode. In this mode, OpenCGA will validate that all
1141
+ parameters and prerequisites are correctly set for successful
1142
+ execution, but the job will not actually run.
1143
+ """
1144
+
1145
+ return self._post(category='analysis', resource='run', subcategory='cvdb/index', data=data, **options)
1146
+
1147
+ def aggregate_interpretation(self, **options):
1148
+ """
1149
+ Calculate and fetch clinical interpretation aggregation stats.
1150
+ PATH: /{apiVersion}/analysis/cvdb/interpretation/aggregate
1151
+
1152
+ :param str project: Project ID.
1153
+ :param str study: Study ID (or list of study IDs separated by commas).
1154
+ :param str ca_id: Clinical analysis ID (or list of IDs separated by
1155
+ commas).
1156
+ :param str ca_description: Clinical analysis description (word or list
1157
+ of words contained in the text, if the words are separated by a
1158
+ comma an OR will be applied; if the words are separated by a
1159
+ semicolon, an AND will be applied).
1160
+ :param str ca_type: Clinical analysis type (or list of types separated
1161
+ by commas).
1162
+ :param str ca_disorder_id: Clinical analysis disorder ID (or list of
1163
+ IDs separated by commas).
1164
+ :param str ca_filename: Clinical analysis filename (or list of
1165
+ filenames separated by commas).
1166
+ :param str ca_proband_id: Clinical analysis proband ID (or list of IDs
1167
+ separated by commas).
1168
+ :param str ca_proband_disorder_id: Clinical analysis proband disorder
1169
+ ID (or list of disorder IDs separated by commas).
1170
+ :param str ca_proband_phenotype_name: Clinical analysis proband
1171
+ phenotype name (or list of phenotype names separated by commas).
1172
+ :param str ca_family_id: Clinical analysis family ID (or list of IDs
1173
+ separated by commas).
1174
+ :param str ca_family_phenotype_name: Clinical analysis family
1175
+ phenotype names (or list of names separated by commas).
1176
+ :param str ca_family_member_id: Clinical analysis family member ID (or
1177
+ list of IDs separated by commas).
1178
+ :param str ca_report: Clinical analysis report text (word or list of
1179
+ words contained in the text, if the words are separated by a comma
1180
+ an OR will be applied; if the words are separated by a semicolon,
1181
+ an AND will be applied).
1182
+ :param str ca_status: Clinical analysis status (or list of status
1183
+ separated by commas).
1184
+ :param bool ca_locked: Clinical analysis locked (true or false).
1185
+ :param str ci_id: Clinical interpretation ID (or list of IDs separated
1186
+ by commas).
1187
+ :param bool ci_primary: Clinical interpretation primary (true or
1188
+ false).
1189
+ :param str ci_description: Clinical interpretation description (word
1190
+ or list of words contained in the text, if the words are separated
1191
+ by a comma an OR will be applied; if the words are separated by a
1192
+ semicolon, an AND will be applied).
1193
+ :param str ci_panel_id: Clinical interpretation panel ID or name (or
1194
+ list of IDs or names separated by commas).
1195
+ :param str ci_analyst_id: Clinical interpretation analyst ID (or list
1196
+ of IDs separated by commas).
1197
+ :param str ci_analyst_name: Clinical interpretation analyst name (or
1198
+ list of names separated by commas).
1199
+ :param str ci_analyst_email: Clinical interpretation analyst e-mail
1200
+ (or list of e-mails separated by commas).
1201
+ :param str ci_analyst_assigned_by: Clinical interpretation analyst
1202
+ assignee name (or list of names separated by commas).
1203
+ :param str ci_analyst_date: Clinical interpretation analyst date (or
1204
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1205
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1206
+ 20231001000000-20231101000000.
1207
+ :param str ci_method_name: Clinical interpretation method name (or
1208
+ list of names separated by commas).
1209
+ :param str ci_method_version: Clinical interpretation method version
1210
+ (or list of versions separated by commas).
1211
+ :param str ci_method_commit: Clinical interpretation method commit (or
1212
+ list of commits separated by commas).
1213
+ :param str ci_method_dependencies: Clinical interpretation method
1214
+ dependencies (word or list of words contained in the text, if the
1215
+ words are separated by a comma an OR will be applied; if the words
1216
+ are separated by a semicolon, an AND will be applied).
1217
+ :param str ci_comments: Clinical interpretation comment text (word or
1218
+ list of words contained in the text, if the words are separated by
1219
+ a comma an OR will be applied; if the words are separated by a
1220
+ semicolon, an AND will be applied).
1221
+ :param bool ci_locked: Clinical interpretation locked (true or false).
1222
+ :param str ci_status_id: Clinical interpretation status ID (or list of
1223
+ IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
1224
+ CLOSED.
1225
+ :param str ci_status_name: Clinical interpretation status name (or
1226
+ list of names separated by commas).
1227
+ :param str ci_status_description: Clinical interpretation status
1228
+ description (word or list of words contained in the text, if the
1229
+ words are separated by a comma an OR will be applied; if the words
1230
+ are separated by a semicolon, an AND will be applied).
1231
+ :param str ci_status_date: Clinical interpretation status date (or
1232
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1233
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1234
+ 20231001000000-20231101000000.
1235
+ :param str ci_creation_date: Clinical interpretation creation date (or
1236
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1237
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1238
+ 20231001000000-20231101000000.
1239
+ :param str ci_modification_date: Clinical interpretation modification
1240
+ date (or list of dates separated by commas), with format
1241
+ YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
1242
+ start_date-end_date, e.g.: 20231001000000-20231101000000.
1243
+ :param int ci_version: Clinical interpretation version number (or list
1244
+ of versions separated by commas).
1245
+ :param str cv_id: Clinical variant ID (or list of IDs separated by
1246
+ commas).
1247
+ :param str cv_variant_id: Variant ID (or list of IDs separated by
1248
+ commas).
1249
+ :param bool cv_primary_finding: Clinical variant is a primary finding
1250
+ (true or false).
1251
+ :param bool cv_primary_interpretation: Clinical variant belongs to the
1252
+ primary interpretation (true or false).
1253
+ :param str cv_comments: Clinical variant comment text (word or list of
1254
+ words contained in the text, if the words are separated by a comma
1255
+ an OR will be applied; if the words are separated by a semicolon,
1256
+ an AND will be applied).
1257
+ :param str cv_discussion_author: Clinical variant discussion author
1258
+ (or list of authors separated by commas).
1259
+ :param str cv_discussion_date: Clinical variant discussion date (or
1260
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1261
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1262
+ 20231001000000-20231101000000.
1263
+ :param str cv_discussion_text: Clinical variant discussion text (word
1264
+ or list of words contained in the text, if the words are separated
1265
+ by a comma an OR will be applied; if the words are separated by a
1266
+ semicolon, an AND will be applied).
1267
+ :param str cv_confidence_value: Clinical variant confidence value (or
1268
+ list of values separated by commas).
1269
+ :param str cv_confidence_author: Clinical variant confidence author
1270
+ (or list of authors separated by commas).
1271
+ :param str cv_confidence_date: Clinical variant confidence date (or
1272
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1273
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1274
+ 20231001000000-20231101000000.
1275
+ :param str cv_tag: Clinical variant tag (or list of tags separated by
1276
+ commas).
1277
+ :param str cv_status: Clinical variant status (or list of status
1278
+ separated by commas).
