dandelion.base.core.Dandelion.update_metadata

Dandelion.update_metadata(retrieve=None, clone_key=None, retrieve_mode='split and merge', collapse_alleles=True, reinitialize=True, by_celltype=False, report_status_productive=True, genotyped_v_call=True, custom_isotype_dict=None)

A Dandelion initialisation function to update and populate the .metadata slot.

Parameters:

• retrieve (list[str] | str | None, optional) – column name in .data slot to retrieve and update the metadata.

• clone_key (str | None, optional) – column name of clone id. None defaults to ‘clone_id’.

• retrieve_mode (Literal[“split and unique only”, “merge and unique only”, “split and merge”, “split and sum”, “split and average”, “split”, “merge”, “sum”, “average”, ], optional) –

  one of:

  split and unique only

  returns the retrieval splitted into two columns, i.e. one for VDJ and one for VJ chains, separated by | for unique elements.

  merge and unique only

  returns the retrieval merged into one column, separated by | for unique elements.

  split and merge

  returns the retrieval splitted into two columns, i.e. one for VDJ and one for VJ chains, separated by | for every elements.

  split

  returns the retrieval splitted into separate columns for each contig.

  merge

  returns the retrieval merged into one columns for each contig, separated by | for unique elements.

  split and sum

  returns the retrieval sum in the VDJ and VJ columns (separately).

  split and average

  returns the retrieval averaged in the VDJ and VJ columns (separately).

  sum

  returns the retrieval sum into one column for all contigs.

  average

  returns the retrieval averaged into one column for all contigs.

• collapse_alleles (bool, optional) – returns the V(D)J genes with allelic calls if False.

• reinitialize (bool, optional) – whether or not to reinitialize the current metadata. useful when updating older versions of dandelion to newer version.

• by_celltype (bool, optional) – whether to return the query/update by celltype.

• report_status_productive (bool, optional) – whether to report the locus and chain status for only productive contigs.

• genotyped_v_call (bool, optional) – whether or not to use genotyped v_call data to initialize metadata if available.

• custom_isotype_dict (dict[str, str] | None, optional) – custom isotype dictionary to update the default isotype dictionary.

Raises:

• KeyError – if columns provided not found in Dandelion.data.

• ValueError – if missing columns in Dandelion.data.

Return type:

None