def sample_times(node, num_times):
assert hasattr(
GC, 'transmissions'
), "No transmission network found in global context! Run this after the transmission network simulation is done"
first_time = node.get_first_infection_time()
if first_time is None:
return []
windows = []
last_time = first_time
for u, v, t in GC.transmissions:
if u == node and v == node:
if last_time is not None and t > last_time:
windows.append((last_time, t))
last_time = None
elif last_time is None and v == node:
last_time = t
if last_time is not None and t > last_time:
windows.append((last_time, GC.time))
if len(windows) == 0:
windows.append((first_time, GC.time))
weighted_die = {}
for start, end in windows:
weighted_die[(start, end)] = end - start
if len(weighted_die) == 0:
return []
if len(weighted_die) == 1:
weighted_die[list(weighted_die.keys())[0]] = 1
out = []
for _ in range(num_times):
start, end = GC.roll(weighted_die)
out.append(uniform(start, end))
return out
def subsample_transmission_network():
nodes = {GC.contact_network.get_node(n) for n in GC.final_sequences}
die = {}
for u, v, t in GC.contact_network.get_transmissions():
if u not in die:
die[u] = 1
else:
die[u] += 1
if v not in die:
die[v] = 1
else:
die[v] += 1
die = {n: die[n] for n in nodes if n in die}
num_sample = GC.node_sample_fraction * len(die.keys())
out = []
while len(die) != 0 and len(out) < num_sample:
n = GC.roll(die)
out.append(n)
die.pop(n)
return out
def prep_GEMF():
# check for gender attribute in contact network nodes
for node in GC.contact_network.nodes_iter():
attr = node.get_attribute()
assert 'MALE' in attr or 'FEMALE' in attr, "All nodes must have MALE or FEMALE in their attributes"
assert not ('MALE' in attr and 'FEMALE'
in attr), "Nodes cannot be both MALE and FEMALE"
# write GEMF parameter file
orig_dir = getcwd()
GC.gemf_path = expanduser(GC.gemf_path.strip())
makedirs(GC.gemf_out_dir, exist_ok=True)
f = open(GC.gemf_out_dir + "/para.txt", 'w')
f.write("[NODAL_TRAN_MATRIX]\n0\t" + str(GC.gon_ma_to_ms) +
"\t0\t0\t0\t0\t0\t0\n" + str(GC.gon_ms_to_ma) + "\t0\t" +
str(GC.gon_ms_to_mis_seed) + "\t" +
str(GC.gon_ms_to_mia_seed) + "\t0\t0\t0\t0\n" +
str(GC.gon_mis_to_ma) + "\t" + str(GC.gon_mis_to_ms) +
"\t0\t0\t0\t0\t0\t0\n" + str(GC.gon_mia_to_ma) + "\t" +
str(GC.gon_mia_to_ms) + "\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t" +
str(GC.gon_fa_to_fs) + "\t0\t0\n0\t0\t0\t0\t" +
str(GC.gon_fs_to_fa) + "\t0\t" + str(GC.gon_fs_to_fis_seed) +
"\t" + str(GC.gon_fs_to_fia_seed) + "\n0\t0\t0\t0\t" +
str(GC.gon_fis_to_fa) + "\t" + str(GC.gon_fis_to_fs) +
"\t0\t0\n0\t0\t0\t0\t" + str(GC.gon_fia_to_fa) + "\t" +
str(GC.gon_fia_to_fs) + "\t0\t0\n\n") # Gonorrhea-specific
f.write("[EDGED_TRAN_MATRIX]\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.gon_ms_to_mis_by_mis) +
"\t" + str(GC.gon_ms_to_mia_by_mis) +
"\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t"
+ str(GC.gon_fs_to_fis_by_mis) + "\t" +
str(GC.gon_fs_to_fia_by_mis) +
"\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.gon_ms_to_mis_by_mia) +
"\t" + str(GC.gon_ms_to_mia_by_mia) +
"\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t"
+ str(GC.gon_fs_to_fis_by_mia) + "\t" +
str(GC.gon_fs_to_fia_by_mia) +
"\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.gon_ms_to_mis_by_fis) +
"\t" + str(GC.gon_ms_to_mia_by_fis) +
"\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t"
+ str(GC.gon_fs_to_fis_by_fis) + "\t" +
str(GC.gon_fs_to_fia_by_fis) +
"\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.gon_ms_to_mis_by_fia) +
"\t" + str(GC.gon_ms_to_mia_by_fia) +
"\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t"
+ str(GC.gon_fs_to_fis_by_fia) + "\t" +
str(GC.gon_fs_to_fia_by_fia) +
"\n0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write("[STATUS_BEGIN]\n0\n\n")
infectious = ['MIS', 'MIA', 'FIS', 'FIA']
f.write("[INDUCER_LIST]\n" +
' '.join([str(GC.gemf_state_to_num[e])
for e in infectious]) + "\n\n")
f.write("[SIM_ROUNDS]\n1\n\n")
f.write("[INTERVAL_NUM]\n1\n\n")
f.write("[MAX_TIME]\n" + str(GC.end_time) + "\n\n")
f.write("[MAX_EVENTS]\n" + str(GC.C_INT_MAX) + "\n\n")
f.write("[DIRECTED]\n1\n\n")
f.write("[SHOW_INDUCER]\n1\n\n")
f.write(
"[DATA_FILE]\nnetwork.txt\nnetwork.txt\nnetwork.txt\nnetwork.txt\n\n"
)
f.write("[STATUS_FILE]\nstatus.txt\n\n")
if GC.random_number_seed is not None:
f.write("[RANDOM_SEED]\n%d\n\n" % GC.random_number_seed)
f.write("[OUT_FILE]\noutput.txt")
f.close()
# write GEMF network file
f = open(GC.gemf_out_dir + "/network.txt", 'w')
num2node = {}
node2num = {}
for edge in GC.contact_network.edges_iter():
u = edge.get_from()
v = edge.get_to()
if u not in node2num:
num = len(node2num) + 1
node2num[u] = num
num2node[num] = u
if v not in node2num:
num = len(node2num) + 1
node2num[v] = num
num2node[num] = v
f.write(str(node2num[u]) + '\t' + str(node2num[v]) + '\n')
f.close()
# write GEMF to original mapping
f = open(GC.gemf_out_dir + "/gemf2orig.json", 'w')
f.write(str({num: num2node[num].get_name() for num in num2node}))
f.close()
# write GEMF status file (MA = 0, MS = 1, MIS = 2, MIA = 3, FA = 4, FS = 5, FIS = 6, FIA = 7)
f = open(GC.gemf_out_dir + "/status.txt", 'w')