1279
+ :param str cv_region: Variant region (or list of regions, these can be
1280
+ just a single chromosome name or regions in the format
1281
+ chr:start-end, e.g.: 2,3:100000-200000).
1282
+ :param str cv_biotype: Variant biotype, e.g. protein_coding (or list
1283
+ of biotypes separated by commas).
1284
+ :param str cv_ct: Variant SO consequence type (or list of SOs
1285
+ separated by commas), e.g. missense_variant,stop_lost or
1286
+ SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
1287
+ 'protein_altering'.
1288
+ :param str cv_transcript_flag: Variant transcript flag (or list of
1289
+ flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
1290
+ Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
1291
+ :param str cv_gene: Variant gene (or list genes separated by commas),
1292
+ most gene IDs are accepted (HGNC, Ensembl gene, ...).
1293
+ :param str cv_xref: Variant external reference (or list of references
1294
+ separated by commas), these can be genes, proteins or variants.
1295
+ Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
1296
+ Cosmic, ...
1297
+ :param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
1298
+ (or list of roles separated by commas).
1299
+ :param str cv_type: Variant type or list of types, accepted values are
1300
+ SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
1301
+ COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
1302
+ TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
1303
+ :param str cv_protein_substitution: Variant protein substitution score
1304
+ (or list of scores separated by commas), include SIFT and PolyPhen.
1305
+ You can query using the score {protein_score}[<|>|<=|>=]{number} or
1306
+ the description {protein_score}[~=|=]{description} e.g.
1307
+ polyphen>0.1,sift=tolerant.
1308
+ :param str cv_conservation: Variant conservation score (or list of
1309
+ scores separated by commas) with the format
1310
+ {conservation_score}[<|>|<=|>=]{number} e.g.
1311
+ phastCons>0.5,phylop<0.1,gerp>0.1.
1312
+ :param str cv_functional_score: Variant functional score (or list of
1313
+ scores separated by commas) with the format
1314
+ {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
1315
+ cadd_raw<=0.3.
1316
+ :param str cv_population_frequency_alt: Variant alternate population
1317
+ frequency (or list of frequencies separated by commas), with the
1318
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
1319
+ 1000G:ALL<0.01.
1320
+ :param str cv_population_frequency_maf: Variant population minor
1321
+ allele frequency (or list of frequencies separated by commas), with
1322
+ the format {study}:{population}[<|>|<=|>=]{number}. e.g.
1323
+ 1000G:ALL<0.01.
1324
+ :param str cv_population_frequency_ref: Variant reference population
1325
+ frequency (or list of frequences separated by commas), with the
1326
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
1327
+ 1000G:ALL<0.01.
1328
+ :param str cv_cohort_stats_alt: Variant alternate allele frequency (or
1329
+ list of frequencies separated by commas), with the format
1330
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1331
+ :param str cv_cohort_stats_maf: Variant minor allele frequency (or
1332
+ list of frequencies separated by commas), with the format
1333
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1334
+ :param str cv_cohort_stats_ref: Variant reference allele frequency (or
1335
+ list of frequencies separated by commas), with the foramt
1336
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1337
+ :param str cv_cohort_stats_pass: Variant filter PASS frequency (or
1338
+ list of frequencies separated by commas), with the format
1339
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
1340
+ :param str cv_score: Variant score (or list of scores separated by
1341
+ commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
1342
+ :param str cv_annot_go_genes: Variant gene GO (or list of GOs
1343
+ separated by commas).
1344
+ :param str cv_annot_expression_genes: Variant gene expression (or list
1345
+ of expressions separated by commas).
1346
+ :param str cv_gene_trait_id: Variant gene trait association ID (or
1347
+ list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
1348
+ 'OMIM:269600'.
1349
+ :param str cv_trait: Variant Trait (or list of traits separated by
1350
+ commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
1351
+ descriptions,...
1352
+ :param str cv_protein_keyword: Uniprot protein variant annotation
1353
+ keyword (or list of keywords separated by commas).
1354
+ :param str cve_variant_id: Variant ID (or list of IDs separated by
1355
+ commas).
1356
+ :param bool cve_primary_finding: Clinical variant evidence belongs to
1357
+ a primary finding (true or false).
1358
+ :param bool cve_primary_interpretation: Clinical variant evidence
1359
+ belongs to the primary interpretation (true or false).
1360
+ :param str cve_phenotype_name: Clinical variant evidence phenotype
1361
+ name (or names separated by commas).
1362
+ :param str cve_gene_name: Clinical variant evidence gene name (or
1363
+ names separated by commas).
1364
+ :param str cve_transcript_id: Clinical variant evidence transcript ID
1365
+ (or IDs separated by commas).
1366
+ :param str cve_so_term_name: Clinical variant evidence sequence
1367
+ ontology name (or names separated by commas).
1368
+ :param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
1369
+ separated by commas).
1370
+ :param str cve_panel_id: Clinical variant evidence panel ID (or IDs
1371
+ separated by commas).
1372
+ :param str cve_moi: Clinical variant evidence mode of inheritance (or
1373
+ list of modes of inheritance separated by commas), valid values:
1374
+ AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
1375
+ X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
1376
+ MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
1377
+ :param str cve_penetrance: Clinical variant evidence penetrance (or
1378
+ list of penetrance values separated by commas), valid values:
1379
+ COMPLETE, INCOMPLETE, UNKNOWN.
1380
+ :param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
1381
+ separated by commas).
1382
+ :param str cve_tier: Clinical variant evidence tier (or list of tier
1383
+ values separated by commas).
1384
+ :param str cve_clinical_significance: Clinical variant evidence
1385
+ clinical significance (or list of clinical significances separated
1386
+ by commas).
1387
+ :param str cve_drug_response: Clinical variant evidence drug response
1388
+ (or list of drug responses separated by commas).
1389
+ :param str cve_trait_association: Clinical variant evidence trait
1390
+ association (or list of traits separated by commas).
1391
+ :param str cve_functional_effect: Clinical variant evidence functional
1392
+ effect (or list of functional effects separated by commas).
1393
+ :param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
1394
+ (or list of tumorigenesis values separated by commas).
1395
+ :param str cve_other_classification: Clinical variant evidence
1396
+ other-classification (or list of other classification values
1397
+ separated by commas).
1398
+ :param str cve_role_in_cancer: Clinical variant evidence role in
1399
+ cancer (or roles in cancer separated by commas).
1400
+ :param str cve_review_acmg: Clinical variant evidence review ACMG (or
1401
+ ACGMs separated by commas).
1402
+ :param str cve_review_tier: Clinical variant evidence review tier (or
1403
+ list of tier values separated by commas).
1404
+ :param str cve_review_clinical_significance: Clinical variant evidence
1405
+ review clinical significance (or list of clinical significances
1406
+ separated by commas).
1407
+ :param str cve_review_text: Clinical variant evidence review text
1408
+ (word or list of words contained in the text, if the words are
1409
+ separated by a comma an OR will be applied; if the words are
1410
+ separated by a semicolon, an AND will be applied).
1411
+ :param str field: List of facet fields separated by semicolons, e.g.:
1412
+ panelIds;methodName. For nested faceted fields use >>, e.g.:
1413
+ panelIds>>methodName. Accepted values: caId, studyId, primary,
1414
+ panelIds, analystId, analystName, analystEmail, analystAssignedBy,
1415
+ analystDate, methodName, methodVersion, methodCommit, statusId,
1416
+ statusDescription, statusType, statusDate, creationDate,
1417
+ modificationDate, version.
