scirpy.io.read_tracer

scirpy.io.read_tracer(path)

Read data from TraCeR ([SLonnbergP+16]).

Requires the TraCeR output directory which contains a folder for each cell. Unfortunately the results files generated by tracer summarize do not contain all required information.

The function will read TCR information from the filtered_TCR_seqs/<CELL_ID>.pkl files.

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, PathUnion[str, Path]

Path to the TraCeR output folder.

Return type

AnnDataAnnData

Returns

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