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
# Basic validation
designed_region = solution.sequence
valid = validateCDS(designed_region)
# # No internal Promoters - e coli specific
# (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 - only for bacterial genomes?
# score = Functions.look_for_terminators(seq=designed_region, outdir=self.root_dir)
# 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 configureSolution(self, solution):
solution.valid = validateCDS(solution.sequence[49:])
if solution.valid:
#CAI
cai_obj = CAI.CAI(solution=solution,
label="cds",
args={'cai_range': (49, len(solution.sequence))})
#Look for RBS
dup_obj1 = RNADuplexRNAFold.RNADuplexRNAFoldRibosome(
solution1=solution,
label="sd16s",
args={'rnaMolecule1region': (25, 48)})
dup_mfe = RNADuplexRNAFold.RNADuplexRNAFoldMFE(dup_obj1)
dup_obj1.add_subfeature(dup_mfe)
#MFE [-30,30]
st1_obj = StructureRNAFold.StructureRNAFold(
solution=solution,
label="utr",
args={'structure_range': (49 - 30, 49 + 30)})
st_mfe = StructureRNAFold.StructureRNAFoldMFE(st1_obj)
st1_obj.add_subfeature(st_mfe)
solution.add_feature(cai_obj)
solution.add_feature(dup_obj1)
solution.add_feature(st1_obj)
def configureSolution(self, solution):
try:
solution.valid = validateCDS(
solution.sequence,
check_frame=self.check_frame,
check_start=self.check_start,
check_end_stop=self.check_end_stop,
check_within_stop=self.check_within_stop)
except DTailorException:
logger.error('Solution invalid')
solution.valid = False
if solution.valid:
if self.ramp:
# CAI - entire sequence
cai_all_obj = CAI(solution=solution,
label="all",
cai_table=self.cai_table,
args={
'cai_range': (0, len(solution.sequence)),
'mutable_region':
range(0, len(solution.sequence))
})
solution.add_feature(cai_all_obj)
# CAI - ramp only
cai_ramp_obj = CAI(solution=solution,
label="ramp",
cai_table=self.cai_table,
args={
'cai_range': (0, self.ramp_from_to[1]),
'mutable_region':
range(0, self.ramp_from_to[1])
})
solution.add_feature(cai_ramp_obj)
# CAI - not ramp only
# If sequence is too short just redo the CAI calc
if len(solution.sequence) <= self.ramp_from_to[1]:
cai_rest_obj = CAI(solution=solution,
label="rest",
cai_table=self.cai_table,
args={
'cai_range':
(0, self.ramp_from_to[1]),
'mutable_region':
range(0, self.ramp_from_to[1])
})
else:
cai_rest_obj = CAI(solution=solution,
label="rest",
cai_table=self.cai_table,
args={
'cai_range':
(self.ramp_from_to[1],
len(solution.sequence)),
'mutable_region':
range(self.ramp_from_to[1],
len(solution.sequence))
})
solution.add_feature(cai_rest_obj)
# MFE - ramp only
st1_obj = StructureRNAFold(solution=solution,
label="mfe",
args={
'structure_range':
(self.ramp_from_to[0],
self.ramp_from_to[1]),
'mutable_region':
range(self.ramp_from_to[0],
self.ramp_from_to[1])
})
st_mfe = StructureRNAFoldMFE(structureObject=st1_obj)
st1_obj.add_subfeature(st_mfe)
solution.add_feature(st1_obj)
else:
# CAI - entire sequence
cai_all_obj = CAI(solution=solution,
label="all",
cai_table=self.cai_table,
args={
'cai_range': (0, len(solution.sequence)),
'mutable_region':
range(0, len(solution.sequence))
})
solution.add_feature(cai_all_obj)