def create_gtr(params):
"""
parse the arguments referring to the GTR model and return a GTR structure
"""
model = params.gtr
gtr_params = params.gtr_params
if model == 'infer':
gtr = GTR.standard('jc', alphabet='aa' if params.aa else 'nuc')
else:
try:
kwargs = {}
if gtr_params is not None:
for param in gtr_params:
keyval = param.split('=')
if len(keyval)!=2: continue
if keyval[0] in ['pis', 'pi', 'Pi', 'Pis']:
keyval[0] = 'pi'
keyval[1] = list(map(float, keyval[1].split(',')))
elif keyval[0] not in ['alphabet']:
keyval[1] = float(keyval[1])
kwargs[keyval[0]] = keyval[1]
else:
print ("GTR params are not specified. Creating GTR model with default parameters")
gtr = GTR.standard(model, **kwargs)
infer_gtr = False
except KeyError as e:
print("\nUNKNOWN SUBSTITUTION MODEL\n")
raise e
return gtr
def create_gtr(params):
"""
parse the arguments referring to the GTR model and return a GTR structure
"""
model = params.gtr
gtr_params = params.gtr_params
if model == 'infer':
gtr = GTR.standard('jc', alphabet='aa' if params.aa else 'nuc')
else:
try:
kwargs = {}
if gtr_params is not None:
for param in gtr_params:
keyval = param.split('=')
if len(keyval)!=2: continue
if keyval[0] in ['pis', 'pi', 'Pi', 'Pis']:
keyval[0] = 'pi'
keyval[1] = list(map(float, keyval[1].split(',')))
elif keyval[0] not in ['alphabet']:
keyval[1] = float(keyval[1])
kwargs[keyval[0]] = keyval[1]
else:
print ("GTR params are not specified. Creating GTR model with default parameters")
gtr = GTR.standard(model, **kwargs)
infer_gtr = False
except:
print ("Could not create GTR model from input arguments. Using default (Jukes-Cantor 1969)")
gtr = GTR.standard('jc', alphabet='aa' if params.aa else 'nuc')
infer_gtr = False
return gtr
def create_gtr(params):
"""
parse the arguments referring to the GTR model and return a GTR structure
"""
model = params.gtr
gtr_params = params.gtr_params
if model == 'infer':
gtr = GTR.standard('jc')
else:
try:
kwargs = {}
if gtr_params is not None:
for param in gtr_params:
keyval = param.split('=')
if len(keyval) != 2: continue
if keyval[0] in ['pis', 'pi', 'Pi', 'Pis']:
keyval[0] = 'pi'
keyval[1] = list(map(float, keyval[1].split(',')))
elif keyval[0] not in ['alphabet']:
keyval[1] = float(keyval[1])
kwargs[keyval[0]] = keyval[1]
else:
print(
"GTR params are not specified. Creating GTR model with default parameters"
)
gtr = GTR.standard(model, **kwargs)
infer_gtr = False
except:
print(
"Could not create GTR model from input arguments. Using default (Jukes-Cantor 1969)"
)
gtr = GTR.standard('jc')
infer_gtr = False
return gtr
def test_GTR():
from treetime import GTR
import numpy as np
for model in ['Jukes-Cantor']:
print('testing GTR, model:',model)
myGTR = GTR.standard(model, alphabet='nuc')
print('Frequency sum:', myGTR.Pi.sum())
assert (myGTR.Pi.sum() - 1.0)**2<1e-14
# the matrix is the rate matrix
assert abs(myGTR.Q.sum(0)).sum() < 1e-14
# eigendecomposition is made correctly
n_states = myGTR.v.shape[0]
assert abs((myGTR.v.dot(myGTR.v_inv) - np.identity(n_states)).sum() < 1e-10)
assert np.abs(myGTR.v.sum()) > 1e-10 # **and** v is not zero
def test_GTR():
from treetime import GTR
import numpy as np
for model in ['Jukes-Cantor', 'random']:
print('testing GTR, model:',model)
myGTR = GTR.standard(model, alphabet='nuc')
print('Frequency sum:', myGTR.Pi.sum())
assert (myGTR.Pi.sum() - 1.0)**2<1e-14
# the matrix is the rate matrix
assert abs(myGTR.Q.sum(0)).sum() < 1e-14
# eigendecomposition is made correctly
n_states = myGTR.v.shape[0]
assert abs((myGTR.v.dot(myGTR.v_inv) - np.identity(n_states)).sum() < 1e-10)
assert np.abs(myGTR.v.sum()) > 1e-10 # **and** v is not zero
if params.tree is None:
from treetime.utils import tree_inference
params.tree = os.path.basename(params.aln) + '.nwk'
print("No tree given: inferring tree")
tmp_dir = 'homoplasy_scanner_tmp_files'
tree_inference(params.aln, params.tree, tmp_dir=tmp_dir)
if os.path.isdir(tmp_dir):
shutil.rmtree(tmp_dir)
###########################################################################
### GTR SET-UP
###########################################################################
model = params.gtr
gtr_params = params.gtr_params
if model == 'infer':
gtr = GTR.standard('jc')
infer_gtr = True
else:
infer_gtr = False
try:
kwargs = {}
if gtr_params is not None:
for param in gtr_params:
keyval = param.split('=')
if len(keyval) != 2: continue
if keyval[0] in ['pis', 'pi', 'Pi', 'Pis']:
keyval[1] = map(float, keyval[1].split(','))
elif keyval[0] not in ['alphabet']:
keyval[1] = float(keyval[1])
kwargs[keyval[0]] = keyval[1]
else: