RepTaxonomy

class RepTaxonomy(taxonomy, taxonomy_columns=None, **kwargs)

An essential class for handling taxonomy data.

Constructor for RepTaxonomy

Parameters

• taxonomy (Union[pandas.core.frame.DataFrame, pandas.core.series.Series, str]) – Data containing feature taxonomy

• taxonomy_columns (Union[str, int, Sequence[Union[int, str]]]) – Column(s) containing taxonomy data

• kwargs (Any) – Passed to read_csv() or biome loader.

Return type

None

Attributes

avail_ranks	List of available taxonomic ranks.
controller	Active essentials controller instance.
data	Actual data representation as pd.DataFrame.
duplicated	List of duplicated feature indices.
is_buckled	Is current essentials instance is mounted or not.
is_mounted	True if current essentials instance is mounted or not.
metadata	The essential instance metadata.
name	The essential instance name.
shape	Return the shape/size of the essential instance.
xrid	Feature indices as pd.Index.

Methods

copy()	Copy of the instance.
drop_feature_by_id(ids, **kwargs)	Remove features by feature ids.
drop_features_without_ranks(ranks[, any])	Remove features that do not contain ranks
drop_features_without_taxa(**kwargs)	Remove features that do not contain taxonomy.
export(output_fp, *args[, _add_ext, sep])	Exports the taxonomy into the specified file.
find_features_by_pattern(pattern_str[, …])	Searches for features with taxa that matches pattern_str
find_features_without_taxa()	Find features without taxa.
from_biom(filepath, **kwargs)	Factory method to construct a RepTaxonomy from biom file.
from_csv(filepath[, taxonomy_columns])	Factory method to construct a RepTaxonomy from CSV file.
get_feature_ids([dtype])	This function and its sample twin is a rescue method to fix RepPhylogeny index problem.
get_lineage_by_id([ids, missing_rank, …])	Get taxonomy lineages by feature ids.
get_subset([rids])	Get subset of the RepTaxonomy.
get_taxonomy_by_id([ids])	Get taxonomy DataFrame by feature ids.
merge_duplicated_features(**kwargs)	Merge features with duplicated taxonomy.
merge_features_by_rank(level, **kwargs)	Merge features by taxonomic rank/level.