NCBIMediator¶

class NCBIMediator(entrez, seq_method='asis', seq_aligner=None, **kwargs)[source]¶

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

Constructor for NCBIMediator

Parameters

entrez (pmaf.remote._entrez._metakit.EntrezBackboneMetabase) – Working/active instance of pmaf.remote.Entrez
seq_method (str) – Method of sequence retrieval. - The “asis” will retrieve multiple sequences as-is. - The “consensus” will attempt to align sequences using seq_aligner and return the consensus sequence
seq_aligner (Optional[pmaf.alignment._multiple._metakit.MultiSequenceAlignerBackboneMetabase]) – Sequence aligner to use when seq_method is set to “consensus”
kwargs (Any) – Compatibility

Attributes

`client`	Current active client that mediator mediates.
`configs`	All current configs.
`state`	State of the mediator(client).

Methods

`get_accession_by_identifier`(docker, factor, …)	Get accessions from identifier.
`get_identifier_by_accession`(docker, factor, …)	Get identifier from accession number.
`get_identifier_by_sequence`(docker, factor, …)	Get identifier from sequence.
`get_identifier_by_taxonomy`(docker, factor, …)	Get identifier from taxonomy.
`get_sequence_by_identifier`(docker, factor, …)	Get sequence from identifier.
`get_taxonomy_by_identifier`(docker, factor, …)	Get taxonomy from identifiers.
`reconfig`(name, value)	Set config name to value
`verify_factor`(factor)	Verify factor compatibility with mediator.