def write_file_and_test_fitness_full_model(self, error_file, intrascaff_file, f2_file):
#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)-1], [0.01 for i in range(len(chrom_list)-1)]
rates_and_lnLk = fitness(fnm, my_R_rates, myUGaps,
lines_file = f2_file,
error_rates = error_file,
intra_scaff_rates_file=intrascaff_file)
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, error_file, intrascaff_file, f2_file):
# 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) - 1], [0.01 for i in range(len(chrom_list) - 1)]
rates_and_lnLk = fitness(
fnm, my_R_rates, myUGaps, lines_file=f2_file, error_rates=error_file, intra_scaff_rates_file=intrascaff_file
)
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, error_file, intrascaff_file, f2_file):
#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
if fnm in self.memo:
self.Fitness = self.memo[fnm][0]
self.Rates = self.memo[fnm][1]
self.runtime = time.time() - starttime
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,
lines_file = f2_file,
error_rates = error_file,
intra_scaff_rates_file=intrascaff_file)
rates = rates_and_lnLk[:-1]
myfitness = rates_and_lnLk[-1]
self.Fitness = myfitness
self.Rates = rates
os.remove(fnm)
self.runtime = time.time() - starttime
