from __future__ import absolute_import, print_function, division from base.trait import GeneralTrait from base import data_set from base.species import TheSpecies def get_species_dataset_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" self.dataset = data_set.create_dataset(start_vars['dataset']) print("After creating dataset") self.species = TheSpecies(dataset=self.dataset) print("After creating species") self.this_trait = GeneralTrait(dataset=self.dataset, name=start_vars['trait_id'], cellid=None) print("After creating trait") #if read_genotype: #self.dataset.group.read_genotype_file() #self.genotype = self.dataset.group.genotype def get_trait_db_obs(self, trait_db_list): self.trait_list = [] for i, trait_db in enumerate(trait_db_list): if i == (len(trait_db_list) - 1): break trait_name, dataset_name = trait_db.split(":") #print("dataset_name:", dataset_name) dataset_ob = data_set.create_dataset(dataset_name) trait_ob = GeneralTrait(dataset=dataset_ob, name=trait_name, cellid=None) self.trait_list.append((trait_ob, dataset_ob))