'''
Generate a list of all pairwise comparisons of the exact matches
'''
import sys
import re
from phage import Phage
phage = Phage()
try:
f = sys.argv[1]
except:
sys.exit("Exact match file, probably phage.kmers.bacteria.rc.txt")
bg = phage.completeBacteriaIDs()
pg = phage.phageIDs()
matches = {}
for p in pg:
matches[p] = {}
for b in bg:
matches[p][b] = 0
with open(f, 'r') as fin:
for l in fin:
p = l.strip().split("\t")
m = re.findall('NC_\d+', l)
if len(m) != 2:
#sys.stderr.write("Error parsing two NC ids from " + l)
continue
def get_phagename_and_refseq(row, phage_finder):
phage = Phage(row, phage_finder)
return phage.name, phage.refseq
else:
return np.exp(-0.5 *
(np.square(x - mu) / sigma_r)) # gaussian r: ~(39.7, 10)
new_host = Host(
c0=10**5,
g_max=0.036, #lit: 0.012
yield_coeff=0.000000000001,
half_sat=0.00000125,
death_rate=0.001,
t_dep=temperature_dependency_new_host,
)
original_phage = Phage(
c0=10**9,
adsorption_rate=0.000000000001,
burst_size=100,
death_rate=0.00272,
)
new_phage = Phage(
c0=10**6,
adsorption_rate=0.0000000001,
burst_size=100,
death_rate=0.00272,
)
s0 = 0.0000025 #stock concentration of nutrient (g/mL) #0.0000025
R_pnn = 1 / 1000 # fraction of new phage in library
def c_nutr_b(tt, c_host_b, c_inf_poo, c_inf_pnn, c_nutr_a):
return -new_host.yield_coeff * new_host.per_cell_growth_rate(
def lyse(self):
model.things = set([i for i in model.things if i != self])
for i in range(self._burst_size):
model.add(Phage(self.get_location()[0], self.get_location()[1]))
def __init__(self):
# simulation time and resolution of samples
self.dt = 0.1
self.xs = np.linspace(0, 120, 120 / self.dt)
self.fluxA = 0.0
self.fluxB = 0.0
self.new_host = Host(
c0=10**5,
g_max=0.036, # lit: 0.012
yield_coeff=0.000000000001,
half_sat=0.00000125,
death_rate=0.001,
t_dep=self.temperature_dependency_new_host,
)
self.original_phage = Phage(
c0=10**9,
adsorption_rate=0.000000000001,
burst_size=100,
death_rate=0.00272,
)
self.new_phage = Phage(
c0=10**6,
adsorption_rate=0.0000000001,
burst_size=100,
death_rate=0.00272,
)
self.s0 = 0.0000025 # stock concentration of nutrient (g/mL) #0.0000025
self.R_pnn = 1 / 1000 # fraction of new phage in library
self.myinterpolator = scipy.interpolate.interp1d(
np.array([0 - 1, 0]), # X
np.array([0, 1]).T, # Y
kind="linear",
bounds_error=False,
fill_value=0)
self.d = 13.3 # lysis time delay
self.dd = 13
# dt *=10
self.q_h_inf_poo = deque([0])
self.q_h_inf_pnn = deque([0])
for i in range(100):
self.q_h_inf_poo.append(0)
self.q_h_inf_pnn.append(0)
data = ddeint(self.model,
self.initial_conditions,
self.xs,
fargs=(self.d, ))
plt.figure(figsize=(16, 16))
plt.subplot(3, 3, 1)
plt.plot(self.xs, [data[t][0] for t in range(len(self.xs))],
label="reactor A")
plt.xlabel('time [min]')
plt.ylabel('concentration [#bacteria/mL]')
plt.title('Host Concentration A over Time')
plt.legend()
plt.subplot(3, 3, 2)
plt.plot(self.xs, [data[t][1] for t in range(len(self.xs))],
label="reactor A")
plt.xlabel('time [min]')
plt.ylabel('concentration [g/mL]')
plt.title('Nutrient A over Time')
plt.legend()
plt.subplot(3, 3, 3)
plt.plot(self.xs, [data[t][2] for t in range(len(self.xs))])
plt.xlabel('time [min]')
plt.ylabel('concentration [#bacteria/mL]')
plt.title('Host Concentration B over Time')
plt.subplot(3, 3, 4)
plt.plot(self.xs, [data[t][3] for t in range(len(self.xs))])
plt.xlabel('time [min]')
plt.ylabel('concentration [g/mL]')
plt.title('Nutrient B over Time')
plt.subplot(3, 3, 5)
plt.plot(self.xs, [data[t][4] for t in range(len(self.xs))])
plt.xlabel('time [min]')
plt.ylabel('concentration [#bacteria/mL]')
plt.title('Host infected OO over Time')
plt.subplot(3, 3, 6)
plt.plot(self.xs, [data[t][5] for t in range(len(self.xs))])
plt.xlabel('time [min]')
plt.ylabel('concentration [#bacteria/mL]')
plt.title('Host infected NN over Time')
plt.subplot(3, 3, 8)
plt.plot(self.xs, [data[t][6] for t in range(len(self.xs))])
plt.xlabel('time [min]')
plt.ylabel('concentration [#phage/mL]')
plt.title('Phage OO over Time')
plt.subplot(3, 3, 9)
plt.plot(self.xs, [data[t][7] for t in range(len(self.xs))])
plt.xlabel('time [min]')
plt.ylabel('concentration [#phage/mL]')
plt.title('Phage NN over Time')
plt.subplot(3, 3, 7)
plt.plot(self.xs, [data[t][6] for t in range(len(self.xs))],
label="original")
plt.plot(self.xs, [data[t][7] for t in range(len(self.xs))],
label="new")
plt.xlabel('time [min]')
plt.ylabel('concentration [#phage/mL]')
plt.title('Phage over Time')
plt.legend()
plt.subplots_adjust(wspace=0.4, hspace=0.4)
plt.show()
def test_phage_finder(phage_finder, input, refseq, name):
result = Phage(input, phage_finder)
assert refseq == result.refseq
assert name == result.name