BioMartManager

class openomics.database.annotation.BioMartManager(dataset, attributes, host, filename)

Bases: object

A base class with functions to query Ensembl Biomarts “https://www.ensembl.org/biomart”.

Methods Summary

cache_dataset(dataset, dataframe, save_filename)	param dataset
query_biomart(dataset, attributes[, host, ...])	param dataset
retrieve_dataset(host, dataset, attributes, ...)	param host

Methods Documentation

cache_dataset(dataset, dataframe, save_filename)

Parameters

• dataset –

• dataframe –

• save_filename –

query_biomart(dataset, attributes, host='www.ensembl.org', cache=True, save_filename=None, blocksize=None)

Parameters

• dataset –

• attributes –

• host –

• cache –

• save_filename –

• blocksize –

retrieve_dataset(host, dataset, attributes, filename, blocksize=None)

Parameters

• host –

• dataset –

• attributes –

• filename –

• blocksize –