1418
+ """
1419
+
1420
+ return self._get(category='analysis', resource='aggregate', subcategory='cvdb/interpretation', **options)
1421
+
1422
+ def query_interpretation(self, **options):
1423
+ """
1424
+ Filter and fetch clinical interpretations from CVDB.
1425
+ PATH: /{apiVersion}/analysis/cvdb/interpretation/query
1426
+
1427
+ :param str project: Project ID.
1428
+ :param str study: Study ID (or list of study IDs separated by commas).
1429
+ :param str include: Fields included in the response, whole JSON path
1430
+ must be provided.
1431
+ :param str exclude: Fields excluded in the response, whole JSON path
1432
+ must be provided.
1433
+ :param int limit: Number of results to be returned.
1434
+ :param int skip: Number of results to skip.
1435
+ :param str ca_id: Clinical analysis ID (or list of IDs separated by
1436
+ commas).
1437
+ :param str ca_description: Clinical analysis description (word or list
1438
+ of words contained in the text, if the words are separated by a
1439
+ comma an OR will be applied; if the words are separated by a
1440
+ semicolon, an AND will be applied).
1441
+ :param str ca_type: Clinical analysis type (or list of types separated
1442
+ by commas).
1443
+ :param str ca_disorder_id: Clinical analysis disorder ID (or list of
1444
+ IDs separated by commas).
1445
+ :param str ca_filename: Clinical analysis filename (or list of
1446
+ filenames separated by commas).
1447
+ :param str ca_proband_id: Clinical analysis proband ID (or list of IDs
1448
+ separated by commas).
1449
+ :param str ca_proband_disorder_id: Clinical analysis proband disorder
1450
+ ID (or list of disorder IDs separated by commas).
1451
+ :param str ca_proband_phenotype_name: Clinical analysis proband
1452
+ phenotype name (or list of phenotype names separated by commas).
1453
+ :param str ca_family_id: Clinical analysis family ID (or list of IDs
1454
+ separated by commas).
1455
+ :param str ca_family_phenotype_name: Clinical analysis family
1456
+ phenotype names (or list of names separated by commas).
1457
+ :param str ca_family_member_id: Clinical analysis family member ID (or
1458
+ list of IDs separated by commas).
1459
+ :param str ca_report: Clinical analysis report text (word or list of
1460
+ words contained in the text, if the words are separated by a comma
1461
+ an OR will be applied; if the words are separated by a semicolon,
1462
+ an AND will be applied).
1463
+ :param str ca_status: Clinical analysis status (or list of status
1464
+ separated by commas).
1465
+ :param bool ca_locked: Clinical analysis locked (true or false).
1466
+ :param str ci_id: Clinical interpretation ID (or list of IDs separated
1467
+ by commas).
1468
+ :param bool ci_primary: Clinical interpretation primary (true or
1469
+ false).
1470
+ :param str ci_description: Clinical interpretation description (word
1471
+ or list of words contained in the text, if the words are separated
1472
+ by a comma an OR will be applied; if the words are separated by a
1473
+ semicolon, an AND will be applied).
1474
+ :param str ci_panel_id: Clinical interpretation panel ID or name (or
1475
+ list of IDs or names separated by commas).
1476
+ :param str ci_analyst_id: Clinical interpretation analyst ID (or list
1477
+ of IDs separated by commas).
1478
+ :param str ci_analyst_name: Clinical interpretation analyst name (or
1479
+ list of names separated by commas).
1480
+ :param str ci_analyst_email: Clinical interpretation analyst e-mail
1481
+ (or list of e-mails separated by commas).
1482
+ :param str ci_analyst_assigned_by: Clinical interpretation analyst
1483
+ assignee name (or list of names separated by commas).
1484
+ :param str ci_analyst_date: Clinical interpretation analyst date (or
1485
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1486
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1487
+ 20231001000000-20231101000000.
1488
+ :param str ci_method_name: Clinical interpretation method name (or
1489
+ list of names separated by commas).
1490
+ :param str ci_method_version: Clinical interpretation method version
1491
+ (or list of versions separated by commas).
1492
+ :param str ci_method_commit: Clinical interpretation method commit (or
1493
+ list of commits separated by commas).
1494
+ :param str ci_method_dependencies: Clinical interpretation method
1495
+ dependencies (word or list of words contained in the text, if the
1496
+ words are separated by a comma an OR will be applied; if the words
1497
+ are separated by a semicolon, an AND will be applied).
1498
+ :param str ci_comments: Clinical interpretation comment text (word or
1499
+ list of words contained in the text, if the words are separated by
1500
+ a comma an OR will be applied; if the words are separated by a
1501
+ semicolon, an AND will be applied).
1502
+ :param bool ci_locked: Clinical interpretation locked (true or false).
1503
+ :param str ci_status_id: Clinical interpretation status ID (or list of
1504
+ IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
1505
+ CLOSED.
1506
+ :param str ci_status_name: Clinical interpretation status name (or
1507
+ list of names separated by commas).
1508
+ :param str ci_status_description: Clinical interpretation status
1509
+ description (word or list of words contained in the text, if the
1510
+ words are separated by a comma an OR will be applied; if the words
1511
+ are separated by a semicolon, an AND will be applied).
1512
+ :param str ci_status_date: Clinical interpretation status date (or
1513
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1514
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1515
+ 20231001000000-20231101000000.
1516
+ :param str ci_creation_date: Clinical interpretation creation date (or
1517
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1518
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1519
+ 20231001000000-20231101000000.
1520
+ :param str ci_modification_date: Clinical interpretation modification
1521
+ date (or list of dates separated by commas), with format
1522
+ YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
1523
+ start_date-end_date, e.g.: 20231001000000-20231101000000.
1524
+ :param int ci_version: Clinical interpretation version number (or list
1525
+ of versions separated by commas).
1526
+ :param str cv_id: Clinical variant ID (or list of IDs separated by
1527
+ commas).
1528
+ :param str cv_variant_id: Variant ID (or list of IDs separated by
1529
+ commas).
1530
+ :param bool cv_primary_finding: Clinical variant is a primary finding
1531
+ (true or false).
1532
+ :param bool cv_primary_interpretation: Clinical variant belongs to the
1533
+ primary interpretation (true or false).
1534
+ :param str cv_comments: Clinical variant comment text (word or list of
1535
+ words contained in the text, if the words are separated by a comma
1536
+ an OR will be applied; if the words are separated by a semicolon,
1537
+ an AND will be applied).
1538
+ :param str cv_discussion_author: Clinical variant discussion author
1539
+ (or list of authors separated by commas).
1540
+ :param str cv_discussion_date: Clinical variant discussion date (or
1541
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1542
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1543
+ 20231001000000-20231101000000.
1544
+ :param str cv_discussion_text: Clinical variant discussion text (word
1545
+ or list of words contained in the text, if the words are separated
1546
+ by a comma an OR will be applied; if the words are separated by a
1547
+ semicolon, an AND will be applied).
1548
+ :param str cv_confidence_value: Clinical variant confidence value (or
1549
+ list of values separated by commas).
1550
+ :param str cv_confidence_author: Clinical variant confidence author
1551
+ (or list of authors separated by commas).
1552
+ :param str cv_confidence_date: Clinical variant confidence date (or
1553
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1554
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1555
+ 20231001000000-20231101000000.
1556
+ :param str cv_tag: Clinical variant tag (or list of tags separated by
1557
+ commas).
1558
+ :param str cv_status: Clinical variant status (or list of status
1559
+ separated by commas).
