MirBase

class openomics.database.sequence.MirBase(path='http://mirbase.org/ftp/CURRENT/', file_resources=None, species_id='9606', index_col='mirbase_id', col_rename=None, **kwargs)

Bases: openomics.database.sequence.SequenceDatabase

Loads the MirBase database from https://mirbase.org .

Default path: “ftp://mirbase.org/pub/mirbase/CURRENT/” . Default file_resources: {

“aliases.txt”: “aliases.txt.gz”, “mature.fa”: “mature.fa.gz”, “hairpin.fa”: “hairpin.fa.gz”, “rnacentral.mirbase.tsv”: “ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/mirbase.tsv”,

}

Methods Summary

get_sequences([index, omic, agg])	param index
load_dataframe(file_resources[, blocksize])	param file_resources

Methods Documentation

get_sequences(index='gene_name', omic=None, agg='all', **kwargs)

Parameters

• index –

• omic –

• agg –

• **kwargs –

load_dataframe(file_resources, blocksize=None)

Parameters

• file_resources –

• blocksize –