seeds = {seed
for seed in GC.seed_nodes
} # seed nodes are assumed to be asymptomatic
for num in sorted(num2node.keys()):
node = num2node[num]
attr = node.get_attribute()
if node in seeds:
if 'MALE' in attr:
f.write(str(GC.gemf_state_to_num['MIA']) +
"\n") # Gonorrhea-specific
node.gemf_state = GC.gemf_state_to_num['MIA']
else:
f.write(str(GC.gemf_state_to_num['FIA']) +
"\n") # Gonorrhea-specific
node.gemf_state = GC.gemf_state_to_num['FIA']
else:
if 'MALE' in attr:
f.write(str(GC.gemf_state_to_num['MS']) +
"\n") # Gonorrhea-specific
node.gemf_state = GC.gemf_state_to_num['MS']
else:
f.write(str(GC.gemf_state_to_num['FS']) +
"\n") # Gonorrhea-specific
node.gemf_state = GC.gemf_state_to_num['FS']
f.close()
# run GEMF
chdir(GC.gemf_out_dir)
try:
call([GC.gemf_path], stdout=open("log.txt", 'w'))
except FileNotFoundError:
chdir(GC.START_DIR)
assert False, "GEMF executable was not found: %s" % GC.gemf_path
chdir(orig_dir)
# reload edge-based matrices for ease of use
matrices = open(GC.gemf_out_dir + '/para.txt').read().strip()
outside_infection_matrix = [[
float(e) for e in l.split()
] for l in matrices[matrices.index('[NODAL_TRAN_MATRIX]'):matrices.
index('\n\n[EDGED_TRAN_MATRIX]')].replace(
'[NODAL_TRAN_MATRIX]\n', '').splitlines()]
matrices = [[
[float(e) for e in l.split()] for l in m.splitlines()
] for m in matrices[matrices.index('[EDGED_TRAN_MATRIX]'):matrices.
index('\n\n[STATUS_BEGIN]')].replace(
'[EDGED_TRAN_MATRIX]\n', '').split('\n\n')]
matrices = {
GC.gemf_state_to_num[infectious[i]]: matrices[i]
for i in range(len(infectious))
}
matrices[GC.gemf_state_to_num['MS']] = outside_infection_matrix
matrices[GC.gemf_state_to_num['FS']] = outside_infection_matrix
# convert GEMF output to FAVITES transmission network format
GC.transmission_num = 0
GC.transmission_state = set() # 'node' and 'time'
NUM_INFECTED = len(seeds)
GC.transmission_file = []
for line in open(GC.gemf_out_dir + "/output.txt"):
t, rate, vNum, pre, post, num0, num1, num2, num3, num4, num5, num6, num7, lists = [
i.strip() for i in line.split()
]
pre, post = int(pre), int(post)
vName = num2node[int(vNum)].get_name()
lists = lists.split('],[')
lists[0] += ']'
lists[-1] = '[' + lists[-1]
for i in range(1, len(lists) - 1):
if '[' not in lists[i]:
lists[i] = '[' + lists[i] + ']'
lists = [eval(l) for l in lists]
uNums = []
for l in lists:
uNums.extend(l)
if post in {
GC.gemf_state_to_num[i]
for i in ['MA', 'MS', 'FA', 'FS']
} and pre in {
GC.gemf_state_to_num[i]
for i in ['MIS', 'MIA', 'FIS', 'FIA']
}:
NUM_INFECTED -= 1
GC.transmission_file.append((vName, vName, float(t)))
if GC.VERBOSE:
print(
'[%s] Uninfection\tTime %s\tNode %s (%s->%s)\tTotal Infected: %d\tTotal Uninfected: %d'
% (datetime.now(), t, vName, GC.gemf_num_to_state[pre],
GC.gemf_num_to_state[post], NUM_INFECTED,
len(num2node) - NUM_INFECTED),
file=stderr)
elif GC.gemf_num_to_state[pre] in [
'MS', 'FS'
] and GC.gemf_num_to_state[post] in ['MIS', 'MIA', 'FIS', 'FIA']:
NUM_INFECTED += 1
v = num2node[int(vNum)]
uNodes = [num2node[num] for num in uNums]
uRates = [
matrices[uNode.gemf_state][pre][post] for uNode in uNodes
]
die = {
uNodes[i]: GC.prob_exp_min(i, uRates)
for i in range(len(uNodes))
}
if len(die) != 0:
u = GC.roll(
die
) # roll die weighted by exponential infectious rates
uName = u.get_name()
if GC.VERBOSE:
print(
'[%s] Infection\tTime %s\tFrom Node %s (%s)\tTo Node %s (%s->%s)\tTotal Infected: %d\tTotal Uninfected: %d'
% (datetime.now(), t, uName,
GC.gemf_num_to_state[u.gemf_state], vName,
GC.gemf_num_to_state[pre],
GC.gemf_num_to_state[post], NUM_INFECTED,
len(num2node) - NUM_INFECTED),
file=stderr)
elif len(die) == 0 or u == v: # new seed
uName = None
if GC.VERBOSE:
print(
'[%s] Seed\tTime %s\tNode %s\tTotal Infected: %d\tTotal Uninfected: %d'
% (datetime.now(), t, vName, NUM_INFECTED,
len(num2node) - NUM_INFECTED),
file=stderr)
GC.transmission_file.append((uName, v.get_name(), float(t)))
elif GC.VERBOSE:
print('[%s] Transition\tTime %s\tNode %s (%s->%s)' %
(datetime.now(), t, vName, GC.gemf_num_to_state[pre],
GC.gemf_num_to_state[post]),
file=stderr)
num2node[int(vNum)].gemf_state = post
assert len(
GC.transmission_file) != 0, "GEMF didn't output any transmissions"
GC.gemf_ready = True
def prep_GEMF():
# check for attributes in contact network nodes
for node in GC.contact_network.nodes_iter():
attr = node.get_attribute()
assert 'MALE' in attr or 'FEMALE' in attr, "All nodes must have MALE or FEMALE in their attributes"
assert not ('MALE' in attr and 'FEMALE'
in attr), "Nodes cannot be both MALE and FEMALE"
if 'MALE' in attr:
assert 'CIRCUMCISED' in attr or 'UNCIRCUMCISED' in attr, "MALE nodes must be either CIRCUMCISED or UNCIRCUMCISED"
else:
assert 'CIRCUMCISED' not in attr, "FEMALE nodes cannot be CIRCUMCISED"
# write GEMF parameter file
orig_dir = getcwd()
GC.gemf_path = expanduser(GC.gemf_path.strip())
makedirs(GC.gemf_out_dir, exist_ok=True)
f = open(GC.gemf_out_dir + "/para.txt", 'w')
f.write("[NODAL_TRAN_MATRIX]\n")
f.write(
"0\t" + str(GC.hiv_msu_to_mspc) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_msu_to_d) + "\n")
