pyxetabase 4.0.0.dev56__py3-none-any.whl
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- pyxetabase/__init__.py +0 -0
- pyxetabase/commons.py +347 -0
- pyxetabase/exceptions.py +8 -0
- pyxetabase/opencga_client.py +344 -0
- pyxetabase/opencga_config.py +211 -0
- pyxetabase/rest_clients/__init__.py +0 -0
- pyxetabase/rest_clients/_parent_rest_clients.py +144 -0
- pyxetabase/rest_clients/admin_client.py +179 -0
- pyxetabase/rest_clients/alignment_client.py +373 -0
- pyxetabase/rest_clients/clinical_analysis_client.py +1216 -0
- pyxetabase/rest_clients/cohort_client.py +349 -0
- pyxetabase/rest_clients/cvdb_client.py +2285 -0
- pyxetabase/rest_clients/disease_panel_client.py +345 -0
- pyxetabase/rest_clients/family_client.py +355 -0
- pyxetabase/rest_clients/federation_client.py +133 -0
- pyxetabase/rest_clients/file_client.py +710 -0
- pyxetabase/rest_clients/ga4gh_client.py +86 -0
- pyxetabase/rest_clients/individual_client.py +435 -0
- pyxetabase/rest_clients/job_client.py +416 -0
- pyxetabase/rest_clients/meta_client.py +85 -0
- pyxetabase/rest_clients/organization_client.py +216 -0
- pyxetabase/rest_clients/project_client.py +128 -0
- pyxetabase/rest_clients/sample_client.py +446 -0
- pyxetabase/rest_clients/study_client.py +462 -0
- pyxetabase/rest_clients/user_client.py +212 -0
- pyxetabase/rest_clients/user_tool_client.py +471 -0
- pyxetabase/rest_clients/variant_client.py +1378 -0
- pyxetabase/rest_clients/variant_operation_client.py +718 -0
- pyxetabase/rest_clients/workflow_client.py +263 -0
- pyxetabase/rest_response.py +220 -0
- pyxetabase/retry.py +57 -0
- pyxetabase-4.0.0.dev56.dist-info/METADATA +159 -0
- pyxetabase-4.0.0.dev56.dist-info/RECORD +36 -0
- pyxetabase-4.0.0.dev56.dist-info/WHEEL +5 -0
- pyxetabase-4.0.0.dev56.dist-info/licenses/LICENSE +202 -0
- pyxetabase-4.0.0.dev56.dist-info/top_level.txt +1 -0
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"""
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WARNING: AUTOGENERATED CODE
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This code was generated by a tool.
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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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from pyxetabase.rest_clients._parent_rest_clients import _ParentRestClient
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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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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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def update_acl(self, data=None, **options):
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"""
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Update the set of permissions granted in CVDB for the OpenCGA users
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that have access to the clinical analyses.
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PATH: /{apiVersion}/analysis/cvdb/acl/update
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:param dict data: Parameters for the ACL updating task
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(cvdb-acl-update). (REQUIRED)
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:param str study: Study [[organization@]project:]study where study and
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project can be either the ID or UUID.
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:param str job_id: Job ID. It must be a unique string within the
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study. An ID will be autogenerated automatically if not provided.
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:param str job_description: Job description.
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:param str job_depends_on: Comma separated list of existing job IDs
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the job will depend on.
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:param str job_tags: Job tags.
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:param str job_scheduled_start_time: Time when the job is scheduled to
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start.
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:param str job_priority: Priority of the job.
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:param bool job_dry_run: Flag indicating that the job will be executed
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in dry-run mode. In this mode, OpenCGA will validate that all
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parameters and prerequisites are correctly set for successful
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execution, but the job will not actually run.
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"""
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return self._post(category='analysis', resource='update', subcategory='cvdb/acl', data=data, **options)
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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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: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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242
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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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246
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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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256
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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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258
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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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264
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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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266
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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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268
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+
:param str cve_so_term_name: Clinical variant evidence sequence
|
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269
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+
ontology name (or names separated by commas).
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270
|
+
: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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274
|
+
:param str cve_moi: Clinical variant evidence mode of inheritance (or
|
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275
|
+
list of modes of inheritance separated by commas), valid values:
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276
|
+
AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
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277
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+
X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
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278
|
+
MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
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279
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+
:param str cve_penetrance: Clinical variant evidence penetrance (or
|
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280
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+
list of penetrance values separated by commas), valid values:
|
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281
|
+
COMPLETE, INCOMPLETE, UNKNOWN.
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282
|
+
:param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
|
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283
|
+
separated by commas).
|
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284
|
+
:param str cve_tier: Clinical variant evidence tier (or list of tier
|
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|
+
values separated by commas).
|
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286
|
+
:param str cve_clinical_significance: Clinical variant evidence
|
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287
|
+
clinical significance (or list of clinical significances separated
|
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288
|
+
by commas).
|
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289
|
+
: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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291
|
+
:param str cve_trait_association: Clinical variant evidence trait
|
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292
|
+
association (or list of traits separated by commas).
|
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293
|
+
:param str cve_functional_effect: Clinical variant evidence functional
|
|
294
|
+
effect (or list of functional effects separated by commas).
|
|
295
|
+
:param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
|
|
296
|
+
(or list of tumorigenesis values separated by commas).
|
|
297
|
+
:param str cve_other_classification: Clinical variant evidence
|
|
298
|
+
other-classification (or list of other classification values
|
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299
|
+
separated by commas).
|
|
300
|
+
:param str cve_role_in_cancer: Clinical variant evidence role in
|
|
301
|
+
cancer (or roles in cancer separated by commas).
|
|
302
|
+
:param str cve_review_acmg: Clinical variant evidence review ACMG (or
|
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303
|
+
ACGMs separated by commas).
|
|
304
|
+
:param str cve_review_tier: Clinical variant evidence review tier (or
|
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305
|
+
list of tier values separated by commas).
|
|
306
|
+
:param str cve_review_clinical_significance: Clinical variant evidence
|
|
307
|
+
review clinical significance (or list of clinical significances
|
|
308
|
+
separated by commas).
|
|
309
|
+
:param str cve_review_text: Clinical variant evidence review text
|
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310
|
+
(word or list of words contained in the text, if the words are
|
|
311
|
+
separated by a comma an OR will be applied; if the words are
|
|
312
|
+
separated by a semicolon, an AND will be applied).
|
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313
|
+
:param str field: List of facet fields separated by semicolons, e.g.:
|
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314
|
+
type;disorderId. For nested faceted fields use >>, e.g.:
|
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315
|
+
type>>disorderId. Accepted values: studyId, type, disorderId,
|
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316
|
+
fileNames, probandId, probandDisorderIds, probandPhenotypeNames,
|
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317
|
+
familyId, familyPhenotypeNames, familyMemberIds, panelIds, status.
|
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318
|
+
"""
|
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319
|
+
|
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320
|
+
return self._get(category='analysis', resource='aggregate', subcategory='cvdb/analysis', **options)
|
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+
|
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322
|
+
def query_analysis(self, **options):
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+
"""
|
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324
|
+
Filter and fetch clinical analyses from CVDB.
|
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325
|
+
PATH: /{apiVersion}/analysis/cvdb/analysis/query
|
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|
+
|
|
327
|
+
:param str project: Project ID.
|
|
328
|
+
:param str study: Study ID (or list of study IDs separated by commas).
|
|
329
|
+
:param str include: Fields included in the response, whole JSON path
|
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330
|
+
must be provided.
|
|
331
|
+
:param str exclude: Fields excluded in the response, whole JSON path
|
|
332
|
+
must be provided.
|
|
333
|
+
:param int limit: Number of results to be returned.
|
|
334
|
+
:param int skip: Number of results to skip.
|
|
335
|
+
:param str ca_id: Clinical analysis ID (or list of IDs separated by
|
|
336
|
+
commas).
|
|
337
|
+
:param str ca_description: Clinical analysis description (word or list
|
|
338
|
+
of words contained in the text, if the words are separated by a
|
|
339
|
+
comma an OR will be applied; if the words are separated by a
|
|
340
|
+
semicolon, an AND will be applied).
|
|
341
|
+
:param str ca_type: Clinical analysis type (or list of types separated
|
|
342
|
+
by commas).
|
|
343
|
+
:param str ca_disorder_id: Clinical analysis disorder ID (or list of
|
|
344
|
+
IDs separated by commas).
|
|
345
|
+
:param str ca_filename: Clinical analysis filename (or list of
|
|
346
|
+
filenames separated by commas).
|
|
347
|
+
:param str ca_proband_id: Clinical analysis proband ID (or list of IDs
|
|
348
|
+
separated by commas).
|
|
349
|
+
:param str ca_proband_disorder_id: Clinical analysis proband disorder
|
|
350
|
+
ID (or list of disorder IDs separated by commas).
|
|
351
|
+
:param str ca_proband_phenotype_name: Clinical analysis proband
|
|
352
|
+
phenotype name (or list of phenotype names separated by commas).
|
|
353
|
+
:param str ca_family_id: Clinical analysis family ID (or list of IDs
|
|
354
|
+
separated by commas).
|
|
355
|
+
:param str ca_family_phenotype_name: Clinical analysis family
|
|
356
|
+
phenotype names (or list of names separated by commas).
|
|
357
|
+
:param str ca_family_member_id: Clinical analysis family member ID (or
|
|
358
|
+
list of IDs separated by commas).
|
|
359
|
+
:param str ca_report: Clinical analysis report text (word or list of
|
|
360
|
+
words contained in the text, if the words are separated by a comma
|
|
361
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
362
|
+
an AND will be applied).
|
|
363
|
+
:param str ca_status: Clinical analysis status (or list of status
|
|
364
|
+
separated by commas).
|
|
365
|
+
:param bool ca_locked: Clinical analysis locked (true or false).
|
|
366
|
+
:param str ci_id: Clinical interpretation ID (or list of IDs separated
|
|
367
|
+
by commas).
|
|
368
|
+
:param bool ci_primary: Clinical interpretation primary (true or
|
|
369
|
+
false).
|
|
370
|
+
:param str ci_description: Clinical interpretation description (word
|
|
371
|
+
or list of words contained in the text, if the words are separated
|
|
372
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
373
|
+
semicolon, an AND will be applied).
|
|
374
|
+
:param str ci_panel_id: Clinical interpretation panel ID or name (or
|
|
375
|
+
list of IDs or names separated by commas).
|
|
376
|
+
:param str ci_analyst_id: Clinical interpretation analyst ID (or list
|
|
377
|
+
of IDs separated by commas).
|
|
378
|
+
:param str ci_analyst_name: Clinical interpretation analyst name (or
|
|
379
|
+
list of names separated by commas).
|
|
380
|
+
:param str ci_analyst_email: Clinical interpretation analyst e-mail
|
|
381
|
+
(or list of e-mails separated by commas).
|
|
382
|
+
:param str ci_analyst_assigned_by: Clinical interpretation analyst
|
|
383
|
+
assignee name (or list of names separated by commas).
|
|
384
|
+
:param str ci_analyst_date: Clinical interpretation analyst date (or
|
|
385
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
386
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
387
|
+
20231001000000-20231101000000.
|
|
388
|
+
:param str ci_method_name: Clinical interpretation method name (or
|
|
389
|
+
list of names separated by commas).
|
|
390
|
+
:param str ci_method_version: Clinical interpretation method version
|
|
391
|
+
(or list of versions separated by commas).
|
|
392
|
+
:param str ci_method_commit: Clinical interpretation method commit (or
|
|
393
|
+
list of commits separated by commas).
|
|
394
|
+
:param str ci_method_dependencies: Clinical interpretation method
|
|
395
|
+
dependencies (word or list of words contained in the text, if the
|
|
396
|
+
words are separated by a comma an OR will be applied; if the words
|
|
397
|
+
are separated by a semicolon, an AND will be applied).
|
|
398
|
+
:param str ci_comments: Clinical interpretation comment text (word or
|
|
399
|
+
list of words contained in the text, if the words are separated by
|
|
400
|
+
a comma an OR will be applied; if the words are separated by a
|
|
401
|
+
semicolon, an AND will be applied).
|
|
402
|
+
:param bool ci_locked: Clinical interpretation locked (true or false).
|
|
403
|
+
:param str ci_status_id: Clinical interpretation status ID (or list of
|
|
404
|
+
IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
|
|
405
|
+
CLOSED.
|
|
406
|
+
:param str ci_status_name: Clinical interpretation status name (or
|
|
407
|
+
list of names separated by commas).
|
|
408
|
+
:param str ci_status_description: Clinical interpretation status
|
|
409
|
+
description (word or list of words contained in the text, if the
|
|
410
|
+
words are separated by a comma an OR will be applied; if the words
|
|
411
|
+
are separated by a semicolon, an AND will be applied).
|
|
412
|
+
:param str ci_status_date: Clinical interpretation status date (or
|
|
413
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
414
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
415
|
+
20231001000000-20231101000000.
|
|
416
|
+
:param str ci_creation_date: Clinical interpretation creation date (or
|
|
417
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
418
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
419
|
+
20231001000000-20231101000000.
|
|
420
|
+
:param str ci_modification_date: Clinical interpretation modification
|
|
421
|
+
date (or list of dates separated by commas), with format
|
|
422
|
+
YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
|
|
423
|
+
start_date-end_date, e.g.: 20231001000000-20231101000000.
|
|
424
|
+
:param int ci_version: Clinical interpretation version number (or list
|
|
425
|
+
of versions separated by commas).
|
|
426
|
+
:param str cv_id: Clinical variant ID (or list of IDs separated by
|
|
427
|
+
commas).
|
|
428
|
+
:param str cv_variant_id: Variant ID (or list of IDs separated by
|
|
429
|
+
commas).
|
|
430
|
+
:param bool cv_primary_finding: Clinical variant is a primary finding
|
|
431
|
+
(true or false).
|
|
432
|
+
:param bool cv_primary_interpretation: Clinical variant belongs to the
|
|
433
|
+
primary interpretation (true or false).
|
|
434
|
+
:param str cv_comments: Clinical variant comment text (word or list of
|
|
435
|
+
words contained in the text, if the words are separated by a comma
|
|
436
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
437
|
+
an AND will be applied).
|
|
438
|
+
:param str cv_discussion_author: Clinical variant discussion author
|
|
439
|
+
(or list of authors separated by commas).
|
|
440
|
+
:param str cv_discussion_date: Clinical variant discussion date (or
|
|
441
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
442
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
443
|
+
20231001000000-20231101000000.
|
|
444
|
+
:param str cv_discussion_text: Clinical variant discussion text (word
|
|
445
|
+
or list of words contained in the text, if the words are separated
|
|
446
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
447
|
+
semicolon, an AND will be applied).
|
|
448
|
+
:param str cv_confidence_value: Clinical variant confidence value (or
|
|
449
|
+
list of values separated by commas).
|
|
450
|
+
:param str cv_confidence_author: Clinical variant confidence author
|
|
451
|
+
(or list of authors separated by commas).
|
|
452
|
+
:param str cv_confidence_date: Clinical variant confidence date (or
|
|
453
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
454
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
455
|
+
20231001000000-20231101000000.
|
|
456
|
+
:param str cv_tag: Clinical variant tag (or list of tags separated by
|
|
457
|
+
commas).
|
|
458
|
+
:param str cv_status: Clinical variant status (or list of status
|
|
459
|
+
separated by commas).
|
|
460
|
+
:param str cv_region: Variant region (or list of regions, these can be
|
|
461
|
+
just a single chromosome name or regions in the format
|
|
462
|
+
chr:start-end, e.g.: 2,3:100000-200000).
|
|
463
|
+
:param str cv_biotype: Variant biotype, e.g. protein_coding (or list
|
|
464
|
+
of biotypes separated by commas).
|
|
465
|
+
:param str cv_ct: Variant SO consequence type (or list of SOs
|
|
466
|
+
separated by commas), e.g. missense_variant,stop_lost or
|
|
467
|
+
SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
|
|
468
|
+
'protein_altering'.
|
|
469
|
+
:param str cv_transcript_flag: Variant transcript flag (or list of
|
|
470
|
+
flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
|
|
471
|
+
Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
|
|
472
|
+
:param str cv_gene: Variant gene (or list genes separated by commas),
|
|
473
|
+
most gene IDs are accepted (HGNC, Ensembl gene, ...).
|
|
474
|
+
:param str cv_xref: Variant external reference (or list of references
|
|
475
|
+
separated by commas), these can be genes, proteins or variants.
|
|
476
|
+
Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
|
|
477
|
+
Cosmic, ...
|
|
478
|
+
:param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
|
|
479
|
+
(or list of roles separated by commas).
