dipper.sources.RGD module

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

Bases: dipper.sources.Source.Source

Ingest of Rat Genome Database gene to mammalian phenotype gaf file

RGD_BASE = 'ftp://ftp.rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/'

fetch(is_dl_forced=False)

Override Source.fetch() Fetches resources from rat_genome_database using the rat_genome_database ftp site Args:

param is_dl_forced (bool):  Force download

Returns:

:return None

files = {'rat_gene2mammalian_phenotype': {'url': 'ftp://ftp.rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/rattus_genes_mp', 'file': 'rattus_genes_mp'}}

make_association(record)

contstruct the association :param record: :return: modeled association of genotype to mammalian phenotype

parse(limit=None)

Override Source.parse() Args:

:param limit (int, optional) limit the number of rows processed

Returns:

:return None