rotifer.taxonomy.utils.lineage

rotifer.taxonomy.utils.lineage(data=None, preferred_taxa=None, column='classification', insep='; ', outsep='>', case=<method 'lower' of 'str' objects>)

Transform detailed linearized taxonomies into reduced lineages using a set of preferred taxa.

Available arguments:

data : may be Pandas Series or DataFrames preferred_taxa : list of clades that should be kept column : for dataframes, name of the column containing the taxonomies insep : clade name separator in input data outsep : clade name separator in the returned stream case : subroutine to handle case independent matching, set to None to disable