EnsemblGenes

class openomics.database.annotation.EnsemblGenes(biomart='hsapiens_gene_ensembl', attributes=None, host='www.ensembl.org', npartitions=None)

Bases: openomics.database.annotation.BioMartManager, openomics.database.base.Database

Attributes Summary

COLUMNS_RENAME_DICT

Methods Summary

get_functional_annotations(index)	param index
get_rename_dict([from_index, to_index])	param from_index
load_data(dataset, attributes, host[, …])	param dataset

Attributes Documentation

COLUMNS_RENAME_DICT = {'ensembl_gene_id': 'gene_id', 'ensembl_transcript_id': 'transcript_id', 'external_gene_name': 'gene_name', 'external_transcript_name': 'transcript_name', 'rfam': 'Rfams'}

Methods Documentation

get_functional_annotations(index)

Parameters

index –

get_rename_dict(from_index='gene_id', to_index='gene_name')

Parameters

• from_index –

• to_index –

load_data(dataset, attributes, host, filename=None, npartitions=None)

Parameters

• dataset –

• attributes –

• host –

• filename –

• npartitions –