def complement(self, clone=True):
if clone:
rval = self.clone()
else:
rval = self
if rval.is_DNA():
rval.sequence = transform.DNA_complement(rval.sequence)
else:
rval.sequence = transform.RNA_complement(rval.sequence)
return rval
def complement( self, clone = True ):
#need to override how color space is complemented
if clone:
rval = self.clone()
else:
rval = self
if rval.has_adapter_base(): #No adapter, color space stays the same
adapter = rval.sequence[0]
sequence = rval.sequence[1:]
if adapter.lower() != 'u':
adapter = transform.DNA_complement( adapter )
else:
adapter = transform.RNA_complement( adapter )
rval.sequence = "%s%s" % ( adapter, sequence )
return rval
def complement(self, clone=True):
"""return a new object with a complemented self.sequence strand
call using my_object.complement(clone=False) if you wish to complement
and return the current object.
"""
if clone:
rval = self.clone()
else:
rval = self
if rval.is_DNA():
rval.sequence = transform.DNA_complement(rval.sequence)
else:
rval.sequence = transform.RNA_complement(rval.sequence)
return rval