|
|
480
|
+
:param str cv_type: Variant type or list of types, accepted values are
|
|
481
|
+
SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
|
|
482
|
+
COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
|
|
483
|
+
TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
|
|
484
|
+
:param str cv_protein_substitution: Variant protein substitution score
|
|
485
|
+
(or list of scores separated by commas), include SIFT and PolyPhen.
|
|
486
|
+
You can query using the score {protein_score}[<|>|<=|>=]{number} or
|
|
487
|
+
the description {protein_score}[~=|=]{description} e.g.
|
|
488
|
+
polyphen>0.1,sift=tolerant.
|
|
489
|
+
:param str cv_conservation: Variant conservation score (or list of
|
|
490
|
+
scores separated by commas) with the format
|
|
491
|
+
{conservation_score}[<|>|<=|>=]{number} e.g.
|
|
492
|
+
phastCons>0.5,phylop<0.1,gerp>0.1.
|
|
493
|
+
:param str cv_functional_score: Variant functional score (or list of
|
|
494
|
+
scores separated by commas) with the format
|
|
495
|
+
{functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
|
|
496
|
+
cadd_raw<=0.3.
|
|
497
|
+
:param str cv_population_frequency_alt: Variant alternate population
|
|
498
|
+
frequency (or list of frequencies separated by commas), with the
|
|
499
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
500
|
+
1000G:ALL<0.01.
|
|
501
|
+
:param str cv_population_frequency_maf: Variant population minor
|
|
502
|
+
allele frequency (or list of frequencies separated by commas), with
|
|
503
|
+
the format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
504
|
+
1000G:ALL<0.01.
|
|
505
|
+
:param str cv_population_frequency_ref: Variant reference population
|
|
506
|
+
frequency (or list of frequences separated by commas), with the
|
|
507
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
508
|
+
1000G:ALL<0.01.
|
|
509
|
+
:param str cv_cohort_stats_alt: Variant alternate allele frequency (or
|
|
510
|
+
list of frequencies separated by commas), with the format
|
|
511
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
512
|
+
:param str cv_cohort_stats_maf: Variant minor allele frequency (or
|
|
513
|
+
list of frequencies separated by commas), with the format
|
|
514
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
515
|
+
:param str cv_cohort_stats_ref: Variant reference allele frequency (or
|
|
516
|
+
list of frequencies separated by commas), with the foramt
|
|
517
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
518
|
+
:param str cv_cohort_stats_pass: Variant filter PASS frequency (or
|
|
519
|
+
list of frequencies separated by commas), with the format
|
|
520
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
|
|
521
|
+
:param str cv_score: Variant score (or list of scores separated by
|
|
522
|
+
commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
|
|
523
|
+
:param str cv_annot_go_genes: Variant gene GO (or list of GOs
|
|
524
|
+
separated by commas).
|
|
525
|
+
:param str cv_annot_expression_genes: Variant gene expression (or list
|
|
526
|
+
of expressions separated by commas).
|
|
527
|
+
:param str cv_gene_trait_id: Variant gene trait association ID (or
|
|
528
|
+
list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
|
|
529
|
+
'OMIM:269600'.
|
|
530
|
+
:param str cv_trait: Variant Trait (or list of traits separated by
|
|
531
|
+
commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
|
|
532
|
+
descriptions,...
|
|
533
|
+
:param str cv_protein_keyword: Uniprot protein variant annotation
|
|
534
|
+
keyword (or list of keywords separated by commas).
|
|
535
|
+
:param str cve_variant_id: Variant ID (or list of IDs separated by
|
|
536
|
+
commas).
|
|
537
|
+
:param bool cve_primary_finding: Clinical variant evidence belongs to
|
|
538
|
+
a primary finding (true or false).
|
|
539
|
+
:param bool cve_primary_interpretation: Clinical variant evidence
|
|
540
|
+
belongs to the primary interpretation (true or false).
|
|
541
|
+
:param str cve_phenotype_name: Clinical variant evidence phenotype
|
|
542
|
+
name (or names separated by commas).
|
|
543
|
+
:param str cve_gene_name: Clinical variant evidence gene name (or
|
|
544
|
+
names separated by commas).
|
|
545
|
+
:param str cve_transcript_id: Clinical variant evidence transcript ID
|
|
546
|
+
(or IDs separated by commas).
|
|
547
|
+
:param str cve_so_term_name: Clinical variant evidence sequence
|
|
548
|
+
ontology name (or names separated by commas).
|
|
549
|
+
:param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
|
|
550
|
+
separated by commas).
|
|
551
|
+
:param str cve_panel_id: Clinical variant evidence panel ID (or IDs
|
|
552
|
+
separated by commas).
|
|
553
|
+
:param str cve_moi: Clinical variant evidence mode of inheritance (or
|
|
554
|
+
list of modes of inheritance separated by commas), valid values:
|
|
555
|
+
AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
|
|
556
|
+
X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
|
|
557
|
+
MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
|
|
558
|
+
:param str cve_penetrance: Clinical variant evidence penetrance (or
|
|
559
|
+
list of penetrance values separated by commas), valid values:
|
|
560
|
+
COMPLETE, INCOMPLETE, UNKNOWN.
|
|
561
|
+
:param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
|
|
562
|
+
separated by commas).
|
|
563
|
+
:param str cve_tier: Clinical variant evidence tier (or list of tier
|
|
564
|
+
values separated by commas).
|
|
565
|
+
:param str cve_clinical_significance: Clinical variant evidence
|
|
566
|
+
clinical significance (or list of clinical significances separated
|
|
567
|
+
by commas).
|
|
568
|
+
:param str cve_drug_response: Clinical variant evidence drug response
|
|
569
|
+
(or list of drug responses separated by commas).
|
|
570
|
+
:param str cve_trait_association: Clinical variant evidence trait
|
|
571
|
+
association (or list of traits separated by commas).
|
|
572
|
+
:param str cve_functional_effect: Clinical variant evidence functional
|
|
573
|
+
effect (or list of functional effects separated by commas).
|
|
574
|
+
:param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
|
|
575
|
+
(or list of tumorigenesis values separated by commas).
|
|
576
|
+
:param str cve_other_classification: Clinical variant evidence
|
|
577
|
+
other-classification (or list of other classification values
|
|
578
|
+
separated by commas).
|
|
579
|
+
:param str cve_role_in_cancer: Clinical variant evidence role in
|
|
580
|
+
cancer (or roles in cancer separated by commas).
|
|
581
|
+
:param str cve_review_acmg: Clinical variant evidence review ACMG (or
|
|
582
|
+
ACGMs separated by commas).
|
|
583
|
+
:param str cve_review_tier: Clinical variant evidence review tier (or
|
|
584
|
+
list of tier values separated by commas).
|
|
585
|
+
:param str cve_review_clinical_significance: Clinical variant evidence
|
|
586
|
+
review clinical significance (or list of clinical significances
|
|
587
|
+
separated by commas).
|
|
588
|
+
:param str cve_review_text: Clinical variant evidence review text
|
|
589
|
+
(word or list of words contained in the text, if the words are
|
|
590
|
+
separated by a comma an OR will be applied; if the words are
|
|
591
|
+
separated by a semicolon, an AND will be applied).
|
|
592
|
+
"""
|
|
593
|
+
|
|
594
|
+
return self._get(category='analysis', resource='query', subcategory='cvdb/analysis', **options)
|
|
595
|
+
|
|
596
|
+
def aggregate_evidence(self, **options):
|
|
597
|
+
"""
|
|
598
|
+
Calculate and fetch clinical variant evidence aggregation stats.
|
|
599
|
+
PATH: /{apiVersion}/analysis/cvdb/evidence/aggregate
|
|
600
|
+
|
|
601
|
+
:param str project: Project ID.
|
|
602
|
+
:param str study: Study ID (or list of study IDs separated by commas).
|
|
603
|
+
:param str ca_id: Clinical analysis ID (or list of IDs separated by
|
|
604
|
+
commas).
|
|
605
|
+
:param str ca_description: Clinical analysis description (word or list
|
|
606
|
+
of words contained in the text, if the words are separated by a
|
|
607
|
+
comma an OR will be applied; if the words are separated by a
|
|
608
|
+
semicolon, an AND will be applied).
|
|
609
|
+
:param str ca_type: Clinical analysis type (or list of types separated
|
|
610
|
+
by commas).
|
|
611
|
+
:param str ca_disorder_id: Clinical analysis disorder ID (or list of
|
|
612
|
+
IDs separated by commas).
|
|
613
|
+
:param str ca_filename: Clinical analysis filename (or list of
|
|
614
|
+
filenames separated by commas).
|
|
615
|
+
:param str ca_proband_id: Clinical analysis proband ID (or list of IDs
|
|
616
|
+
separated by commas).
|
|
617
|
+
:param str ca_proband_disorder_id: Clinical analysis proband disorder
|
|
618
|
+
ID (or list of disorder IDs separated by commas).
|
|
619
|
+
:param str ca_proband_phenotype_name: Clinical analysis proband
|
|
620
|
+
phenotype name (or list of phenotype names separated by commas).
|
|
621
|
+
:param str ca_family_id: Clinical analysis family ID (or list of IDs
|
|
622
|
+
separated by commas).
|
|
623
|
+
:param str ca_family_phenotype_name: Clinical analysis family
|
|
624
|
+
phenotype names (or list of names separated by commas).
|
|
625
|
+
:param str ca_family_member_id: Clinical analysis family member ID (or
|
|
626
|
+
list of IDs separated by commas).
|
|
627
|
+
:param str ca_report: Clinical analysis report text (word or list of
|
|
628
|
+
words contained in the text, if the words are separated by a comma
|
|
629
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
630
|
+
an AND will be applied).
|
|
631
|
+
:param str ca_status: Clinical analysis status (or list of status
|
|
632
|
+
separated by commas).
|
|
633
|
+
:param bool ca_locked: Clinical analysis locked (true or false).
|
|
634
|
+
:param str ci_id: Clinical interpretation ID (or list of IDs separated
|
|
635
|
+
by commas).
|
|
636
|
+
:param bool ci_primary: Clinical interpretation primary (true or
|
|
637
|
+
false).
|
|
638
|
+
:param str ci_description: Clinical interpretation description (word
|
|
639
|
+
or list of words contained in the text, if the words are separated
|
|
640
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
641
|
+
semicolon, an AND will be applied).
|
|
642
|
+
:param str ci_panel_id: Clinical interpretation panel ID or name (or
|
|
643
|
+
list of IDs or names separated by commas).
|
|
644
|
+
:param str ci_analyst_id: Clinical interpretation analyst ID (or list
|
|
645
|
+
of IDs separated by commas).
|
|
646
|
+
:param str ci_analyst_name: Clinical interpretation analyst name (or
|
|
647
|
+
list of names separated by commas).
|
|
648
|
+
:param str ci_analyst_email: Clinical interpretation analyst e-mail
|
|
649
|
+
(or list of e-mails separated by commas).
|
|
650
|
+
:param str ci_analyst_assigned_by: Clinical interpretation analyst
|
|
651
|
+
assignee name (or list of names separated by commas).
|
|
652
|
+
:param str ci_analyst_date: Clinical interpretation analyst date (or
|
|
653
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
654
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
655
|
+
20231001000000-20231101000000.
|
|
656
|
+
:param str ci_method_name: Clinical interpretation method name (or
|
|
657
|
+
list of names separated by commas).
|
|
658
|
+
:param str ci_method_version: Clinical interpretation method version
|
|
659
|
+
(or list of versions separated by commas).
|
|
660
|
+
:param str ci_method_commit: Clinical interpretation method commit (or
|
|
661
|
+
list of commits separated by commas).
|
|
662
|
+
:param str ci_method_dependencies: Clinical interpretation method
|
|
663
|
+
dependencies (word or list of words contained in the text, if the
|
|
664
|
+
words are separated by a comma an OR will be applied; if the words
|
|
665
|
+
are separated by a semicolon, an AND will be applied).
|
|
666
|
+
:param str ci_comments: Clinical interpretation comment text (word or
|
|
667
|
+
list of words contained in the text, if the words are separated by
|
|
668
|
+
a comma an OR will be applied; if the words are separated by a
|
|
669
|
+
semicolon, an AND will be applied).
|
|
670
|
+
:param bool ci_locked: Clinical interpretation locked (true or false).
|
|
671
|
+
:param str ci_status_id: Clinical interpretation status ID (or list of
|
|
672
|
+
IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
|
|
673
|
+
CLOSED.
|
|
674
|
+
:param str ci_status_name: Clinical interpretation status name (or
|
|
675
|
+
list of names separated by commas).
|
|
676
|
+
:param str ci_status_description: Clinical interpretation status
|
|
677
|
+
description (word or list of words contained in the text, if the
|
|
678
|
+
words are separated by a comma an OR will be applied; if the words
|
|
679
|
+
are separated by a semicolon, an AND will be applied).
|
|
680
|
+
:param str ci_status_date: Clinical interpretation status date (or
|
|
681
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
682
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
683
|
+
20231001000000-20231101000000.
|
|
684
|
+
:param str ci_creation_date: Clinical interpretation creation date (or
|
|
685
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
686
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
687
|
+
20231001000000-20231101000000.
|
|
688
|
+
:param str ci_modification_date: Clinical interpretation modification
|
|
689
|
+
date (or list of dates separated by commas), with format
|
|
690
|
+
YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
|
|
691
|
+
start_date-end_date, e.g.: 20231001000000-20231101000000.
|
|
692
|
+
:param int ci_version: Clinical interpretation version number (or list
|
|
693
|
+
of versions separated by commas).
|
|
694
|
+
:param str cv_id: Clinical variant ID (or list of IDs separated by
|
|
695
|
+
commas).
|
|
696
|
+
:param str cv_variant_id: Variant ID (or list of IDs separated by
|
|
697
|
+
commas).
|
|
698
|
+
:param bool cv_primary_finding: Clinical variant is a primary finding
|
|
699
|
+
(true or false).
|
|
700
|
+
:param bool cv_primary_interpretation: Clinical variant belongs to the
|
|
701
|
+
primary interpretation (true or false).
|
|
702
|
+
:param str cv_comments: Clinical variant comment text (word or list of
|
|
703
|
+
words contained in the text, if the words are separated by a comma
|
|
704
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
705
|
+
an AND will be applied).
|
|
706
|
+
:param str cv_discussion_author: Clinical variant discussion author
|
|
707
|
+
(or list of authors separated by commas).
|
|
708
|
+
:param str cv_discussion_date: Clinical variant discussion date (or
|
|
709
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
710
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
711
|
+
20231001000000-20231101000000.
|
|
712
|
+
:param str cv_discussion_text: Clinical variant discussion text (word
|
|
713
|
+
or list of words contained in the text, if the words are separated
|
|
714
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
715
|
+
semicolon, an AND will be applied).
|
|
716
|
+
:param str cv_confidence_value: Clinical variant confidence value (or
|
|
717
|
+
list of values separated by commas).
|
|
718
|
+
:param str cv_confidence_author: Clinical variant confidence author
|
|
719
|
+
(or list of authors separated by commas).
|
|
720
|
+
:param str cv_confidence_date: Clinical variant confidence date (or
|
|
721
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
722
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
723
|
+
20231001000000-20231101000000.
|
|
724
|
+
:param str cv_tag: Clinical variant tag (or list of tags separated by
|
|
725
|
+
commas).
|
|
726
|
+
:param str cv_status: Clinical variant status (or list of status
|
|
727
|
+
separated by commas).
|
|
728
|
+
:param str cv_region: Variant region (or list of regions, these can be
|
|
729
|
+
just a single chromosome name or regions in the format
|
|
730
|
+
chr:start-end, e.g.: 2,3:100000-200000).
|
|
731
|
+
:param str cv_biotype: Variant biotype, e.g. protein_coding (or list
|
|
732
|
+
of biotypes separated by commas).
|
|
733
|
+
:param str cv_ct: Variant SO consequence type (or list of SOs
|
|
734
|
+
separated by commas), e.g. missense_variant,stop_lost or
|
|
735
|
+
SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
|
|
736
|
+
'protein_altering'.
|
|
737
|
+
:param str cv_transcript_flag: Variant transcript flag (or list of
|
|
738
|
+
flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
|
|
739
|
+
Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
|
|
740
|
+
:param str cv_gene: Variant gene (or list genes separated by commas),
|
|
741
|
+
most gene IDs are accepted (HGNC, Ensembl gene, ...).
|
|
742
|
+
:param str cv_xref: Variant external reference (or list of references
|
|
743
|
+
separated by commas), these can be genes, proteins or variants.
|
|
744
|
+
Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
|
|
745
|
+
Cosmic, ...
|
|
746
|
+
:param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
|
|
747
|
+
(or list of roles separated by commas).
|
|
748
|
+
:param str cv_type: Variant type or list of types, accepted values are
|
|
749
|
+
SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
|
|
750
|
+
COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
|
|
751
|
+
TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
|
|
752
|
+
:param str cv_protein_substitution: Variant protein substitution score
|
|
753
|
+
(or list of scores separated by commas), include SIFT and PolyPhen.
