def mutation_sources(): sources = {} for name, source in Mutation.sources_dict.items(): if name == 'user': continue sources[name] = Mutation.get_source_model(name) return sources
def with_significant_genes(self, significant_gene_list_name): query = request.args.get('query', '') gene_list = GeneList.query.filter_by( name=significant_gene_list_name).first_or_404() dataset = Mutation.get_source_model(gene_list.mutation_source_name) return template('pathway/significant.html', gene_list=gene_list, dataset=dataset, endpoint='significant_data', endpoint_kwargs={'gene_list_id': gene_list.id}, query=query)
def __init__(self, protein, filter_manager, include_kinases_from_groups=False): super().__init__(protein, filter_manager, include_kinases_from_groups) sites, kinases, kinase_groups = self.get_sites_and_kinases( only_sites_with_kinases=False) tracks = prepare_tracks(protein, self.protein_mutations) source = filter_manager.get_value('Mutation.sources') source_model = Mutation.get_source_model(source) value_type = source_model.value_type parsed_mutations = self.represent_needles() self.json_data = { 'value_type': value_type, 'log_scale': (value_type == 'frequency'), 'mutations': parsed_mutations, 'sites': prepare_sites(sites), 'tracks': tracks }