f.write(
"0\t0\t" + str(GC.hiv_mspc_to_msch) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_mspc_to_d) + "\n")
f.write(
"0\t0\t0\t" + str(GC.hiv_msch_to_msc) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_msch_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_msc_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t" + str(GC.hiv_miah_to_mia) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_miah_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mia_to_mi1) + "\t" +
str(GC.hiv_mia_to_mi2) + "\t" + str(GC.hiv_mia_to_mi3) + "\t" +
str(GC.hiv_mia_to_mi4) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_mia_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mi1_to_mi2) + "\t0\t0\t" +
str(GC.hiv_mi1_to_mj1) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_mi1_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mi2_to_mi3) + "\t0\t0\t" +
str(GC.hiv_mi2_to_mj2) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_mi2_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mi3_to_mi4) +
"\t0\t0\t" + str(GC.hiv_mi3_to_mj3) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_mi3_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_mi4_to_mj4) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_mi4_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mj1_to_mj2) +
"\t0\t0\t" + str(GC.hiv_mj1_to_mt1) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_mj1_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mj2_to_mj3) +
"\t0\t0\t" + str(GC.hiv_mj2_to_mt2) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_mj2_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_mj3_to_mj4) + "\t0\t0\t" + str(GC.hiv_mj3_to_mt3) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_mj3_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_mj4_to_mt4) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_mj4_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mt1_to_mi1) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mt1_to_mt2) +
"\t0\t0\t" + str(GC.hiv_mt1_to_ma1) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_mt1_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mt2_to_mi2) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mt2_to_mt3) +
"\t0\t0\t" + str(GC.hiv_mt2_to_ma2) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_mt2_to_d) + "\n")
f.write("0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mt3_to_mi3) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mt3_to_mt4) +
"\t0\t0\t" + str(GC.hiv_mt3_to_ma3) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_mt3_to_d) + "\n")
f.write("0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_mt4_to_mi4) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_mt4_to_ma4) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_mt4_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t" + str(GC.hiv_ma1_to_mi1) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_ma1_to_ma2) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_ma1_to_d) + "\n")
f.write("0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_ma2_to_mi2) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_ma2_to_ma3) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_ma2_to_d) + "\n")
f.write("0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_ma3_to_mi3) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_ma3_to_ma4) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_ma3_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_ma4_to_mi4) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_ma4_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fs_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fia_to_fi1) + "\t" + str(GC.hiv_fia_to_fi2) + "\t" +
str(GC.hiv_fia_to_fi3) + "\t" + str(GC.hiv_fia_to_fi4) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_fia_to_d) +
"\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fi1_to_fi2) + "\t0\t0\t" + str(GC.hiv_fi1_to_fj1) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_fi1_to_d) +
"\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fi2_to_fi3) + "\t0\t0\t" + str(GC.hiv_fi2_to_fj2) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_fi2_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fi3_to_fi4) + "\t0\t0\t" + str(GC.hiv_fi3_to_fj3) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_fi3_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fi4_to_fj4) + "\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_fi4_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fj1_to_fj2) + "\t0\t0\t" + str(GC.hiv_fj1_to_ft1) +
"\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_fj1_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fj2_to_fj3) + "\t0\t0\t" + str(GC.hiv_fj2_to_ft2) +
"\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_fj2_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fj3_to_fj4) + "\t0\t0\t" + str(GC.hiv_fj3_to_ft3) +
"\t0\t0\t0\t0\t0\t" + str(GC.hiv_fj3_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fj4_to_ft4) + "\t0\t0\t0\t0\t" +
