genotype_browser package

Module contents

Genotype browser routes for browsing and listing variants in studies.

class genotype_browser.views.GenotypeBrowserQueryView

Bases: QueryDatasetView

Genotype browser queries view.

MAX_SHOWN_VARIANTS = 1000

post(request: Request) → Response

Query for variants from a dataset.

Request:

POST /genotype_browser/preview/variants HTTP/1.1 Host: example.com Content-Type: application/json Accept: text/event-stream

{

“datasetId”: “iossifov_2014”, “maxVariantsCount”: 1000

}

Response:

HTTP/1.1 200 OK Vary: Accept Content-Type: text/event-stream [

[col1,col2,col3,col4…..]

,

[col1,col2,col3,col4…..]

,

[col1,col2,col3,col4…..]

]

Status codes:

200: Successfully fetched variants 403: User has no permissions for dataset 400: Invalid request body 404: Dataset does not exist

Request JSON parameters:

datasetId (string): ID of the dataset to query. download (boolean): Change response type for easier download. genomicScores (json): Genomic score range filter. maxVariantsCount (integer): Maximum amount of variants to query. sources (list): List of name-source objects: columns to fetch. summaryVariantIds (list): List of summary variant IDs for filter. querySummary (boolean): True if should query only summary variants. uniqueFamilyVariants (boolean): Query for unique variants only. regions (list): List of regions as strings to filter with. presentInChild (json): Roles object to filter with. presentInParent (json): Roles object to filter with. inheritanceTypeFilter (list): Inheritance filtering. geneScores (list): Gene score range filter. gender (list): Gender filter. variantTypes (list): Filter by variant type. effectTypes (list): Filter by effect type. studyFilters (list): Filter by study ID (dataset only). personFilters (list): Filter with person filters. familyFilters (list): Filter with family filters. personIds (list): Filter by person IDs. familyTypes (list): Filter by family type. familyIds (list): Filter by family IDs. affectedStatus (list): Filter by affected status. tagIntersection (boolean): Change Family tags interesection mode selectedFamilyTags (list): Family tags to include deselectedFamilyTags (list): Family tags to exlude