def _getSequence(self, slic):
data = self.data[slic]
SNPTypes = self.chromosome.genome.SNPTypes
if SNPTypes is None or self.refOnly:
return data
iterators = []
for setName, SNPType in SNPTypes.iteritems():
f = RabaQuery(str(SNPType),
namespace=self.chromosome._raba_namespace)
f.addFilter({
'start >=': slic.start,
'start <': slic.stop,
'setName': str(setName),
'chromosomeNumber': self.chromosome.number
})
# conf.db.enableDebug(True)
iterators.append(f.iterRun(sqlTail='ORDER BY start'))
if len(iterators) < 1:
return data
polys = {}
for iterator in iterators:
for poly in iterator:
if poly.start not in polys:
polys[poly.start] = {poly.setName: poly}
else:
polys[poly.start][poly.setName] = poly
data = list(data)
for start, setPolys in polys.iteritems():
seqPos = start - slic.start
sequenceModifier = self.SNPFilter.filter(self.chromosome,
**setPolys)
# print sequenceModifier.alleles
if sequenceModifier is not None:
if sequenceModifier.__class__ is SF.SequenceDel:
data = data[:seqPos] + data[seqPos +
sequenceModifier.length:]
elif sequenceModifier.__class__ is SF.SequenceSNP:
data[seqPos] = sequenceModifier.alleles
elif sequenceModifier.__class__ is SF.SequenceInsert:
data[seqPos] = "%s%s" % (sequenceModifier.bases,
data[seqPos])
else:
raise TypeError(
"sequenceModifier on chromosome: %s starting at: %s is of unknown type: %s"
% (self.chromosome.number, snp.start,
sequenceModifier.__class__))
# print data
return ''.join(data)
def getSequenceData(self, slic) :
data = self.data[slic].decode('utf-8')
SNPTypes = self.chromosome.genome.SNPTypes
if SNPTypes is None or self.refOnly :
return data
iterators = []
for setName, SNPType in SNPTypes.items() :
f = RabaQuery(str(SNPType), namespace = self.chromosome._raba_namespace)
chromosomeNumber = self.chromosome.number
if chromosomeNumber == 'MT':
chromosomeNumber = 'M'
f.addFilter({'start >=' : slic.start, 'start <' : slic.stop, 'setName' : str(setName), 'chromosomeNumber' : chromosomeNumber})
# conf.db.enableDebug(True)
iterators.append(f.run(sqlTail = 'ORDER BY start', gen=True))
if len(iterators) < 1 :
return data
polys = {}
for iterator in iterators :
for poly in iterator :
if poly.start not in polys :
polys[poly.start] = {poly.setName : poly}
else :
try :
polys[poly.start][poly.setName].append(poly)
except :
polys[poly.start][poly.setName] = [polys[poly.start][poly.setName]]
polys[poly.start][poly.setName].append(poly)
data = list(data)
for start, setPolys in polys.items() :
seqPos = start - slic.start
sequenceModifier = self.SNPFilter.filter(self.chromosome, **setPolys)
# print sequenceModifier.alleles
if sequenceModifier is not None :
if sequenceModifier.__class__ is SF.SequenceDel :
seqPos = seqPos + sequenceModifier.offset
#To avoid to change the length of the sequence who can create some bug or side effect
data[seqPos:(seqPos + sequenceModifier.length)] = [''] * sequenceModifier.length
elif sequenceModifier.__class__ is SF.SequenceSNP :
data[seqPos] = sequenceModifier.alleles
elif sequenceModifier.__class__ is SF.SequenceInsert :
seqPos = seqPos + sequenceModifier.offset
data[seqPos] = "%s%s" % (data[seqPos], sequenceModifier.bases)
else :
raise TypeError("sequenceModifier on chromosome: %s starting at: %s is of unknown type: %s" % (self.chromosome.number, snp.start, sequenceModifier.__class__))
return data
def _makeLoadQuery(self, objectType, *args, **coolArgs) : # conf.db.enableDebug(True) f = RabaQuery(objectType._wrapped_class, namespace = self._wrapped_class._raba_namespace) coolArgs[self._wrapped_class.__name__[:-5]] = self.wrapped_object #[:-5] removes _Raba from class name if len(args) > 0 and type(args[0]) is types.ListType : for a in args[0] : if type(a) is types.DictType : f.addFilter(**a) else : f.addFilter(*args, **coolArgs) return f
def _makeLoadQuery(self, objectType, *args, **coolArgs) : if issubclass(objectType, SNP_INDEL) : f = RabaQuery(objectType, namespace = self._wrapped_class._raba_namespace) coolArgs['species'] = self.genome.species coolArgs['chromosomeNumber'] = self.number if len(args) > 0 and type(args[0]) is types.ListType : for a in args[0] : if type(a) is types.DictType : f.addFilter(**a) else : f.addFilter(*args, **coolArgs) return f return pyGenoRabaObjectWrapper._makeLoadQuery(self, objectType, *args, **coolArgs)