API Reference#

IO#

`base_adapter.BaseAdapter`(bc[, cache_dir, ...])	Base class for all adapters.
`cedar_adapter.CEDARAdapter`(bc[, cache_dir, ...])	BioCypher adapter for the Cancer Epitope Database and Analysis Resource CEDAR.
`iedb_adapter.IEDBAdapter`(bc[, cache_dir, ...])	BioCypher adapter for the Immune Epitope Database IEDB.
`mcpas_adapter.MCPASAdapter`(bc[, cache_dir, ...])	BioCypher adapter for the manually-curated catalogue of pathology-associated T cell receptor sequences McPAS-TCR.
`neotcr_adapter.NEOTCRAdapter`(bc[, ...])	BioCypher adapter for the NeoTCR dataset.
`tcr3d_adapter.TCR3DAdapter`(bc[, cache_dir, ...])	BioCypher adapter for the TCR3D database.
`trait_adapter.TRAITAdapter`(bc[, cache_dir, ...])	A Comprehensive Database for T-cell Receptor-Antigen Interactions TRAIT.
`vdjdb_adapter.VDJDBAdapter`(bc[, cache_dir, ...])	BioCypher adapter for the VDJDB database.

`mapping_utils`	This module contains utility functions for cleaning up species terms and cleaning antigen names
`utils`	This module contains utility functions for harmonizing data for iggytop