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
}