str(GC.hiv_fj4_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_ft1_to_fi1) + "\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_ft1_to_ft2) + "\t0\t0\t" + str(GC.hiv_ft1_to_fa1) +
"\t0\t0\t0\t" + str(GC.hiv_ft1_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_ft2_to_fi2) + "\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_ft2_to_ft3) + "\t0\t0\t" + str(GC.hiv_ft2_to_fa2) +
"\t0\t0\t" + str(GC.hiv_ft2_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_ft3_to_fi3) + "\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_ft3_to_ft4) + "\t0\t0\t" + str(GC.hiv_ft3_to_fa3) +
"\t0\t" + str(GC.hiv_ft3_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_ft4_to_fi4) + "\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" +
str(GC.hiv_ft4_to_fa4) + "\t" + str(GC.hiv_ft4_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fa1_to_fi1) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_fa1_to_fa2) +
"\t0\t0\t" + str(GC.hiv_fa1_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fa2_to_fi2) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_fa2_to_fa3) +
"\t0\t" + str(GC.hiv_fa2_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fa3_to_fi3) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_fa3_to_fa4) +
"\t" + str(GC.hiv_fa3_to_d) + "\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(GC.hiv_fa4_to_fi4) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_fa4_to_d) +
"\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write("\n")
infectious = [
'MIAH', 'MIA', 'MI1', 'MI2', 'MI3', 'MI4', 'MJ1', 'MJ2', 'MJ3',
'MJ4', 'MT1', 'MT2', 'MT3', 'MT4', 'MA1', 'MA2', 'MA3', 'MA4',
'FIA', 'FI1', 'FI2', 'FI3', 'FI4', 'FJ1', 'FJ2', 'FJ3', 'FJ4',
'FT1', 'FT2', 'FT3', 'FT4', 'FA1', 'FA2', 'FA3', 'FA4'
]
f.write("[EDGED_TRAN_MATRIX]\n")
for _ in infectious:
by = _.lower()
f.write(
"0\t0\t0\t0\t0\t" +
str(getattr(GC, 'hiv_msu_to_mia_by_' + by)) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t" +
str(getattr(GC, 'hiv_mspc_to_mia_by_' + by)) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t" +
str(getattr(GC, 'hiv_msch_to_miah_by_' + by)) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t" +
str(getattr(GC, 'hiv_msc_to_mia_by_' + by)) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"
+ str(getattr(GC, 'hiv_fs_to_fia_by_' + by)) +
"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n")
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write(
"0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n"
)
f.write('\n')
f.write("[STATUS_BEGIN]\n0\n\n")
f.write("[INDUCER_LIST]\n" +
' '.join([str(GC.gemf_state_to_num[i])
for i in infectious]) + "\n\n")
f.write("[SIM_ROUNDS]\n1\n\n")
f.write("[INTERVAL_NUM]\n1\n\n")
f.write("[MAX_TIME]\n" + str(GC.end_time) + "\n\n")
f.write("[MAX_EVENTS]\n" + str(GC.C_INT_MAX) + "\n\n")
f.write("[DIRECTED]\n" + str(int(GC.contact_network.is_directed())) +
"\n\n")
f.write("[SHOW_INDUCER]\n1\n\n")
f.write("[DATA_FILE]\n" +
'\n'.join(["network.txt"] * len(infectious)) + "\n\n")
f.write("[STATUS_FILE]\nstatus.txt\n\n")
if GC.random_number_seed is not None:
f.write("[RANDOM_SEED]\n%d\n\n" % GC.random_number_seed)
f.write("[OUT_FILE]\noutput.txt")
f.close()
# write GEMF network file
f = open(GC.gemf_out_dir + "/network.txt", 'w')
num2node = {}
node2num = {}
for edge in GC.contact_network.edges_iter():
u = edge.get_from()
v = edge.get_to()
if u not in node2num:
num = len(node2num) + 1
node2num[u] = num
num2node[num] = u
if v not in node2num:
num = len(node2num) + 1
node2num[v] = num
num2node[num] = v
f.write(str(node2num[u]) + '\t' + str(node2num[v]) + '\n')
f.close()
# write GEMF to original mapping
f = open(GC.gemf_out_dir + "/gemf2orig.json", 'w')
f.write(str({num: num2node[num].get_name() for num in num2node}))
f.close()
# write GEMF status file (see above for the states)
f = open(GC.gemf_out_dir + "/status.txt", 'w')
seeds = {seed
for seed in GC.seed_nodes
} # seed nodes are assumed to be in acute infection
for num in sorted(num2node.keys()):
node = num2node[num]
attr = node.get_attribute()
if node in seeds:
if 'MALE' in attr:
f.write(str(GC.gemf_state_to_num['MIA']) +
"\n") # PopART-specific
node.gemf_state = GC.gemf_state_to_num['MIA']
else:
f.write(str(GC.gemf_state_to_num['FIA']) +
"\n") # PopART-specific
node.gemf_state = GC.gemf_state_to_num['FIA']
else:
if 'MALE' in attr:
if 'CIRCUMCISED' in attr:
f.write(str(GC.gemf_state_to_num['MSC']) +
"\n") # PopART-specific
node.gemf_state = GC.gemf_state_to_num['MSC']
else:
f.write(str(GC.gemf_state_to_num['MSU']) +
"\n") # PopART-specific
node.gemf_state = GC.gemf_state_to_num['MSU']
else:
f.write(str(GC.gemf_state_to_num['FS']) +
"\n") # PopART-specific
node.gemf_state = GC.gemf_state_to_num['FS']
f.close()
# run GEMF
chdir(GC.gemf_out_dir)
try:
call([GC.gemf_path], stdout=open("log.txt", 'w'))
except FileNotFoundError:
chdir(GC.START_DIR)
assert False, "GEMF executable was not found: %s" % GC.gemf_path
chdir(orig_dir)
# reload edge-based matrices for ease of use
matrices = open(GC.gemf_out_dir + '/para.txt').read().strip()
matrices = [[
[float(e) for e in l.split()] for l in m.splitlines()
] for m in matrices[matrices.index('[EDGED_TRAN_MATRIX]'):matrices.
