def __init__(self, config=None):
'''
Constructor
'''
self.restrictionEnzymeList = list()
self.speciesList = list()
resDir = os.path.join(PathUtils.getCwd(), "res")
self.SPSUMHandler = KazusaSPSUMHandler(resDir)
if config:
self.loadConfig(config)
self.possibleOptimizationStrategies = ["Fastest Codons", "Adapt Speed To Source", "Random Adapt To Target"]
self.optimizer = None
# self.speciesList.append(("1234", "Testus specius"))
self.sourceSequence = ""
self.optimizedSequence = ""
class OptimizerApp:
'''
classdocs
'''
def __init__(self, config=None):
'''
Constructor
'''
self.restrictionEnzymeList = list()
self.speciesList = list()
resDir = os.path.join(PathUtils.getCwd(), "res")
self.SPSUMHandler = KazusaSPSUMHandler(resDir)
if config:
self.loadConfig(config)
self.possibleOptimizationStrategies = ["Fastest Codons", "Adapt Speed To Source", "Random Adapt To Target"]
self.optimizer = None
# self.speciesList.append(("1234", "Testus specius"))
self.sourceSequence = ""
self.optimizedSequence = ""
def setOptimizer(self, sourceTaxid, targetTaxid, strategy):
if not strategy in self.possibleOptimizationStrategies:
return
if strategy == "Fastest Codons":
self.optimizer = MostFrequentCodonOptimizer(self.SPSUMHandler.getCUTable(sourceTaxid), self.SPSUMHandler.getCUTable(targetTaxid))
elif strategy == "Adapt Speed To Source":
self.optimizer = AdaptingCodonOptimizer(self.SPSUMHandler.getCUTable(sourceTaxid), self.SPSUMHandler.getCUTable(targetTaxid))
elif strategy == "Random Adapt To Target":
self.optimizer = RandomTargetAdaptingCodonOptimizer(self.SPSUMHandler.getCUTable(sourceTaxid), self.SPSUMHandler.getCUTable(targetTaxid))
else:
return
def setSourceSeq(self, seq):
self.sourceSequence = seq.upper()
def setOptimizedSeq(self, seq):
self.optimizedSequence = seq.upper()
def runOptimization(self):
self.optimizedSequence = self.optimizer.getBestSequence(self.sourceSequence)
# print("optimized to: " + self.optimizedSequence)
if not sys.platform == "darwin":
assert Seq(self.sourceSequence).translate() == Seq(self.optimizedSequence).translate()
def runRestricionRemoval(self):
restrictionSequences = list()
for r in self.restrictionEnzymeList:
restrictionSequences.append(rest_dict[r]['site'])
self.optimizedSequence = self.optimizer.removeRestrictionSites(self.sourceSequence, self.optimizedSequence, restrictionSequences)
if not sys.platform == "darwin":
# this assertion fails on macs?
# we look the other way for now
assert Seq(self.sourceSequence).translate() == Seq(self.optimizedSequence).translate()
def getCodonsForPrint(self, source=True):
if self.optimizer:
restrictionSequences = list()
for r in self.restrictionEnzymeList:
restrictionSequences.append(rest_dict[r]['site'])
if source:
return self.optimizer.SequenceToPrint(self.sourceSequence, restrictionSequences, source)
else:
return self.optimizer.SequenceToPrint(self.optimizedSequence, restrictionSequences, source)
else:
return None
def testPrint(self):
print(self.optimizer)
print(self.sourceSequence)
def saveConfig(self, path):
cp = configparser.ConfigParser()
taxids = list()
names = list()
for t, s in self.speciesList:
taxids.append(t)
names.append(s)
restrictionEnzymes = list()
for r in self.restrictionEnzymeList:
restrictionEnzymes.append(r)
cp['config'] = {"speciesTaxids" : ",".join(taxids), "speciesNames" : ",".join(names), "restrictionEnzymes" :",".join(restrictionEnzymes)}
with open(path, 'w') as configfile:
# print("writing config")
cp.write(configfile)
def loadConfig(self, path):
if not os.path.exists(path):
return
cp = configparser.ConfigParser()
cp.read(path)
taxids = list()
for t in cp["config"]["speciesTaxids"].split(","):
if t:
taxids.append(t)
names = list()
for n in cp["config"]["speciesNames"].split(","):
if n:
names.append(n)
restrictionEnzymes = list()
for r in cp["config"]["restrictionEnzymes"].split(","):
if r:
restrictionEnzymes.append(r)
for i in range(len(taxids)):
self.speciesList.append((taxids[i], names[i]))
self.restrictionEnzymeList = restrictionEnzymes
def setTest(self):
self.sourceSequence = "ATGC"