scirpy.io.read_bracer

scirpy.io.read_bracer(path)

Read data from BraCeR ([LEM+18]).

Requires the changeodb.tab file as input which is created by the bracer summarise step.

Note

Reading data into Scirpy has the following constraints:

  • Each cell can have up to four productive chains chains (Dual IR): two VJ and two VDJ chains.

  • Excess chains are ignored (those with lowest read count/UMI count) and cells flagged as Multichain-cell.

  • Non-productive chains are ignored.

  • Chain loci must be valid IMGT locus names.

  • Excess chains, non-productive chains, chains without a CDR3 sequence, or chains with invalid loci are serialized to JSON and stored in the extra_chains column. They are not used by scirpy except when exporting the AnnData object to AIRR format.

For more information, see Immune receptor (IR) model.

Parameters
path : str | PathUnion[str, Path]

Path to the changeodb.tab file.

Return type

AnnData

Returns

AnnData object with BCR data in obs for each cell. For more details see Data structure.