|
|
754
|
+
You can query using the score {protein_score}[<|>|<=|>=]{number} or
|
|
755
|
+
the description {protein_score}[~=|=]{description} e.g.
|
|
756
|
+
polyphen>0.1,sift=tolerant.
|
|
757
|
+
:param str cv_conservation: Variant conservation score (or list of
|
|
758
|
+
scores separated by commas) with the format
|
|
759
|
+
{conservation_score}[<|>|<=|>=]{number} e.g.
|
|
760
|
+
phastCons>0.5,phylop<0.1,gerp>0.1.
|
|
761
|
+
:param str cv_functional_score: Variant functional score (or list of
|
|
762
|
+
scores separated by commas) with the format
|
|
763
|
+
{functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
|
|
764
|
+
cadd_raw<=0.3.
|
|
765
|
+
:param str cv_population_frequency_alt: Variant alternate population
|
|
766
|
+
frequency (or list of frequencies separated by commas), with the
|
|
767
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
768
|
+
1000G:ALL<0.01.
|
|
769
|
+
:param str cv_population_frequency_maf: Variant population minor
|
|
770
|
+
allele frequency (or list of frequencies separated by commas), with
|
|
771
|
+
the format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
772
|
+
1000G:ALL<0.01.
|
|
773
|
+
:param str cv_population_frequency_ref: Variant reference population
|
|
774
|
+
frequency (or list of frequences separated by commas), with the
|
|
775
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
776
|
+
1000G:ALL<0.01.
|
|
777
|
+
:param str cv_cohort_stats_alt: Variant alternate allele frequency (or
|
|
778
|
+
list of frequencies separated by commas), with the format
|
|
779
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
780
|
+
:param str cv_cohort_stats_maf: Variant minor allele frequency (or
|
|
781
|
+
list of frequencies separated by commas), with the format
|
|
782
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
783
|
+
:param str cv_cohort_stats_ref: Variant reference allele frequency (or
|
|
784
|
+
list of frequencies separated by commas), with the foramt
|
|
785
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
786
|
+
:param str cv_cohort_stats_pass: Variant filter PASS frequency (or
|
|
787
|
+
list of frequencies separated by commas), with the format
|
|
788
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
|
|
789
|
+
:param str cv_score: Variant score (or list of scores separated by
|
|
790
|
+
commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
|
|
791
|
+
:param str cv_annot_go_genes: Variant gene GO (or list of GOs
|
|
792
|
+
separated by commas).
|
|
793
|
+
:param str cv_annot_expression_genes: Variant gene expression (or list
|
|
794
|
+
of expressions separated by commas).
|
|
795
|
+
:param str cv_gene_trait_id: Variant gene trait association ID (or
|
|
796
|
+
list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
|
|
797
|
+
'OMIM:269600'.
|
|
798
|
+
:param str cv_trait: Variant Trait (or list of traits separated by
|
|
799
|
+
commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
|
|
800
|
+
descriptions,...
|
|
801
|
+
:param str cv_protein_keyword: Uniprot protein variant annotation
|
|
802
|
+
keyword (or list of keywords separated by commas).
|
|
803
|
+
:param str cve_variant_id: Variant ID (or list of IDs separated by
|
|
804
|
+
commas).
|
|
805
|
+
:param bool cve_primary_finding: Clinical variant evidence belongs to
|
|
806
|
+
a primary finding (true or false).
|
|
807
|
+
:param bool cve_primary_interpretation: Clinical variant evidence
|
|
808
|
+
belongs to the primary interpretation (true or false).
|
|
809
|
+
:param str cve_phenotype_name: Clinical variant evidence phenotype
|
|
810
|
+
name (or names separated by commas).
|
|
811
|
+
:param str cve_gene_name: Clinical variant evidence gene name (or
|
|
812
|
+
names separated by commas).
|
|
813
|
+
:param str cve_transcript_id: Clinical variant evidence transcript ID
|
|
814
|
+
(or IDs separated by commas).
|
|
815
|
+
:param str cve_so_term_name: Clinical variant evidence sequence
|
|
816
|
+
ontology name (or names separated by commas).
|
|
817
|
+
:param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
|
|
818
|
+
separated by commas).
|
|
819
|
+
:param str cve_panel_id: Clinical variant evidence panel ID (or IDs
|
|
820
|
+
separated by commas).
|
|
821
|
+
:param str cve_moi: Clinical variant evidence mode of inheritance (or
|
|
822
|
+
list of modes of inheritance separated by commas), valid values:
|
|
823
|
+
AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
|
|
824
|
+
X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
|
|
825
|
+
MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
|
|
826
|
+
:param str cve_penetrance: Clinical variant evidence penetrance (or
|
|
827
|
+
list of penetrance values separated by commas), valid values:
|
|
828
|
+
COMPLETE, INCOMPLETE, UNKNOWN.
|
|
829
|
+
:param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
|
|
830
|
+
separated by commas).
|
|
831
|
+
:param str cve_tier: Clinical variant evidence tier (or list of tier
|
|
832
|
+
values separated by commas).
|
|
833
|
+
:param str cve_clinical_significance: Clinical variant evidence
|
|
834
|
+
clinical significance (or list of clinical significances separated
|
|
835
|
+
by commas).
|
|
836
|
+
:param str cve_drug_response: Clinical variant evidence drug response
|
|
837
|
+
(or list of drug responses separated by commas).
|
|
838
|
+
:param str cve_trait_association: Clinical variant evidence trait
|
|
839
|
+
association (or list of traits separated by commas).
|
|
840
|
+
:param str cve_functional_effect: Clinical variant evidence functional
|
|
841
|
+
effect (or list of functional effects separated by commas).
|
|
842
|
+
:param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
|
|
843
|
+
(or list of tumorigenesis values separated by commas).
|
|
844
|
+
:param str cve_other_classification: Clinical variant evidence
|
|
845
|
+
other-classification (or list of other classification values
|
|
846
|
+
separated by commas).
|
|
847
|
+
:param str cve_role_in_cancer: Clinical variant evidence role in
|
|
848
|
+
cancer (or roles in cancer separated by commas).
|
|
849
|
+
:param str cve_review_acmg: Clinical variant evidence review ACMG (or
|
|
850
|
+
ACGMs separated by commas).
|
|
851
|
+
:param str cve_review_tier: Clinical variant evidence review tier (or
|
|
852
|
+
list of tier values separated by commas).
|
|
853
|
+
:param str cve_review_clinical_significance: Clinical variant evidence
|
|
854
|
+
review clinical significance (or list of clinical significances
|
|
855
|
+
separated by commas).
|
|
856
|
+
:param str cve_review_text: Clinical variant evidence review text
|
|
857
|
+
(word or list of words contained in the text, if the words are
|
|
858
|
+
separated by a comma an OR will be applied; if the words are
|
|
859
|
+
separated by a semicolon, an AND will be applied).
|
|
860
|
+
:param str field: List of facet fields separated by semicolons, e.g.:
|
|
861
|
+
geneName;tier. For nested faceted fields use >>, e.g.:
|
|
862
|
+
geneName>>tier. Accepted values: caId, ciId, cvId, variantId,
|
|
863
|
+
studyId, phenotypeNames, geneName, transcriptId, soTermNames,
|
|
864
|
+
xrefIds, panelId, mois, penetrance, acmgs, tier,
|
|
865
|
+
clinicalSignificance, drugResponse, traitAssociation,
|
|
866
|
+
functionalEffect, tumorigenesis, otherClassifications,
|
|
867
|
+
rolesInCancer, reviewAcmgs, reviewTier, reviewClinicalSignificance.
|
|
868
|
+
"""
|
|
869
|
+
|
|
870
|
+
return self._get(category='analysis', resource='aggregate', subcategory='cvdb/evidence', **options)
|
|
871
|
+
|
|
872
|
+
def query_evidence(self, **options):
|
|
873
|
+
"""
|
|
874
|
+
Filter and fetch clinical variant evidences from CVDB.
|
|
875
|
+
PATH: /{apiVersion}/analysis/cvdb/evidence/query
|
|
876
|
+
|
|
877
|
+
:param str project: Project ID.
|
|
878
|
+
:param str study: Study ID (or list of study IDs separated by commas).
|
|
879
|
+
:param str include: Fields included in the response, whole JSON path
|
|
880
|
+
must be provided.
|
|
881
|
+
:param str exclude: Fields excluded in the response, whole JSON path
|
|
882
|
+
must be provided.
|
|
883
|
+
:param int limit: Number of results to be returned.
|
|
884
|
+
:param int skip: Number of results to skip.
|
|
885
|
+
:param str ca_id: Clinical analysis ID (or list of IDs separated by
|
|
886
|
+
commas).
|
|
887
|
+
:param str ca_description: Clinical analysis description (word or list
|
|
888
|
+
of words contained in the text, if the words are separated by a
|
|
889
|
+
comma an OR will be applied; if the words are separated by a
|
|
890
|
+
semicolon, an AND will be applied).
|
|
891
|
+
:param str ca_type: Clinical analysis type (or list of types separated
|
|
892
|
+
by commas).
|
|
893
|
+
:param str ca_disorder_id: Clinical analysis disorder ID (or list of
|
|
894
|
+
IDs separated by commas).
|
|
895
|
+
:param str ca_filename: Clinical analysis filename (or list of
|
|
896
|
+
filenames separated by commas).
|
|
897
|
+
:param str ca_proband_id: Clinical analysis proband ID (or list of IDs
|
|
898
|
+
separated by commas).
|
|
899
|
+
:param str ca_proband_disorder_id: Clinical analysis proband disorder
|
|
900
|
+
ID (or list of disorder IDs separated by commas).
|
|
901
|
+
:param str ca_proband_phenotype_name: Clinical analysis proband
|
|
902
|
+
phenotype name (or list of phenotype names separated by commas).
|
|
903
|
+
:param str ca_family_id: Clinical analysis family ID (or list of IDs
|
|
904
|
+
separated by commas).
|
|
905
|
+
:param str ca_family_phenotype_name: Clinical analysis family
|
|
906
|
+
phenotype names (or list of names separated by commas).
|
|
907
|
+
:param str ca_family_member_id: Clinical analysis family member ID (or
|
|
908
|
+
list of IDs separated by commas).
|
|
909
|
+
:param str ca_report: Clinical analysis report text (word or list of
|
|
910
|
+
words contained in the text, if the words are separated by a comma
|
|
911
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
912
|
+
an AND will be applied).
|
|
913
|
+
:param str ca_status: Clinical analysis status (or list of status
|
|
914
|
+
separated by commas).
|
|
915
|
+
:param bool ca_locked: Clinical analysis locked (true or false).
|
|
916
|
+
:param str ci_id: Clinical interpretation ID (or list of IDs separated
|
|
917
|
+
by commas).
|
|
918
|
+
:param bool ci_primary: Clinical interpretation primary (true or
|
|
919
|
+
false).
|
|
920
|
+
:param str ci_description: Clinical interpretation description (word
|
|
921
|
+
or list of words contained in the text, if the words are separated
|
|
922
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
923
|
+
semicolon, an AND will be applied).
|
|
924
|
+
:param str ci_panel_id: Clinical interpretation panel ID or name (or
|
|
925
|
+
list of IDs or names separated by commas).
|
|
926
|
+
:param str ci_analyst_id: Clinical interpretation analyst ID (or list
|
|
927
|
+
of IDs separated by commas).
|
|
928
|
+
:param str ci_analyst_name: Clinical interpretation analyst name (or
|
|
929
|
+
list of names separated by commas).
|
|
930
|
+
:param str ci_analyst_email: Clinical interpretation analyst e-mail
|
|
931
|
+
(or list of e-mails separated by commas).
|
|
932
|
+
:param str ci_analyst_assigned_by: Clinical interpretation analyst
|
|
933
|
+
assignee name (or list of names separated by commas).
|
|
934
|
+
:param str ci_analyst_date: Clinical interpretation analyst date (or
|
|
935
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
936
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
937
|
+
20231001000000-20231101000000.
|
|
938
|
+
:param str ci_method_name: Clinical interpretation method name (or
|
|
939
|
+
list of names separated by commas).
|
|
940
|
+
:param str ci_method_version: Clinical interpretation method version
|
|
941
|
+
(or list of versions separated by commas).
|
|
942
|
+
:param str ci_method_commit: Clinical interpretation method commit (or
|
|
943
|
+
list of commits separated by commas).
|
|
944
|
+
:param str ci_method_dependencies: Clinical interpretation method
|
|
945
|
+
dependencies (word or list of words contained in the text, if the
|
|
946
|
+
words are separated by a comma an OR will be applied; if the words
|
|
947
|
+
are separated by a semicolon, an AND will be applied).
|
|
948
|
+
:param str ci_comments: Clinical interpretation comment text (word or
|
|
949
|
+
list of words contained in the text, if the words are separated by
|
|
950
|
+
a comma an OR will be applied; if the words are separated by a
|
|
951
|
+
semicolon, an AND will be applied).
|
|
952
|
+
:param bool ci_locked: Clinical interpretation locked (true or false).
|
|
953
|
+
:param str ci_status_id: Clinical interpretation status ID (or list of
|
|
954
|
+
IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
|
|
955
|
+
CLOSED.
|
|
956
|
+
:param str ci_status_name: Clinical interpretation status name (or
|
|
957
|
+
list of names separated by commas).
|
|
958
|
+
:param str ci_status_description: Clinical interpretation status
|
|
959
|
+
description (word or list of words contained in the text, if the
|
|
960
|
+
words are separated by a comma an OR will be applied; if the words
|
|
961
|
+
are separated by a semicolon, an AND will be applied).
|
|
962
|
+
:param str ci_status_date: Clinical interpretation status date (or
|
|
963
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
964
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
965
|
+
20231001000000-20231101000000.
|
|
966
|
+
:param str ci_creation_date: Clinical interpretation creation date (or
|
|
967
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
968
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
969
|
+
20231001000000-20231101000000.
|
|
970
|
+
:param str ci_modification_date: Clinical interpretation modification
|
|
971
|
+
date (or list of dates separated by commas), with format
|
|
972
|
+
YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
|
|
973
|
+
start_date-end_date, e.g.: 20231001000000-20231101000000.
|
|
974
|
+
:param int ci_version: Clinical interpretation version number (or list
|
|
975
|
+
of versions separated by commas).
|
|
976
|
+
:param str cv_id: Clinical variant ID (or list of IDs separated by
|
|
977
|
+
commas).
|
|
978
|
+
:param str cv_variant_id: Variant ID (or list of IDs separated by
|
|
979
|
+
commas).
|
|
980
|
+
:param bool cv_primary_finding: Clinical variant is a primary finding
|
|
981
|
+
(true or false).
|
|
982
|
+
:param bool cv_primary_interpretation: Clinical variant belongs to the
|
|
983
|
+
primary interpretation (true or false).
|
|
984
|
+
:param str cv_comments: Clinical variant comment text (word or list of
|
|
985
|
+
words contained in the text, if the words are separated by a comma
|
|
986
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
987
|
+
an AND will be applied).
|
|
988
|
+
:param str cv_discussion_author: Clinical variant discussion author
|
|
989
|
+
(or list of authors separated by commas).
|
|
990
|
+
:param str cv_discussion_date: Clinical variant discussion date (or
|
|
991
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
992
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
993
|
+
20231001000000-20231101000000.
|
|
994
|
+
:param str cv_discussion_text: Clinical variant discussion text (word
|
|
995
|
+
or list of words contained in the text, if the words are separated
|
|
996
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
997
|
+
semicolon, an AND will be applied).
|
|
998
|
+
:param str cv_confidence_value: Clinical variant confidence value (or
|
|
999
|
+
list of values separated by commas).
|
|
1000
|
+
:param str cv_confidence_author: Clinical variant confidence author
|
|
1001
|
+
(or list of authors separated by commas).
|
|
1002
|
+
:param str cv_confidence_date: Clinical variant confidence date (or
|
|
1003
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1004
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1005
|
+
20231001000000-20231101000000.
|
|
1006
|
+
:param str cv_tag: Clinical variant tag (or list of tags separated by
|
|
1007
|
+
commas).
|
|
1008
|
+
:param str cv_status: Clinical variant status (or list of status
|
|
1009
|
+
separated by commas).
|
|
1010
|
+
:param str cv_region: Variant region (or list of regions, these can be
|
|
1011
|
+
just a single chromosome name or regions in the format
|
|
1012
|
+
chr:start-end, e.g.: 2,3:100000-200000).
|
|
1013
|
+
:param str cv_biotype: Variant biotype, e.g. protein_coding (or list
|
|
1014
|
+
of biotypes separated by commas).
