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')