mgkit.mappings.go module

Module containing classes and functions to deal with Gene Ontology data

class mgkit.mappings.go.Kegg2GOMapper(fname=None)

Bases: mgkit.kegg.KeggMapperBase

Class holding mappings KOs->GO

columns_string = 'go-id'

load_go_names(fname)

load_goslim_mapping(f_handle)

map_kos_go(kos, contact, skip=False)

Map a list of KOs to GO ids

query_string = 'database:(type:ko {0})'

write_association_file(f_handle)

mgkit.mappings.go.download_data(contact, kegg_data='kegg.pickle', go_data='go_data.pickle')

Function to download Gene Ontology data