|
|
1015
|
+
:param str cv_ct: Variant SO consequence type (or list of SOs
|
|
1016
|
+
separated by commas), e.g. missense_variant,stop_lost or
|
|
1017
|
+
SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
|
|
1018
|
+
'protein_altering'.
|
|
1019
|
+
:param str cv_transcript_flag: Variant transcript flag (or list of
|
|
1020
|
+
flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
|
|
1021
|
+
Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
|
|
1022
|
+
:param str cv_gene: Variant gene (or list genes separated by commas),
|
|
1023
|
+
most gene IDs are accepted (HGNC, Ensembl gene, ...).
|
|
1024
|
+
:param str cv_xref: Variant external reference (or list of references
|
|
1025
|
+
separated by commas), these can be genes, proteins or variants.
|
|
1026
|
+
Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
|
|
1027
|
+
Cosmic, ...
|
|
1028
|
+
:param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
|
|
1029
|
+
(or list of roles separated by commas).
|
|
1030
|
+
:param str cv_type: Variant type or list of types, accepted values are
|
|
1031
|
+
SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
|
|
1032
|
+
COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
|
|
1033
|
+
TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
|
|
1034
|
+
:param str cv_protein_substitution: Variant protein substitution score
|
|
1035
|
+
(or list of scores separated by commas), include SIFT and PolyPhen.
|
|
1036
|
+
You can query using the score {protein_score}[<|>|<=|>=]{number} or
|
|
1037
|
+
the description {protein_score}[~=|=]{description} e.g.
|
|
1038
|
+
polyphen>0.1,sift=tolerant.
|
|
1039
|
+
:param str cv_conservation: Variant conservation score (or list of
|
|
1040
|
+
scores separated by commas) with the format
|
|
1041
|
+
{conservation_score}[<|>|<=|>=]{number} e.g.
|
|
1042
|
+
phastCons>0.5,phylop<0.1,gerp>0.1.
|
|
1043
|
+
:param str cv_functional_score: Variant functional score (or list of
|
|
1044
|
+
scores separated by commas) with the format
|
|
1045
|
+
{functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
|
|
1046
|
+
cadd_raw<=0.3.
|
|
1047
|
+
:param str cv_population_frequency_alt: Variant alternate population
|
|
1048
|
+
frequency (or list of frequencies separated by commas), with the
|
|
1049
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1050
|
+
1000G:ALL<0.01.
|
|
1051
|
+
:param str cv_population_frequency_maf: Variant population minor
|
|
1052
|
+
allele frequency (or list of frequencies separated by commas), with
|
|
1053
|
+
the format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1054
|
+
1000G:ALL<0.01.
|
|
1055
|
+
:param str cv_population_frequency_ref: Variant reference population
|
|
1056
|
+
frequency (or list of frequences separated by commas), with the
|
|
1057
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1058
|
+
1000G:ALL<0.01.
|
|
1059
|
+
:param str cv_cohort_stats_alt: Variant alternate allele frequency (or
|
|
1060
|
+
list of frequencies separated by commas), with the format
|
|
1061
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1062
|
+
:param str cv_cohort_stats_maf: Variant minor allele frequency (or
|
|
1063
|
+
list of frequencies separated by commas), with the format
|
|
1064
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1065
|
+
:param str cv_cohort_stats_ref: Variant reference allele frequency (or
|
|
1066
|
+
list of frequencies separated by commas), with the foramt
|
|
1067
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1068
|
+
:param str cv_cohort_stats_pass: Variant filter PASS frequency (or
|
|
1069
|
+
list of frequencies separated by commas), with the format
|
|
1070
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
|
|
1071
|
+
:param str cv_score: Variant score (or list of scores separated by
|
|
1072
|
+
commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
|
|
1073
|
+
:param str cv_annot_go_genes: Variant gene GO (or list of GOs
|
|
1074
|
+
separated by commas).
|
|
1075
|
+
:param str cv_annot_expression_genes: Variant gene expression (or list
|
|
1076
|
+
of expressions separated by commas).
|
|
1077
|
+
:param str cv_gene_trait_id: Variant gene trait association ID (or
|
|
1078
|
+
list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
|
|
1079
|
+
'OMIM:269600'.
|
|
1080
|
+
:param str cv_trait: Variant Trait (or list of traits separated by
|
|
1081
|
+
commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
|
|
1082
|
+
descriptions,...
|
|
1083
|
+
:param str cv_protein_keyword: Uniprot protein variant annotation
|
|
1084
|
+
keyword (or list of keywords separated by commas).
|
|
1085
|
+
:param str cve_variant_id: Variant ID (or list of IDs separated by
|
|
1086
|
+
commas).
|
|
1087
|
+
:param bool cve_primary_finding: Clinical variant evidence belongs to
|
|
1088
|
+
a primary finding (true or false).
|
|
1089
|
+
:param bool cve_primary_interpretation: Clinical variant evidence
|
|
1090
|
+
belongs to the primary interpretation (true or false).
|
|
1091
|
+
:param str cve_phenotype_name: Clinical variant evidence phenotype
|
|
1092
|
+
name (or names separated by commas).
|
|
1093
|
+
:param str cve_gene_name: Clinical variant evidence gene name (or
|
|
1094
|
+
names separated by commas).
|
|
1095
|
+
:param str cve_transcript_id: Clinical variant evidence transcript ID
|
|
1096
|
+
(or IDs separated by commas).
|
|
1097
|
+
:param str cve_so_term_name: Clinical variant evidence sequence
|
|
1098
|
+
ontology name (or names separated by commas).
|
|
1099
|
+
:param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
|
|
1100
|
+
separated by commas).
|
|
1101
|
+
:param str cve_panel_id: Clinical variant evidence panel ID (or IDs
|
|
1102
|
+
separated by commas).
|
|
1103
|
+
:param str cve_moi: Clinical variant evidence mode of inheritance (or
|
|
1104
|
+
list of modes of inheritance separated by commas), valid values:
|
|
1105
|
+
AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
|
|
1106
|
+
X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
|
|
1107
|
+
MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
|
|
1108
|
+
:param str cve_penetrance: Clinical variant evidence penetrance (or
|
|
1109
|
+
list of penetrance values separated by commas), valid values:
|
|
1110
|
+
COMPLETE, INCOMPLETE, UNKNOWN.
|
|
1111
|
+
:param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
|
|
1112
|
+
separated by commas).
|
|
1113
|
+
:param str cve_tier: Clinical variant evidence tier (or list of tier
|
|
1114
|
+
values separated by commas).
|
|
1115
|
+
:param str cve_clinical_significance: Clinical variant evidence
|
|
1116
|
+
clinical significance (or list of clinical significances separated
|
|
1117
|
+
by commas).
|
|
1118
|
+
:param str cve_drug_response: Clinical variant evidence drug response
|
|
1119
|
+
(or list of drug responses separated by commas).
|
|
1120
|
+
:param str cve_trait_association: Clinical variant evidence trait
|
|
1121
|
+
association (or list of traits separated by commas).
|
|
1122
|
+
:param str cve_functional_effect: Clinical variant evidence functional
|
|
1123
|
+
effect (or list of functional effects separated by commas).
|
|
1124
|
+
:param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
|
|
1125
|
+
(or list of tumorigenesis values separated by commas).
|
|
1126
|
+
:param str cve_other_classification: Clinical variant evidence
|
|
1127
|
+
other-classification (or list of other classification values
|
|
1128
|
+
separated by commas).
|
|
1129
|
+
:param str cve_role_in_cancer: Clinical variant evidence role in
|
|
1130
|
+
cancer (or roles in cancer separated by commas).
|
|
1131
|
+
:param str cve_review_acmg: Clinical variant evidence review ACMG (or
|
|
1132
|
+
ACGMs separated by commas).
|
|
1133
|
+
:param str cve_review_tier: Clinical variant evidence review tier (or
|
|
1134
|
+
list of tier values separated by commas).
|
|
1135
|
+
:param str cve_review_clinical_significance: Clinical variant evidence
|
|
1136
|
+
review clinical significance (or list of clinical significances
|
|
1137
|
+
separated by commas).
|
|
1138
|
+
:param str cve_review_text: Clinical variant evidence review text
|
|
1139
|
+
(word or list of words contained in the text, if the words are
|
|
1140
|
+
separated by a comma an OR will be applied; if the words are
|
|
1141
|
+
separated by a semicolon, an AND will be applied).
|
|
1142
|
+
"""
|
|
1143
|
+
|
|
1144
|
+
return self._get(category='analysis', resource='query', subcategory='cvdb/evidence', **options)
|
|
1145
|
+
|
|
1146
|
+
def run_index(self, data=None, **options):
|
|
1147
|
+
"""
|
|
1148
|
+
Index clinical analyses of a OpenCGA project, a study or a list of
|
|
1149
|
+
clinical analyses into CVDB.
|
|
1150
|
+
PATH: /{apiVersion}/analysis/cvdb/index/run
|
|
1151
|
+
|
|
1152
|
+
:param dict data: Parameters: Index clinical analyses of a OpenCGA
|
|
1153
|
+
project, a study or a list of clinical analyses into CVDB.
|
|
1154
|
+
(REQUIRED)
|
|
1155
|
+
:param str study: Study [[organization@]project:]study where study and
|
|
1156
|
+
project can be either the ID or UUID.
|
|
1157
|
+
:param str job_id: Job ID. It must be a unique string within the
|
|
1158
|
+
study. An ID will be autogenerated automatically if not provided.
|
|
1159
|
+
:param str job_description: Job description.
|
|
1160
|
+
:param str job_depends_on: Comma separated list of existing job IDs
|
|
1161
|
+
the job will depend on.
|
|
1162
|
+
:param str job_tags: Job tags.
|
|
1163
|
+
:param str job_scheduled_start_time: Time when the job is scheduled to
|
|
1164
|
+
start.
|
|
1165
|
+
:param str job_priority: Priority of the job.
|
|
1166
|
+
:param bool job_dry_run: Flag indicating that the job will be executed
|
|
1167
|
+
in dry-run mode. In this mode, OpenCGA will validate that all
|
|
1168
|
+
parameters and prerequisites are correctly set for successful
|
|
1169
|
+
execution, but the job will not actually run.
|
|
1170
|
+
"""
|
|
1171
|
+
|
|
1172
|
+
return self._post(category='analysis', resource='run', subcategory='cvdb/index', data=data, **options)
|
|
1173
|
+
|
|
1174
|
+
def aggregate_interpretation(self, **options):
|
|
1175
|
+
"""
|
|
1176
|
+
Calculate and fetch clinical interpretation aggregation stats.
|
|
1177
|
+
PATH: /{apiVersion}/analysis/cvdb/interpretation/aggregate
|
|
1178
|
+
|
|
1179
|
+
:param str project: Project ID.
|
|
1180
|
+
:param str study: Study ID (or list of study IDs separated by commas).
|
|
1181
|
+
:param str ca_id: Clinical analysis ID (or list of IDs separated by
|
|
1182
|
+
commas).
|
|
1183
|
+
:param str ca_description: Clinical analysis description (word or list
|
|
1184
|
+
of words contained in the text, if the words are separated by a
|
|
1185
|
+
comma an OR will be applied; if the words are separated by a
|
|
1186
|
+
semicolon, an AND will be applied).
|
|
1187
|
+
:param str ca_type: Clinical analysis type (or list of types separated
|
|
1188
|
+
by commas).
|
|
1189
|
+
:param str ca_disorder_id: Clinical analysis disorder ID (or list of
|
|
1190
|
+
IDs separated by commas).
|
|
1191
|
+
:param str ca_filename: Clinical analysis filename (or list of
|
|
1192
|
+
filenames separated by commas).
|
|
1193
|
+
:param str ca_proband_id: Clinical analysis proband ID (or list of IDs
|
|
1194
|
+
separated by commas).
|
|
1195
|
+
:param str ca_proband_disorder_id: Clinical analysis proband disorder
|
|
1196
|
+
ID (or list of disorder IDs separated by commas).
|
|
1197
|
+
:param str ca_proband_phenotype_name: Clinical analysis proband
|
|
1198
|
+
phenotype name (or list of phenotype names separated by commas).
|
|
1199
|
+
:param str ca_family_id: Clinical analysis family ID (or list of IDs
|
|
1200
|
+
separated by commas).
|
|
1201
|
+
:param str ca_family_phenotype_name: Clinical analysis family
|
|
1202
|
+
phenotype names (or list of names separated by commas).
|
|
1203
|
+
:param str ca_family_member_id: Clinical analysis family member ID (or
|
|
1204
|
+
list of IDs separated by commas).
|
|
1205
|
+
:param str ca_report: Clinical analysis report text (word or list of
|
|
1206
|
+
words contained in the text, if the words are separated by a comma
|
|
1207
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
1208
|
+
an AND will be applied).
|
|
1209
|
+
:param str ca_status: Clinical analysis status (or list of status
|
|
1210
|
+
separated by commas).
|
|
1211
|
+
:param bool ca_locked: Clinical analysis locked (true or false).
|
|
1212
|
+
:param str ci_id: Clinical interpretation ID (or list of IDs separated
|
|
1213
|
+
by commas).
|
|
1214
|
+
:param bool ci_primary: Clinical interpretation primary (true or
|
|
1215
|
+
false).
|
|
1216
|
+
:param str ci_description: Clinical interpretation description (word
|
|
1217
|
+
or list of words contained in the text, if the words are separated
|
|
1218
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
1219
|
+
semicolon, an AND will be applied).
|
|
1220
|
+
:param str ci_panel_id: Clinical interpretation panel ID or name (or
|
|
1221
|
+
list of IDs or names separated by commas).
|
|
1222
|
+
:param str ci_analyst_id: Clinical interpretation analyst ID (or list
|
|
1223
|
+
of IDs separated by commas).
|
|
1224
|
+
:param str ci_analyst_name: Clinical interpretation analyst name (or
|
|
1225
|
+
list of names separated by commas).
|
|
1226
|
+
:param str ci_analyst_email: Clinical interpretation analyst e-mail
|
|
1227
|
+
(or list of e-mails separated by commas).
|
|
1228
|
+
:param str ci_analyst_assigned_by: Clinical interpretation analyst
|
|
1229
|
+
assignee name (or list of names separated by commas).
|
|
1230
|
+
:param str ci_analyst_date: Clinical interpretation analyst date (or
|
|
1231
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1232
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1233
|
+
20231001000000-20231101000000.
|
|
1234
|
+
:param str ci_method_name: Clinical interpretation method name (or
|
|
1235
|
+
list of names separated by commas).
|
|
1236
|
+
:param str ci_method_version: Clinical interpretation method version
|
|
1237
|
+
(or list of versions separated by commas).
|
|
1238
|
+
:param str ci_method_commit: Clinical interpretation method commit (or
|
|
1239
|
+
list of commits separated by commas).
|
|
1240
|
+
:param str ci_method_dependencies: Clinical interpretation method
|
|
1241
|
+
dependencies (word or list of words contained in the text, if the
|
|
1242
|
+
words are separated by a comma an OR will be applied; if the words
|
|
1243
|
+
are separated by a semicolon, an AND will be applied).
|
|
1244
|
+
:param str ci_comments: Clinical interpretation comment text (word or
|
|
1245
|
+
list of words contained in the text, if the words are separated by
|
|
1246
|
+
a comma an OR will be applied; if the words are separated by a
|
|
1247
|
+
semicolon, an AND will be applied).
|
|
1248
|
+
:param bool ci_locked: Clinical interpretation locked (true or false).
|
|
1249
|
+
:param str ci_status_id: Clinical interpretation status ID (or list of
|
|
1250
|
+
IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
|
|
1251
|
+
CLOSED.
|
|
1252
|
+
:param str ci_status_name: Clinical interpretation status name (or
|
|
1253
|
+
list of names separated by commas).
|
|
1254
|
+
:param str ci_status_description: Clinical interpretation status
|
|
1255
|
+
description (word or list of words contained in the text, if the
|
|
1256
|
+
words are separated by a comma an OR will be applied; if the words
|
|
1257
|
+
are separated by a semicolon, an AND will be applied).
|
|
1258
|
+
:param str ci_status_date: Clinical interpretation status date (or
|
|
1259
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1260
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1261
|
+
20231001000000-20231101000000.
|
|
1262
|
+
:param str ci_creation_date: Clinical interpretation creation date (or
|
|
1263
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1264
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1265
|
+
20231001000000-20231101000000.
|
|
1266
|
+
:param str ci_modification_date: Clinical interpretation modification
|
|
1267
|
+
date (or list of dates separated by commas), with format
|
|
1268
|
+
YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
|
|
1269
|
+
start_date-end_date, e.g.: 20231001000000-20231101000000.
|
|
1270
|
+
:param int ci_version: Clinical interpretation version number (or list
|
|
1271
|
+
of versions separated by commas).