1560
+ :param str cv_region: Variant region (or list of regions, these can be
1561
+ just a single chromosome name or regions in the format
1562
+ chr:start-end, e.g.: 2,3:100000-200000).
1563
+ :param str cv_biotype: Variant biotype, e.g. protein_coding (or list
1564
+ of biotypes separated by commas).
1565
+ :param str cv_ct: Variant SO consequence type (or list of SOs
1566
+ separated by commas), e.g. missense_variant,stop_lost or
1567
+ SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
1568
+ 'protein_altering'.
1569
+ :param str cv_transcript_flag: Variant transcript flag (or list of
1570
+ flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
1571
+ Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
1572
+ :param str cv_gene: Variant gene (or list genes separated by commas),
1573
+ most gene IDs are accepted (HGNC, Ensembl gene, ...).
1574
+ :param str cv_xref: Variant external reference (or list of references
1575
+ separated by commas), these can be genes, proteins or variants.
1576
+ Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
1577
+ Cosmic, ...
1578
+ :param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
1579
+ (or list of roles separated by commas).
1580
+ :param str cv_type: Variant type or list of types, accepted values are
1581
+ SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
1582
+ COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
1583
+ TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
1584
+ :param str cv_protein_substitution: Variant protein substitution score
1585
+ (or list of scores separated by commas), include SIFT and PolyPhen.
1586
+ You can query using the score {protein_score}[<|>|<=|>=]{number} or
1587
+ the description {protein_score}[~=|=]{description} e.g.
1588
+ polyphen>0.1,sift=tolerant.
1589
+ :param str cv_conservation: Variant conservation score (or list of
1590
+ scores separated by commas) with the format
1591
+ {conservation_score}[<|>|<=|>=]{number} e.g.
1592
+ phastCons>0.5,phylop<0.1,gerp>0.1.
1593
+ :param str cv_functional_score: Variant functional score (or list of
1594
+ scores separated by commas) with the format
1595
+ {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
1596
+ cadd_raw<=0.3.
1597
+ :param str cv_population_frequency_alt: Variant alternate population
1598
+ frequency (or list of frequencies separated by commas), with the
1599
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
1600
+ 1000G:ALL<0.01.
1601
+ :param str cv_population_frequency_maf: Variant population minor
1602
+ allele frequency (or list of frequencies separated by commas), with
1603
+ the format {study}:{population}[<|>|<=|>=]{number}. e.g.
1604
+ 1000G:ALL<0.01.
1605
+ :param str cv_population_frequency_ref: Variant reference population
1606
+ frequency (or list of frequences separated by commas), with the
1607
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
1608
+ 1000G:ALL<0.01.
1609
+ :param str cv_cohort_stats_alt: Variant alternate allele frequency (or
1610
+ list of frequencies separated by commas), with the format
1611
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1612
+ :param str cv_cohort_stats_maf: Variant minor allele frequency (or
1613
+ list of frequencies separated by commas), with the format
1614
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1615
+ :param str cv_cohort_stats_ref: Variant reference allele frequency (or
1616
+ list of frequencies separated by commas), with the foramt
1617
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1618
+ :param str cv_cohort_stats_pass: Variant filter PASS frequency (or
1619
+ list of frequencies separated by commas), with the format
1620
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
1621
+ :param str cv_score: Variant score (or list of scores separated by
1622
+ commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
1623
+ :param str cv_annot_go_genes: Variant gene GO (or list of GOs
1624
+ separated by commas).
1625
+ :param str cv_annot_expression_genes: Variant gene expression (or list
1626
+ of expressions separated by commas).
1627
+ :param str cv_gene_trait_id: Variant gene trait association ID (or
1628
+ list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
1629
+ 'OMIM:269600'.
1630
+ :param str cv_trait: Variant Trait (or list of traits separated by
1631
+ commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
1632
+ descriptions,...
1633
+ :param str cv_protein_keyword: Uniprot protein variant annotation
1634
+ keyword (or list of keywords separated by commas).
1635
+ :param str cve_variant_id: Variant ID (or list of IDs separated by
1636
+ commas).
1637
+ :param bool cve_primary_finding: Clinical variant evidence belongs to
1638
+ a primary finding (true or false).
1639
+ :param bool cve_primary_interpretation: Clinical variant evidence
1640
+ belongs to the primary interpretation (true or false).
1641
+ :param str cve_phenotype_name: Clinical variant evidence phenotype
1642
+ name (or names separated by commas).
1643
+ :param str cve_gene_name: Clinical variant evidence gene name (or
1644
+ names separated by commas).
1645
+ :param str cve_transcript_id: Clinical variant evidence transcript ID
1646
+ (or IDs separated by commas).
1647
+ :param str cve_so_term_name: Clinical variant evidence sequence
1648
+ ontology name (or names separated by commas).
1649
+ :param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
1650
+ separated by commas).
1651
+ :param str cve_panel_id: Clinical variant evidence panel ID (or IDs
1652
+ separated by commas).
1653
+ :param str cve_moi: Clinical variant evidence mode of inheritance (or
1654
+ list of modes of inheritance separated by commas), valid values:
1655
+ AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
1656
+ X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
1657
+ MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
1658
+ :param str cve_penetrance: Clinical variant evidence penetrance (or
1659
+ list of penetrance values separated by commas), valid values:
1660
+ COMPLETE, INCOMPLETE, UNKNOWN.
1661
+ :param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
1662
+ separated by commas).
1663
+ :param str cve_tier: Clinical variant evidence tier (or list of tier
1664
+ values separated by commas).
1665
+ :param str cve_clinical_significance: Clinical variant evidence
1666
+ clinical significance (or list of clinical significances separated
1667
+ by commas).
1668
+ :param str cve_drug_response: Clinical variant evidence drug response
1669
+ (or list of drug responses separated by commas).
1670
+ :param str cve_trait_association: Clinical variant evidence trait
1671
+ association (or list of traits separated by commas).
1672
+ :param str cve_functional_effect: Clinical variant evidence functional
1673
+ effect (or list of functional effects separated by commas).
1674
+ :param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
1675
+ (or list of tumorigenesis values separated by commas).
1676
+ :param str cve_other_classification: Clinical variant evidence
1677
+ other-classification (or list of other classification values
1678
+ separated by commas).
1679
+ :param str cve_role_in_cancer: Clinical variant evidence role in
1680
+ cancer (or roles in cancer separated by commas).
1681
+ :param str cve_review_acmg: Clinical variant evidence review ACMG (or
1682
+ ACGMs separated by commas).
1683
+ :param str cve_review_tier: Clinical variant evidence review tier (or
1684
+ list of tier values separated by commas).
1685
+ :param str cve_review_clinical_significance: Clinical variant evidence
1686
+ review clinical significance (or list of clinical significances
1687
+ separated by commas).
1688
+ :param str cve_review_text: Clinical variant evidence review text
1689
+ (word or list of words contained in the text, if the words are
1690
+ separated by a comma an OR will be applied; if the words are
1691
+ separated by a semicolon, an AND will be applied).
1692
+ """
1693
+
1694
+ return self._get(category='analysis', resource='query', subcategory='cvdb/interpretation', **options)
1695
+
1696
+ def aggregate_variant(self, **options):
1697
+ """
1698
+ Calculate and fetch clinical variant aggregation stats.
1699
+ PATH: /{apiVersion}/analysis/cvdb/variant/aggregate
1700
+
1701
+ :param str project: Project ID.
1702
+ :param str study: Study ID (or list of study IDs separated by commas).
