def write_file_and_test_fitness(self):
#this writes a file, and calls JKK's fitness code and points it to the file
#and retrieves the lnL (aka fitness) and then cleans up the file
#also uses a cache ("memo") to check if the fitness has already been calculated for a particular order
#this saves on the expensive compute
##6/27/16, further modifications also now allow it to search through precomputed local values and pass in those
##in place of full estimates.
starttime = time.time()
fnm = sha.sha(str(self.chrom_list)).hexdigest()
self.tag = fnm
# print 'running', self.chrom_list, self.tag
if fnm in self.memo:
#print 'hit:', fnm
self.Fitness = self.memo[fnm][0]
self.Rates = self.memo[fnm][1]
self.runtime = time.time() - starttime
#update_subset_memo(self.chrom_list, self.Rates)
else: #we haven't tested this one yet
b = open(fnm, 'w')
for i in self.chrom_list:
scaff = self.scaff_lookup[abs(i)]
output = self.chrom_dict[scaff]
if i < 0: output = list(reversed(output))
for j in output: b.write(scaff+'\t'+j+'\n')
b.close()
myUGaps, my_R_rates = fill_in_rates_return_UGaps_and_new_R_rates(self.chrom_list, self.subset_memo)
rates_and_lnLk = fitness(fnm, my_R_rates, myUGaps)
rates = rates_and_lnLk[:-1]
myfitness = rates_and_lnLk[-1]
self.Fitness = myfitness
self.Rates = rates
os.remove(fnm)
self.runtime = time.time() - starttime
def write_file_and_test_fitness(self):
#this writes a file, and calls JKK's fitness code and points it to the file
#and retrieves the lnL (aka fitness) and then cleans up the file
#also uses a cache ("memo") to check if the fitness has already been calculated for a particular order
#this saves on the expensive compute
##6/27/16, further modifications also now allow it to search through precomputed local values and pass in those
##in place of full estimates.
starttime = time.time()
fnm = sha.sha(str(self.chrom_list)).hexdigest()
self.tag = fnm
# print 'running', self.chrom_list, self.tag
if fnm in self.memo:
#print 'hit:', fnm
self.Fitness = self.memo[fnm][0]
self.Rates = self.memo[fnm][1]
self.runtime = time.time() - starttime
#update_subset_memo(self.chrom_list, self.Rates)
else: #we haven't tested this one yet
b = open(fnm, 'w')
for i in self.chrom_list:
scaff = self.scaff_lookup[abs(i)]
output = self.chrom_dict[scaff]
if i < 0: output = list(reversed(output))
for j in output:
b.write(scaff + '\t' + j + '\n')
b.close()
myUGaps, my_R_rates = fill_in_rates_return_UGaps_and_new_R_rates(
self.chrom_list, self.subset_memo)
rates_and_lnLk = fitness(fnm, my_R_rates, myUGaps)
rates = rates_and_lnLk[:-1]
myfitness = rates_and_lnLk[-1]
self.Fitness = myfitness
self.Rates = rates
os.remove(fnm)
self.runtime = time.time() - starttime
def write_file_and_test_fitness(self):
#this writes a file, and calls JKK's fitness code and points it to the file
#and retrieves the lnL (aka fitness) and then cleans up the file
#also uses a cache ("memo") to check if the fitness has already been calculated for a particular order
#this saves on the expensive compute
##6/27/16, further modifications also now allow it to search through precomputed local values and pass in those
##in place of full estimates.
fnm = sha.sha(str(self.chrom_list)).hexdigest()
self.tag = fnm
# print 'running', self.chrom_list, self.tag
if fnm in self.memo:
print 'hit:', fnm
self.Fitness = self.memo[fnm][0]
self.Rates = self.memo[fnm][1]
#update_subset_memo(self.chrom_list, self.Rates)
else: #we haven't tested this one yet
b = open(fnm, 'w')
for i in self.chrom_list:
scaff = self.scaff_lookup[abs(i)]
output = self.chrom_dict[scaff]
if i < 0: output = list(reversed(output))
for j in output: b.write(scaff+'\t'+j+'\n')
b.close()
# print self.tag
myUGaps, my_R_rates = fill_in_rates_return_UGaps_and_new_R_rates(self.chrom_list, self.subset_memo, intra_scaff = 0.31)
#print 'run!'
