iggytop.adapters.vdjdb_adapter.VDJDBAdapter

class iggytop.adapters.vdjdb_adapter.VDJDBAdapter(bc, cache_dir=None, receptors_to_include=('TCR', 'BCR'), test=False)

BioCypher adapter for the VDJDB database.

This adapter handles the downloading, reading, and processing of the VDJDB database.

__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 VDJDB database from GitHub.
get_nodes()	Yield BioCypher nodes generated via OntoWeaver.
read_table(bc, table_path, receptors[, test])	Reads and processes the VDJdb 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_FNAME	File name of the database.
DB_NAME	Name of the database.
REPO_NAME	GitHub repository name for the VDJDB database.
airr_cells	Property to get the list of AIRR cells.
available_receptors	Receptor types available in VDJDB.
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.

_process_single_chain(df, chain_type)

Process single chain data (TRA or TRB only).

Parameters:

• df – The input DataFrame containing the single chain data.

• chain_type – The type of chain, either “tra” or “trb”.

Returns:

A DataFrame with the processed single chain data.

_transform_paired_data_efficient(df)

Efficient transformation that handles ALL cases correctly. This is required to properly pair TRA and TRB chains based on complex.id. (They are on different rows in the raw database) :type df: :param df: The input DataFrame containing the VDJdb data.

Returns:

A DataFrame with the transformed paired data.

get_edges()

Yield BioCypher edges generated via OntoWeaver.

get_latest_release(bc)

Retrieves the latest release of the VDJDB database from GitHub.

Parameters:

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

Return type:

str

Returns:

The file path of the downloaded database.

Raises:

FileNotFoundError – If the database file cannot be found after downloading.

get_nodes()

Yield BioCypher nodes generated via OntoWeaver.

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

Reads and processes the VDJdb 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_DIR = 'vdjdb_latest'

Directory name for the downloaded database.

DB_FNAME = 'vdjdb.txt'

File name of the database.

DB_NAME: str = 'VDJDB'

Name of the database.

REPO_NAME = 'antigenomics/vdjdb-db'

GitHub repository name for the VDJDB database.

_abc_impl = <_abc._abc_data object>

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

Receptor types available in VDJDB.