BBClient Module

bbclient

Classes

BBClient

BBClient(cache_folder=DEFAULT_CACHE_FOLDER, bedbase_api=DEFAULT_BEDBASE_API)

Bases: BedCacheManager

BBClient to deal with download files from bedbase and caching them.

Parameters:

Name	Type	Description	Default
`cache_folder`	`Union[str, PathLike]`	path to local folder as cache of files from bedbase, if not given it will be the environment variable `BBCLIENT_CACHE`	`DEFAULT_CACHE_FOLDER`
`bedbase_api`	`str`	url to bedbase	`DEFAULT_BEDBASE_API`

Functions

load_bedset

load_bedset(bedset_id)

Load a BEDset from cache, or download and add it to the cache with its BED files

Parameters:

Name	Type	Description	Default
`bedset_id`	`str`	unique identifier of a BED set	required

Returns:

Type	Description
`BedSet`	the BedSet object

load_bed

load_bed(bed_id)

Loads a BED file from cache, or downloads and caches it if it doesn't exist

Parameters:

Name	Type	Description	Default
`bed_id`	`str`	unique identifier of a BED file	required

Returns:

Type	Description
`RegionSet`	the RegionSet object

add_bedset_to_cache

add_bedset_to_cache(bedset)

Add a BED set to the cache

Parameters:

Name	Type	Description	Default
`bedset`	`BedSet`	the BED set to be added, a BedSet class	required

Returns:

Type	Description
`str`	the identifier if the BedSet object

add_bed_to_cache

add_bed_to_cache(bedfile, force=False)

Add a BED file to the cache

Parameters:

Name	Type	Description	Default
`bedfile`	`Union[RegionSet, str]`	a RegionSet object or a path or url to the BED file	required
`force`	`bool`	whether to overwrite the existing file in cache	`False`

Returns:

Type	Description
`RegionSet`	the RegionSet identifier

add_bed_tokens_to_cache

add_bed_tokens_to_cache(bed_id, universe_id)

Add a tokenized BED file to the cache

Parameters:

Name	Type	Description	Default
`bed_id`	`str`	the identifier of the BED file	required
`universe_id`	`str`	the identifier of the universe	required

Returns:

Type	Description
`None`	the identifier of the tokenized BED file

load_bed_tokens

load_bed_tokens(bed_id, universe_id)

Load a tokenized BED file from cache, or download and cache it if it doesn't exist

Parameters:

Name	Type	Description	Default
`bed_id`	`str`	the identifier of the BED file	required
`universe_id`	`str`	the identifier of the universe	required

Returns:

Type	Description
`Array`	the zarr array of tokens

remove_tokens

remove_tokens(bed_id, universe_id)

Remove all tokenized BED files from cache

cache_tokens

cache_tokens(bed_id, universe_id, tokens)

Cache tokenized BED file

Parameters:

Name	Type	Description	Default
`bed_id`	`str`	the identifier of the BED file	required
`universe_id`	`str`	the identifier of the universe	required
`tokens`	`Union[list, Array]`	the list of tokens	required

Returns:

Type	Description
`None`	None

add_bed_to_s3

add_bed_to_s3(identifier, bucket=DEFAULT_BUCKET_NAME, endpoint_url=None, aws_access_key_id=None, aws_secret_access_key=None, s3_path=DEFAULT_BUCKET_FOLDER)

Add a cached BED file to S3

Parameters:

Name	Type	Description	Default
`identifier`	`str`	the unique identifier of the BED file	required
`bucket`	`str`	the name of the bucket	`DEFAULT_BUCKET_NAME`
`endpoint_url`	`str`	the URL of the S3 endpoint [Default: set up by the environment vars]	`None`
`aws_access_key_id`	`str`	the access key of the AWS account [Default: set up by the environment vars]	`None`
`aws_secret_access_key`	`str`	the secret access key of the AWS account [Default: set up by the environment vars]	`None`
`s3_path`	`str`	the path on S3	`DEFAULT_BUCKET_FOLDER`

Returns:

Type	Description
`str`	full path on S3

get_bed_from_s3

get_bed_from_s3(identifier, bucket=DEFAULT_BUCKET_NAME, endpoint_url=None, aws_access_key_id=None, aws_secret_access_key=None, s3_path=DEFAULT_BUCKET_FOLDER)

Get a cached BED file from S3 and cache it locally

Parameters:

Name	Type	Description	Default
`identifier`	`str`	the unique identifier of the BED file	required
`bucket`	`str`	the name of the bucket	`DEFAULT_BUCKET_NAME`
`endpoint_url`	`str`	the URL of the S3 endpoint [Default: set up by the environment vars]	`None`
`aws_access_key_id`	`str`	the access key of the AWS account [Default: set up by the environment vars]	`None`
`aws_secret_access_key`	`str`	the secret access key of the AWS account [Default: set up by the environment vars]	`None`
`s3_path`	`str`	the path on S3	`DEFAULT_BUCKET_FOLDER`

Returns:

Type	Description
`str`	bed file id

Raises:

Type	Description
`FileNotFoundError`	if the identifier does not exist in cache

seek

seek(identifier)

Get local path to BED file or BED set with specific identifier

Parameters:

Name	Type	Description	Default
`identifier`	`str`	the unique identifier	required

Returns:

Type	Description
`str`	the local path of the file

Raises:

Type	Description
`FileNotFoundError`	if the identifier does not exist in cache

remove_bedset_from_cache

remove_bedset_from_cache(bedset_id, remove_bed_files=False)

Remove a BED set from cache

Parameters:

Name	Type	Description	Default
`bedset_id`	`str`	the identifier of BED set	required
`remove_bed_files`	`bool`	whether also remove BED files in the BED set	`False`

Raises:

Type	Description
`FileNotFoundError`	if the BED set does not exist in cache

list_beds

list_beds()

List all BED files in cache

Returns:

Type	Description
`Dict[str, str]`	the list of identifiers of BED files

list_bedsets

list_bedsets()

List all BED sets in cache

Returns:

Type	Description
`Dict[str, str]`	the list of identifiers of BED sets

remove_bedfile_from_cache

remove_bedfile_from_cache(bedfile_id)

Remove a BED file from cache

Parameters:

Name	Type	Description	Default
`bedfile_id`	`str`	the identifier of BED file	required

Raises:

Type	Description
`FileNotFoundError`	if the BED set does not exist in cache