1703
+ :param str ca_id: Clinical analysis ID (or list of IDs separated by
1704
+ commas).
1705
+ :param str ca_description: Clinical analysis description (word or list
1706
+ of words contained in the text, if the words are separated by a
1707
+ comma an OR will be applied; if the words are separated by a
1708
+ semicolon, an AND will be applied).
1709
+ :param str ca_type: Clinical analysis type (or list of types separated
1710
+ by commas).
1711
+ :param str ca_disorder_id: Clinical analysis disorder ID (or list of
1712
+ IDs separated by commas).
1713
+ :param str ca_filename: Clinical analysis filename (or list of
1714
+ filenames separated by commas).
1715
+ :param str ca_proband_id: Clinical analysis proband ID (or list of IDs
1716
+ separated by commas).
1717
+ :param str ca_proband_disorder_id: Clinical analysis proband disorder
1718
+ ID (or list of disorder IDs separated by commas).
1719
+ :param str ca_proband_phenotype_name: Clinical analysis proband
1720
+ phenotype name (or list of phenotype names separated by commas).
1721
+ :param str ca_family_id: Clinical analysis family ID (or list of IDs
1722
+ separated by commas).
1723
+ :param str ca_family_phenotype_name: Clinical analysis family
1724
+ phenotype names (or list of names separated by commas).
1725
+ :param str ca_family_member_id: Clinical analysis family member ID (or
1726
+ list of IDs separated by commas).
1727
+ :param str ca_report: Clinical analysis report text (word or list of
1728
+ words contained in the text, if the words are separated by a comma
1729
+ an OR will be applied; if the words are separated by a semicolon,
1730
+ an AND will be applied).
1731
+ :param str ca_status: Clinical analysis status (or list of status
1732
+ separated by commas).
1733
+ :param bool ca_locked: Clinical analysis locked (true or false).
1734
+ :param str ci_id: Clinical interpretation ID (or list of IDs separated
1735
+ by commas).
1736
+ :param bool ci_primary: Clinical interpretation primary (true or
1737
+ false).
1738
+ :param str ci_description: Clinical interpretation description (word
1739
+ or list of words contained in the text, if the words are separated
1740
+ by a comma an OR will be applied; if the words are separated by a
1741
+ semicolon, an AND will be applied).
1742
+ :param str ci_panel_id: Clinical interpretation panel ID or name (or
1743
+ list of IDs or names separated by commas).
1744
+ :param str ci_analyst_id: Clinical interpretation analyst ID (or list
1745
+ of IDs separated by commas).
1746
+ :param str ci_analyst_name: Clinical interpretation analyst name (or
1747
+ list of names separated by commas).
1748
+ :param str ci_analyst_email: Clinical interpretation analyst e-mail
1749
+ (or list of e-mails separated by commas).
1750
+ :param str ci_analyst_assigned_by: Clinical interpretation analyst
1751
+ assignee name (or list of names separated by commas).
1752
+ :param str ci_analyst_date: Clinical interpretation analyst date (or
1753
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1754
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1755
+ 20231001000000-20231101000000.
1756
+ :param str ci_method_name: Clinical interpretation method name (or
1757
+ list of names separated by commas).
1758
+ :param str ci_method_version: Clinical interpretation method version
1759
+ (or list of versions separated by commas).
1760
+ :param str ci_method_commit: Clinical interpretation method commit (or
1761
+ list of commits separated by commas).
1762
+ :param str ci_method_dependencies: Clinical interpretation method
1763
+ dependencies (word or list of words contained in the text, if the
1764
+ words are separated by a comma an OR will be applied; if the words
1765
+ are separated by a semicolon, an AND will be applied).
1766
+ :param str ci_comments: Clinical interpretation comment text (word or
1767
+ list of words contained in the text, if the words are separated by
1768
+ a comma an OR will be applied; if the words are separated by a
1769
+ semicolon, an AND will be applied).
1770
+ :param bool ci_locked: Clinical interpretation locked (true or false).
1771
+ :param str ci_status_id: Clinical interpretation status ID (or list of
1772
+ IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
1773
+ CLOSED.
1774
+ :param str ci_status_name: Clinical interpretation status name (or
1775
+ list of names separated by commas).
1776
+ :param str ci_status_description: Clinical interpretation status
1777
+ description (word or list of words contained in the text, if the
1778
+ words are separated by a comma an OR will be applied; if the words
1779
+ are separated by a semicolon, an AND will be applied).
1780
+ :param str ci_status_date: Clinical interpretation status date (or
1781
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1782
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1783
+ 20231001000000-20231101000000.
1784
+ :param str ci_creation_date: Clinical interpretation creation date (or
1785
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1786
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1787
+ 20231001000000-20231101000000.
1788
+ :param str ci_modification_date: Clinical interpretation modification
1789
+ date (or list of dates separated by commas), with format
1790
+ YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
1791
+ start_date-end_date, e.g.: 20231001000000-20231101000000.
1792
+ :param int ci_version: Clinical interpretation version number (or list
1793
+ of versions separated by commas).
1794
+ :param str cv_id: Clinical variant ID (or list of IDs separated by
1795
+ commas).
1796
+ :param str cv_variant_id: Variant ID (or list of IDs separated by
1797
+ commas).
1798
+ :param bool cv_primary_finding: Clinical variant is a primary finding
1799
+ (true or false).
1800
+ :param bool cv_primary_interpretation: Clinical variant belongs to the
1801
+ primary interpretation (true or false).
1802
+ :param str cv_comments: Clinical variant comment text (word or list of
1803
+ words contained in the text, if the words are separated by a comma
1804
+ an OR will be applied; if the words are separated by a semicolon,
1805
+ an AND will be applied).
1806
+ :param str cv_discussion_author: Clinical variant discussion author
1807
+ (or list of authors separated by commas).
1808
+ :param str cv_discussion_date: Clinical variant discussion date (or
1809
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1810
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1811
+ 20231001000000-20231101000000.
1812
+ :param str cv_discussion_text: Clinical variant discussion text (word
1813
+ or list of words contained in the text, if the words are separated
1814
+ by a comma an OR will be applied; if the words are separated by a
1815
+ semicolon, an AND will be applied).
1816
+ :param str cv_confidence_value: Clinical variant confidence value (or
1817
+ list of values separated by commas).
1818
+ :param str cv_confidence_author: Clinical variant confidence author
1819
+ (or list of authors separated by commas).
1820
+ :param str cv_confidence_date: Clinical variant confidence date (or
1821
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
1822
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
1823
+ 20231001000000-20231101000000.
1824
+ :param str cv_tag: Clinical variant tag (or list of tags separated by
1825
+ commas).
1826
+ :param str cv_status: Clinical variant status (or list of status
1827
+ separated by commas).
1828
+ :param str cv_region: Variant region (or list of regions, these can be
1829
+ just a single chromosome name or regions in the format
1830
+ chr:start-end, e.g.: 2,3:100000-200000).
1831
+ :param str cv_biotype: Variant biotype, e.g. protein_coding (or list
1832
+ of biotypes separated by commas).
1833
+ :param str cv_ct: Variant SO consequence type (or list of SOs
1834
+ separated by commas), e.g. missense_variant,stop_lost or
1835
+ SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
1836
+ 'protein_altering'.
1837
+ :param str cv_transcript_flag: Variant transcript flag (or list of
1838
+ flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
1839
+ Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
1840
+ :param str cv_gene: Variant gene (or list genes separated by commas),
1841
+ most gene IDs are accepted (HGNC, Ensembl gene, ...).