index('\n\n[STATUS_BEGIN]')].replace(
'[EDGED_TRAN_MATRIX]\n', '').split('\n\n')]
matrices = {
GC.gemf_state_to_num[infectious[i]]: matrices[i]
for i in range(len(infectious))
}
# convert GEMF output to FAVITES transmission network format
GC.transmission_num = 0
GC.transmission_state = set() # 'node' and 'time'
GC.transmission_file = []
for line in open(GC.gemf_out_dir + "/output.txt"):
parts = [i.strip() for i in line.split()]
t = parts[0]
rate = parts[1]
vNum = parts[2]
pre = int(parts[3])
post = int(parts[4])
lists = parts[-1]
lists = lists.split('],[')
lists[0] += ']'
lists[-1] = '[' + lists[-1]
for i in range(1, len(lists) - 1):
if '[' not in lists[i]:
lists[i] = '[' + lists[i] + ']'
lists = [eval(l) for l in lists]
uNums = []
for l in lists:
uNums.extend(l)
if post == GC.gemf_state_to_num['D']:
vName = num2node[int(vNum)].get_name()
GC.transmission_file.append((vName, vName, float(t)))
elif len(lists[0]) == 0:
v = num2node[int(vNum)]
uNodes = [num2node[num] for num in uNums]
uRates = [
matrices[uNode.gemf_state][pre][post] for uNode in uNodes
]
die = {
uNodes[i]: GC.prob_exp_min(i, uRates)
for i in range(len(uNodes))
}
if len(die) != 0:
uName = GC.roll(die).get_name(
) # roll die weighted by exponential infectious rates
elif len(die) == 0 or u == v: # new seed
uName = None
GC.transmission_file.append((uName, v.get_name(), float(t)))
num2node[int(vNum)].gemf_state = post
assert len(
GC.transmission_file) != 0, "GEMF didn't output any transmissions"
GC.gemf_ready = True
def prep_GEMF():
# write GEMF parameter file
orig_dir = getcwd()
GC.gemf_path = expanduser(GC.gemf_path.strip())
makedirs(GC.gemf_out_dir, exist_ok=True)
f = open(GC.gemf_out_dir + "/para.txt",'w')
f.write("[NODAL_TRAN_MATRIX]\n0\t" + str(GC.hiv_ns_to_s) + "\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_ns_to_d) + "\n0\t0\t" + str(GC.hiv_s_to_i1_seed) + "\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_s_to_d) + "\n0\t0\t0\t" + str(GC.hiv_i1_to_i2) + "\t0\t0\t" + str(GC.hiv_i1_to_a1) + "\t0\t0\t0\t" + str(GC.hiv_i1_to_d) + "\n0\t0\t0\t0\t" + str(GC.hiv_i2_to_i3) + "\t0\t0\t" + str(GC.hiv_i2_to_a2) + "\t0\t0\t" + str(GC.hiv_i2_to_d) + "\n0\t0\t0\t0\t0\t" + str(GC.hiv_i3_to_i4) + "\t0\t0\t" + str(GC.hiv_i3_to_a3) + "\t0\t" + str(GC.hiv_i3_to_d) + "\n0\t0\t0\t0\t0\t0\t0\t0\t0\t" + str(GC.hiv_i4_to_a4) + "\t" + str(GC.hiv_i4_to_d) + "\n0\t0\t" + str(GC.hiv_a1_to_i1) + "\t0\t0\t0\t0\t" + str(GC.hiv_a1_to_a2) + "\t0\t0\t" + str(GC.hiv_a1_to_d) + "\n0\t0\t0\t" + str(GC.hiv_a2_to_i2) + "\t0\t0\t0\t0\t" + str(GC.hiv_a2_to_a3) + "\t0\t" + str(GC.hiv_a2_to_d) + "\n0\t0\t0\t0\t" + str(GC.hiv_a3_to_i3) + "\t0\t0\t0\t0\t" + str(GC.hiv_a3_to_a4) + "\t" + str(GC.hiv_a3_to_d) + "\n0\t0\t0\t0\t0\t" + str(GC.hiv_a4_to_i4) + "\t0\t0\t0\t0\t" + str(GC.hiv_a4_to_d) + "\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n\n") # HIV-ART-specific
f.write("[EDGED_TRAN_MATRIX]\n")
f.write("0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.hiv_s_to_i1_by_i1) + "\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write("0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.hiv_s_to_i1_by_i2) + "\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write("0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.hiv_s_to_i1_by_i3) + "\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write("0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.hiv_s_to_i1_by_i4) + "\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write("0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.hiv_s_to_i1_by_a1) + "\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write("0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.hiv_s_to_i1_by_a2) + "\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write("0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.hiv_s_to_i1_by_a3) + "\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write("0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t" + str(GC.hiv_s_to_i1_by_a4) + "\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n\n")
f.write("[STATUS_BEGIN]\n0\n\n")
infectious = ['I1','I2','I3','I4','A1','A2','A3','A4']
f.write("[INDUCER_LIST]\n" + ' '.join([str(GC.gemf_state_to_num[i]) for i in infectious]) + "\n\n")
