scirpy.io.read_tracer

scirpy.io.read_tracer(path, **kwargs)

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

Since scirpy v0.13, there are no restrictions on the AIRR data that can be stored in the scirpy data structure, except that each receptor chain needs to be associated with a cell.

The scirpy Immune receptor (IR) model is now applied in later step using the index_chains() function.

For more information, see Storing AIRR rearrangement data in AnnData.

Parameters

path : str | PathUnion[str, Path]: Path to the TraCeR output folder.
**kwargs: are passed to from_airr_cells().

Return type

AnnData

Returns

AnnData object with AIRR data in obsm["airr"] for each cell. For more details see Storing AIRR rearrangement data in AnnData.