1842
+ :param str cv_xref: Variant external reference (or list of references
1843
+ separated by commas), these can be genes, proteins or variants.
1844
+ Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
1845
+ Cosmic, ...
1846
+ :param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
1847
+ (or list of roles separated by commas).
1848
+ :param str cv_type: Variant type or list of types, accepted values are
1849
+ SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
1850
+ COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
1851
+ TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
1852
+ :param str cv_protein_substitution: Variant protein substitution score
1853
+ (or list of scores separated by commas), include SIFT and PolyPhen.
1854
+ You can query using the score {protein_score}[<|>|<=|>=]{number} or
1855
+ the description {protein_score}[~=|=]{description} e.g.
1856
+ polyphen>0.1,sift=tolerant.
1857
+ :param str cv_conservation: Variant conservation score (or list of
1858
+ scores separated by commas) with the format
1859
+ {conservation_score}[<|>|<=|>=]{number} e.g.
1860
+ phastCons>0.5,phylop<0.1,gerp>0.1.
1861
+ :param str cv_functional_score: Variant functional score (or list of
1862
+ scores separated by commas) with the format
1863
+ {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
1864
+ cadd_raw<=0.3.
1865
+ :param str cv_population_frequency_alt: Variant alternate population
1866
+ frequency (or list of frequencies separated by commas), with the
1867
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
1868
+ 1000G:ALL<0.01.
1869
+ :param str cv_population_frequency_maf: Variant population minor
1870
+ allele frequency (or list of frequencies separated by commas), with
1871
+ the format {study}:{population}[<|>|<=|>=]{number}. e.g.
1872
+ 1000G:ALL<0.01.
1873
+ :param str cv_population_frequency_ref: Variant reference population
1874
+ frequency (or list of frequences separated by commas), with the
1875
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
1876
+ 1000G:ALL<0.01.
1877
+ :param str cv_cohort_stats_alt: Variant alternate allele frequency (or
1878
+ list of frequencies separated by commas), with the format
1879
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1880
+ :param str cv_cohort_stats_maf: Variant minor allele frequency (or
1881
+ list of frequencies separated by commas), with the format
1882
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1883
+ :param str cv_cohort_stats_ref: Variant reference allele frequency (or
1884
+ list of frequencies separated by commas), with the foramt
1885
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
1886
+ :param str cv_cohort_stats_pass: Variant filter PASS frequency (or
1887
+ list of frequencies separated by commas), with the format
1888
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
1889
+ :param str cv_score: Variant score (or list of scores separated by
1890
+ commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
1891
+ :param str cv_annot_go_genes: Variant gene GO (or list of GOs
1892
+ separated by commas).
1893
+ :param str cv_annot_expression_genes: Variant gene expression (or list
1894
+ of expressions separated by commas).
1895
+ :param str cv_gene_trait_id: Variant gene trait association ID (or
1896
+ list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
1897
+ 'OMIM:269600'.
1898
+ :param str cv_trait: Variant Trait (or list of traits separated by
1899
+ commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
1900
+ descriptions,...
1901
+ :param str cv_protein_keyword: Uniprot protein variant annotation
1902
+ keyword (or list of keywords separated by commas).
1903
+ :param str cve_variant_id: Variant ID (or list of IDs separated by
1904
+ commas).
1905
+ :param bool cve_primary_finding: Clinical variant evidence belongs to
1906
+ a primary finding (true or false).
1907
+ :param bool cve_primary_interpretation: Clinical variant evidence
1908
+ belongs to the primary interpretation (true or false).
1909
+ :param str cve_phenotype_name: Clinical variant evidence phenotype
1910
+ name (or names separated by commas).
1911
+ :param str cve_gene_name: Clinical variant evidence gene name (or
1912
+ names separated by commas).
1913
+ :param str cve_transcript_id: Clinical variant evidence transcript ID
1914
+ (or IDs separated by commas).
1915
+ :param str cve_so_term_name: Clinical variant evidence sequence
1916
+ ontology name (or names separated by commas).
1917
+ :param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
1918
+ separated by commas).
1919
+ :param str cve_panel_id: Clinical variant evidence panel ID (or IDs
1920
+ separated by commas).
1921
+ :param str cve_moi: Clinical variant evidence mode of inheritance (or
1922
+ list of modes of inheritance separated by commas), valid values:
1923
+ AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
1924
+ X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
1925
+ MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
1926
+ :param str cve_penetrance: Clinical variant evidence penetrance (or
1927
+ list of penetrance values separated by commas), valid values:
1928
+ COMPLETE, INCOMPLETE, UNKNOWN.
1929
+ :param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
1930
+ separated by commas).
1931
+ :param str cve_tier: Clinical variant evidence tier (or list of tier
1932
+ values separated by commas).
1933
+ :param str cve_clinical_significance: Clinical variant evidence
1934
+ clinical significance (or list of clinical significances separated
1935
+ by commas).
1936
+ :param str cve_drug_response: Clinical variant evidence drug response
1937
+ (or list of drug responses separated by commas).
1938
+ :param str cve_trait_association: Clinical variant evidence trait
1939
+ association (or list of traits separated by commas).
1940
+ :param str cve_functional_effect: Clinical variant evidence functional
1941
+ effect (or list of functional effects separated by commas).
1942
+ :param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
1943
+ (or list of tumorigenesis values separated by commas).
1944
+ :param str cve_other_classification: Clinical variant evidence
1945
+ other-classification (or list of other classification values
1946
+ separated by commas).
1947
+ :param str cve_role_in_cancer: Clinical variant evidence role in
1948
+ cancer (or roles in cancer separated by commas).
1949
+ :param str cve_review_acmg: Clinical variant evidence review ACMG (or
1950
+ ACGMs separated by commas).
1951
+ :param str cve_review_tier: Clinical variant evidence review tier (or
1952
+ list of tier values separated by commas).
1953
+ :param str cve_review_clinical_significance: Clinical variant evidence
1954
+ review clinical significance (or list of clinical significances
1955
+ separated by commas).
1956
+ :param str cve_review_text: Clinical variant evidence review text
1957
+ (word or list of words contained in the text, if the words are
1958
+ separated by a comma an OR will be applied; if the words are
1959
+ separated by a semicolon, an AND will be applied).
1960
+ :param str field: List of facet fields separated by semicolons, e.g.:
1961
+ type;biotypes. For nested faceted fields use >>, e.g.:
1962
+ type>>biotypes. Accepted values: caId, ciId, variantId, studyId,
1963
+ primary, discussionAuthor, discussionDate,discussionText,
1964
+ confidenceValue, confidenceAuthor, confidenceDate, tags, status,
1965
+ chromosome, start, end, xrefs, type, release, studies, phastCons,
1966
+ phylop, gerp, caddRaw, caddScaled, sift, siftDesc, polyphen,
1967
+ polyphenDesc, genes, biotypes, soAcc, clinicalSig.
1968
+ """
1969
+
1970
+ return self._get(category='analysis', resource='aggregate', subcategory='cvdb/variant', **options)
1971
+
1972
+ def query_variant(self, **options):
1973
+ """
1974
+ Filter and fetch clinical variants from CVDB.
1975
+ PATH: /{apiVersion}/analysis/cvdb/variant/query
1976
+
1977
+ :param str project: Project ID.
1978
+ :param str study: Study ID (or list of study IDs separated by commas).
1979
+ :param str include: Fields included in the response, whole JSON path
1980
+ must be provided.
