dipper.sources.HGNC module

class dipper.sources.HGNC.HGNC(graph_type, are_bnodes_skolemized, tax_ids=None, gene_ids=None)

Bases: dipper.sources.Source.Source

This is the processing module for HGNC.

We create equivalences between HGNC identifiers and ENSEMBL and NCBIGene. We also add the links to cytogenic locations for the gene features.

fetch(is_dl_forced=False)

abstract method to fetch all data from an external resource. this should be overridden by subclasses :return: None

files = {'genes': {'url': 'ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt', 'file': 'hgnc_complete_set.txt'}}

getTestSuite()

An abstract method that should be overwritten with tests appropriate for the specific source. :return:

get_symbol_id_map()

A convenience method to create a mapping between the HGNC symbols and their identifiers. :return:

parse(limit=None)

abstract method to parse all data from an external resource, that was fetched in fetch() this should be overridden by subclasses :return: None