SequenceDatabase#

class openomics.database.sequence.SequenceDatabase(**kwargs)[source][source]#

Bases: openomics.database.base.Database

Provides a series of methods to extract sequence data from SequenceDataset.

Methods Summary

get_sequences(index, omic, agg, **kwargs)

Returns a dictionary where keys are 'index' and values are sequence(s).

Methods Documentation

abstract get_sequences(index, omic, agg, **kwargs)[source][source]#

Returns a dictionary where keys are ‘index’ and values are sequence(s).

Parameters

  • index (str) – {“gene_id”, “gene_name”, “transcript_id”, “transcript_name”}

  • omic (str) – {“lncRNA”, “microRNA”, “messengerRNA”}

  • agg (str) – {“all”, “shortest”, “longest”}

  • **kwargs – any additional argument to pass to SequenceDataset.get_sequences()

Return type

Union[Series, Dict]