moonstone.parsers.counts.taxonomy.Metaphlan2Parser

class moonstone.parsers.counts.taxonomy.Metaphlan2Parser(*args, analysis_type='rel_ab', **kwargs)

Parse output from Metaphlan2 merged table.

__init__(*args, analysis_type='rel_ab', **kwargs)

Parameters

analysis_type (str) – output type of Metaphlan3 (see -t option of metaphlan3)

Methods

__init__(*args[, analysis_type])	type analysis_type str
compare_difference_between_two_levels(…)	rtype DataFrame
remove_duplicates(df)	rtype DataFrame
rows_differences(dataframe1, dataframe2)	rtype DataFrame
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.
plotter	Access to instance dedicated to visualization for this type of data.
rank_level	retrieves rank_level
taxa_column
taxonomical_names