def to_file_extra(self, output_filename):
home_dir = support.get_home_dir()
with open(os.path.join(home_dir, 'extra_params_template')) as t:
string = t.readlines()
string = ''.join(string)
with open(output_filename, 'w') as out:
out.write(
string.format(
str(self.min_N),
str(self.max_N),
str(self.min_T),
str(self.max_T),
str(self.min_M),
str(self.max_M),
str(self.ls_verbose),
str(self.ls_flush_delay),
str(self.ls_epsilon),
str(self.ls_gtol),
str(self.ls_maxiter),
str(self.hc_mutation_rate),
str(self.hc_const_for_mutation_rate),
str(self.hc_stop_iter),
str(self.random_N_A),
str(self.multinom_cross),
str(self.multinom_mutate),
str(self.time_for_print),
str(self.distribution),
str(self.std)
))
def to_file(self, output_filename):
def comma_sep_repr(l):
if l is None:
return 'None'
if len(l) == 1:
return str(l[0])
return ', '.join([str(x) for x in l])
home_dir = support.get_home_dir()
with open(os.path.join(home_dir, "params_template")) as t:
string = t.readlines()
string = ''.join(string)
with open(output_filename, 'w') as out:
out.write(
string.format(
self.output_dir,
self.resume_dir,
self.only_models,
self.input_file,
comma_sep_repr(self.pop_labels),
comma_sep_repr(self.ns),
str(self.theta),
str(self.gen_time),
'moments' if self.moments_scenario else 'dadi',
str(self.multinom),
comma_sep_repr(self.dadi_pts),
comma_sep_repr(self.initial_structure),
comma_sep_repr(self.final_structure),
str(self.split_1_lim),
str(self.split_2_lim),
str(self.relative_params),
str(self.no_mig),
str(self.size_of_generation),
comma_sep_repr(self.fracs),
str(self.mutation_strength),
str(self.const_for_mut_strength),
str(self.mutation_rate),
str(self.const_for_mut_rate),
str(self.epsilon),
str(self.stop_iter),
str(self.optimize_name),
str(self.draw_iter),
str(self.code_iter),
'Thousand Years' if self.gen_time_units == 1000 else 'Years',
str(self.silence),
str(self.repeats),
str(self.processes),
str(self.only_sudden),
str(self.model_func_file),
comma_sep_repr(self.lower_bound),
comma_sep_repr(self.upper_bound),
comma_sep_repr(self.p_ids),
str(self.linked_snp),
str(self.boot_dir)
))
def test_args():
'''
Put default args for test case.
'''
global options_storage
import tempfile
options_storage.output_dir = tempfile.mkdtemp("gadma_test_dir")
options_storage.output_dir = support.ensure_dir_existence(
options_storage.output_dir)
options_storage.input_file = os.path.join(support.get_home_dir(), "..",
"fs_examples", "test.fs")
options_storage.input_data, options_storage.ns, options_storage.pop_labels = support.load_spectrum(
options_storage.input_file, None, None)
options_storage.ns = np.array(options_storage.ns)
options_storage.number_of_populations = 1
options_storage.linked_snp = False
options_storage.theta = 0.37976
options_storage.gen_time = 25
options_storage.initial_structure = np.array([1])
options_storage.final_structure = np.array([2])
options_storage.size_of_generation = 5
options_storage.fracs = [
float(x) for x in options_storage.fracs.split(",")
]
options_storage.frac_of_old_models = options_storage.fracs[0]
options_storage.frac_of_mutated_models = options_storage.fracs[1]
options_storage.frac_of_crossed_models = options_storage.fracs[2]
options_storage.optimize_name = 'hill_climbing'
options_storage.moments_scenario = True
options_storage.relative_params = False
options_storage.dadi_pts = [20, 30, 40]
options_storage.repeats = 2
options_storage.processes = 2
options_storage.epsilon = 1
options_storage.test = True
options_storage.multinom = True
options_storage.final_check()
return options_storage