|
|
1272
|
+
:param str cv_id: Clinical variant ID (or list of IDs separated by
|
|
1273
|
+
commas).
|
|
1274
|
+
:param str cv_variant_id: Variant ID (or list of IDs separated by
|
|
1275
|
+
commas).
|
|
1276
|
+
:param bool cv_primary_finding: Clinical variant is a primary finding
|
|
1277
|
+
(true or false).
|
|
1278
|
+
:param bool cv_primary_interpretation: Clinical variant belongs to the
|
|
1279
|
+
primary interpretation (true or false).
|
|
1280
|
+
:param str cv_comments: Clinical variant comment text (word or list of
|
|
1281
|
+
words contained in the text, if the words are separated by a comma
|
|
1282
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
1283
|
+
an AND will be applied).
|
|
1284
|
+
:param str cv_discussion_author: Clinical variant discussion author
|
|
1285
|
+
(or list of authors separated by commas).
|
|
1286
|
+
:param str cv_discussion_date: Clinical variant discussion date (or
|
|
1287
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1288
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1289
|
+
20231001000000-20231101000000.
|
|
1290
|
+
:param str cv_discussion_text: Clinical variant discussion text (word
|
|
1291
|
+
or list of words contained in the text, if the words are separated
|
|
1292
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
1293
|
+
semicolon, an AND will be applied).
|
|
1294
|
+
:param str cv_confidence_value: Clinical variant confidence value (or
|
|
1295
|
+
list of values separated by commas).
|
|
1296
|
+
:param str cv_confidence_author: Clinical variant confidence author
|
|
1297
|
+
(or list of authors separated by commas).
|
|
1298
|
+
:param str cv_confidence_date: Clinical variant confidence date (or
|
|
1299
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1300
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1301
|
+
20231001000000-20231101000000.
|
|
1302
|
+
:param str cv_tag: Clinical variant tag (or list of tags separated by
|
|
1303
|
+
commas).
|
|
1304
|
+
:param str cv_status: Clinical variant status (or list of status
|
|
1305
|
+
separated by commas).
|
|
1306
|
+
:param str cv_region: Variant region (or list of regions, these can be
|
|
1307
|
+
just a single chromosome name or regions in the format
|
|
1308
|
+
chr:start-end, e.g.: 2,3:100000-200000).
|
|
1309
|
+
:param str cv_biotype: Variant biotype, e.g. protein_coding (or list
|
|
1310
|
+
of biotypes separated by commas).
|
|
1311
|
+
:param str cv_ct: Variant SO consequence type (or list of SOs
|
|
1312
|
+
separated by commas), e.g. missense_variant,stop_lost or
|
|
1313
|
+
SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
|
|
1314
|
+
'protein_altering'.
|
|
1315
|
+
:param str cv_transcript_flag: Variant transcript flag (or list of
|
|
1316
|
+
flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
|
|
1317
|
+
Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
|
|
1318
|
+
:param str cv_gene: Variant gene (or list genes separated by commas),
|
|
1319
|
+
most gene IDs are accepted (HGNC, Ensembl gene, ...).
|
|
1320
|
+
:param str cv_xref: Variant external reference (or list of references
|
|
1321
|
+
separated by commas), these can be genes, proteins or variants.
|
|
1322
|
+
Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
|
|
1323
|
+
Cosmic, ...
|
|
1324
|
+
:param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
|
|
1325
|
+
(or list of roles separated by commas).
|
|
1326
|
+
:param str cv_type: Variant type or list of types, accepted values are
|
|
1327
|
+
SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
|
|
1328
|
+
COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
|
|
1329
|
+
TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
|
|
1330
|
+
:param str cv_protein_substitution: Variant protein substitution score
|
|
1331
|
+
(or list of scores separated by commas), include SIFT and PolyPhen.
|
|
1332
|
+
You can query using the score {protein_score}[<|>|<=|>=]{number} or
|
|
1333
|
+
the description {protein_score}[~=|=]{description} e.g.
|
|
1334
|
+
polyphen>0.1,sift=tolerant.
|
|
1335
|
+
:param str cv_conservation: Variant conservation score (or list of
|
|
1336
|
+
scores separated by commas) with the format
|
|
1337
|
+
{conservation_score}[<|>|<=|>=]{number} e.g.
|
|
1338
|
+
phastCons>0.5,phylop<0.1,gerp>0.1.
|
|
1339
|
+
:param str cv_functional_score: Variant functional score (or list of
|
|
1340
|
+
scores separated by commas) with the format
|
|
1341
|
+
{functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
|
|
1342
|
+
cadd_raw<=0.3.
|
|
1343
|
+
:param str cv_population_frequency_alt: Variant alternate population
|
|
1344
|
+
frequency (or list of frequencies separated by commas), with the
|
|
1345
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1346
|
+
1000G:ALL<0.01.
|
|
1347
|
+
:param str cv_population_frequency_maf: Variant population minor
|
|
1348
|
+
allele frequency (or list of frequencies separated by commas), with
|
|
1349
|
+
the format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1350
|
+
1000G:ALL<0.01.
|
|
1351
|
+
:param str cv_population_frequency_ref: Variant reference population
|
|
1352
|
+
frequency (or list of frequences separated by commas), with the
|
|
1353
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1354
|
+
1000G:ALL<0.01.
|
|
1355
|
+
:param str cv_cohort_stats_alt: Variant alternate allele frequency (or
|
|
1356
|
+
list of frequencies separated by commas), with the format
|
|
1357
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1358
|
+
:param str cv_cohort_stats_maf: Variant minor allele frequency (or
|
|
1359
|
+
list of frequencies separated by commas), with the format
|
|
1360
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1361
|
+
:param str cv_cohort_stats_ref: Variant reference allele frequency (or
|
|
1362
|
+
list of frequencies separated by commas), with the foramt
|
|
1363
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1364
|
+
:param str cv_cohort_stats_pass: Variant filter PASS frequency (or
|
|
1365
|
+
list of frequencies separated by commas), with the format
|
|
1366
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
|
|
1367
|
+
:param str cv_score: Variant score (or list of scores separated by
|
|
1368
|
+
commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
|
|
1369
|
+
:param str cv_annot_go_genes: Variant gene GO (or list of GOs
|
|
1370
|
+
separated by commas).
|
|
1371
|
+
:param str cv_annot_expression_genes: Variant gene expression (or list
|
|
1372
|
+
of expressions separated by commas).
|
|
1373
|
+
:param str cv_gene_trait_id: Variant gene trait association ID (or
|
|
1374
|
+
list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
|
|
1375
|
+
'OMIM:269600'.
|
|
1376
|
+
:param str cv_trait: Variant Trait (or list of traits separated by
|
|
1377
|
+
commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
|
|
1378
|
+
descriptions,...
|
|
1379
|
+
:param str cv_protein_keyword: Uniprot protein variant annotation
|
|
1380
|
+
keyword (or list of keywords separated by commas).
|
|
1381
|
+
:param str cve_variant_id: Variant ID (or list of IDs separated by
|
|
1382
|
+
commas).
|
|
1383
|
+
:param bool cve_primary_finding: Clinical variant evidence belongs to
|
|
1384
|
+
a primary finding (true or false).
|
|
1385
|
+
:param bool cve_primary_interpretation: Clinical variant evidence
|
|
1386
|
+
belongs to the primary interpretation (true or false).
|
|
1387
|
+
:param str cve_phenotype_name: Clinical variant evidence phenotype
|
|
1388
|
+
name (or names separated by commas).
|
|
1389
|
+
:param str cve_gene_name: Clinical variant evidence gene name (or
|
|
1390
|
+
names separated by commas).
|
|
1391
|
+
:param str cve_transcript_id: Clinical variant evidence transcript ID
|
|
1392
|
+
(or IDs separated by commas).
|
|
1393
|
+
:param str cve_so_term_name: Clinical variant evidence sequence
|
|
1394
|
+
ontology name (or names separated by commas).
|
|
1395
|
+
:param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
|
|
1396
|
+
separated by commas).
|
|
1397
|
+
:param str cve_panel_id: Clinical variant evidence panel ID (or IDs
|
|
1398
|
+
separated by commas).
|
|
1399
|
+
:param str cve_moi: Clinical variant evidence mode of inheritance (or
|
|
1400
|
+
list of modes of inheritance separated by commas), valid values:
|
|
1401
|
+
AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
|
|
1402
|
+
X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
|
|
1403
|
+
MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
|
|
1404
|
+
:param str cve_penetrance: Clinical variant evidence penetrance (or
|
|
1405
|
+
list of penetrance values separated by commas), valid values:
|
|
1406
|
+
COMPLETE, INCOMPLETE, UNKNOWN.
|
|
1407
|
+
:param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
|
|
1408
|
+
separated by commas).
|
|
1409
|
+
:param str cve_tier: Clinical variant evidence tier (or list of tier
|
|
1410
|
+
values separated by commas).
|
|
1411
|
+
:param str cve_clinical_significance: Clinical variant evidence
|
|
1412
|
+
clinical significance (or list of clinical significances separated
|
|
1413
|
+
by commas).
|
|
1414
|
+
:param str cve_drug_response: Clinical variant evidence drug response
|
|
1415
|
+
(or list of drug responses separated by commas).
|
|
1416
|
+
:param str cve_trait_association: Clinical variant evidence trait
|
|
1417
|
+
association (or list of traits separated by commas).
|
|
1418
|
+
:param str cve_functional_effect: Clinical variant evidence functional
|
|
1419
|
+
effect (or list of functional effects separated by commas).
|
|
1420
|
+
:param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
|
|
1421
|
+
(or list of tumorigenesis values separated by commas).
|
|
1422
|
+
:param str cve_other_classification: Clinical variant evidence
|
|
1423
|
+
other-classification (or list of other classification values
|
|
1424
|
+
separated by commas).
|
|
1425
|
+
:param str cve_role_in_cancer: Clinical variant evidence role in
|
|
1426
|
+
cancer (or roles in cancer separated by commas).
|
|
1427
|
+
:param str cve_review_acmg: Clinical variant evidence review ACMG (or
|
|
1428
|
+
ACGMs separated by commas).
|
|
1429
|
+
:param str cve_review_tier: Clinical variant evidence review tier (or
|
|
1430
|
+
list of tier values separated by commas).
|
|
1431
|
+
:param str cve_review_clinical_significance: Clinical variant evidence
|
|
1432
|
+
review clinical significance (or list of clinical significances
|
|
1433
|
+
separated by commas).
|
|
1434
|
+
:param str cve_review_text: Clinical variant evidence review text
|
|
1435
|
+
(word or list of words contained in the text, if the words are
|
|
1436
|
+
separated by a comma an OR will be applied; if the words are
|
|
1437
|
+
separated by a semicolon, an AND will be applied).
|
|
1438
|
+
:param str field: List of facet fields separated by semicolons, e.g.:
|
|
1439
|
+
panelIds;methodName. For nested faceted fields use >>, e.g.:
|
|
1440
|
+
panelIds>>methodName. Accepted values: caId, studyId, primary,
|
|
1441
|
+
panelIds, analystId, analystName, analystEmail, analystAssignedBy,
|
|
1442
|
+
analystDate, methodName, methodVersion, methodCommit, statusId,
|
|
1443
|
+
statusDescription, statusType, statusDate, creationDate,
|
|
1444
|
+
modificationDate, version.
|
|
1445
|
+
"""
|
|
1446
|
+
|
|
1447
|
+
return self._get(category='analysis', resource='aggregate', subcategory='cvdb/interpretation', **options)
|
|
1448
|
+
|
|
1449
|
+
def query_interpretation(self, **options):
|
|
1450
|
+
"""
|
|
1451
|
+
Filter and fetch clinical interpretations from CVDB.
|
|
1452
|
+
PATH: /{apiVersion}/analysis/cvdb/interpretation/query
|
|
1453
|
+
|
|
1454
|
+
:param str project: Project ID.
|
|
1455
|
+
:param str study: Study ID (or list of study IDs separated by commas).
|
|
1456
|
+
:param str include: Fields included in the response, whole JSON path
|
|
1457
|
+
must be provided.
|
|
1458
|
+
:param str exclude: Fields excluded in the response, whole JSON path
|
|
1459
|
+
must be provided.
|
|
1460
|
+
:param int limit: Number of results to be returned.
|
|
1461
|
+
:param int skip: Number of results to skip.
|
|
1462
|
+
:param str ca_id: Clinical analysis ID (or list of IDs separated by
|
|
1463
|
+
commas).
|
|
1464
|
+
:param str ca_description: Clinical analysis description (word or list
|
|
1465
|
+
of words contained in the text, if the words are separated by a
|
|
1466
|
+
comma an OR will be applied; if the words are separated by a
|
|
1467
|
+
semicolon, an AND will be applied).
|
|
1468
|
+
:param str ca_type: Clinical analysis type (or list of types separated
|
|
1469
|
+
by commas).
|
|
1470
|
+
:param str ca_disorder_id: Clinical analysis disorder ID (or list of
|
|
1471
|
+
IDs separated by commas).
|
|
1472
|
+
:param str ca_filename: Clinical analysis filename (or list of
|
|
1473
|
+
filenames separated by commas).
|
|
1474
|
+
:param str ca_proband_id: Clinical analysis proband ID (or list of IDs
|
|
1475
|
+
separated by commas).
|
|
1476
|
+
:param str ca_proband_disorder_id: Clinical analysis proband disorder
|
|
1477
|
+
ID (or list of disorder IDs separated by commas).
|
|
1478
|
+
:param str ca_proband_phenotype_name: Clinical analysis proband
|
|
1479
|
+
phenotype name (or list of phenotype names separated by commas).
|
|
1480
|
+
:param str ca_family_id: Clinical analysis family ID (or list of IDs
|
|
1481
|
+
separated by commas).
|
|
1482
|
+
:param str ca_family_phenotype_name: Clinical analysis family
|
|
1483
|
+
phenotype names (or list of names separated by commas).
|
|
1484
|
+
:param str ca_family_member_id: Clinical analysis family member ID (or
|
|
1485
|
+
list of IDs separated by commas).
|
|
1486
|
+
:param str ca_report: Clinical analysis report text (word or list of
|
|
1487
|
+
words contained in the text, if the words are separated by a comma
|
|
1488
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
1489
|
+
an AND will be applied).
|
|
1490
|
+
:param str ca_status: Clinical analysis status (or list of status
|
|
1491
|
+
separated by commas).
|
|
1492
|
+
:param bool ca_locked: Clinical analysis locked (true or false).
|
|
1493
|
+
:param str ci_id: Clinical interpretation ID (or list of IDs separated
|
|
1494
|
+
by commas).
|
|
1495
|
+
:param bool ci_primary: Clinical interpretation primary (true or
|
|
1496
|
+
false).
|
|
1497
|
+
:param str ci_description: Clinical interpretation description (word
|
|
1498
|
+
or list of words contained in the text, if the words are separated
|
|
1499
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
1500
|
+
semicolon, an AND will be applied).
|
|
1501
|
+
:param str ci_panel_id: Clinical interpretation panel ID or name (or
|
|
1502
|
+
list of IDs or names separated by commas).
|
|
1503
|
+
:param str ci_analyst_id: Clinical interpretation analyst ID (or list
|
|
1504
|
+
of IDs separated by commas).
|
|
1505
|
+
:param str ci_analyst_name: Clinical interpretation analyst name (or
|
|
1506
|
+
list of names separated by commas).
|
|
1507
|
+
:param str ci_analyst_email: Clinical interpretation analyst e-mail
|
|
1508
|
+
(or list of e-mails separated by commas).
|
|
1509
|
+
:param str ci_analyst_assigned_by: Clinical interpretation analyst
|
|
1510
|
+
assignee name (or list of names separated by commas).
|
|
1511
|
+
:param str ci_analyst_date: Clinical interpretation analyst date (or
|
|
1512
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1513
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1514
|
+
20231001000000-20231101000000.
|
|
1515
|
+
:param str ci_method_name: Clinical interpretation method name (or
|
|
1516
|
+
list of names separated by commas).
|
|
1517
|
+
:param str ci_method_version: Clinical interpretation method version
|
|
1518
|
+
(or list of versions separated by commas).
|
|
1519
|
+
:param str ci_method_commit: Clinical interpretation method commit (or
|
|
1520
|
+
list of commits separated by commas).
|
|
1521
|
+
:param str ci_method_dependencies: Clinical interpretation method
|
|
1522
|
+
dependencies (word or list of words contained in the text, if the
|
|
1523
|
+
words are separated by a comma an OR will be applied; if the words
|
|
1524
|
+
are separated by a semicolon, an AND will be applied).
|
|
1525
|
+
:param str ci_comments: Clinical interpretation comment text (word or
|
|
1526
|
+
list of words contained in the text, if the words are separated by
|
|
1527
|
+
a comma an OR will be applied; if the words are separated by a
|
|
1528
|
+
semicolon, an AND will be applied).
