dipper.sources.Decipher module

class dipper.sources.Decipher.Decipher(graph_type, are_bnodes_skolemized)

Bases: dipper.sources.Source.Source

The Decipher group curates and assembles the Development Disorder Genotype Phenotype Database (DDG2P) which is a curated list of genes reported to be associated with developmental disorders, compiled by clinicians as part of the DDD study to facilitate clinical feedback of likely causal variants.

Beware that the redistribution of this data is a bit unclear from the [license](https://decipher.sanger.ac.uk/legal). If you intend to distribute this data, be sure to have the appropriate licenses in place.

fetch(is_dl_forced=False)

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

files = {'annot': {'url': 'https://decipher.sanger.ac.uk/files/ddd/ddg2p.zip', 'file': 'ddg2p.zip'}}

make_allele_by_consequence(consequence, gene_id, gene_symbol)

Given a “consequence” label that describes a variation type, create an anonymous variant of the specified gene as an instance of that consequence type.

Parameters:

• consequence –
• gene_id –
• gene_symbol –

Returns:

allele_id

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