pegasusio.read_molecule_info

pegasusio.read_molecule_info(molecule_info_h5)[source]

Load molecule info from hdf5 file as a pandas DataFrame. Only support cumulus_feature_barcoding format as the following structure:

  • /barcode_idx: Integer array of length n_mol (number of molecules). Each entry is the index of the molecule’s cell barcode, which can be found in /barcodes;

  • /barcodes: String array of length n_cell (number of cell barcodes). Each entry is a cell barcode;

  • /feature_idx: Integer array of length n_mol. Each entry is the index of the molecule’s feature name, which can be found in /features;

  • /features: String array of length n_feature (number of features). Each entry is a feature name;

  • /umi: String array of length n_mol. Each entry is the molecule’s UMI barcode;

  • /count: Integer array of length n_mol. Each entry is the molecule’s count of reads.

Parameters:

molecule_info_h5 (str) – The hdf5 format file containing UMI information.

Return type:

DataFrame

Returns:

  • A data frame with each row representing a UMI, and columns as –

    • Barcode for cell barcodes

    • Feature for feature names

    • UMI for UMI barcodes

    • Count for count of reads

Examples

>>> io.read_molecule_info("molecule_info.h5")