.long

proteopy.read.long(intensities, *, level=None, sep=None, sample_annotation=None, var_annotation=None, fill_na=None, column_map=None, sort_obs_by_annotation=False)[source]

Read long-format peptide or protein files into an AnnData container.

Parameters:

  • intensities (str | Path | pd.DataFrame) – Long-form intensities data. Accepts a file path (str or Path) or a pandas DataFrame. When a file path is provided, the separator is auto-detected from the extension (.csv -> ‘,’, .tsv -> ‘t’) unless sep is explicitly specified.

  • level ({"peptide", "protein"}, default None) – Select whether to process peptide- or protein-level inputs. This argument is required.

  • sep (str, optional) – Delimiter passed to pandas.read_csv. If None (the default), the separator is auto-detected from the file extension. Ignored when input is a DataFrame.

  • sample_annotation (str | Path | pd.DataFrame, optional) – Optional obs annotations. Accepts a file path or DataFrame.

  • var_annotation (str | Path | pd.DataFrame, optional) – Optional var annotations merged into adata.var. Accepts a file path or DataFrame. Interpreted as peptide annotations when level="peptide" and as protein annotations when level="protein".

  • fill_na (float, optional) – Optional replacement value for missing intensity entries.

  • column_map (dict, optional) – Optional mapping that specifies custom column names for the expected keys: peptide_id, protein_id, sample_id, intensity.

  • sort_obs_by_annotation (bool, default False) – When True, reorder observations to match the order of samples in the annotation (if supplied) or the original intensity table.

Returns:

Structured representation of the long-form intensities ready for downstream analysis.

Return type:

AnnData