def differential_mut(name,
gen_name = None,
geo_name = 'star',
mut = mu0,
delta = deltamu,
dim = 20,
**kwargs):
#CONFIG PARAMETERS
mut_rate_source = 2
params_dict = {'MUT_RATE_SOURCE':mut_rate_source,
'DIVIDE_INS_PROB':0.0,
'DIVIDE_DEL_PROB':0.0,
'COPY_MUT_PROB':0.00}
#deal with filenames in KWARGS
env = kwargs
configure_paths(params_dict, env)
globals().update(env)
#make GEOMETRY
geometry = make_geometry(params_dict,
name = geo_name,
dim = dim)
ntot =geometry['n']
nofs = ntot/2
globals().update(geometry)
#STERILIZE
ca.alter_eve(eve_fname, 'i KillRectangle 0 0 '+str(x)\
+ ' ' + str(y))
#BUILD LINEAGES AND INJECT
linfun = diffmut_lin;
linints= [0,nofs,ntot-1]
make_lineage_squares(linints, linfun, mut, delta)
#get a default set of resources, tasks, rxns and corresponding params
make_resources_and_tasks(params_dict,
n = ntot)
#EXIT
ca.alter_eve(eve_fname, 'g ' + str(default_gens) + ' Exit')
#NOW THAT ALL OF THE PARAMETERS HAVE BEEN SET
#MAKE THE GENESIS FILES AND GENOMES
genesis = ca.make_gen(name,\
params_dict,
gen_name)
make_genomes(genesis)
out = {'geometry': geometry}
return out
def differential_mut(name,
gen_name=None,
geo_name='star',
mut=mu0,
delta=deltamu,
dim=20,
**kwargs):
#CONFIG PARAMETERS
mut_rate_source = 2
params_dict = {
'MUT_RATE_SOURCE': mut_rate_source,
'DIVIDE_INS_PROB': 0.0,
'DIVIDE_DEL_PROB': 0.0,
'COPY_MUT_PROB': 0.00
}
#deal with filenames in KWARGS
env = kwargs
configure_paths(params_dict, env)
globals().update(env)
#make GEOMETRY
geometry = make_geometry(params_dict, name=geo_name, dim=dim)
ntot = geometry['n']
nofs = ntot / 2
globals().update(geometry)
#STERILIZE
ca.alter_eve(eve_fname, 'i KillRectangle 0 0 '+str(x)\
+ ' ' + str(y))
#BUILD LINEAGES AND INJECT
linfun = diffmut_lin
linints = [0, nofs, ntot - 1]
make_lineage_squares(linints, linfun, mut, delta)
#get a default set of resources, tasks, rxns and corresponding params
make_resources_and_tasks(params_dict, n=ntot)
#EXIT
ca.alter_eve(eve_fname, 'g ' + str(default_gens) + ' Exit')
#NOW THAT ALL OF THE PARAMETERS HAVE BEEN SET
#MAKE THE GENESIS FILES AND GENOMES
genesis = ca.make_gen(name,\
params_dict,
gen_name)
make_genomes(genesis)
out = {'geometry': geometry}
return out
def make_lineage_squares(endpts, linfun, mut, delta):
#convert from pythonic endpoints (zero based, open ended)
#to avida's endpoint style
intervals = [(e[0], e[1]) for e in zip(endpts, roll(endpts, -1))][:-1]
#CALL LINFUN TO SET UP CONDITIONS FOR EACH LINEAGE
lineage_lines = linfun(intervals, mut, delta)
for l in lineage_lines:
ca.alter_eve(eve_fname, l)
#INJECT EACH LINEAGE
for i, e in enumerate(intervals):
ca.alter_eve(eve_fname,
'i InjectRange '+org_fname+\
' {0} {1} '.format(*e)+\
' -1 {0}'.format(i))
def make_lineage_squares(endpts, linfun,mut,delta):
#convert from pythonic endpoints (zero based, open ended)
#to avida's endpoint style
intervals = [(e[0], e[1] )
for e in zip(endpts, roll(endpts ,-1))][:-1]
#CALL LINFUN TO SET UP CONDITIONS FOR EACH LINEAGE
lineage_lines = linfun(intervals, mut,delta)
for l in lineage_lines: ca.alter_eve(eve_fname, l)
#INJECT EACH LINEAGE
for i,e in enumerate(intervals):
ca.alter_eve(eve_fname,
'i InjectRange '+org_fname+\
' {0} {1} '.format(*e)+\
' -1 {0}'.format(i))
def make_cfg(plot_params,
name=default_name,
geo='square',
mut=.002,
delta=.0005,
dim=20):
if not os.path.isdir(name):
os.mkdir(name)
import shutil
flist = os.listdir(name)
cfg_start = cfg.dataPath('avida_default_cfgfiles')
for r, d, files in os.walk(cfg_start):
for f in files:
if f in flist:
continue
shutil.copyfile(os.path.join(r, f), os.path.join(name, f))
#default_file = open(os.path.join(name,'avida.cfg'))
outfile = open(os.path.join(name, 'avida.cfg.auto'), 'w')
outfile.write('#avida.cfg generated by python.')
