def simulate_from_record(
self, record, output_dir, name, tmpdir, datatype=None, allow_nonsense=False, split_lengths=None, gene_names=None
):
if not datatype:
datatype = self.datatype
if datatype == "protein":
SeqSim.simulate_from_record_WAG(record, output_dir, name, tmpdir, allow_nonsense, split_lengths, gene_names)
elif datatype == "dna":
SeqSim.simulate_from_record_GTR(record, output_dir, name, tmpdir, allow_nonsense, split_lengths, gene_names)
else:
print "datatype {0} is not recognised".format(datatype)
def simulate_from_record(
self,
record,
output_dir,
name,
tmpdir,
datatype=None,
allow_nonsense=False,
split_lengths=None,
gene_names=None,
):
if not datatype:
datatype = self.datatype
if datatype == 'protein':
SeqSim.simulate_from_record_WAG(
record,
output_dir,
name,
tmpdir,
allow_nonsense,
split_lengths,
gene_names,
)
elif datatype == 'dna':
SeqSim.simulate_from_record_GTR(
record,
output_dir,
name,
tmpdir,
allow_nonsense,
split_lengths,
gene_names,
)
else:
print 'datatype {0} is not recognised'.format(datatype)
tune = args['tune']
regime = args['regime']
permutation_strength = args['permutations']
permutation_type = args['class_permuter']
master_tree_generator = args['master']
filepath = args['directory']
if 'TEMPORARY_DIRECTORY' in os.environ:
tmpdir = os.environ['TEMPORARY_DIRECTORY']
else:
tmpdir = args['temp_directory']
indels = args['indels']
ratevar = args['ratevar']
quiet = args['quiet']
gtp_path = args['geodesic']
sim = SeqSim('base')
sim.hky_model(
alpha=3.551,
beta=1,
Afreq=0.31,
Cfreq=0.18,
Gfreq=0.21,
Tfreq=0.3,
)
if indels:
sim.indels()
if ratevar:
sim.rate_variation()