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circuit_epistasis.py
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circuit_epistasis.py
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from three_way_epistasis import list_epistasis, list_epistasis_signed, get_next_ordering, ordering_to_fitness
__author__ = "@gavruskin"
def get_positives_list():
return [{1, 7}, # 1 a
{2, 8}, # 2 b
{1, 6}, # 3 c
{3, 8}, # 4 d
{1, 5}, # 5 e
{4, 8}, # 6 f
{1, 8}, # 7 g
{2, 7}, # 8 h
{1, 8}, # 9 i
{2, 7}, # 10 j
{1, 8}, # 11 k
{3, 6}, # 12 l
{2, 3, 4}, # 13 m
{5, 6, 7}, # 14 n
{3, 4, 8}, # 15 o
{1, 5, 6}, # 16 p
{2, 4, 8}, # 17 q
{1, 5, 7}, # 18 r
{1, 6, 7}, # 19 s
{2, 3, 8}, # 20 t
{1, 4, 5, 8}, # 21 u_011
{1, 3, 6, 8}, # 22 u_101
{1, 2, 7, 8}, # 23 u_110
{1, 5, 6, 7}] # 24 u_111
def get_negatives_list():
return [{3, 4}, # 1 a
{5, 6}, # 2 b
{2, 4}, # 3 c
{5, 7}, # 4 d
{2, 3}, # 5 e
{6, 7}, # 6 f
{5, 4}, # 7 g
{3, 6}, # 8 h
{3, 6}, # 9 i
{5, 4}, # 10 j
{2, 7}, # 11 k
{5, 4}, # 12 l
{8, 1}, # 13 m
{1, 8}, # 14 n
{2, 7}, # 15 o
{7, 2}, # 16 p
{3, 6}, # 17 q
{6, 3}, # 18 r
{5, 4}, # 19 s
{4, 5}, # 20 t
{2, 6, 3, 7}, # 21 u_011
{2, 5, 4, 7}, # 22 u_101
{3, 5, 4, 6}, # 23 u_110
{4, 3, 2, 8}] # 24 u_111
# Returns the list of coefficients that corresponds to circuit number n from {1, ..., 24}.
# Will return all coefficients 1 if the circuit number is out of range.
def get_repetitions_from_circuit_number(n):
if n == 13:
return [2, 1, 1, 1, 1, 1, 1, 1]
elif n == 14:
return [1, 1, 1, 1, 1, 1, 1, 2]
elif n == 15:
return [1, 1, 1, 1, 1, 1, 2, 1]
elif n == 16:
return [1, 2, 1, 1, 1, 1, 1, 1]
elif n == 17:
return [1, 1, 1, 1, 1, 2, 1, 1]
elif n == 18:
return [1, 1, 2, 1, 1, 1, 1, 1]
elif n == 19:
return [1, 1, 1, 2, 1, 1, 1, 1]
elif n == 20:
return [1, 1, 1, 1, 2, 1, 1, 1]
else:
return [1, 1, 1, 1, 1, 1, 1, 1]