1981
+ :param str exclude: Fields excluded in the response, whole JSON path
1982
+ must be provided.
1983
+ :param int limit: Number of results to be returned.
1984
+ :param int skip: Number of results to skip.
1985
+ :param str ca_id: Clinical analysis ID (or list of IDs separated by
1986
+ commas).
1987
+ :param str ca_description: Clinical analysis description (word or list
1988
+ of words contained in the text, if the words are separated by a
1989
+ comma an OR will be applied; if the words are separated by a
1990
+ semicolon, an AND will be applied).
1991
+ :param str ca_type: Clinical analysis type (or list of types separated
1992
+ by commas).
1993
+ :param str ca_disorder_id: Clinical analysis disorder ID (or list of
1994
+ IDs separated by commas).
1995
+ :param str ca_filename: Clinical analysis filename (or list of
1996
+ filenames separated by commas).
1997
+ :param str ca_proband_id: Clinical analysis proband ID (or list of IDs
1998
+ separated by commas).
1999
+ :param str ca_proband_disorder_id: Clinical analysis proband disorder
2000
+ ID (or list of disorder IDs separated by commas).
2001
+ :param str ca_proband_phenotype_name: Clinical analysis proband
2002
+ phenotype name (or list of phenotype names separated by commas).
2003
+ :param str ca_family_id: Clinical analysis family ID (or list of IDs
2004
+ separated by commas).
2005
+ :param str ca_family_phenotype_name: Clinical analysis family
2006
+ phenotype names (or list of names separated by commas).
2007
+ :param str ca_family_member_id: Clinical analysis family member ID (or
2008
+ list of IDs separated by commas).
2009
+ :param str ca_report: Clinical analysis report text (word or list of
2010
+ words contained in the text, if the words are separated by a comma
2011
+ an OR will be applied; if the words are separated by a semicolon,
2012
+ an AND will be applied).
2013
+ :param str ca_status: Clinical analysis status (or list of status
2014
+ separated by commas).
2015
+ :param bool ca_locked: Clinical analysis locked (true or false).
2016
+ :param str ci_id: Clinical interpretation ID (or list of IDs separated
2017
+ by commas).
2018
+ :param bool ci_primary: Clinical interpretation primary (true or
2019
+ false).
2020
+ :param str ci_description: Clinical interpretation description (word
2021
+ or list of words contained in the text, if the words are separated
2022
+ by a comma an OR will be applied; if the words are separated by a
2023
+ semicolon, an AND will be applied).
2024
+ :param str ci_panel_id: Clinical interpretation panel ID or name (or
2025
+ list of IDs or names separated by commas).
2026
+ :param str ci_analyst_id: Clinical interpretation analyst ID (or list
2027
+ of IDs separated by commas).
2028
+ :param str ci_analyst_name: Clinical interpretation analyst name (or
2029
+ list of names separated by commas).
2030
+ :param str ci_analyst_email: Clinical interpretation analyst e-mail
2031
+ (or list of e-mails separated by commas).
2032
+ :param str ci_analyst_assigned_by: Clinical interpretation analyst
2033
+ assignee name (or list of names separated by commas).
2034
+ :param str ci_analyst_date: Clinical interpretation analyst date (or
2035
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
2036
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
2037
+ 20231001000000-20231101000000.
2038
+ :param str ci_method_name: Clinical interpretation method name (or
2039
+ list of names separated by commas).
2040
+ :param str ci_method_version: Clinical interpretation method version
2041
+ (or list of versions separated by commas).
2042
+ :param str ci_method_commit: Clinical interpretation method commit (or
2043
+ list of commits separated by commas).
2044
+ :param str ci_method_dependencies: Clinical interpretation method
2045
+ dependencies (word or list of words contained in the text, if the
2046
+ words are separated by a comma an OR will be applied; if the words
2047
+ are separated by a semicolon, an AND will be applied).
2048
+ :param str ci_comments: Clinical interpretation comment text (word or
2049
+ list of words contained in the text, if the words are separated by
2050
+ a comma an OR will be applied; if the words are separated by a
2051
+ semicolon, an AND will be applied).
2052
+ :param bool ci_locked: Clinical interpretation locked (true or false).
2053
+ :param str ci_status_id: Clinical interpretation status ID (or list of
2054
+ IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
2055
+ CLOSED.
2056
+ :param str ci_status_name: Clinical interpretation status name (or
2057
+ list of names separated by commas).
2058
+ :param str ci_status_description: Clinical interpretation status
2059
+ description (word or list of words contained in the text, if the
2060
+ words are separated by a comma an OR will be applied; if the words
2061
+ are separated by a semicolon, an AND will be applied).
2062
+ :param str ci_status_date: Clinical interpretation status date (or
2063
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
2064
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
2065
+ 20231001000000-20231101000000.
2066
+ :param str ci_creation_date: Clinical interpretation creation date (or
2067
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
2068
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
2069
+ 20231001000000-20231101000000.
2070
+ :param str ci_modification_date: Clinical interpretation modification
2071
+ date (or list of dates separated by commas), with format
2072
+ YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
2073
+ start_date-end_date, e.g.: 20231001000000-20231101000000.
2074
+ :param int ci_version: Clinical interpretation version number (or list
2075
+ of versions separated by commas).
2076
+ :param str cv_id: Clinical variant ID (or list of IDs separated by
2077
+ commas).
2078
+ :param str cv_variant_id: Variant ID (or list of IDs separated by
2079
+ commas).
2080
+ :param bool cv_primary_finding: Clinical variant is a primary finding
2081
+ (true or false).
2082
+ :param bool cv_primary_interpretation: Clinical variant belongs to the
2083
+ primary interpretation (true or false).
2084
+ :param str cv_comments: Clinical variant comment text (word or list of
2085
+ words contained in the text, if the words are separated by a comma
2086
+ an OR will be applied; if the words are separated by a semicolon,
2087
+ an AND will be applied).
2088
+ :param str cv_discussion_author: Clinical variant discussion author
2089
+ (or list of authors separated by commas).
2090
+ :param str cv_discussion_date: Clinical variant discussion date (or
2091
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
2092
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
2093
+ 20231001000000-20231101000000.
2094
+ :param str cv_discussion_text: Clinical variant discussion text (word
2095
+ or list of words contained in the text, if the words are separated
2096
+ by a comma an OR will be applied; if the words are separated by a
2097
+ semicolon, an AND will be applied).
2098
+ :param str cv_confidence_value: Clinical variant confidence value (or
2099
+ list of values separated by commas).
2100
+ :param str cv_confidence_author: Clinical variant confidence author
2101
+ (or list of authors separated by commas).
2102
+ :param str cv_confidence_date: Clinical variant confidence date (or
2103
+ list of dates separated by commas), with format YYYYMMDDhhmmss,
2104
+ e.g.: 20231026120345; range is available start_date-end_date, e.g.:
2105
+ 20231001000000-20231101000000.
2106
+ :param str cv_tag: Clinical variant tag (or list of tags separated by
2107
+ commas).
2108
+ :param str cv_status: Clinical variant status (or list of status
2109
+ separated by commas).
2110
+ :param str cv_region: Variant region (or list of regions, these can be
2111
+ just a single chromosome name or regions in the format
2112
+ chr:start-end, e.g.: 2,3:100000-200000).
2113
+ :param str cv_biotype: Variant biotype, e.g. protein_coding (or list
2114
+ of biotypes separated by commas).
