dandelion.tools.find_clones

dandelion.tools.find_clones(self, identity=0.85, clustering_by=None, by_alleles=None, key_added=None, calculate_junction_length=True)[source]

Find clones based on heavy chain and light chain CDR3 junction hamming distance.

Parameters

  • self (Dandelion, DataFrame, str) – Dandelion object, pandas DataFrame in changeo/airr format, or file path to changeo/airr file after clones have been determined.

  • identity (float) – Junction similarity parameter. Default 0.85

  • clustering_by (str, optional) – modes for clustering: ‘nt’ or ‘aa’. None defaults to ‘aa’.

  • by_alleles (bool, optional) – Whether or not to collapse alleles to genes. None defaults to True.

  • key_added (str, optional) – If specified, this will be the column name for clones. None defaults to ‘clone_id’

  • calculate_junction_length (bool) – Whether or not to re-calculate junction length, rather than rely on parsed assignment (which occasionally is wrong). Default is True

Returns

Return type

Dandelion object with clone_id annotated in .data slot and .metadata initialized.