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():
# 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():
# 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.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