2115
+ :param str cv_ct: Variant SO consequence type (or list of SOs
2116
+ separated by commas), e.g. missense_variant,stop_lost or
2117
+ SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
2118
+ 'protein_altering'.
2119
+ :param str cv_transcript_flag: Variant transcript flag (or list of
2120
+ flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
2121
+ Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
2122
+ :param str cv_gene: Variant gene (or list genes separated by commas),
2123
+ most gene IDs are accepted (HGNC, Ensembl gene, ...).
2124
+ :param str cv_xref: Variant external reference (or list of references
2125
+ separated by commas), these can be genes, proteins or variants.
2126
+ Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
2127
+ Cosmic, ...
2128
+ :param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
2129
+ (or list of roles separated by commas).
2130
+ :param str cv_type: Variant type or list of types, accepted values are
2131
+ SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
2132
+ COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
2133
+ TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
2134
+ :param str cv_protein_substitution: Variant protein substitution score
2135
+ (or list of scores separated by commas), include SIFT and PolyPhen.
2136
+ You can query using the score {protein_score}[<|>|<=|>=]{number} or
2137
+ the description {protein_score}[~=|=]{description} e.g.
2138
+ polyphen>0.1,sift=tolerant.
2139
+ :param str cv_conservation: Variant conservation score (or list of
2140
+ scores separated by commas) with the format
2141
+ {conservation_score}[<|>|<=|>=]{number} e.g.
2142
+ phastCons>0.5,phylop<0.1,gerp>0.1.
2143
+ :param str cv_functional_score: Variant functional score (or list of
2144
+ scores separated by commas) with the format
2145
+ {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
2146
+ cadd_raw<=0.3.
2147
+ :param str cv_population_frequency_alt: Variant alternate population
2148
+ frequency (or list of frequencies separated by commas), with the
2149
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
2150
+ 1000G:ALL<0.01.
2151
+ :param str cv_population_frequency_maf: Variant population minor
2152
+ allele frequency (or list of frequencies separated by commas), with
2153
+ the format {study}:{population}[<|>|<=|>=]{number}. e.g.
2154
+ 1000G:ALL<0.01.
2155
+ :param str cv_population_frequency_ref: Variant reference population
2156
+ frequency (or list of frequences separated by commas), with the
2157
+ format {study}:{population}[<|>|<=|>=]{number}. e.g.
2158
+ 1000G:ALL<0.01.
2159
+ :param str cv_cohort_stats_alt: Variant alternate allele frequency (or
2160
+ list of frequencies separated by commas), with the format
2161
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
2162
+ :param str cv_cohort_stats_maf: Variant minor allele frequency (or
2163
+ list of frequencies separated by commas), with the format
2164
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
2165
+ :param str cv_cohort_stats_ref: Variant reference allele frequency (or
2166
+ list of frequencies separated by commas), with the foramt
2167
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
2168
+ :param str cv_cohort_stats_pass: Variant filter PASS frequency (or
2169
+ list of frequencies separated by commas), with the format
2170
+ [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
2171
+ :param str cv_score: Variant score (or list of scores separated by
2172
+ commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
2173
+ :param str cv_annot_go_genes: Variant gene GO (or list of GOs
2174
+ separated by commas).
2175
+ :param str cv_annot_expression_genes: Variant gene expression (or list
2176
+ of expressions separated by commas).
2177
+ :param str cv_gene_trait_id: Variant gene trait association ID (or
2178
+ list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
2179
+ 'OMIM:269600'.
2180
+ :param str cv_trait: Variant Trait (or list of traits separated by
2181
+ commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
2182
+ descriptions,...
2183
+ :param str cv_protein_keyword: Uniprot protein variant annotation
2184
+ keyword (or list of keywords separated by commas).
2185
+ :param str cve_variant_id: Variant ID (or list of IDs separated by
2186
+ commas).
2187
+ :param bool cve_primary_finding: Clinical variant evidence belongs to
2188
+ a primary finding (true or false).
2189
+ :param bool cve_primary_interpretation: Clinical variant evidence
2190
+ belongs to the primary interpretation (true or false).
2191
+ :param str cve_phenotype_name: Clinical variant evidence phenotype
2192
+ name (or names separated by commas).
2193
+ :param str cve_gene_name: Clinical variant evidence gene name (or
2194
+ names separated by commas).
2195
+ :param str cve_transcript_id: Clinical variant evidence transcript ID
2196
+ (or IDs separated by commas).
2197
+ :param str cve_so_term_name: Clinical variant evidence sequence
2198
+ ontology name (or names separated by commas).
2199
+ :param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
2200
+ separated by commas).
2201
+ :param str cve_panel_id: Clinical variant evidence panel ID (or IDs
2202
+ separated by commas).
2203
+ :param str cve_moi: Clinical variant evidence mode of inheritance (or
2204
+ list of modes of inheritance separated by commas), valid values:
2205
+ AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
2206
+ X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
2207
+ MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
2208
+ :param str cve_penetrance: Clinical variant evidence penetrance (or
2209
+ list of penetrance values separated by commas), valid values:
2210
+ COMPLETE, INCOMPLETE, UNKNOWN.
2211
+ :param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
2212
+ separated by commas).
2213
+ :param str cve_tier: Clinical variant evidence tier (or list of tier
2214
+ values separated by commas).
2215
+ :param str cve_clinical_significance: Clinical variant evidence
2216
+ clinical significance (or list of clinical significances separated
2217
+ by commas).
2218
+ :param str cve_drug_response: Clinical variant evidence drug response
2219
+ (or list of drug responses separated by commas).
2220
+ :param str cve_trait_association: Clinical variant evidence trait
2221
+ association (or list of traits separated by commas).
2222
+ :param str cve_functional_effect: Clinical variant evidence functional
2223
+ effect (or list of functional effects separated by commas).
2224
+ :param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
2225
+ (or list of tumorigenesis values separated by commas).
2226
+ :param str cve_other_classification: Clinical variant evidence
2227
+ other-classification (or list of other classification values
2228
+ separated by commas).
2229
+ :param str cve_role_in_cancer: Clinical variant evidence role in
2230
+ cancer (or roles in cancer separated by commas).
2231
+ :param str cve_review_acmg: Clinical variant evidence review ACMG (or
2232
+ ACGMs separated by commas).
2233
+ :param str cve_review_tier: Clinical variant evidence review tier (or
2234
+ list of tier values separated by commas).
2235
+ :param str cve_review_clinical_significance: Clinical variant evidence
2236
+ review clinical significance (or list of clinical significances
2237
+ separated by commas).
2238
+ :param str cve_review_text: Clinical variant evidence review text
2239
+ (word or list of words contained in the text, if the words are
2240
+ separated by a comma an OR will be applied; if the words are
2241
+ separated by a semicolon, an AND will be applied).
2242
+ """
2243
+
2244
+ return self._get(category='analysis', resource='query', subcategory='cvdb/variant', **options)
2245
+
2246
+ def stats_variant(self, variant_id, **options):
2247
+ """
2248
+ Get clinical variant summary from CVDB.
2249
+ PATH: /{apiVersion}/analysis/cvdb/variant/{variantId}/stats
2250
+
2251
+ :param str variant_id: Variant ID (or comma separated list of variant
2252
+ IDs). (REQUIRED)
2253
+ :param str project: Project ID(or command separated list of project
2254
+ IDs).
2255
+ """
2256
+
2257
+ return self._get(category='analysis', resource='stats', subcategory='cvdb/variant', second_query_id=variant_id, **options)
2258
+