f.write("[SIM_ROUNDS]\n1\n\n")
f.write("[INTERVAL_NUM]\n1\n\n")
f.write("[MAX_TIME]\n" + str(GC.end_time) + "\n\n")
f.write("[MAX_EVENTS]\n" + str(GC.C_INT_MAX) + "\n\n")
f.write("[DIRECTED]\n" + str(int(GC.contact_network.is_directed())) + "\n\n")
f.write("[SHOW_INDUCER]\n1\n\n")
f.write("[DATA_FILE]\n" + '\n'.join(["network.txt"]*len(infectious)) + "\n\n")
f.write("[STATUS_FILE]\nstatus.txt\n\n")
if GC.random_number_seed is not None:
f.write("[RANDOM_SEED]\n%d\n\n"%GC.random_number_seed)
f.write("[OUT_FILE]\noutput.txt")
f.close()
# write GEMF network file
f = open(GC.gemf_out_dir + "/network.txt",'w')
num2node = {}
node2num = {}
for edge in GC.contact_network.edges_iter():
u = edge.get_from()
v = edge.get_to()
if u not in node2num:
num = len(node2num) + 1
node2num[u] = num
num2node[num] = u
if v not in node2num:
num = len(node2num) + 1
node2num[v] = num
num2node[num] = v
f.write(str(node2num[u]) + '\t' + str(node2num[v]) + '\n')
f.close()
# write GEMF to original mapping
f = open(GC.gemf_out_dir + "/gemf2orig.json",'w')
f.write(str({num:num2node[num].get_name() for num in num2node}))
f.close()
# write GEMF status file (NS = 0, S = 1, I1 = 2, I2 = 3, I3 = 4, I4 = 5, A1 = 6, A2 = 7, A3 = 8, A4 = 9, D = 10)
leftover = len(num2node)
start_states = {'seed':[], 'other':[]}
for s in infectious:
k = "hiv_freq_%s"%s.lower()
if isinstance(getattr(GC,k), float):
n = int(len(num2node)*getattr(GC,k))
else:
n = getattr(GC,k)
start_states['seed'] += [GC.gemf_state_to_num[s]]*n
leftover -= n
assert len(start_states['seed']) == len(GC.seed_nodes), "At time 0, A1+A2+A3+A4+I1+I2+I3+I4 = %d, but there are %d seed nodes. Fix hiv_freq_* parameters accordingly" % (len(start_states['seed']),len(GC.seed_nodes))
for s in ['NS','S']:
k = "hiv_freq_%s"%s.lower()
if isinstance(getattr(GC,k), float):
n = int(len(num2node)*getattr(GC,k))
else:
n = getattr(GC,k)
start_states['other'] += [GC.gemf_state_to_num[s]]*n
leftover -= n
start_states['other'] += [GC.gemf_state_to_num['D']]*leftover
shuffle(start_states['seed']); shuffle(start_states['other'])
f = open(GC.gemf_out_dir + "/status.txt",'w')
seeds = {seed for seed in GC.seed_nodes} # seed nodes are assumed to be in I1 and non-seeds to be in NS
for num in sorted(num2node.keys()):
node = num2node[num]
if node in seeds:
s = start_states['seed'].pop()
f.write("%d\n"%s)
node.gemf_state = s
else:
s = start_states['other'].pop()
f.write("%d\n"%s)
node.gemf_state = s
f.close()
# run GEMF
chdir(GC.gemf_out_dir)
try:
call([GC.gemf_path], stdout=open("log.txt",'w'))
except FileNotFoundError:
chdir(GC.START_DIR)
assert False, "GEMF executable was not found: %s" % GC.gemf_path
chdir(orig_dir)
# reload edge-based matrices for ease of use
matrices = open(GC.gemf_out_dir + '/para.txt').read().strip()
outside_infection_matrix = [[float(e) for e in l.split()] for l in matrices[matrices.index('[NODAL_TRAN_MATRIX]'):matrices.index('\n\n[EDGED_TRAN_MATRIX]')].replace('[NODAL_TRAN_MATRIX]\n','').splitlines()]
matrices = [[[float(e) for e in l.split()] for l in m.splitlines()] for m in matrices[matrices.index('[EDGED_TRAN_MATRIX]'):matrices.index('\n\n[STATUS_BEGIN]')].replace('[EDGED_TRAN_MATRIX]\n','').split('\n\n')]
matrices = {GC.gemf_state_to_num[infectious[i]]:matrices[i] for i in range(len(infectious))}
matrices[GC.gemf_state_to_num['S']] = outside_infection_matrix
# convert GEMF output to FAVITES transmission network format
GC.transmission_num = 0
GC.transmission_state = set() # 'node' and 'time'
NUM_INFECTED = len(seeds)
GC.transmission_file = []
for line in open(GC.gemf_out_dir + "/output.txt"):
t,rate,vNum,pre,post,num0,num1,num2,num3,num4,num5,num6,num7,num8,num9,num10,lists = [i.strip() for i in line.split()]
pre,post = int(pre),int(post)
vName = num2node[int(vNum)].get_name()
lists = lists.split('],[')
lists[0] += ']'
lists[-1] = '[' + lists[-1]
for i in range(1,len(lists)-1):
if '[' not in lists[i]:
lists[i] = '[' + lists[i] + ']'
lists = [eval(l) for l in lists]
uNums = []
for l in lists:
uNums.extend(l)
if post == GC.gemf_state_to_num['D']:
NUM_INFECTED -= 1
GC.transmission_file.append((vName,vName,float(t)))
