MediatorLocalPhylogenyMixin

class MediatorLocalPhylogenyMixin(database, phy_method='infer', phy_sub_nodes=True, phy_ignore_tips=False, phy_refrep='tid', **kwargs)[source]

Mixin class for local mediator that handle phylogeny data.

Mixin class constructor for MediatorLocalPhylogenyMixin

Parameters

  • database (pmaf.database._metakit.DatabasePhylogenyMetabase) – Instance of DatabaseBase and DatabasePhylogenyMixin

  • phy_method (str) – Phylogeny retrieval method. Can be either “infer” or “prune”

  • phy_sub_nodes (bool) – Whether mediator should include subs

  • phy_ignore_tips (bool) – Ignore duplicated tips

  • phy_refrep (str) – Taxonomy lookup level. Can be either “tid” for tids or “rid” for rids

  • kwargs (Any) – Compatibility

Attributes

PHYLO_EXTRACT_METHODS

client

Current active client that mediator mediates.

configs

All current configs.

state

State of the mediator(client)

Methods

get_identifier_by_phylogeny(docker, factor, …)

meta private

get_phylogeny_by_identifier(docker, factor, …)

Get phylogeny data that matches identifiers in docker within local database client.

reconfig(name, value)

Set config name to value

verify_factor(factor)

Verify/validate compatibility of the current mediator and factor