#print self.chrom_list
#print self.Rates
#print self.UGaps
rates_and_lnLk = fitness(fnm, my_R_rates, myUGaps)
full_fitness_and_rates = fitness(fnm, my_R_rates, [[], 17])
info_dump = {'carryoverFitness': rates_and_lnLk[-1], 'fullFitness':full_fitness_and_rates[-1],
'carryoverRates': rates_and_lnLk[:-1], 'fullRates':full_fitness_and_rates[:-1], 'ord':self.chrom_list,
'num_carryover':len(myUGaps[0]) }
self.info = info_dump
#print rates_and_lnLk
#print subset_memo
#print memo
rates = rates_and_lnLk[:-1]
myfitness = rates_and_lnLk[-1]
self.Fitness = myfitness
self.Rates = rates
os.remove(fnm)
def write_file_and_test_fitness_full_model(self):
starttime = time.time()
fnm = sha.sha(str(self.chrom_list)).hexdigest()
self.tag = fnm
b = open(fnm, 'w')
for i in self.chrom_list:
scaff = self.scaff_lookup[abs(i)]
output = self.chrom_dict[scaff]
if i < 0: output = list(reversed(output))
for j in output: b.write(scaff+'\t'+j+'\n')
b.close()
myUGaps, my_R_rates = [[], len(self.chrom_list)], [0.1 for i in range(len(chrom_list))]
rates_and_lnLk = fitness(fnm, my_R_rates, myUGaps)
rates = rates_and_lnLk[:-1]
myfitness = rates_and_lnLk[-1]
self.Fitness = myfitness
self.Rates = rates
os.remove(fnm)
self.runtime = time.time() - starttime
def write_file_and_test_fitness_full_model(self):
starttime = time.time()
fnm = sha.sha(str(self.chrom_list)).hexdigest()
self.tag = fnm
b = open(fnm, 'w')
for i in self.chrom_list:
scaff = self.scaff_lookup[abs(i)]
output = self.chrom_dict[scaff]
if i < 0: output = list(reversed(output))
for j in output:
b.write(scaff + '\t' + j + '\n')
b.close()
myUGaps, my_R_rates = [[], len(self.chrom_list)
], [0.1 for i in range(len(chrom_list))]
rates_and_lnLk = fitness(fnm, my_R_rates, myUGaps)
rates = rates_and_lnLk[:-1]
myfitness = rates_and_lnLk[-1]
self.Fitness = myfitness
self.Rates = rates
os.remove(fnm)
self.runtime = time.time() - starttime
def write_file_and_test_fitness_full_model(self):
#THIS VERSION DOES NOT CARRY OVER ANY RATES. INSTEAD IT RUNS FULL LIKELIHOOD MODEL
#USED ONLY ON CONTIG ORDERS THAT BREAK THEIR WAY INTO THE ELITE GROUP.
#I.E. WE BURN THE COMPUTES TO GET THE LIKELIHOOD REALY ACCURATE ONLY ON THE MOST PROMISING CONTIG ORDERS
starttime = time.time()
fnm = sha.sha(str(self.chrom_list)).hexdigest()
self.tag = fnm
b = open(fnm, 'w')
for i in self.chrom_list:
scaff = self.scaff_lookup[abs(i)]
output = self.chrom_dict[scaff]
if i < 0: output = list(reversed(output))
for j in output: b.write(scaff+'\t'+j+'\n')
b.close()
myUGaps, my_R_rates = [[], len(self.chrom_list)], [0.1 for i in range(len(chrom_list))]
rates_and_lnLk = fitness(fnm, my_R_rates, myUGaps)
rates = rates_and_lnLk[:-1]
myfitness = rates_and_lnLk[-1]
self.Fitness = myfitness
self.Rates = rates
os.remove(fnm)
self.runtime = time.time() - starttime
