def Score(
self,
scoreMatrix={
'HP': 1000,
'PD': 10,
'GC': 10000,
'rep': 10000,
'Tm': 100,
'CyclePenalty': 1000
}):
###score is from best to worst highest score is worst probe
score = 0
if 'Tm' in scoreMatrix:
score = score + abs(self.Params['TmMin'] -
self.Tm) * scoreMatrix['Tm']
if 'HP' in scoreMatrix:
score = score + self.HPScore * scoreMatrix['HP']
if 'PD' in scoreMatrix:
score = score + self.PDScore * scoreMatrix['PD']
if 'GC' in scoreMatrix:
score = score + self.GCScore * scoreMatrix['GC']
if 'rep' in scoreMatrix:
score = score + self.repScore * scoreMatrix['rep']
if 'PCRGC' in scoreMatrix:
gcpcr = MB.perGC(self.seq[-6:]) / 100 * 6
gcpcr = int(gcpcr)
gcpcrScore = 0
if gcpcr == 0:
gcpcrScore = 3
if gcpcr == 1 or gcpcr == 6:
gcpcrScore = 2
if gcpcr == 2 or gcpcr == 5:
gcpcrScore = 1
score = score + gcpcrScore * scoreMatrix['PCRGC']
##print self.seq + 'gcpcr is ' + str(gcpcr) + ' score = ' + str(score)
# if 'self-Anneal' in scoreMatrix:
# val = self.ComputeSelfAnneal()
# val = max(0, val -30000)
# score = score + val*scoreMatrix['self-Anneal']
if 'CyclePenalty' in scoreMatrix:
cycleIndex = max(
0, (self.SynthCycles - self.Params['MaxSynthCycles']))
score = score + cycleIndex * scoreMatrix['CyclePenalty']
self.score = score
return score
def CharacterizeProbe(probeSeq, filtparams={}):
"""CharacterizeProbe
|(probeObj, FilterParams = None, returnLabel = None, Verbose = 1)
|probe object needs to be of the form [label, seq, len, anything else, , , ]
|
|"""
Limits = DefaultProbeFilterParameters
Limits.update(
filtparams) ##this is if you have a special set of conditions
#['ProbeGood','HP','PD','repeatNum','GC','HPstruct','PDstruct','failreason']
MaxHPTm = float(Limits['MaxHPTm'])
MaxPalindrome = float(Limits['MaxPalindrome'])
MaxRepeats = int(Limits['MaxRepeats'])
MaxGC = float(Limits['MaxGC'])
MinGC = float(Limits['MinGC'])
if 'MaxSynthCycles' in Limits:
MaxSynthCycles = int(Limits['MaxSynthCycles'])
else:
MaxSynthCycles = 160
failreason = 'good'
ProbeGood = 1
for base in probeSeq:
if not (base in 'GATCgatc'):
ProbeGood = 0
failreason = 'badBase'
break
if failreason == 'badBase':
return [0, 0, 0, 0, 0, 0, 0, 0, 0]
probeSeqSSLst = MB.SecStruct(probeSeq, MinAnneal=4)
HPLst = []
PDLst = []
for obj in probeSeqSSLst:
if obj[2] > 0:
HPLst.append(obj)
else:
PDLst.append(obj)
PDobj = MB.StabSecStruct(PDLst, Pal=1, OutType=1)
PD = PDobj[0]
PDstruct = PDobj[1]
HPobj = MB.StabSecStruct(HPLst, OutType=1)
HP = HPobj[0]
HPstruct = HPobj[1]
if PD > MaxPalindrome:
ProbeGood = 0
failreason = 'PD > ' + str(MaxPalindrome)
if HP > MaxHPTm:
ProbeGood = 0
failreason = 'HP > ' + str(MaxHPTm)
GC = MB.perGC(probeSeq)
if GC > MaxGC:
ProbeGood = 0
failreason = '%GC > ' + str(MaxGC)
if GC < MinGC:
ProbeGood = 0
failreason = '%GC < ' + str(MinGC)
repeatNum = MB.repeats(probeSeq)
repeatType = int((repeatNum - math.floor(repeatNum)) * 10)
if repeatNum > MaxRepeats:
ProbeGood = 0
failreason = 'repeats > ' + str(MaxRepeats) + '-' + str(repeatType)
SynthCycles = CyclesToSynth(probeSeq)
if SynthCycles > MaxSynthCycles:
ProbeGood = 0
failreason = 'SynthCycles %i>%i(max)' % (SynthCycles, MaxSynthCycles)
probeObj = [
SynthCycles, ProbeGood, HP, PD, repeatNum, GC, HPstruct, PDstruct,
failreason
]
#print str(probeObj)
return probeObj