if GC.VERBOSE:
print('[%s] Uninfection\tTime %s\tNode %s (%s->%s)\tTotal Infected: %d\tTotal Uninfected: %d' % (datetime.now(),t,vName,GC.gemf_num_to_state[pre],GC.gemf_num_to_state[post],NUM_INFECTED,len(num2node)-NUM_INFECTED), file=stderr)
elif GC.gemf_num_to_state[pre] == 'S' and GC.gemf_num_to_state[post] == 'I1':
NUM_INFECTED += 1
v = num2node[int(vNum)]
uNodes = [num2node[num] for num in uNums]
uRates = [matrices[uNode.gemf_state][pre][post] for uNode in uNodes]
die = {uNodes[i]:GC.prob_exp_min(i, uRates) for i in range(len(uNodes))}
if len(die) != 0:
u = GC.roll(die) # roll die weighted by exponential infectious rates
uName = u.get_name()
if GC.VERBOSE:
print('[%s] Infection\tTime %s\tFrom Node %s (%s)\tTo Node %s (%s->%s)\tTotal Infected: %d\tTotal Uninfected: %d' % (datetime.now(),t,uName,GC.gemf_num_to_state[u.gemf_state],vName,GC.gemf_num_to_state[pre],GC.gemf_num_to_state[post],NUM_INFECTED,len(num2node)-NUM_INFECTED), file=stderr)
elif len(die) == 0 or u == v: # new seed
uName = None
if GC.VERBOSE:
print('[%s] Seed\tTime %s\tNode %s\tTotal Infected: %d\tTotal Uninfected: %d' % (datetime.now(),t,vName,NUM_INFECTED,len(num2node)-NUM_INFECTED), file=stderr)
GC.transmission_file.append((uName,v.get_name(),float(t)))
elif GC.VERBOSE:
print('[%s] Transition\tTime %s\tNode %s (%s->%s)' % (datetime.now(),t,vName,GC.gemf_num_to_state[pre],GC.gemf_num_to_state[post]), file=stderr)
num2node[int(vNum)].gemf_state = post
assert len(GC.transmission_file) != 0, "GEMF didn't output any transmissions"
GC.gemf_ready = True
GC.gemf_num2node = num2node
def prep_GEMF():
# write GEMF parameter file
orig_dir = getcwd()
GC.gemf_path = expanduser(GC.gemf_path.strip())
makedirs(GC.gemf_out_dir, exist_ok=True)
f = open(GC.gemf_out_dir + "/para.txt", 'w')
f.write("[NODAL_TRAN_MATRIX]\n0\t" + str(GC.seir_beta_seed) +
"\t0\t0\n0\t0\t" + str(GC.seir_lambda) + "\t0\n0\t0\t0\t" +
str(GC.seir_delta) + "\n0\t0\t0\t0\n\n") # SEIR-specific
f.write(
"[EDGED_TRAN_MATRIX]\n0\t" + str(GC.seir_beta_by_i) +
"\t0\t0\n0\t0\t0\t0\n0\t0\t0\t0\n0\t0\t0\t0\n\n") # SEIR-specific
f.write("[STATUS_BEGIN]\n0\n\n")
f.write("[INDUCER_LIST]\n" + str(GC.gemf_state_to_num['I']) + "\n\n")
f.write("[SIM_ROUNDS]\n1\n\n")
f.write("[INTERVAL_NUM]\n1\n\n")
f.write("[MAX_TIME]\n" + str(GC.end_time) + "\n\n")
f.write("[MAX_EVENTS]\n" + str(GC.C_INT_MAX) + "\n\n")
f.write("[DIRECTED]\n" + str(int(GC.contact_network.is_directed())) +
"\n\n")
f.write("[SHOW_INDUCER]\n1\n\n")
f.write("[DATA_FILE]\nnetwork.txt\n\n")
f.write("[STATUS_FILE]\nstatus.txt\n\n")
if GC.random_number_seed is not None:
f.write("[RANDOM_SEED]\n%d\n\n" % GC.random_number_seed)
f.write("[OUT_FILE]\noutput.txt")
f.close()
# write GEMF network file
f = open(GC.gemf_out_dir + "/network.txt", 'w')
num2node = {}
node2num = {}
for edge in GC.contact_network.edges_iter():
u = edge.get_from()
v = edge.get_to()
if u not in node2num:
num = len(node2num) + 1
node2num[u] = num
num2node[num] = u
if v not in node2num:
num = len(node2num) + 1
node2num[v] = num
num2node[num] = v
f.write(str(node2num[u]) + '\t' + str(node2num[v]) + '\n')
f.close()
# write GEMF to original mapping
f = open(GC.gemf_out_dir + "/gemf2orig.json", 'w')
f.write(str({num: num2node[num].get_name() for num in num2node}))
f.close()
# write GEMF status file (0 = S, 1 = E, 2 = I, 3 = R)
f = open(GC.gemf_out_dir + "/status.txt", 'w')
seeds = {seed for seed in GC.seed_nodes}
for num in sorted(num2node.keys()):
node = num2node[num]
if node in seeds:
f.write(str(GC.gemf_state_to_num['I']) + "\n") # SEIR-specific
node.gemf_state = GC.gemf_state_to_num['I']
else:
f.write(str(GC.gemf_state_to_num['S']) + "\n") # SEIR-specific
node.gemf_state = GC.gemf_state_to_num['S']
f.close()
# run GEMF
chdir(GC.gemf_out_dir)
try:
call([GC.gemf_path], stdout=open("log.txt", 'w'))
except FileNotFoundError:
chdir(GC.START_DIR)
assert False, "GEMF executable was not found: %s" % GC.gemf_path
chdir(orig_dir)
# reload edge-based matrices for ease of use
matrices = open(GC.gemf_out_dir + '/para.txt').read().strip()
outside_infection_matrix = [[
float(e) for e in l.split()
] for l in matrices[matrices.index('[NODAL_TRAN_MATRIX]'):matrices.
