dandelion.base.io.read_parse_airr

dandelion.base.io.read_parse_airr(file, prefix=None, suffix=None, sep='_', remove_trailing_hyphen_number=False, verbose=False, **kwargs)[source]

Read the TCR or BCR _annotation_airr.tsv produced from Parse Biosciences Evercode technology.

This is not to be used for any airr rearrangement file, but specifically for the one produced by Parse Biosciences. For standard airr rearrangement files e.g. all_contig_dandelion.tsv, use ddl.Dandelion or ddl.read_airr directly.

Parameters:

  • file (Path | str) – path to _annotation_airr.tsv

  • prefix (str | None, optional) – Prefix to append to sequence_id and cell_id.

  • suffix (str | None, optional) – Suffix to append to sequence_id and cell_id.

  • sep (str, optional) – the separator to append suffix/prefix.

  • remove_trailing_hyphen_number (bool, optional) – whether or not to remove the trailing hyphen number e.g. ‘-1’ from the cell/contig barcodes.

  • verbose (bool, optional) – whether or not to print messages during creation of the Dandelion object.

  • **kwargs – additional keyword arguments passed to Dandelion.

Returns:

Dandelion object from Parse AIRR file.

Return type:

Dandelion