lnschema_covim.ingest_markers

lnschema_covim.ingest_markers(meta, curate_function=None, *, basedir=None, var_key='marker', update=False)

Ingest data from the CovimBiosampleForm.

Parameters:

  • meta (DataFrame) – DataFrame containing the metadata from CovimBiosampleForm.xlsx.

  • curate_function (Callable | None, default: None) – Function which is applied to a here created AnnData object for curation.

  • basedir (Path | str | None, default: None) – Path to the directory containing the files.

  • var_key (str, default: 'marker') – The var key of the AnnData object to curate.

  • update (bool, default: False) – Whether to update existing records.

Return type:

Biosample | list[Biosample]

Returns:

Biosample record/s.