browser_handlers

Request handlers for the variant browser.

class Autocomplete(application: tornado.web.Application, request: tornado.httputil.HTTPServerRequest, **kwargs)

Bases: handlers.UnsafeHandler

Provide autocompletion for protein names based on current query.

get(dataset: str, query: str, ds_version: str = None)

Provide autocompletion for protein names based on current query.

Parameters:

• dataset (str) – dataset short name
• query (str) – query
• ds_version (str) – dataset version

class Download(application: tornado.web.Application, request: tornado.httputil.HTTPServerRequest, **kwargs)

Bases: handlers.UnsafeHandler

Download variants in CSV format.

get(dataset: str, datatype: str, item: str, ds_version: str = None, filter_type: str = None)

Download variants in CSV format.

Will filter the variants if filter_type is provided.

Parameters:

• dataset (str) – dataset short name
• datatype (str) – type of data
• item (str) – query item
• ds_version (str) – dataset version
• filter_type (str) – type of filter to apply

class GetCoverage(application: tornado.web.Application, request: tornado.httputil.HTTPServerRequest, **kwargs)

Bases: handlers.UnsafeHandler

Retrieve coverage.

get(dataset: str, datatype: str, item: str, ds_version: str = None)

Retrieve coverage.

Parameters:

• dataset (str) – dataset short name
• datatype (str) – type of data
• item (str) – query item
• ds_version (str) – dataset version

class GetCoveragePos(application: tornado.web.Application, request: tornado.httputil.HTTPServerRequest, **kwargs)

Bases: handlers.UnsafeHandler

Retrieve coverage range.

get(dataset: str, datatype: str, item: str, ds_version: str = None)

Retrieve coverage range.

Parameters:

• dataset (str) – dataset short name
• datatype (str) – type of data
• item (str) – query item
• ds_version (str) – dataset version

class GetGene(application: tornado.web.Application, request: tornado.httputil.HTTPServerRequest, **kwargs)

Bases: handlers.UnsafeHandler

Request information about a gene.

get(dataset: str, gene: str, ds_version: str = None)

Request information about a gene.

Parameters:

• dataset (str) – short name of the dataset
• gene (str) – the gene id
• ds_version (str) – dataset version

class GetRegion(application: tornado.web.Application, request: tornado.httputil.HTTPServerRequest, **kwargs)

Bases: handlers.UnsafeHandler

Request information about genes in a region.

get(dataset: str, region: str, ds_version: str = None)

Request information about genes in a region.

Parameters:

• dataset (str) – short name of the dataset
• region (str) – the region in the format chr-startpos-endpos
• ds_version (str) – dataset version

class GetTranscript(application: tornado.web.Application, request: tornado.httputil.HTTPServerRequest, **kwargs)

Bases: handlers.UnsafeHandler

Request information about a transcript.

get(dataset: str, transcript: str, ds_version: str = None)

Request information about a transcript.

Parameters:

• dataset (str) – short name of the dataset
• transcript (str) – the transcript id

Returns:

transcript (transcript and exons), gene (gene information)

Return type:

dict

class GetVariant(application: tornado.web.Application, request: tornado.httputil.HTTPServerRequest, **kwargs)

Bases: handlers.UnsafeHandler

Request information about a gene.

get(dataset: str, variant: str, ds_version: str = None)

Request information about a gene.

Parameters:

• dataset (str) – short name of the dataset
• variant (str) – variant in the format chrom-pos-ref-alt

class GetVariants(application: tornado.web.Application, request: tornado.httputil.HTTPServerRequest, **kwargs)

Bases: handlers.UnsafeHandler

Retrieve variants.

get(dataset: str, datatype: str, item: str, ds_version: str = None)

Retrieve variants.

Parameters:

• dataset (str) – short name of the dataset
• datatype (str) – gene, region, or transcript
• item (str) – item to query

class Search(application: tornado.web.Application, request: tornado.httputil.HTTPServerRequest, **kwargs)

Bases: handlers.UnsafeHandler

Perform a search for the wanted object.

get(dataset: str, query: str, ds_version: str = None)

Perform a search for the wanted object.

Parameters:

• dataset (str) – short name of the dataset
• query (str) – search query