moonstone.parsers.counts.taxonomy.SunbeamKraken2Parser

class moonstone.parsers.counts.taxonomy.SunbeamKraken2Parser(*args, **kwargs)

Parse output from Kraken2 merge table from Sunbeam pipeline.

__init__(*args, **kwargs)

Parameters

• file_path – path of the input file to be parsed

• sep – delimiter to use (same behaviour as read_csv from pandas)

• no_header – set to True if table has no header

• parsing_options – Extra parsing options for read_csv method, (see pandas documentation)

Methods

__init__(*args, **kwargs)	param file_path path of the input file to be parsed
split_taxa_fill_none(df[, sep, taxo_prefix, …])	type terms_to_remove Optional[List]

Attributes

dataframe	Retrieve the pandas dataframe constructed from the input file.
new_otu_id_name
plotter	Access to instance dedicated to visualization for this type of data.
rank_level	retrieves rank_level
taxa_column
taxonomical_names