def removeRestrictionSites(self, sourceSeq, optimizedSeq, restrictionSites):
'''
get the best sequence that does not contain any restriction sites
by re-randomizing until no restriction site remains
'''
codons = re.findall('...', optimizedSeq)
remainder = SeqUtils.getRemainderSuffix(optimizedSeq)
restrictionSites = SeqUtils.expandAmbiguousMult(restrictionSites)
restrictionLocations = SeqUtils.searchSubseqs(optimizedSeq, restrictionSites)
restrictionCodons = SeqUtils.getCodonsForRanges(restrictionLocations)
# try to re-randomize a finite amount of times
ITERMAX = 10000
iteration = 0
while iteration < ITERMAX:
for i in restrictionCodons:
codons[i] = self.getRandomOptimizedCodon(codons[i])
tSeq = "".join(codons) + remainder
tRL = SeqUtils.searchSubseqs(tSeq, restrictionSites)
tRC = SeqUtils.getCodonsForRanges(tRL)
if not tRC:
return tSeq
iteration += 1
return None
def getBestSequence(self, sourceSequence):
sourceCodons = re.findall('...', sourceSequence)
remainder = SeqUtils.getRemainderSuffix(sourceSequence)
result = ""
for co in sourceCodons:
result += self.getBestCodon(co)
result += remainder
return result
def SequenceToPrint(self, seq, restrictionSites, source=True):
'''
return tuples of the form (codon, usage, isRestrictionSite) for the sequence
'''
codons = re.findall('...', seq)
remainder = SeqUtils.getRemainderSuffix(seq)
result = list()
restrictionSites = SeqUtils.expandAmbiguousMult(restrictionSites)
restrictionLocations = SeqUtils.searchSubseqs(seq, restrictionSites)
restrictionCodons = SeqUtils.getCodonsForRanges(restrictionLocations)
for i in range(len(codons)):
usage = self.sourceCU.getCodonRelativeUsage(codons[i]) if source else self.targetCU.getCodonRelativeUsage(codons[i])
result.append((codons[i], usage, i in restrictionCodons))
if remainder:
result.append((remainder, None, None))
return result
def getPossibleOneStepChanges(self, sourceSeq, optimizedSeq, codonsToConsider):
'''
get all possible sequences resulting from substituting the codons to consider
in the optimized Seq with the next best codons
'''
sourceCodons = re.findall('...', sourceSeq) # list of codons
optCodons = re.findall("...", optimizedSeq)
remainder = SeqUtils.getRemainderSuffix(optimizedSeq)
res = list()
for i in range(len(optCodons)):
if i in codonsToConsider:
nextBestCodon = self.getNextBestCodon(sourceCodons[i], optCodons[i])
if nextBestCodon:
tCodons = optCodons
tCodons[i] = nextBestCodon
tSeq = "".join(tCodons)
tSeq += remainder
res.append(tSeq)
return res
