def init():
try:
global pyvolve
import pyvolve
except:
from os import chdir
chdir(GC.START_DIR)
assert False, "Error loading Pyvolve. Install with: pip3 install pyvolve"
# config validity checks
custom_model_params = {}
GC.ecm_type = GC.ecm_type.strip()
if GC.ecm_type == 'restricted':
GC.ecm_type = 'ECMrest'
elif GC.ecm_type == 'unrestricted':
GC.ecm_type = 'ECMunrest'
else:
assert False, 'ecm_type must be "restricted" or "unrestricted"'
if isinstance(GC.ecm_alpha, str):
GC.ecm_alpha = GC.ecm_alpha.strip()
if len(GC.ecm_alpha) != 0:
custom_model_params['alpha'] = float(GC.ecm_alpha)
else:
custom_model_params['alpha'] = float(GC.ecm_alpha)
if isinstance(GC.ecm_beta, str):
GC.ecm_beta = GC.ecm_beta.strip()
if len(GC.ecm_beta) != 0:
custom_model_params['beta'] = float(GC.ecm_beta)
else:
custom_model_params['beta'] = float(GC.ecm_beta)
if isinstance(GC.ecm_omega, str):
GC.ecm_omega = GC.ecm_omega.strip()
if len(GC.ecm_omega) != 0:
custom_model_params['omega'] = float(GC.ecm_omega)
else:
custom_model_params['omega'] = float(GC.ecm_omega)
assert isinstance(
GC.ecm_codon_frequencies_dictionary, dict
), "Specified ecm_codon_frequencies_dictionary is not a dictionary"
if len(GC.ecm_codon_frequencies_dictionary) != 0:
codons = set(GC.generate_all_kmers(3, 'ACGT'))
codons.difference_update({'TGA', 'TAA',
'TAG'}) # remove STOP codons
for key in GC.ecm_codon_frequencies_dictionary:
assert key in codons, "%s is not a valid codon for ecm_codon_frequencies_dictionary. Only include 3-mers of the DNA alphabet, excluding the STOP codons (TGA, TAA, and TAG)"
assert abs(
sum(GC.ecm_codon_frequencies_dictionary.values()) - 1
) < 0.000000001, "Frequencies in ecm_codon_frequencies_dictionary must sum to 1"
custom_model_params[
'state_freqs'] = GC.ecm_codon_frequencies_dictionary
# set up Pyvolve
if len(custom_model_params) == 0:
GC.pyvolve_model = pyvolve.Model(GC.ecm_type)
else:
GC.pyvolve_model = pyvolve.Model(GC.ecm_type, custom_model_params)
def init():
try:
global pyvolve
import pyvolve
except:
from os import chdir
chdir(GC.START_DIR)
assert False, "Error loading Pyvolve. Install with: pip3 install pyvolve"
# config validity checks
custom_model_params = {}
GC.mcm_style = GC.mcm_style.strip()
assert GC.mcm_style in {'GY', 'MG'}
if isinstance(GC.mcm_alpha, str):
GC.mcm_alpha = GC.mcm_alpha.strip()
if len(GC.mcm_alpha) != 0:
custom_model_params['alpha'] = float(GC.mcm_alpha)
else:
custom_model_params['alpha'] = float(GC.mcm_alpha)
if isinstance(GC.mcm_beta, str):
GC.mcm_beta = GC.mcm_beta.strip()
if len(GC.mcm_beta) != 0:
custom_model_params['beta'] = float(GC.mcm_beta)
else:
custom_model_params['beta'] = float(GC.mcm_beta)
if isinstance(GC.mcm_omega, str):
GC.mcm_omega = GC.mcm_omega.strip()
if len(GC.mcm_omega) != 0:
custom_model_params['omega'] = float(GC.mcm_omega)
else:
custom_model_params['omega'] = float(GC.mcm_omega)
if isinstance(GC.mcm_kappa, str):
GC.mcm_kappa = GC.mcm_kappa.strip()
if len(GC.mcm_kappa) != 0:
custom_model_params['kappa'] = float(GC.mcm_kappa)
else:
custom_model_params['kappa'] = float(GC.mcm_kappa)
assert isinstance(
GC.mcm_codon_frequencies_dictionary, dict
), "Specified mcm_codon_frequencies_dictionary is not a dictionary"
if len(GC.mcm_codon_frequencies_dictionary) != 0:
codons = set(GC.generate_all_kmers(3, 'ACGT'))
codons.difference_update({'TGA', 'TAA',
'TAG'}) # remove STOP codons
for key in GC.mcm_codon_frequencies_dictionary:
assert key in codons, "%s is not a valid codon for mcm_codon_frequencies_dictionary. Only include 3-mers of the DNA alphabet, excluding the STOP codons (TGA, TAA, and TAG)"
assert abs(
sum(GC.mcm_codon_frequencies_dictionary.values()) - 1
) < 0.000000001, "Frequencies in mcm_codon_frequencies_dictionary must sum to 1"
custom_model_params[
'state_freqs'] = GC.mcm_codon_frequencies_dictionary
assert isinstance(
GC.mcm_mutation_rates_dictionary, dict
), "Specified mcm_mutation_rates_dictionary is not a dictionary"
if len(GC.mcm_mutation_rates_dictionary) != 0:
custom_model_params['mu'] = GC.mcm_mutation_rates_dictionary
assert 'beta' in custom_model_params or 'omega' in custom_model_params, "Must specify a dN value using either mcm_beta or mcm_omega"
assert not (
'kappa' in custom_model_params
and 'mcm_mutation_rates_dictionary' in custom_model_params
), "Cannot use custom values for both mcm_kappa and mcm_mutation_rates_dictionary: only one of the two"
# set up Pyvolve
if len(custom_model_params) == 0:
GC.pyvolve_model = pyvolve.Model(GC.mcm_style,
neutral_scaling=True)
else:
GC.pyvolve_model = pyvolve.Model(GC.mcm_style,
custom_model_params,
neutral_scaling=True)