from os import path
# Module is scripts/helper_functions.py
from helper_functions import verify_file_locs, move_files, display_msg, run_avida
EVN = "environment.cfg"
CUSTOM_EVNS = ["native_environment.cfg", "invasive_environment.cfg"] # Required configuration files for this script
EVENTS = "events.cfg"
CUSTOM_EVENTS = "create_pop_events.cfg"
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:
CUSTOM_ANALYZE = "invasive_analyze.cfg"
POPULATION_FILES = ["native-detail-100000.spop", "invasive-detail-100000.spop"]
NUM_OF_TRIALS = 5
NUM_OF_INVADERS = 5
# move the population files
username = raw_input("Please enter your first name or the name of the directory\nin the 'saved_data' directory: ").lower()
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()
from helper_functions import verify_file_locs, move_files, display_msg, run_avida
EVN = "environment.cfg"
CUSTOM_EVNS = ["native_environment.cfg", "invasive_environment.cfg"
] # Required configuration files for this script
EVENTS = "events.cfg"
CUSTOM_EVENTS = "create_pop_events.cfg"
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)
NUM_OF_INVADERS = 5
# move the population files
username = raw_input(
"Please enter your first name or the name of the directory\nin the 'saved_data' directory: "
).lower()
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):