|
|
1529
|
+
:param bool ci_locked: Clinical interpretation locked (true or false).
|
|
1530
|
+
:param str ci_status_id: Clinical interpretation status ID (or list of
|
|
1531
|
+
IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
|
|
1532
|
+
CLOSED.
|
|
1533
|
+
:param str ci_status_name: Clinical interpretation status name (or
|
|
1534
|
+
list of names separated by commas).
|
|
1535
|
+
:param str ci_status_description: Clinical interpretation status
|
|
1536
|
+
description (word or list of words contained in the text, if the
|
|
1537
|
+
words are separated by a comma an OR will be applied; if the words
|
|
1538
|
+
are separated by a semicolon, an AND will be applied).
|
|
1539
|
+
:param str ci_status_date: Clinical interpretation status date (or
|
|
1540
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1541
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1542
|
+
20231001000000-20231101000000.
|
|
1543
|
+
:param str ci_creation_date: Clinical interpretation creation date (or
|
|
1544
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1545
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1546
|
+
20231001000000-20231101000000.
|
|
1547
|
+
:param str ci_modification_date: Clinical interpretation modification
|
|
1548
|
+
date (or list of dates separated by commas), with format
|
|
1549
|
+
YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
|
|
1550
|
+
start_date-end_date, e.g.: 20231001000000-20231101000000.
|
|
1551
|
+
:param int ci_version: Clinical interpretation version number (or list
|
|
1552
|
+
of versions separated by commas).
|
|
1553
|
+
:param str cv_id: Clinical variant ID (or list of IDs separated by
|
|
1554
|
+
commas).
|
|
1555
|
+
:param str cv_variant_id: Variant ID (or list of IDs separated by
|
|
1556
|
+
commas).
|
|
1557
|
+
:param bool cv_primary_finding: Clinical variant is a primary finding
|
|
1558
|
+
(true or false).
|
|
1559
|
+
:param bool cv_primary_interpretation: Clinical variant belongs to the
|
|
1560
|
+
primary interpretation (true or false).
|
|
1561
|
+
:param str cv_comments: Clinical variant comment text (word or list of
|
|
1562
|
+
words contained in the text, if the words are separated by a comma
|
|
1563
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
1564
|
+
an AND will be applied).
|
|
1565
|
+
:param str cv_discussion_author: Clinical variant discussion author
|
|
1566
|
+
(or list of authors separated by commas).
|
|
1567
|
+
:param str cv_discussion_date: Clinical variant discussion date (or
|
|
1568
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1569
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1570
|
+
20231001000000-20231101000000.
|
|
1571
|
+
:param str cv_discussion_text: Clinical variant discussion text (word
|
|
1572
|
+
or list of words contained in the text, if the words are separated
|
|
1573
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
1574
|
+
semicolon, an AND will be applied).
|
|
1575
|
+
:param str cv_confidence_value: Clinical variant confidence value (or
|
|
1576
|
+
list of values separated by commas).
|
|
1577
|
+
:param str cv_confidence_author: Clinical variant confidence author
|
|
1578
|
+
(or list of authors separated by commas).
|
|
1579
|
+
:param str cv_confidence_date: Clinical variant confidence date (or
|
|
1580
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1581
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1582
|
+
20231001000000-20231101000000.
|
|
1583
|
+
:param str cv_tag: Clinical variant tag (or list of tags separated by
|
|
1584
|
+
commas).
|
|
1585
|
+
:param str cv_status: Clinical variant status (or list of status
|
|
1586
|
+
separated by commas).
|
|
1587
|
+
:param str cv_region: Variant region (or list of regions, these can be
|
|
1588
|
+
just a single chromosome name or regions in the format
|
|
1589
|
+
chr:start-end, e.g.: 2,3:100000-200000).
|
|
1590
|
+
:param str cv_biotype: Variant biotype, e.g. protein_coding (or list
|
|
1591
|
+
of biotypes separated by commas).
|
|
1592
|
+
:param str cv_ct: Variant SO consequence type (or list of SOs
|
|
1593
|
+
separated by commas), e.g. missense_variant,stop_lost or
|
|
1594
|
+
SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
|
|
1595
|
+
'protein_altering'.
|
|
1596
|
+
:param str cv_transcript_flag: Variant transcript flag (or list of
|
|
1597
|
+
flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
|
|
1598
|
+
Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
|
|
1599
|
+
:param str cv_gene: Variant gene (or list genes separated by commas),
|
|
1600
|
+
most gene IDs are accepted (HGNC, Ensembl gene, ...).
|
|
1601
|
+
:param str cv_xref: Variant external reference (or list of references
|
|
1602
|
+
separated by commas), these can be genes, proteins or variants.
|
|
1603
|
+
Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
|
|
1604
|
+
Cosmic, ...
|
|
1605
|
+
:param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
|
|
1606
|
+
(or list of roles separated by commas).
|
|
1607
|
+
:param str cv_type: Variant type or list of types, accepted values are
|
|
1608
|
+
SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
|
|
1609
|
+
COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
|
|
1610
|
+
TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
|
|
1611
|
+
:param str cv_protein_substitution: Variant protein substitution score
|
|
1612
|
+
(or list of scores separated by commas), include SIFT and PolyPhen.
|
|
1613
|
+
You can query using the score {protein_score}[<|>|<=|>=]{number} or
|
|
1614
|
+
the description {protein_score}[~=|=]{description} e.g.
|
|
1615
|
+
polyphen>0.1,sift=tolerant.
|
|
1616
|
+
:param str cv_conservation: Variant conservation score (or list of
|
|
1617
|
+
scores separated by commas) with the format
|
|
1618
|
+
{conservation_score}[<|>|<=|>=]{number} e.g.
|
|
1619
|
+
phastCons>0.5,phylop<0.1,gerp>0.1.
|
|
1620
|
+
:param str cv_functional_score: Variant functional score (or list of
|
|
1621
|
+
scores separated by commas) with the format
|
|
1622
|
+
{functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
|
|
1623
|
+
cadd_raw<=0.3.
|
|
1624
|
+
:param str cv_population_frequency_alt: Variant alternate population
|
|
1625
|
+
frequency (or list of frequencies separated by commas), with the
|
|
1626
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1627
|
+
1000G:ALL<0.01.
|
|
1628
|
+
:param str cv_population_frequency_maf: Variant population minor
|
|
1629
|
+
allele frequency (or list of frequencies separated by commas), with
|
|
1630
|
+
the format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1631
|
+
1000G:ALL<0.01.
|
|
1632
|
+
:param str cv_population_frequency_ref: Variant reference population
|
|
1633
|
+
frequency (or list of frequences separated by commas), with the
|
|
1634
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1635
|
+
1000G:ALL<0.01.
|
|
1636
|
+
:param str cv_cohort_stats_alt: Variant alternate allele frequency (or
|
|
1637
|
+
list of frequencies separated by commas), with the format
|
|
1638
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1639
|
+
:param str cv_cohort_stats_maf: Variant minor allele frequency (or
|
|
1640
|
+
list of frequencies separated by commas), with the format
|
|
1641
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1642
|
+
:param str cv_cohort_stats_ref: Variant reference allele frequency (or
|
|
1643
|
+
list of frequencies separated by commas), with the foramt
|
|
1644
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1645
|
+
:param str cv_cohort_stats_pass: Variant filter PASS frequency (or
|
|
1646
|
+
list of frequencies separated by commas), with the format
|
|
1647
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
|
|
1648
|
+
:param str cv_score: Variant score (or list of scores separated by
|
|
1649
|
+
commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
|
|
1650
|
+
:param str cv_annot_go_genes: Variant gene GO (or list of GOs
|
|
1651
|
+
separated by commas).
|
|
1652
|
+
:param str cv_annot_expression_genes: Variant gene expression (or list
|
|
1653
|
+
of expressions separated by commas).
|
|
1654
|
+
:param str cv_gene_trait_id: Variant gene trait association ID (or
|
|
1655
|
+
list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
|
|
1656
|
+
'OMIM:269600'.
|
|
1657
|
+
:param str cv_trait: Variant Trait (or list of traits separated by
|
|
1658
|
+
commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
|
|
1659
|
+
descriptions,...
|
|
1660
|
+
:param str cv_protein_keyword: Uniprot protein variant annotation
|
|
1661
|
+
keyword (or list of keywords separated by commas).
|
|
1662
|
+
:param str cve_variant_id: Variant ID (or list of IDs separated by
|
|
1663
|
+
commas).
|
|
1664
|
+
:param bool cve_primary_finding: Clinical variant evidence belongs to
|
|
1665
|
+
a primary finding (true or false).
|
|
1666
|
+
:param bool cve_primary_interpretation: Clinical variant evidence
|
|
1667
|
+
belongs to the primary interpretation (true or false).
|
|
1668
|
+
:param str cve_phenotype_name: Clinical variant evidence phenotype
|
|
1669
|
+
name (or names separated by commas).
|
|
1670
|
+
:param str cve_gene_name: Clinical variant evidence gene name (or
|
|
1671
|
+
names separated by commas).
|
|
1672
|
+
:param str cve_transcript_id: Clinical variant evidence transcript ID
|
|
1673
|
+
(or IDs separated by commas).
|
|
1674
|
+
:param str cve_so_term_name: Clinical variant evidence sequence
|
|
1675
|
+
ontology name (or names separated by commas).
|
|
1676
|
+
:param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
|
|
1677
|
+
separated by commas).
|
|
1678
|
+
:param str cve_panel_id: Clinical variant evidence panel ID (or IDs
|
|
1679
|
+
separated by commas).
|
|
1680
|
+
:param str cve_moi: Clinical variant evidence mode of inheritance (or
|
|
1681
|
+
list of modes of inheritance separated by commas), valid values:
|
|
1682
|
+
AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
|
|
1683
|
+
X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
|
|
1684
|
+
MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
|
|
1685
|
+
:param str cve_penetrance: Clinical variant evidence penetrance (or
|
|
1686
|
+
list of penetrance values separated by commas), valid values:
|
|
1687
|
+
COMPLETE, INCOMPLETE, UNKNOWN.
|
|
1688
|
+
:param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
|
|
1689
|
+
separated by commas).
|
|
1690
|
+
:param str cve_tier: Clinical variant evidence tier (or list of tier
|
|
1691
|
+
values separated by commas).
|
|
1692
|
+
:param str cve_clinical_significance: Clinical variant evidence
|
|
1693
|
+
clinical significance (or list of clinical significances separated
|
|
1694
|
+
by commas).
|
|
1695
|
+
:param str cve_drug_response: Clinical variant evidence drug response
|
|
1696
|
+
(or list of drug responses separated by commas).
|
|
1697
|
+
:param str cve_trait_association: Clinical variant evidence trait
|
|
1698
|
+
association (or list of traits separated by commas).
|
|
1699
|
+
:param str cve_functional_effect: Clinical variant evidence functional
|
|
1700
|
+
effect (or list of functional effects separated by commas).
|
|
1701
|
+
:param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
|
|
1702
|
+
(or list of tumorigenesis values separated by commas).
|
|
1703
|
+
:param str cve_other_classification: Clinical variant evidence
|
|
1704
|
+
other-classification (or list of other classification values
|
|
1705
|
+
separated by commas).
|
|
1706
|
+
:param str cve_role_in_cancer: Clinical variant evidence role in
|
|
1707
|
+
cancer (or roles in cancer separated by commas).
|
|
1708
|
+
:param str cve_review_acmg: Clinical variant evidence review ACMG (or
|
|
1709
|
+
ACGMs separated by commas).
|
|
1710
|
+
:param str cve_review_tier: Clinical variant evidence review tier (or
|
|
1711
|
+
list of tier values separated by commas).
|
|
1712
|
+
:param str cve_review_clinical_significance: Clinical variant evidence
|
|
1713
|
+
review clinical significance (or list of clinical significances
|
|
1714
|
+
separated by commas).
|
|
1715
|
+
:param str cve_review_text: Clinical variant evidence review text
|
|
1716
|
+
(word or list of words contained in the text, if the words are
|
|
1717
|
+
separated by a comma an OR will be applied; if the words are
|
|
1718
|
+
separated by a semicolon, an AND will be applied).
|
|
1719
|
+
"""
|
|
1720
|
+
|
|
1721
|
+
return self._get(category='analysis', resource='query', subcategory='cvdb/interpretation', **options)
|
|
1722
|
+
|
|
1723
|
+
def aggregate_variant(self, **options):
|
|
1724
|
+
"""
|
|
1725
|
+
Calculate and fetch clinical variant aggregation stats.
|
|
1726
|
+
PATH: /{apiVersion}/analysis/cvdb/variant/aggregate
|
|
1727
|
+
|
|
1728
|
+
:param str project: Project ID.
|
|
1729
|
+
:param str study: Study ID (or list of study IDs separated by commas).
|
|
1730
|
+
:param str ca_id: Clinical analysis ID (or list of IDs separated by
|
|
1731
|
+
commas).
|
|
1732
|
+
:param str ca_description: Clinical analysis description (word or list
|
|
1733
|
+
of words contained in the text, if the words are separated by a
|
|
1734
|
+
comma an OR will be applied; if the words are separated by a
|
|
1735
|
+
semicolon, an AND will be applied).
|
|
1736
|
+
:param str ca_type: Clinical analysis type (or list of types separated
|
|
1737
|
+
by commas).
|
|
1738
|
+
:param str ca_disorder_id: Clinical analysis disorder ID (or list of
|
|
1739
|
+
IDs separated by commas).
|
|
1740
|
+
:param str ca_filename: Clinical analysis filename (or list of
|
|
1741
|
+
filenames separated by commas).
|
|
1742
|
+
:param str ca_proband_id: Clinical analysis proband ID (or list of IDs
|
|
1743
|
+
separated by commas).
|
|
1744
|
+
:param str ca_proband_disorder_id: Clinical analysis proband disorder
|
|
1745
|
+
ID (or list of disorder IDs separated by commas).
|
|
1746
|
+
:param str ca_proband_phenotype_name: Clinical analysis proband
|
|
1747
|
+
phenotype name (or list of phenotype names separated by commas).
|
|
1748
|
+
:param str ca_family_id: Clinical analysis family ID (or list of IDs
|
|
1749
|
+
separated by commas).
|
|
1750
|
+
:param str ca_family_phenotype_name: Clinical analysis family
|
|
1751
|
+
phenotype names (or list of names separated by commas).
|
|
1752
|
+
:param str ca_family_member_id: Clinical analysis family member ID (or
|
|
1753
|
+
list of IDs separated by commas).
|
|
1754
|
+
:param str ca_report: Clinical analysis report text (word or list of
|
|
1755
|
+
words contained in the text, if the words are separated by a comma
|
|
1756
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
1757
|
+
an AND will be applied).
|
|
1758
|
+
:param str ca_status: Clinical analysis status (or list of status
|
|
1759
|
+
separated by commas).
|
|
1760
|
+
:param bool ca_locked: Clinical analysis locked (true or false).
|
|
1761
|
+
:param str ci_id: Clinical interpretation ID (or list of IDs separated
|
|
1762
|
+
by commas).
|
|
1763
|
+
:param bool ci_primary: Clinical interpretation primary (true or
|
|
1764
|
+
false).
|
|
1765
|
+
:param str ci_description: Clinical interpretation description (word
|
|
1766
|
+
or list of words contained in the text, if the words are separated
|
|
1767
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
1768
|
+
semicolon, an AND will be applied).
|
|
1769
|
+
:param str ci_panel_id: Clinical interpretation panel ID or name (or
|
|
1770
|
+
list of IDs or names separated by commas).
|
|
1771
|
+
:param str ci_analyst_id: Clinical interpretation analyst ID (or list
|
|
1772
|
+
of IDs separated by commas).
|
|
1773
|
+
:param str ci_analyst_name: Clinical interpretation analyst name (or
|
|
1774
|
+
list of names separated by commas).
|
|
1775
|
+
:param str ci_analyst_email: Clinical interpretation analyst e-mail
|
|
1776
|
+
(or list of e-mails separated by commas).
|
|
1777
|
+
:param str ci_analyst_assigned_by: Clinical interpretation analyst
|
|
1778
|
+
assignee name (or list of names separated by commas).
|
|
1779
|
+
:param str ci_analyst_date: Clinical interpretation analyst date (or
|
|
1780
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1781
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1782
|
+
20231001000000-20231101000000.
|
|
1783
|
+
:param str ci_method_name: Clinical interpretation method name (or
|
|
1784
|
+
list of names separated by commas).
|
|
1785
|
+
:param str ci_method_version: Clinical interpretation method version
|
|
1786
|
+
(or list of versions separated by commas).
