pmaf.pipe.agents.mediators

Database Mediators (pmaf.pipe.agents.mediators)

This sub-package mediators contains classes called mediator-classes. These are group of classes that are responsible for exploitation of various remote and local databases. Each mediator class consist of multiple mixin classes composition of which depends on the database instance that will be mediated. Although, mediators are be directly used it is recommended to use miner instance instead.

Local Mediators

LocalMediator(database, **kwargs)

Factory function to create local mediator for given database client.

Mixin Classes for Local Mediator

MediatorLocalAccessionMixin(database[, …])

Mixin class for local mediator that handle accession data.

MediatorLocalPhylogenyMixin(database[, …])

Mixin class for local mediator that handle phylogeny data.

MediatorLocalSequenceMixin(database[, …])

Mixin class for local mediator that handle sequence data.

MediatorLocalTaxonomyMixin(database[, …])

Mixin class for local mediator that handle taxonomy data.

Remote Mediators

NCBIMediator(entrez[, seq_method, seq_aligner])

The NCBI Entrez API Schuler et al. [SEOK96] mediator.