# For every circuit, generates a file that contains orders that imply epistasis.
def orders_to_circuits():
positives_list = get_positives_list()
negatives_list = get_negatives_list()
for shape_number in range(len(positives_list)):
shape_name = shape_number + 1
if shape_name == 21:
shape_name = "u_011"
elif shape_name == 22:
shape_name = "u_101"
elif shape_name == 23:
shape_name = "u_110"
elif shape_name == 24:
shape_name = "u_111"
elif shape_name == 13:
rep = [2, 1, 1, 1, 1, 1, 1, 1]
elif shape_name == 14:
rep = [1, 1, 1, 1, 1, 1, 1, 2]
elif shape_name == 15:
rep = [1, 1, 1, 1, 1, 1, 2, 1]
elif shape_name == 16:
rep = [1, 2, 1, 1, 1, 1, 1, 1]
elif shape_name == 17:
rep = [1, 1, 1, 1, 1, 2, 1, 1]
elif shape_name == 18:
rep = [1, 1, 2, 1, 1, 1, 1, 1]
elif shape_name == 19:
rep = [1, 1, 1, 2, 1, 1, 1, 1]
elif shape_name == 20:
rep = [1, 1, 1, 1, 2, 1, 1, 1]
else:
rep = [1, 1, 1, 1, 1, 1, 1, 1]
list_epistasis(positives_list[shape_number], negatives_list[shape_number], shape_name, rep)
list_epistasis_signed(positives_list[shape_number], negatives_list[shape_number], shape_name, rep)
# Generates a file with shared orders:
def shared_orders(file1, file2):
ranks1 = open("./outputs/circuit_%s_orders.txt" % file1, "r")
ranks2 = open("./outputs/circuit_%s_orders.txt" % file2, "r")
ranks1_set = set()
shared = set()
for line in ranks1:
ranks1_set.add(line)
for line in ranks2:
if line in ranks1_set:
shared.add(line)
shared_file = open("./outputs/ranks_shared_between_%s_and_%s.txt" % (file1, file2), "w")
for x in shared:
shared_file.write(str(x))
ranks1.close()
ranks2.close()
shared_file.close()
# Generates a big file with the list of all rankings.
# A ranking is followed by a list of circuits that imply epistasis.
def circuits_to_orders():
circuits_to_orders_file = open("./outputs/circuits_to_orders.txt", "w")
ordering = [1, 1, 1, 1, 1, 1, 1, 1]
fitness = [1, 2, 3, 4, 5, 6, 7, 8]
line = str(fitness) + "\n"
circuits_to_orders_file.write(line)
for circuit in range(1, 21):
if line in open("./outputs/circuit_%s_orders.txt" % circuit, "r"):
circuits_to_orders_file.write(str(circuit))
while ordering != [8, 7, 6, 5, 4, 3, 2, 1]:
ordering = get_next_ordering(ordering)
fitness = ordering_to_fitness(ordering)
line = str(fitness) + "\n"
circuits_to_orders_file.write("\n" + line)
for circuit in range(1, 21):
if line in open("./outputs/circuit_%s_orders.txt" % circuit, "r"):
circuits_to_orders_file.write(str(circuit) + " ")
circuits_to_orders_file.close()
# Generates a big file with the list of all rankings.
# A ranking is followed by a list of circuits with signs that imply epistasis.
def circuits_to_orders_signed():
circuits_to_orders_file = open("./outputs/circuits_to_orders_signed.txt", "w")
ordering = [1, 1, 1, 1, 1, 1, 1, 1]
fitness = [1, 2, 3, 4, 5, 6, 7, 8]
line = str(fitness) + "\n"
line_positive = str(fitness) + " +" + "\n"
line_negative = str(fitness) + " -" + "\n"
circuits_to_orders_file.write(line)
for circuit in range(1, 21):
if line_positive in open("./outputs/circuit_%s_orders_signed.txt" % circuit, "r"):
circuits_to_orders_file.write("+" + str(circuit) + " ")
elif line_negative in open("./outputs/circuit_%s_orders_signed.txt" % circuit, "r"):
circuits_to_orders_file.write("-" + str(circuit) + " ")
while ordering != [8, 7, 6, 5, 4, 3, 2, 1]:
ordering = get_next_ordering(ordering)
fitness = ordering_to_fitness(ordering)
line = str(fitness) + "\n"
line_positive = str(fitness) + " +" + "\n"
line_negative = str(fitness) + " -" + "\n"
circuits_to_orders_file.write("\n" + line)
for circuit in range(1, 21):
if line_positive in open("./outputs/circuit_%s_orders_signed.txt" % circuit, "r"):
circuits_to_orders_file.write("+" + str(circuit) + " ")
elif line_negative in open("./outputs/circuit_%s_orders_signed.txt" % circuit, "r"):
circuits_to_orders_file.write("-" + str(circuit) + " ")
circuits_to_orders_file.close()
# To generate the big file, call:
# orders_to_circuits()
# circuits_to_orders_signed()