BiomeAssembly

class BiomeAssembly(essentials=None, *args, curb=None, copy=True, **kwargs)[source]

Assembly class for interconnecting and containing essentials

Constructor for BiomeAssembly

Parameters

  • essentials (Optional[Sequence[pmaf.biome.essentials._metakit.EssentialBackboneMetabase]]) – Single or _multiple instances of essentials

  • args (Optional[pmaf.biome.essentials._metakit.EssentialBackboneMetabase]) – Instances of essentials

  • curb (Optional[Union[str, pmaf.biome.essentials._metakit.EssentialBackboneMetabase]]) – Set limiting instance of essentials that will be used to subset remaining essentials to identical axes. If set tp ‘intersect’ intersection will be used as limiter.

  • copy (bool) – Whether to copy essentials or not.

  • kwargs (Any) – Compatibility

Return type

None

Attributes

controller

EssentialsController of essentials

essentials

List of essentials

metadata

The essential instance metadata.

name

The essential instance name.

shape

Return the shape/size of the essential instance.

xrid

Feature identifiers.

xsid

Sample identifiers.

Methods

add_essentials(*args[, curb, copy])

Add instance of essentials to the current instance of BiomeAssembly

copy()

Copy of the instance.

export(output_dir[, prefix, as_otu_table, sep])

Export data from assembly to the directory.

get_feature_ids([dtype])

This function and its sample twin is a rescue method to fix RepPhylogeny index problem.

get_sample_ids([dtype])

This function and its sample twin is a rescue method to fix RepPhylogeny index problem.

get_subset([rids, sids])

Get subset of the BiomeAssembly.

to_otu_table(*args, **kwargs)

Crate an OTU-table DataFrame

write_otu_table(output_fp, *args[, sep])

Write OTU-table to the file.