ovrlpy.io.read_Atera

ovrlpy.io.read_Atera(filepath, *, min_qv=None, remove_features=ATERA_CTRLS, additional_columns=[])

Read a Xenium transcripts file.

Parameters:

  • filepath (PathLike or str) – Path to the Atera transcripts file (.parquet). The Zarr-store is currently not supported.

  • min_qv (float | None, optional) – Minimum Phred-scaled quality value (Q-Score) of a transcript to be included. If None no filtering is performed.

  • remove_features (Collection[str], optional) – List of regex patterns to filter the ‘feature_name’ column, ovrlpy.io.ATERA_CTRLS by default.

  • additional_columns (Collection[str], optional) – Additional columns to load from the transcripts file.

Return type:

polars.DataFrame