#lines = default_file.readlines()
auto_dir = os.path.join(name, os.path.join('autogen'))
if not os.path.isdir(auto_dir):
os.mkdir(auto_dir)
eve_fname = ca.make_eve(name, default_evename)
org_fname = ca.make_org(name, default_orgname)
ana_fname = ca.make_ana(name, default_ananame)
env_fname = ca.make_env(name, default_envname)
ins_fname = ca.make_ins(name, default_insname)
computed = presets.differential_mut(name,
mut=mut,
geo_name=geo,
delta=delta,
dim=dim,
eve_fname=eve_fname,
org_fname=org_fname,
ana_fname=ana_fname,
env_fname=env_fname,
ins_fname=ins_fname,
gen_name=default_genname)
for pp in plot_params:
pp['computed'] = computed
print
print 'setting print params: '
print
for p in plot_params:
if p['type'] == 'ts':
colstr = ''
for col in p.get('command_params', []):
colstr += col + ' '
printstr = p['update'] + ' ' + p['command'] + ' ' + p[
'fname'] + ' ' + colstr
ca.alter_eve(eve_fname, printstr)
elif p['type'] == 'grid':
printstr = p['update'] + ' ' + p['command'] + ' ' + p['fname']
ca.alter_eve(eve_fname, printstr)
f = open(eve_fname).read()
print f
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')
def periodic_res(eve_fname, period, res_name, injection):
ca.alter_eve(eve_fname, period + ' ' + 'SetCellResource ' +'0' + ' ' +res_name+ ' ' + str(injection))
def make_cfg(plot_params,
name =default_name,
geo = 'square',
mut = .002,
delta = .0005,
dim = 20):
if not os.path.isdir(name):
os.mkdir(name)
import shutil
flist = os.listdir(name)
cfg_start = cfg.dataPath('avida_default_cfgfiles')
for r,d,files in os.walk(cfg_start):
for f in files:
if f in flist:
continue
shutil.copyfile(os.path.join(r,f),
os.path.join(name, f))
#default_file = open(os.path.join(name,'avida.cfg'))
outfile = open(os.path.join(name,'avida.cfg.auto'),'w')
outfile.write('#avida.cfg generated by python.')
#lines = default_file.readlines()
auto_dir = os.path.join(name,os.path.join('autogen'))
if not os.path.isdir(auto_dir):
os.mkdir(auto_dir)
eve_fname = ca.make_eve(name,default_evename)
org_fname = ca.make_org(name,default_orgname)
ana_fname = ca.make_ana(name,default_ananame)
env_fname = ca.make_env(name,default_envname)
ins_fname = ca.make_ins(name,default_insname)
computed = presets.differential_mut(name,
mut = mut,
geo_name = geo,
delta = delta,
dim = dim,
eve_fname = eve_fname,
org_fname = org_fname,
ana_fname = ana_fname,
env_fname = env_fname,
ins_fname = ins_fname,
gen_name = default_genname)
for pp in plot_params:
pp['computed'] = computed
print
print 'setting print params: '
print
for p in plot_params:
if p['type'] == 'ts':
colstr = ''
for col in p.get('command_params',[]):
colstr += col + ' '
printstr = p['update']+' '+p['command'] +' '+p['fname'] + ' '+colstr
ca.alter_eve(eve_fname, printstr)
elif p['type'] == 'grid':
printstr = p['update'] + ' ' + p['command'] + ' ' + p['fname']
ca.alter_eve(eve_fname, printstr)
f = open(eve_fname).read()
print f
def periodic_res(eve_fname, period, res_name, injection):
ca.alter_eve(
eve_fname, period + ' ' + 'SetCellResource ' + '0' + ' ' + res_name +
' ' + str(injection))