|
|
1787
|
+
:param str ci_method_commit: Clinical interpretation method commit (or
|
|
1788
|
+
list of commits separated by commas).
|
|
1789
|
+
:param str ci_method_dependencies: Clinical interpretation method
|
|
1790
|
+
dependencies (word or list of words contained in the text, if the
|
|
1791
|
+
words are separated by a comma an OR will be applied; if the words
|
|
1792
|
+
are separated by a semicolon, an AND will be applied).
|
|
1793
|
+
:param str ci_comments: Clinical interpretation comment text (word or
|
|
1794
|
+
list of words contained in the text, if the words are separated by
|
|
1795
|
+
a comma an OR will be applied; if the words are separated by a
|
|
1796
|
+
semicolon, an AND will be applied).
|
|
1797
|
+
:param bool ci_locked: Clinical interpretation locked (true or false).
|
|
1798
|
+
:param str ci_status_id: Clinical interpretation status ID (or list of
|
|
1799
|
+
IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
|
|
1800
|
+
CLOSED.
|
|
1801
|
+
:param str ci_status_name: Clinical interpretation status name (or
|
|
1802
|
+
list of names separated by commas).
|
|
1803
|
+
:param str ci_status_description: Clinical interpretation status
|
|
1804
|
+
description (word or list of words contained in the text, if the
|
|
1805
|
+
words are separated by a comma an OR will be applied; if the words
|
|
1806
|
+
are separated by a semicolon, an AND will be applied).
|
|
1807
|
+
:param str ci_status_date: Clinical interpretation status date (or
|
|
1808
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1809
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1810
|
+
20231001000000-20231101000000.
|
|
1811
|
+
:param str ci_creation_date: Clinical interpretation creation date (or
|
|
1812
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1813
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1814
|
+
20231001000000-20231101000000.
|
|
1815
|
+
:param str ci_modification_date: Clinical interpretation modification
|
|
1816
|
+
date (or list of dates separated by commas), with format
|
|
1817
|
+
YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
|
|
1818
|
+
start_date-end_date, e.g.: 20231001000000-20231101000000.
|
|
1819
|
+
:param int ci_version: Clinical interpretation version number (or list
|
|
1820
|
+
of versions separated by commas).
|
|
1821
|
+
:param str cv_id: Clinical variant ID (or list of IDs separated by
|
|
1822
|
+
commas).
|
|
1823
|
+
:param str cv_variant_id: Variant ID (or list of IDs separated by
|
|
1824
|
+
commas).
|
|
1825
|
+
:param bool cv_primary_finding: Clinical variant is a primary finding
|
|
1826
|
+
(true or false).
|
|
1827
|
+
:param bool cv_primary_interpretation: Clinical variant belongs to the
|
|
1828
|
+
primary interpretation (true or false).
|
|
1829
|
+
:param str cv_comments: Clinical variant comment text (word or list of
|
|
1830
|
+
words contained in the text, if the words are separated by a comma
|
|
1831
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
1832
|
+
an AND will be applied).
|
|
1833
|
+
:param str cv_discussion_author: Clinical variant discussion author
|
|
1834
|
+
(or list of authors separated by commas).
|
|
1835
|
+
:param str cv_discussion_date: Clinical variant discussion date (or
|
|
1836
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1837
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1838
|
+
20231001000000-20231101000000.
|
|
1839
|
+
:param str cv_discussion_text: Clinical variant discussion text (word
|
|
1840
|
+
or list of words contained in the text, if the words are separated
|
|
1841
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
1842
|
+
semicolon, an AND will be applied).
|
|
1843
|
+
:param str cv_confidence_value: Clinical variant confidence value (or
|
|
1844
|
+
list of values separated by commas).
|
|
1845
|
+
:param str cv_confidence_author: Clinical variant confidence author
|
|
1846
|
+
(or list of authors separated by commas).
|
|
1847
|
+
:param str cv_confidence_date: Clinical variant confidence date (or
|
|
1848
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
1849
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
1850
|
+
20231001000000-20231101000000.
|
|
1851
|
+
:param str cv_tag: Clinical variant tag (or list of tags separated by
|
|
1852
|
+
commas).
|
|
1853
|
+
:param str cv_status: Clinical variant status (or list of status
|
|
1854
|
+
separated by commas).
|
|
1855
|
+
:param str cv_region: Variant region (or list of regions, these can be
|
|
1856
|
+
just a single chromosome name or regions in the format
|
|
1857
|
+
chr:start-end, e.g.: 2,3:100000-200000).
|
|
1858
|
+
:param str cv_biotype: Variant biotype, e.g. protein_coding (or list
|
|
1859
|
+
of biotypes separated by commas).
|
|
1860
|
+
:param str cv_ct: Variant SO consequence type (or list of SOs
|
|
1861
|
+
separated by commas), e.g. missense_variant,stop_lost or
|
|
1862
|
+
SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
|
|
1863
|
+
'protein_altering'.
|
|
1864
|
+
:param str cv_transcript_flag: Variant transcript flag (or list of
|
|
1865
|
+
flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
|
|
1866
|
+
Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
|
|
1867
|
+
:param str cv_gene: Variant gene (or list genes separated by commas),
|
|
1868
|
+
most gene IDs are accepted (HGNC, Ensembl gene, ...).
|
|
1869
|
+
:param str cv_xref: Variant external reference (or list of references
|
|
1870
|
+
separated by commas), these can be genes, proteins or variants.
|
|
1871
|
+
Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
|
|
1872
|
+
Cosmic, ...
|
|
1873
|
+
:param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
|
|
1874
|
+
(or list of roles separated by commas).
|
|
1875
|
+
:param str cv_type: Variant type or list of types, accepted values are
|
|
1876
|
+
SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
|
|
1877
|
+
COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
|
|
1878
|
+
TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
|
|
1879
|
+
:param str cv_protein_substitution: Variant protein substitution score
|
|
1880
|
+
(or list of scores separated by commas), include SIFT and PolyPhen.
|
|
1881
|
+
You can query using the score {protein_score}[<|>|<=|>=]{number} or
|
|
1882
|
+
the description {protein_score}[~=|=]{description} e.g.
|
|
1883
|
+
polyphen>0.1,sift=tolerant.
|
|
1884
|
+
:param str cv_conservation: Variant conservation score (or list of
|
|
1885
|
+
scores separated by commas) with the format
|
|
1886
|
+
{conservation_score}[<|>|<=|>=]{number} e.g.
|
|
1887
|
+
phastCons>0.5,phylop<0.1,gerp>0.1.
|
|
1888
|
+
:param str cv_functional_score: Variant functional score (or list of
|
|
1889
|
+
scores separated by commas) with the format
|
|
1890
|
+
{functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
|
|
1891
|
+
cadd_raw<=0.3.
|
|
1892
|
+
:param str cv_population_frequency_alt: Variant alternate population
|
|
1893
|
+
frequency (or list of frequencies separated by commas), with the
|
|
1894
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1895
|
+
1000G:ALL<0.01.
|
|
1896
|
+
:param str cv_population_frequency_maf: Variant population minor
|
|
1897
|
+
allele frequency (or list of frequencies separated by commas), with
|
|
1898
|
+
the format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1899
|
+
1000G:ALL<0.01.
|
|
1900
|
+
:param str cv_population_frequency_ref: Variant reference population
|
|
1901
|
+
frequency (or list of frequences separated by commas), with the
|
|
1902
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
1903
|
+
1000G:ALL<0.01.
|
|
1904
|
+
:param str cv_cohort_stats_alt: Variant alternate allele frequency (or
|
|
1905
|
+
list of frequencies separated by commas), with the format
|
|
1906
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1907
|
+
:param str cv_cohort_stats_maf: Variant minor allele frequency (or
|
|
1908
|
+
list of frequencies separated by commas), with the format
|
|
1909
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1910
|
+
:param str cv_cohort_stats_ref: Variant reference allele frequency (or
|
|
1911
|
+
list of frequencies separated by commas), with the foramt
|
|
1912
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
1913
|
+
:param str cv_cohort_stats_pass: Variant filter PASS frequency (or
|
|
1914
|
+
list of frequencies separated by commas), with the format
|
|
1915
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
|
|
1916
|
+
:param str cv_score: Variant score (or list of scores separated by
|
|
1917
|
+
commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
|
|
1918
|
+
:param str cv_annot_go_genes: Variant gene GO (or list of GOs
|
|
1919
|
+
separated by commas).
|
|
1920
|
+
:param str cv_annot_expression_genes: Variant gene expression (or list
|
|
1921
|
+
of expressions separated by commas).
|
|
1922
|
+
:param str cv_gene_trait_id: Variant gene trait association ID (or
|
|
1923
|
+
list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
|
|
1924
|
+
'OMIM:269600'.
|
|
1925
|
+
:param str cv_trait: Variant Trait (or list of traits separated by
|
|
1926
|
+
commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
|
|
1927
|
+
descriptions,...
|
|
1928
|
+
:param str cv_protein_keyword: Uniprot protein variant annotation
|
|
1929
|
+
keyword (or list of keywords separated by commas).
|
|
1930
|
+
:param str cve_variant_id: Variant ID (or list of IDs separated by
|
|
1931
|
+
commas).
|
|
1932
|
+
:param bool cve_primary_finding: Clinical variant evidence belongs to
|
|
1933
|
+
a primary finding (true or false).
|
|
1934
|
+
:param bool cve_primary_interpretation: Clinical variant evidence
|
|
1935
|
+
belongs to the primary interpretation (true or false).
|
|
1936
|
+
:param str cve_phenotype_name: Clinical variant evidence phenotype
|
|
1937
|
+
name (or names separated by commas).
|
|
1938
|
+
:param str cve_gene_name: Clinical variant evidence gene name (or
|
|
1939
|
+
names separated by commas).
|
|
1940
|
+
:param str cve_transcript_id: Clinical variant evidence transcript ID
|
|
1941
|
+
(or IDs separated by commas).
|
|
1942
|
+
:param str cve_so_term_name: Clinical variant evidence sequence
|
|
1943
|
+
ontology name (or names separated by commas).
|
|
1944
|
+
:param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
|
|
1945
|
+
separated by commas).
|
|
1946
|
+
:param str cve_panel_id: Clinical variant evidence panel ID (or IDs
|
|
1947
|
+
separated by commas).
|
|
1948
|
+
:param str cve_moi: Clinical variant evidence mode of inheritance (or
|
|
1949
|
+
list of modes of inheritance separated by commas), valid values:
|
|
1950
|
+
AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
|
|
1951
|
+
X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
|
|
1952
|
+
MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
|
|
1953
|
+
:param str cve_penetrance: Clinical variant evidence penetrance (or
|
|
1954
|
+
list of penetrance values separated by commas), valid values:
|
|
1955
|
+
COMPLETE, INCOMPLETE, UNKNOWN.
|
|
1956
|
+
:param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
|
|
1957
|
+
separated by commas).
|
|
1958
|
+
:param str cve_tier: Clinical variant evidence tier (or list of tier
|
|
1959
|
+
values separated by commas).
|
|
1960
|
+
:param str cve_clinical_significance: Clinical variant evidence
|
|
1961
|
+
clinical significance (or list of clinical significances separated
|
|
1962
|
+
by commas).
|
|
1963
|
+
:param str cve_drug_response: Clinical variant evidence drug response
|
|
1964
|
+
(or list of drug responses separated by commas).
|
|
1965
|
+
:param str cve_trait_association: Clinical variant evidence trait
|
|
1966
|
+
association (or list of traits separated by commas).
|
|
1967
|
+
:param str cve_functional_effect: Clinical variant evidence functional
|
|
1968
|
+
effect (or list of functional effects separated by commas).
|
|
1969
|
+
:param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
|
|
1970
|
+
(or list of tumorigenesis values separated by commas).
|
|
1971
|
+
:param str cve_other_classification: Clinical variant evidence
|
|
1972
|
+
other-classification (or list of other classification values
|
|
1973
|
+
separated by commas).
|
|
1974
|
+
:param str cve_role_in_cancer: Clinical variant evidence role in
|
|
1975
|
+
cancer (or roles in cancer separated by commas).
|
|
1976
|
+
:param str cve_review_acmg: Clinical variant evidence review ACMG (or
|
|
1977
|
+
ACGMs separated by commas).
|
|
1978
|
+
:param str cve_review_tier: Clinical variant evidence review tier (or
|
|
1979
|
+
list of tier values separated by commas).
|
|
1980
|
+
:param str cve_review_clinical_significance: Clinical variant evidence
|
|
1981
|
+
review clinical significance (or list of clinical significances
|
|
1982
|
+
separated by commas).
|
|
1983
|
+
:param str cve_review_text: Clinical variant evidence review text
|
|
1984
|
+
(word or list of words contained in the text, if the words are
|
|
1985
|
+
separated by a comma an OR will be applied; if the words are
|
|
1986
|
+
separated by a semicolon, an AND will be applied).
|
|
1987
|
+
:param str field: List of facet fields separated by semicolons, e.g.:
|
|
1988
|
+
type;biotypes. For nested faceted fields use >>, e.g.:
|
|
1989
|
+
type>>biotypes. Accepted values: caId, ciId, variantId, studyId,
|
|
1990
|
+
primary, discussionAuthor, discussionDate,discussionText,
|
|
1991
|
+
confidenceValue, confidenceAuthor, confidenceDate, tags, status,
|
|
1992
|
+
chromosome, start, end, xrefs, type, release, studies, phastCons,
|
|
1993
|
+
phylop, gerp, caddRaw, caddScaled, sift, siftDesc, polyphen,
|
|
1994
|
+
polyphenDesc, genes, biotypes, soAcc, clinicalSig.
|
|
1995
|
+
"""
|
|
1996
|
+
|
|
1997
|
+
return self._get(category='analysis', resource='aggregate', subcategory='cvdb/variant', **options)
|
|
1998
|
+
|
|
1999
|
+
def query_variant(self, **options):
|
|
2000
|
+
"""
|
|
2001
|
+
Filter and fetch clinical variants from CVDB.
|
|
2002
|
+
PATH: /{apiVersion}/analysis/cvdb/variant/query
|
|
2003
|
+
|
|
2004
|
+
:param str project: Project ID.
|
|
2005
|
+
:param str study: Study ID (or list of study IDs separated by commas).
|
|
2006
|
+
:param str include: Fields included in the response, whole JSON path
|
|
2007
|
+
must be provided.
|
|
2008
|
+
:param str exclude: Fields excluded in the response, whole JSON path
|
|
2009
|
+
must be provided.
|
|
2010
|
+
:param int limit: Number of results to be returned.
|
|
2011
|
+
:param int skip: Number of results to skip.
|
|
2012
|
+
:param str ca_id: Clinical analysis ID (or list of IDs separated by
|
|
2013
|
+
commas).
|
|
2014
|
+
:param str ca_description: Clinical analysis description (word or list
|
|
2015
|
+
of words contained in the text, if the words are separated by a
|
|
2016
|
+
comma an OR will be applied; if the words are separated by a
|
|
2017
|
+
semicolon, an AND will be applied).
|
|
2018
|
+
:param str ca_type: Clinical analysis type (or list of types separated
|
|
2019
|
+
by commas).
|
|
2020
|
+
:param str ca_disorder_id: Clinical analysis disorder ID (or list of
|
|
2021
|
+
IDs separated by commas).
|
|
2022
|
+
:param str ca_filename: Clinical analysis filename (or list of
|
|
2023
|
+
filenames separated by commas).
|
|
2024
|
+
:param str ca_proband_id: Clinical analysis proband ID (or list of IDs
|
|
2025
|
+
separated by commas).
|
|
2026
|
+
:param str ca_proband_disorder_id: Clinical analysis proband disorder
|
|
2027
|
+
ID (or list of disorder IDs separated by commas).
|
|
2028
|
+
:param str ca_proband_phenotype_name: Clinical analysis proband
|
|
2029
|
+
phenotype name (or list of phenotype names separated by commas).
|
|
2030
|
+
:param str ca_family_id: Clinical analysis family ID (or list of IDs
|
|
2031
|
+
separated by commas).
|
|
2032
|
+
:param str ca_family_phenotype_name: Clinical analysis family
|
|
2033
|
+
phenotype names (or list of names separated by commas).
|
|
2034
|
+
:param str ca_family_member_id: Clinical analysis family member ID (or
|
|
2035
|
+
list of IDs separated by commas).
|
|
2036
|
+
:param str ca_report: Clinical analysis report text (word or list of
|
|
2037
|
+
words contained in the text, if the words are separated by a comma
|
|
2038
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
2039
|
+
an AND will be applied).
|
|
2040
|
+
:param str ca_status: Clinical analysis status (or list of status
|
|
2041
|
+
separated by commas).
|
|
2042
|
+
:param bool ca_locked: Clinical analysis locked (true or false).
