def sim(self):
self.sim_root()
for edge in self.edge_list:
#print edge, self.edge_to_blen[edge]
# Now need to adapt branchsim
# create an instance for each branch
blen = self.edge_to_blen[edge]
num_exon = self.num_exon
x_exon = self.x_exon
x_IGC = deepcopy(self.x_IGC)
log_file = self.log_folder + '_'.join(edge) + '_log.log'
div_file = self.div_folder + '_'.join(edge) + '_div.log'
starting_seq = self.node_to_sequence[edge[0]]
if edge in self.outgroup:
x_IGC[0] = 0.0
self.OneBranchSimulator = OneBranchIGCCodonSimulator(
blen=blen,
num_exon=num_exon,
x_exon=x_exon,
x_IGC=x_IGC,
log_file=log_file,
div_file=div_file,
initial_seq=starting_seq)
blen = self.edge_to_blen[edge]
self.OneBranchSimulator.sim_one_branch(starting_seq, blen)
self.node_to_sequence[
edge[1]] = self.OneBranchSimulator.convert_list_to_seq()
self.total_mut += self.OneBranchSimulator.point_mut_count
self.total_IGC += self.OneBranchSimulator.IGC_total_count
self.total_IGC_sites += self.OneBranchSimulator.IGC_contribution_count
self.total_IGC_changes += self.OneBranchSimulator.IGC_change_sites
self.output_seq()
self.get_log()
self.write_log()