index('\n\n[EDGED_TRAN_MATRIX]')].replace(
'[NODAL_TRAN_MATRIX]\n', '').splitlines()]
matrices = [[
[float(e) for e in l.split()] for l in m.splitlines()
] for m in matrices[matrices.index('[EDGED_TRAN_MATRIX]'):matrices.
index('\n\n[STATUS_BEGIN]')].replace(
'[EDGED_TRAN_MATRIX]\n', '').split('\n\n')]
infectious = ['I']
matrices = {
GC.gemf_state_to_num['S']: outside_infection_matrix,
GC.gemf_state_to_num['I']: matrices[0]
}
# convert GEMF output to FAVITES transmission network format
GC.transmission_num = 0
GC.transmission_state = set() # 'node' and 'time'
NUM_INFECTED = len(seeds)
GC.transmission_file = []
for line in open(GC.gemf_out_dir + "/output.txt"):
t, rate, vNum, pre, post, num0, num1, num2, num3, lists = [
i.strip() for i in line.split()
]
pre, post = int(pre), int(post)
vName = num2node[int(vNum)].get_name()
lists = lists.split('],[')
lists[0] += ']'
lists[-1] = '[' + lists[-1]
for i in range(1, len(lists) - 1):
if '[' not in lists[i]:
lists[i] = '[' + lists[i] + ']'
lists = [eval(l) for l in lists]
uNums = []
for l in lists:
uNums.extend(l)
if post == GC.gemf_state_to_num['R']:
NUM_INFECTED -= 1
GC.transmission_file.append((vName, vName, float(t)))
if GC.VERBOSE:
print(
'[%s] Uninfection\tTime %s\tNode %s (%s->%s)\tTotal Infected: %d\tTotal Uninfected: %d'
% (datetime.now(), t, vName, GC.gemf_num_to_state[pre],
GC.gemf_num_to_state[post], NUM_INFECTED,
len(num2node) - NUM_INFECTED),
file=stderr)
elif post == GC.gemf_state_to_num['E']:
NUM_INFECTED += 1
v = num2node[int(vNum)]
uNodes = [num2node[num] for num in uNums]
uRates = [
matrices[uNode.gemf_state][pre][post] for uNode in uNodes
]
die = {
uNodes[i]: GC.prob_exp_min(i, uRates)
for i in range(len(uNodes))
}
if len(die) != 0:
u = GC.roll(
die
) # roll die weighted by exponential infectious rates
uName = u.get_name()
if GC.VERBOSE:
print(
'[%s] Infection\tTime %s\tFrom Node %s (%s)\tTo Node %s (%s->%s)\tTotal Infected: %d\tTotal Uninfected: %d'
% (datetime.now(), t, uName,
GC.gemf_num_to_state[u.gemf_state], vName,
GC.gemf_num_to_state[pre],
GC.gemf_num_to_state[post], NUM_INFECTED,
len(num2node) - NUM_INFECTED),
file=stderr)
elif len(die) == 0 or u == v: # new seed
uName = None
if GC.VERBOSE:
print(
'[%s] Seed\tTime %s\tNode %s\tTotal Infected: %d\tTotal Uninfected: %d'
% (datetime.now(), t, vName, NUM_INFECTED,
len(num2node) - NUM_INFECTED),
file=stderr)
GC.transmission_file.append((uName, v.get_name(), float(t)))
elif GC.VERBOSE:
print('[%s] Transition\tTime %s\tNode %s (%s->%s)' %
(datetime.now(), t, vName, GC.gemf_num_to_state[pre],
GC.gemf_num_to_state[post]),
file=stderr)
num2node[int(vNum)].gemf_state = post
assert len(
GC.transmission_file) != 0, "GEMF didn't output any transmissions"
GC.gemf_ready = True
def genString(k, pi):
return ''.join([GC.roll(pi) for _ in range(k)])