def validateSolution(self, solution):
'''
Solution validation tests
'''
if solution.sequence == None or ('?' in solution.levels.values()):
sys.stderr.write("SolutionValidator: Level unknown - "+str(solution.levels)+"\n")
solution.valid = False
return 0
#check if solution is valid
valid = True
designed_region = solution.sequence
#No internal Promoters
(score, _, _) = Functions.look_for_promoters(designed_region)
if score >= 15.3990166: #0.95 percentile for Promoter PWM scores
valid = False
sys.stderr.write("SolutionValidator: High Promoter score: "+str(score)+"\n")
#No internal Terminator
score = Functions.look_for_terminators(designed_region)
if score >= 90: #90% confidence from transtermHP
valid = False
sys.stderr.write("SolutionValidator: High Terminator score\n")
#No restriction enzymes
#if 'ggtctc' in designed_region or 'gagacc' in designed_region:
# sys.stderr.write("SolutionValidator: Restriction enzyme found\n")
# valid = False
solution.valid = valid
return valid
def validateSolution(self, solution):
'''
Solution validation tests
'''
return True
if solution.sequence == None:
return 0
valid = True
e_type=None
variable_region = solution.sequence[solution.mutable_region[0]:(solution.mutable_region[-1]+1)]
#No Promoters
promoter_putative_region = solution.sequence[(solution.mutable_region[0]-30):(solution.mutable_region[-1]+31)]
(score, position, spacer) = Functions.look_for_promoters(promoter_putative_region)
if score >= 0.3990166: #0.95 percentile for Promoter PWM scores
valid = False
position = (solution.mutable_region[0]-30) + position
e_type = "prom"
sys.stderr.write("SolutionValidator: High Promoter score\n")
#No RBS
rbs_putative_region = solution.sequence[(solution.mutable_region[0]-12):(solution.mutable_region[-1]+11)]
(score, position) = Functions.look_for_RBS(rbs_putative_region)
if score >= 0.820515: #0.95 percentile for RBS PWM scores
valid = False
position = (solution.mutable_region[0]-12) + position
e_type = "rbs"
sys.stderr.write("SolutionValidator: High RBS score: "+str(score)+" - "+str(position)+"\n")
#No Terminator
term_putative_region = solution.sequence[(solution.mutable_region[0]-30):(solution.mutable_region[-1]+31)]
score = Functions.look_for_terminators(term_putative_region)
if score >= 90: #90% confidence from transtermHP
e_type = "term"
valid = False
sys.stderr.write("SolutionValidator: High Terminator score\n")
#No stop codon
for i in range(0,len(variable_region),3):
if codon2aa_table[variable_region[i:i+3]]=='stop':
sys.stderr.write("SolutionValidator: Stop codon found\n")
e_type = "stopcodon"
valid = False
position = solution.mutable_region[0]+i
break
#No restriction enzymes
rsite_putative_region = solution.sequence[(solution.mutable_region[0]-6):(solution.mutable_region[-1])]
if 'ggtacc' in rsite_putative_region:
e_type = "rsite"
sys.stderr.write("SolutionValidator: Restriction enzyme found\n")
position = (solution.mutable_region[0]-6)+rsite_putative_region.index('ggtacc')
valid = False
if 'ggatcc' in rsite_putative_region:
e_type = "rsite"
sys.stderr.write("SolutionValidator: Restriction enzyme found\n")
position = (solution.mutable_region[0]-6)+rsite_putative_region.index('ggatcc')
valid = False
#No bases run of more than 5nt
repeat_putative_region = solution.sequence[(solution.mutable_region[0]-6):(solution.mutable_region[-1]+7)]
for b_run in ('aaaaaa','tttttt','gggggg','cccccc'):
if b_run in repeat_putative_region:
sys.stderr.write("SolutionValidator: Bases run for more than 5 found\n")
valid = False
position = (solution.mutable_region[0]-6) + repeat_putative_region.index(b_run)
e_type = "repeats"
solution.valid = valid
if valid == True:
return (valid,None,None)
else:
return (valid,position,e_type)