scirpy.io.read_airr

scirpy.io.read_airr(path)

Read AIRR-compliant data.

Reads data organized in the AIRR rearrangement schema.

The following columns are required:

  • cell_id

  • productive

  • locus

  • consensus_count

  • at least one of junction_aa or junction.

Note

Reading data into Scirpy has the following constraints:

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

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

  • non-productive chains are removed

  • chain loci must be IGMT locus names.

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

Parameters
path : str, Sequence[str], Path, Sequence[Path]Union[str, Sequence[str], Path, Sequence[Path]]

Path to the AIRR rearrangement tsv file. If different chains are split up into multiple files, these can be specified as a List, e.g. ["path/to/tcr_alpha.tsv", "path/to/tcr_beta.tsv"].

Return type

AnnDataAnnData

Returns

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