def init():
SeedSequence_Virus.init()
SequenceEvolution_GTRGammaSeqGen.init()
GC.seed_height = float(GC.seed_height)
assert GC.seed_height > 0, "seed_height must be positive"
assert GC.check_eval_str(GC.seed_speciation_rate_func), "Potentially dangerous seed_speciation_rate_func"
GC.check_seqgen_executable()
def init():
SeedSequence_Virus.init()
SequenceEvolution_GTRGammaSeqGen.init()
GC.seed_birth_rate = float(GC.seed_birth_rate)
assert GC.seed_birth_rate > 0, "seed_birth_rate must be positive"
GC.seed_death_rate = float(GC.seed_death_rate)
assert GC.seed_death_rate >= 0, "seed_death_rate must be at least 0"
GC.check_seqgen_executable()
try:
global treesim
from dendropy.simulate import treesim
except:
from os import chdir
chdir(GC.START_DIR)
assert False, "Error loading DendroPy. Install with: pip3 install dendropy"
def init():
SeedSequence_Virus.init()
SequenceEvolution_GTRGammaSeqGen.init()
GC.seed_population = float(GC.seed_population)
assert GC.seed_population > 0, "seed_population must be positive"
GC.check_seqgen_executable()
try:
global TaxonNamespace
from dendropy import TaxonNamespace
global treesim
from dendropy.simulate import treesim
except:
from os import chdir
chdir(GC.START_DIR)
assert False, "Error loading DendroPy. Install with: pip3 install dendropy"
def init():
GC.seqgen_path = expanduser(GC.seqgen_path.strip())
GC.seqgen_args = GC.seqgen_args.strip()
assert '-d' not in GC.seqgen_args, "Do not use the Seq-Gen -d argument"
assert '-k' not in GC.seqgen_args, "Do not use the Seq-Gen -k argument"
assert '-l' not in GC.seqgen_args, "Do not use the Seq-Gen -l argument"
assert '-n' not in GC.seqgen_args, "Do not use the Seq-Gen -n argument"
assert '-o' not in GC.seqgen_args, "Do not use the Seq-Gen -o argument"
assert '-p' not in GC.seqgen_args, "Do not use the Seq-Gen -p argument"
assert '-s' not in GC.seqgen_args, "Do not use the Seq-Gen -s argument"
assert '-m' in GC.seqgen_args, "Must specify a Seq-Gen model using the -m argument"
mode = GC.seqgen_args.split('-m')[1].strip().split(' ')[0]
assert mode in SEQGEN_MODES.split(', '), "Invalid Seq-Gen model (%s). Options: %s" % (mode,SEQGEN_MODES)
GC.check_seqgen_executable()
try:
global read_tree_newick
from treeswift import read_tree_newick
except:
from os import chdir
chdir(GC.START_DIR)
assert False, "Error loading TreeSwift. Install with: pip3 install treeswift"
def init():
GC.msms_path = expanduser(GC.msms_path.strip())
assert MF.modules[
'ContactNetworkGenerator'].__name__ in GC.COMMUNITY_GENERATORS, "Must use a ContactNetworkGenerator that creates communities (%s)" % ', '.join(
sorted(GC.COMMUNITY_GENERATORS))
SeedSequence_Virus.init()
SequenceEvolution_GTRGammaSeqGen.init()
GC.community_seed_scaled_mutation_rate = float(
GC.community_seed_scaled_mutation_rate)
assert GC.community_seed_scaled_mutation_rate > 0, "community_seed_scaled_mutation_rate must be positive"
assert isinstance(
GC.community_seed_populations, list
), "community_seed_populations must be a list of positive integers"
for i in range(len(GC.community_seed_populations)):
GC.community_seed_populations[i] = int(
GC.community_seed_populations[i])
assert GC.community_seed_populations[
i] > 0, "community_seed_populations must be a list of positive integers"
assert isinstance(
GC.community_seed_migration_rates, dict
), "community_seed_migration_rates must be a dictionary of dictionaries of floats"
try:
for i in range(len(GC.community_seed_populations)):
for j in range(len(GC.community_seed_migration_rates)):
if i == j:
assert i not in GC.community_seed_migration_rates[
i] or float(
GC.community_seed_migration_rates[i][i]
) == 0., "Non-zero self-migration rate found in community_seed_migration_rates"
else:
GC.community_seed_migration_rates[i][j] = float(
GC.community_seed_migration_rates[i][j])
assert GC.community_seed_migration_rates[i][
j] >= 0, "Migration rates in community_seed_migration_rates must be at least 0"
except KeyError:
assert False, "Malformed community_seed_migration_rates dictionary. See FAVITES Wiki for usage information"
GC.check_seqgen_executable()
def init():
SeedSequence_Virus.init()
SequenceEvolution_GTRGammaSeqGen.init()
GC.seed_height = float(GC.seed_height)
assert GC.seed_height > 0, "seed_height must be positive"
GC.check_seqgen_executable()