scirpy.io.read_bd_rhapsody

scirpy.io.read_bd_rhapsody(path, **kwargs)

Read IR data from the BD Rhapsody Analysis Pipeline.

Supports *_perCellChain.csv, *_perCellChain_unfiltered.csv, *_VDJ_Dominant_Contigs.csv, and *_VDJ_Unfiltered_Contigs.csv files. The applicable filename depends your version of the BD Rhapsody pipeline.

Note

More recent versions of the pipeline generate data in standardized AIRR Rearragement format. If you have a chance to do so, we recommend reanalysing your data with the most recent version of the BD Rhapsody pipeline and read output filese with scirpy.io.read_airr().

*_perCell files are currently not supported, follow the IO Tutorial to import custom formats and make use of this snippet

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 (Union[str, Path]) – Path to the perCellChain or Contigs file generated by the BD Rhapsody analysis pipeline. May be gzipped.

• **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.