|
|
2043
|
+
:param str ci_id: Clinical interpretation ID (or list of IDs separated
|
|
2044
|
+
by commas).
|
|
2045
|
+
:param bool ci_primary: Clinical interpretation primary (true or
|
|
2046
|
+
false).
|
|
2047
|
+
:param str ci_description: Clinical interpretation description (word
|
|
2048
|
+
or list of words contained in the text, if the words are separated
|
|
2049
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
2050
|
+
semicolon, an AND will be applied).
|
|
2051
|
+
:param str ci_panel_id: Clinical interpretation panel ID or name (or
|
|
2052
|
+
list of IDs or names separated by commas).
|
|
2053
|
+
:param str ci_analyst_id: Clinical interpretation analyst ID (or list
|
|
2054
|
+
of IDs separated by commas).
|
|
2055
|
+
:param str ci_analyst_name: Clinical interpretation analyst name (or
|
|
2056
|
+
list of names separated by commas).
|
|
2057
|
+
:param str ci_analyst_email: Clinical interpretation analyst e-mail
|
|
2058
|
+
(or list of e-mails separated by commas).
|
|
2059
|
+
:param str ci_analyst_assigned_by: Clinical interpretation analyst
|
|
2060
|
+
assignee name (or list of names separated by commas).
|
|
2061
|
+
:param str ci_analyst_date: Clinical interpretation analyst date (or
|
|
2062
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
2063
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
2064
|
+
20231001000000-20231101000000.
|
|
2065
|
+
:param str ci_method_name: Clinical interpretation method name (or
|
|
2066
|
+
list of names separated by commas).
|
|
2067
|
+
:param str ci_method_version: Clinical interpretation method version
|
|
2068
|
+
(or list of versions separated by commas).
|
|
2069
|
+
:param str ci_method_commit: Clinical interpretation method commit (or
|
|
2070
|
+
list of commits separated by commas).
|
|
2071
|
+
:param str ci_method_dependencies: Clinical interpretation method
|
|
2072
|
+
dependencies (word or list of words contained in the text, if the
|
|
2073
|
+
words are separated by a comma an OR will be applied; if the words
|
|
2074
|
+
are separated by a semicolon, an AND will be applied).
|
|
2075
|
+
:param str ci_comments: Clinical interpretation comment text (word or
|
|
2076
|
+
list of words contained in the text, if the words are separated by
|
|
2077
|
+
a comma an OR will be applied; if the words are separated by a
|
|
2078
|
+
semicolon, an AND will be applied).
|
|
2079
|
+
:param bool ci_locked: Clinical interpretation locked (true or false).
|
|
2080
|
+
:param str ci_status_id: Clinical interpretation status ID (or list of
|
|
2081
|
+
IDs separated by commas). Valid values: NOT_STARTED, ACTIVE, DONE,
|
|
2082
|
+
CLOSED.
|
|
2083
|
+
:param str ci_status_name: Clinical interpretation status name (or
|
|
2084
|
+
list of names separated by commas).
|
|
2085
|
+
:param str ci_status_description: Clinical interpretation status
|
|
2086
|
+
description (word or list of words contained in the text, if the
|
|
2087
|
+
words are separated by a comma an OR will be applied; if the words
|
|
2088
|
+
are separated by a semicolon, an AND will be applied).
|
|
2089
|
+
:param str ci_status_date: Clinical interpretation status date (or
|
|
2090
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
2091
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
2092
|
+
20231001000000-20231101000000.
|
|
2093
|
+
:param str ci_creation_date: Clinical interpretation creation date (or
|
|
2094
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
2095
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
2096
|
+
20231001000000-20231101000000.
|
|
2097
|
+
:param str ci_modification_date: Clinical interpretation modification
|
|
2098
|
+
date (or list of dates separated by commas), with format
|
|
2099
|
+
YYYYMMDDhhmmss, e.g.: 20231026120345; range is available
|
|
2100
|
+
start_date-end_date, e.g.: 20231001000000-20231101000000.
|
|
2101
|
+
:param int ci_version: Clinical interpretation version number (or list
|
|
2102
|
+
of versions separated by commas).
|
|
2103
|
+
:param str cv_id: Clinical variant ID (or list of IDs separated by
|
|
2104
|
+
commas).
|
|
2105
|
+
:param str cv_variant_id: Variant ID (or list of IDs separated by
|
|
2106
|
+
commas).
|
|
2107
|
+
:param bool cv_primary_finding: Clinical variant is a primary finding
|
|
2108
|
+
(true or false).
|
|
2109
|
+
:param bool cv_primary_interpretation: Clinical variant belongs to the
|
|
2110
|
+
primary interpretation (true or false).
|
|
2111
|
+
:param str cv_comments: Clinical variant comment text (word or list of
|
|
2112
|
+
words contained in the text, if the words are separated by a comma
|
|
2113
|
+
an OR will be applied; if the words are separated by a semicolon,
|
|
2114
|
+
an AND will be applied).
|
|
2115
|
+
:param str cv_discussion_author: Clinical variant discussion author
|
|
2116
|
+
(or list of authors separated by commas).
|
|
2117
|
+
:param str cv_discussion_date: Clinical variant discussion date (or
|
|
2118
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
2119
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
2120
|
+
20231001000000-20231101000000.
|
|
2121
|
+
:param str cv_discussion_text: Clinical variant discussion text (word
|
|
2122
|
+
or list of words contained in the text, if the words are separated
|
|
2123
|
+
by a comma an OR will be applied; if the words are separated by a
|
|
2124
|
+
semicolon, an AND will be applied).
|
|
2125
|
+
:param str cv_confidence_value: Clinical variant confidence value (or
|
|
2126
|
+
list of values separated by commas).
|
|
2127
|
+
:param str cv_confidence_author: Clinical variant confidence author
|
|
2128
|
+
(or list of authors separated by commas).
|
|
2129
|
+
:param str cv_confidence_date: Clinical variant confidence date (or
|
|
2130
|
+
list of dates separated by commas), with format YYYYMMDDhhmmss,
|
|
2131
|
+
e.g.: 20231026120345; range is available start_date-end_date, e.g.:
|
|
2132
|
+
20231001000000-20231101000000.
|
|
2133
|
+
:param str cv_tag: Clinical variant tag (or list of tags separated by
|
|
2134
|
+
commas).
|
|
2135
|
+
:param str cv_status: Clinical variant status (or list of status
|
|
2136
|
+
separated by commas).
|
|
2137
|
+
:param str cv_region: Variant region (or list of regions, these can be
|
|
2138
|
+
just a single chromosome name or regions in the format
|
|
2139
|
+
chr:start-end, e.g.: 2,3:100000-200000).
|
|
2140
|
+
:param str cv_biotype: Variant biotype, e.g. protein_coding (or list
|
|
2141
|
+
of biotypes separated by commas).
|
|
2142
|
+
:param str cv_ct: Variant SO consequence type (or list of SOs
|
|
2143
|
+
separated by commas), e.g. missense_variant,stop_lost or
|
|
2144
|
+
SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and
|
|
2145
|
+
'protein_altering'.
|
|
2146
|
+
:param str cv_transcript_flag: Variant transcript flag (or list of
|
|
2147
|
+
flags separated by commas), e.g. canonical, CCDS, basic, LRG, MANE
|
|
2148
|
+
Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
|
|
2149
|
+
:param str cv_gene: Variant gene (or list genes separated by commas),
|
|
2150
|
+
most gene IDs are accepted (HGNC, Ensembl gene, ...).
|
|
2151
|
+
:param str cv_xref: Variant external reference (or list of references
|
|
2152
|
+
separated by commas), these can be genes, proteins or variants.
|
|
2153
|
+
Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO,
|
|
2154
|
+
Cosmic, ...
|
|
2155
|
+
:param str cv_annot_role_in_cancer_genes: Variant rol in cancer genes
|
|
2156
|
+
(or list of roles separated by commas).
|
|
2157
|
+
:param str cv_type: Variant type or list of types, accepted values are
|
|
2158
|
+
SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS,
|
|
2159
|
+
COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION,
|
|
2160
|
+
TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
|
|
2161
|
+
:param str cv_protein_substitution: Variant protein substitution score
|
|
2162
|
+
(or list of scores separated by commas), include SIFT and PolyPhen.
|
|
2163
|
+
You can query using the score {protein_score}[<|>|<=|>=]{number} or
|
|
2164
|
+
the description {protein_score}[~=|=]{description} e.g.
|
|
2165
|
+
polyphen>0.1,sift=tolerant.
|
|
2166
|
+
:param str cv_conservation: Variant conservation score (or list of
|
|
2167
|
+
scores separated by commas) with the format
|
|
2168
|
+
{conservation_score}[<|>|<=|>=]{number} e.g.
|
|
2169
|
+
phastCons>0.5,phylop<0.1,gerp>0.1.
|
|
2170
|
+
:param str cv_functional_score: Variant functional score (or list of
|
|
2171
|
+
scores separated by commas) with the format
|
|
2172
|
+
{functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 ,
|
|
2173
|
+
cadd_raw<=0.3.
|
|
2174
|
+
:param str cv_population_frequency_alt: Variant alternate population
|
|
2175
|
+
frequency (or list of frequencies separated by commas), with the
|
|
2176
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
2177
|
+
1000G:ALL<0.01.
|
|
2178
|
+
:param str cv_population_frequency_maf: Variant population minor
|
|
2179
|
+
allele frequency (or list of frequencies separated by commas), with
|
|
2180
|
+
the format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
2181
|
+
1000G:ALL<0.01.
|
|
2182
|
+
:param str cv_population_frequency_ref: Variant reference population
|
|
2183
|
+
frequency (or list of frequences separated by commas), with the
|
|
2184
|
+
format {study}:{population}[<|>|<=|>=]{number}. e.g.
|
|
2185
|
+
1000G:ALL<0.01.
|
|
2186
|
+
:param str cv_cohort_stats_alt: Variant alternate allele frequency (or
|
|
2187
|
+
list of frequencies separated by commas), with the format
|
|
2188
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
2189
|
+
:param str cv_cohort_stats_maf: Variant minor allele frequency (or
|
|
2190
|
+
list of frequencies separated by commas), with the format
|
|
2191
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
2192
|
+
:param str cv_cohort_stats_ref: Variant reference allele frequency (or
|
|
2193
|
+
list of frequencies separated by commas), with the foramt
|
|
2194
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
|
|
2195
|
+
:param str cv_cohort_stats_pass: Variant filter PASS frequency (or
|
|
2196
|
+
list of frequencies separated by commas), with the format
|
|
2197
|
+
[{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
|
|
2198
|
+
:param str cv_score: Variant score (or list of scores separated by
|
|
2199
|
+
commas), with the format: [{study:}]{score}[<|>|<=|>=]{number}.
|
|
2200
|
+
:param str cv_annot_go_genes: Variant gene GO (or list of GOs
|
|
2201
|
+
separated by commas).
|
|
2202
|
+
:param str cv_annot_expression_genes: Variant gene expression (or list
|
|
2203
|
+
of expressions separated by commas).
|
|
2204
|
+
:param str cv_gene_trait_id: Variant gene trait association ID (or
|
|
2205
|
+
list of trait IDs separated by commas), e.g. 'umls:C0007222' ,
|
|
2206
|
+
'OMIM:269600'.
|
|
2207
|
+
:param str cv_trait: Variant Trait (or list of traits separated by
|
|
2208
|
+
commas), based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies,
|
|
2209
|
+
descriptions,...
|
|
2210
|
+
:param str cv_protein_keyword: Uniprot protein variant annotation
|
|
2211
|
+
keyword (or list of keywords separated by commas).
|
|
2212
|
+
:param str cve_variant_id: Variant ID (or list of IDs separated by
|
|
2213
|
+
commas).
|
|
2214
|
+
:param bool cve_primary_finding: Clinical variant evidence belongs to
|
|
2215
|
+
a primary finding (true or false).
|
|
2216
|
+
:param bool cve_primary_interpretation: Clinical variant evidence
|
|
2217
|
+
belongs to the primary interpretation (true or false).
|
|
2218
|
+
:param str cve_phenotype_name: Clinical variant evidence phenotype
|
|
2219
|
+
name (or names separated by commas).
|
|
2220
|
+
:param str cve_gene_name: Clinical variant evidence gene name (or
|
|
2221
|
+
names separated by commas).
|
|
2222
|
+
:param str cve_transcript_id: Clinical variant evidence transcript ID
|
|
2223
|
+
(or IDs separated by commas).
|
|
2224
|
+
:param str cve_so_term_name: Clinical variant evidence sequence
|
|
2225
|
+
ontology name (or names separated by commas).
|
|
2226
|
+
:param str cve_xref_id: Clinical variant evidence Xref ID (or IDs
|
|
2227
|
+
separated by commas).
|
|
2228
|
+
:param str cve_panel_id: Clinical variant evidence panel ID (or IDs
|
|
2229
|
+
separated by commas).
|
|
2230
|
+
:param str cve_moi: Clinical variant evidence mode of inheritance (or
|
|
2231
|
+
list of modes of inheritance separated by commas), valid values:
|
|
2232
|
+
AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_LINKED_DOMINANT,
|
|
2233
|
+
X_LINKED_RECESSIVE, Y_LINKED, MITOCHONDRIAL, DE_NOVO,
|
|
2234
|
+
MENDELIAN_ERROR, COMPOUND_HETEROZYGOUS, UNKNOWN.
|
|
2235
|
+
:param str cve_penetrance: Clinical variant evidence penetrance (or
|
|
2236
|
+
list of penetrance values separated by commas), valid values:
|
|
2237
|
+
COMPLETE, INCOMPLETE, UNKNOWN.
|
|
2238
|
+
:param str cve_acmg: Clinical variant evidence ACMG (or ACGMs
|
|
2239
|
+
separated by commas).
|
|
2240
|
+
:param str cve_tier: Clinical variant evidence tier (or list of tier
|
|
2241
|
+
values separated by commas).
|
|
2242
|
+
:param str cve_clinical_significance: Clinical variant evidence
|
|
2243
|
+
clinical significance (or list of clinical significances separated
|
|
2244
|
+
by commas).
|
|
2245
|
+
:param str cve_drug_response: Clinical variant evidence drug response
|
|
2246
|
+
(or list of drug responses separated by commas).
|
|
2247
|
+
:param str cve_trait_association: Clinical variant evidence trait
|
|
2248
|
+
association (or list of traits separated by commas).
|
|
2249
|
+
:param str cve_functional_effect: Clinical variant evidence functional
|
|
2250
|
+
effect (or list of functional effects separated by commas).
|
|
2251
|
+
:param str cve_tumorigenesis: Clinical variant evidence tumorigenesis
|
|
2252
|
+
(or list of tumorigenesis values separated by commas).
|
|
2253
|
+
:param str cve_other_classification: Clinical variant evidence
|
|
2254
|
+
other-classification (or list of other classification values
|
|
2255
|
+
separated by commas).
|
|
2256
|
+
:param str cve_role_in_cancer: Clinical variant evidence role in
|
|
2257
|
+
cancer (or roles in cancer separated by commas).
|
|
2258
|
+
:param str cve_review_acmg: Clinical variant evidence review ACMG (or
|
|
2259
|
+
ACGMs separated by commas).
|
|
2260
|
+
:param str cve_review_tier: Clinical variant evidence review tier (or
|
|
2261
|
+
list of tier values separated by commas).
|
|
2262
|
+
:param str cve_review_clinical_significance: Clinical variant evidence
|
|
2263
|
+
review clinical significance (or list of clinical significances
|
|
2264
|
+
separated by commas).
|
|
2265
|
+
:param str cve_review_text: Clinical variant evidence review text
|
|
2266
|
+
(word or list of words contained in the text, if the words are
|
|
2267
|
+
separated by a comma an OR will be applied; if the words are
|
|
2268
|
+
separated by a semicolon, an AND will be applied).
|
|
2269
|
+
"""
|
|
2270
|
+
|
|
2271
|
+
return self._get(category='analysis', resource='query', subcategory='cvdb/variant', **options)
|
|
2272
|
+
|
|
2273
|
+
def stats_variant(self, variant_id, **options):
|
|
2274
|
+
"""
|
|
2275
|
+
Get clinical variant summary from CVDB.
|
|
2276
|
+
PATH: /{apiVersion}/analysis/cvdb/variant/{variantId}/stats
|
|
2277
|
+
|
|
2278
|
+
:param str variant_id: Variant ID (or comma separated list of variant
|
|
2279
|
+
IDs). (REQUIRED)
|
|
2280
|
+
:param str project: Project ID(or command separated list of project
|
|
2281
|
+
IDs).
|
|
2282
|
+
"""
|
|
2283
|
+
|
|
2284
|
+
return self._get(category='analysis', resource='stats', subcategory='cvdb/variant', second_query_id=variant_id, **options)
|
|
2285
|
+
|