iggytop.adapters.mcpas_adapter.MCPASAdapter#

class iggytop.adapters.mcpas_adapter.MCPASAdapter(bc, cache_dir=None, receptors_to_include=('TCR', 'BCR'), test=False)#

BioCypher adapter for the manually-curated catalogue of pathology-associated T cell receptor sequences McPAS-TCR.

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

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`()	Yield BioCypher edges generated via OntoWeaver.
`get_latest_release`(bc)	Retrieves the latest release of the McPAS-TCR database.
`get_nodes`()	Yield BioCypher nodes generated via OntoWeaver.
`read_table`(bc, table_path, receptors[, test])	Reads and processes the MCPAS table from the downloaded database file.
`set_metadata`([version, source_url, ...])	Sets the metadata for the adapter.

Attributes

`DB_DIR`	Directory name for the downloaded database.
`DB_NAME`	Name of the database.
`DB_URL`	URL to download the McPAS-TCR database.
`airr_cells`	Property to get the list of AIRR cells.
`available_receptors`	Receptor types available in McPAS-TCR.
`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_latest_release(bc)#

Retrieves the latest release of the McPAS-TCR database.

read_table(bc, table_path, receptors, test=False)#

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

Parameters:

bc (BioCypher) – An instance of the BioCypher class.
table_path (str) – Path to the table file.
receptors (list[str]) – List of receptor types to include in the table. (Ignored as only TCR is available).
test (bool) – If True, loads only a subset of the data for testing (default is False).

Return type:

DataFrame

Returns:

A DataFrame containing the processed table data.

Raises:

FileNotFoundError – If the table file cannot be found.

DB_URL = 'https://friedmanlab.weizmann.ac.il/McPAS-TCR.csv'#: URL to download the McPAS-TCR database.

available_receptors: list[str] = ['TCR']#: Receptor types available in McPAS-TCR.

iggytop.adapters.mcpas_adapter.MCPASAdapter