iggytop.adapters.cedar_adapter.CEDARAdapter

class iggytop.adapters.cedar_adapter.CEDARAdapter(bc, cache_dir=None, receptors_to_include=('TCR', 'BCR'), test=False, filter_10x=False)

BioCypher adapter for the Cancer Epitope Database and Analysis Resource CEDAR.

__init__(bc, cache_dir=None, receptors_to_include=('TCR', 'BCR'), test=False, filter_10x=False)

Initializes the BaseAdapter instance.

Parameters:

• bc (BioCypher) – An instance of the BioCypher class.

• cache_dir (str | None) – Directory to cache data. Defaults to None.

• receptors_to_include (Optional[Sequence[Literal['TCR', 'BCR']]]) – Receptors to include. Defaults to (“TCR”, “BCR”).

• test (bool) – Whether to run in test mode. Defaults to False.

• filter_10x (bool) – Whether to filter out 10X Genomics datasets. Defaults to False.

Methods

__init__(bc[, cache_dir, ...])	Initializes the BaseAdapter instance.
create_anndata()	Creates an Anndata object from the AIRR cell data and saves it to a file in the cache directory.
get_edges()	Abstract method to generate BioCypher edges from the data.
get_latest_release(bc)	Retrieves the latest release of the CEDAR database.
get_nodes()	Abstract method to generate BioCypher nodes from the data.
read_table(bc, table_path, receptors[, ...])	Reads and processes the CEDAR table from the downloaded database file.
set_metadata([version, source_url, ...])	Sets the metadata for the adapter.

Attributes

BCR_FNAME	File name of the BCR data in CEDAR.
DB_DIR	Directory name for the downloaded database.
DB_NAME	Name of the database.
DB_URL	URL to download the CEDAR database.
TCR_FNAME	File name of the TCR data in CEDAR.
airr_cells	Property to get the list of AIRR cells.
available_receptors	Receptor types available in CEDAR.
cache_dir	Property to get the cache directory.
db_name	Property to get the database name.
metadata	Property to get the adapter metadata.
receptors	Property to get the available receptor types.
table	Property to get the data table.

get_edges()

Abstract method to generate BioCypher edges from the data.

This method is intended to call _generate_edges_from_table with the right parameters for each edge type. This requires parameters depending on the adapter used.

Yields:

tuple – A BioCypher edge (id, source, target, type, properties).

get_latest_release(bc)

Retrieves the latest release of the CEDAR database.

Parameters:

bc (BioCypher) – An instance of the BioCypher class.

Return type:

tuple[str, str]

Returns:

Paths to the latest TCR and BCR release files.

get_nodes()

Abstract method to generate BioCypher nodes from the data.

This method is intended to use _generate_nodes_from_table with the right parameters for each edge type. This requires parameters depending on the adapter used.

Yields:

tuple – A BioCypher node (id, type, properties).

read_table(bc, table_path, receptors, test=False, prefer_calculated=True)

Reads and processes the CEDAR table from the downloaded database file.

Parameters:

• bc (BioCypher) – An instance of the BioCypher class.

• table_path (tuple[str, str]) – Paths to the TCR and BCR table files.

• receptors (list[str]) – List of receptor types to include in the table.

• test (bool) – If True, loads only a subset of the data for testing (default is False).

• prefer_calculated (bool) – If True, calculated values are preferred over curated values. Defaults to True.

Return type:

DataFrame

Returns:

A DataFrame containing the processed table data.

Raises:

FileNotFoundError – If the table file cannot be found.

BCR_FNAME = 'bcr_full_v3.csv'

File name of the BCR data in CEDAR.

DB_DIR = 'cedar_latest'

Directory name for the downloaded database.

DB_NAME: str = 'CEDAR'

Name of the database.

DB_URL = 'https://cedar.iedb.org/downloader.php?file_name=doc/receptor_full_v3.zip'

URL to download the CEDAR database.

TCR_FNAME = 'tcr_full_v3.csv'

File name of the TCR data in CEDAR.

_abc_impl = <_abc._abc_data object>

available_receptors: list[str] = ['TCR', 'BCR']

Receptor types available in CEDAR.