def make_genomes(genesis):
#Create a genome and a complementing genome
genome = au.genesis_seqs(genesis)
seqprime = genome
repeats = re.search(re.compile('c{3,}'), seqprime).group()
seqprime = seqprime.replace(repeats, repeats.replace('c', 'b'))
org_fname2 = au.save_genome(genesis, seqprime, org_fname + '.comp')
def make_genomes(genesis):
#Create a genome and a complementing genome
genome = au.genesis_seqs(genesis)
seqprime = genome
repeats = re.search(re.compile('c{3,}'),seqprime).group()
seqprime =seqprime.replace(repeats,repeats.replace('c','b'))
org_fname2 = au.save_genome(genesis, seqprime, org_fname + '.comp')
def differential_mut(name, eve_fname, org_fname, ana_fname, env_fname, ins_fname, gen_name):
#CONFIG PARAMETERS
mut_rate_source = 2
x = default_x
y = default_y
params_dict = {'MUT_RATE_SOURCE':2,
'WORLD_X':x,
'WORLD_Y':y,
'WORLD_GEOMETRY':2,
'ENVIRONMENT_FILE':env_fname,
'ANALYZE_FILE':ana_fname,
'EVENT_FILE':eve_fname,
'INST_SET':ins_fname,
'START_CREATURE':org_fname,
'DIVIDE_INS_PROB':0.0,
'DIVIDE_DEL_PROB':0.0,
'COPY_MUT_PROB':0.00}
genesis = ca.make_gen(name,\
params_dict,\
gen_name)
#Create a genome and a complementing genome
genome = au.genesis_seqs(genesis)
seqprime = genome
repeats = re.search(re.compile('c{3,}'),seqprime).group()
seqprime =seqprime.replace(repeats,repeats.replace('c','b'))
org_fname2 = au.save_genome(genesis, seqprime, org_fname + '.comp')
n = x * y
ntot = x*y
nofs = ntot/2
#STERILIZE
ca.alter_eve(eve_fname, 'i KillRectangle 0 0 '+str(x) + ' ' + str(y))
#SET MUTATION PROBS
highmut_strings = ['i SetMutProb COPY_MUT '+str((mu0 - deltamu)*kmut) + ' 1 '+str(nofs),
'i SetMutProb DIVIDE_INS '+str((mu0 - deltamu)*kdiv) + ' 1 '+str(nofs),
'i SetMutProb DIVIDE_DEL '+str((mu0 - deltamu)*kdiv) + ' 1 '+str(nofs)]
lowmut_strings = ['i SetMutProb COPY_MUT '+str((mu0 + deltamu)*kmut) + ' ' + str(nofs+1) + ' ' +str(ntot),
'i SetMutProb DIVIDE_INS '+str((mu0 + deltamu)*kdiv) + ' ' + str(nofs+1) + ' ' +str(ntot),
'i SetMutProb DIVIDE_DEL '+str((mu0 + deltamu)*kdiv) + ' ' + str(nofs+1) + ' ' +str(ntot)]
for s in highmut_strings:
ca.alter_eve(eve_fname, s)
for s in lowmut_strings:
ca.alter_eve(eve_fname, s)
#INJECT
ca.alter_eve(eve_fname,
'i InjectRange '+org_fname+' 1 '+str(nofs)+' -1 0')
ca.alter_eve(eve_fname,
'i InjectRange '+org_fname+' '+str(nofs+1)+ ' ' +str(ntot) +' -1 1')
#get a default set of resources, tasks, rxns and corresponding params
task_names, res_names, resource_ropts = get_resources()
task_names_b, res_names_b, resource_ropts_b = get_resources(distribution = 'gravity',
ygrav = default_ygrav,
outflow = biproduct_outflow,
inflow = 0,
kind = 'byproduct')
if enable_biproducts:
if biproduct_last: biproducts= shift(res_names_b, -1)
else: biproducts = res_names_b
else:
biproducts = None
rxn_names, rxn_popts, rxn_ropts = get_reactions(res_names,
conversion = conversion,
product_names = biproducts)
if death_chain_reaction: b_prods = res_names_b
else:b_prods = res_names
rslines = au.resource_lines(res_names, resource_ropts)
rxlines = au.reaction_lines(rxn_names, task_names,rxn_popts,rxn_ropts)
ca.append_lines(env_fname, rslines)
if enable_biproducts:
rxn_names_b, rxn_popts_b, rxn_ropts_b = get_reactions(res_names_b,
lethal = lethal_biproduct,
min_count = lethal_dose,
product_names = b_prods,
conversion = death_chain_mag,
bonus_type = 'mult',
values = [0 for i in res_names])
rslines_b = au.resource_lines(res_names_b, resource_ropts_b)
rxlines_b = au.reaction_lines(rxn_names_b, task_names_b,rxn_popts_b,rxn_ropts_b)
ca.append_lines(env_fname, rslines_b)
ca.append_lines(env_fname, rxlines_b)
ca.append_lines(env_fname, rxlines)
#EXIT
ca.alter_eve(eve_fname, 'g ' + str(default_gens) + ' Exit')