AVIDA_DIR = path.join(os.pardir, 'avida') # Relative location of the avida directory
verify_file_locs(CUSTOM_EVNS+[CUSTOM_EVENTS], AVIDA_DIR)
seed = input("Please enter the seed number (digits of UT EID): ")
username = raw_input("Please enter your first name: ").lower()
moved_cfgs = move_files("temp", EVN, EVENTS) # If there already exists an environment.cfg or evemts.cfg file, move it out of the way
try:
os.rename(CUSTOM_EVENTS, EVENTS)
for cfg in CUSTOM_EVNS:
os.rename(cfg, EVN)
run = 1
run_avida(seed)
display_msg("Run "+str(run) +" of avida completed.")
run += 1
os.rename(ENV, cfg)
data_src = path.join('data','detail-100000.spop')
data_dest = path.join(os.pardir, 'saved_data', username)
dest = move_files(data_dest, data_src)
if run == 1:
os.rename(dest[0],path.join(path.dirname(dest[0]), "native-detail-100000.spop"))
if run == 2: #it shouldn't run more than twice, but I don't want it to fail if it does
os.rename(dest[0],path.join(path.dirname(dest[0]), "invasive-detail-100000.spop"))
finally:
os.rename(EVENTS, CUSTOM_EVENTS)
move_files(os.curdir, *moved_cfgs)
display_msg("Script has finished.")
user_pops_dir = path.join(os.pardir, 'saved_data', username)
user_pop_files = []
for pop in POPULATION_FILES:
user_pop_files.append(path.join(user_pops_dir,pop))
required_files = [CUSTOM_EVENTS] + CUSTOM_EVNS + [CUSTOM_ANALYZE] + user_pop_files
verify_file_locs(required_files, AVIDA_DIR)
moved_cfgs = move_files("temp", EVN, ANALYZE) # If there already exists configuration files, move them out of the way
moved_pop_files = move_files(os.curdir, *user_pop_files)
try:
os.rename(CUSTOM_EVNS[0], EVN)
os.rename(CUSTOM_ANALYZE, ANALYZE)
# find the dominant sequence
run_avida(-1)
display_msg("Analysis complete")
moved_cfgs += move_files("temp", EVENTS)
os.rename(ANALYZE, CUSTOM_ANALYZE)
with open("data/dom_genotype.dat") as fp:
for line in fp:
if re.match(r'[^#]\w+', line):
dom_genotype = line.strip()
break
# edit the events.cfg file
with open(CUSTOM_EVENTS) as fp:
detail_line = re.compile(r"(.*InjectSequence\s)(\w+)")
fo = open("events.cfg", "w")
for line in fp:
if detail_line.match(line):
verify_file_locs(CUSTOM_EVNS + [CUSTOM_EVENTS], AVIDA_DIR)
seed = input("Please enter the seed number (digits of UT EID): ")
username = raw_input("Please enter your first name: ").lower()
moved_cfgs = move_files(
"temp", EVN, EVENTS
) # If there already exists an environment.cfg or evemts.cfg file, move it out of the way
try:
os.rename(CUSTOM_EVENTS, EVENTS)
for cfg in CUSTOM_EVNS:
os.rename(cfg, EVN)
run = 1
run_avida(seed)
display_msg("Run " + str(run) + " of avida completed.")
run += 1
os.rename(ENV, cfg)
data_src = path.join('data', 'detail-100000.spop')
data_dest = path.join(os.pardir, 'saved_data', username)
dest = move_files(data_dest, data_src)
if run == 1:
os.rename(
dest[0],
path.join(path.dirname(dest[0]), "native-detail-100000.spop"))
if run == 2: #it shouldn't run more than twice, but I don't want it to fail if it does
os.rename(
dest[0],
path.join(path.dirname(dest[0]),
"invasive-detail-100000.spop"))
user_pop_files.append(path.join(user_pops_dir, pop))
required_files = [CUSTOM_EVENTS] + CUSTOM_EVNS + [CUSTOM_ANALYZE
] + user_pop_files
verify_file_locs(required_files, AVIDA_DIR)
moved_cfgs = move_files(
"temp", EVN, ANALYZE
) # If there already exists configuration files, move them out of the way
moved_pop_files = move_files(os.curdir, *user_pop_files)
try:
os.rename(CUSTOM_EVNS[0], EVN)
os.rename(CUSTOM_ANALYZE, ANALYZE)
# find the dominant sequence
run_avida(-1)
display_msg("Analysis complete")
moved_cfgs += move_files("temp", EVENTS)
os.rename(ANALYZE, CUSTOM_ANALYZE)
with open("data/dom_genotype.dat") as fp:
for line in fp:
if re.match(r'[^#]\w+', line):
dom_genotype = line.strip()
break
# edit the events.cfg file
with open(CUSTOM_EVENTS) as fp:
detail_line = re.compile(r"(.*InjectSequence\s)(\w+)")
fo = open("events.cfg", "w")
for line in fp:
if detail_line.match(line):
