def sequence(self):
temp = self.strand5p()
if not temp:
return None
if temp.sequence():
return ''.join([Strand.sequence(strand) \
for strand in self.strand5p().generator3pStrand()])
else:
return None
def sequence(self):
temp = self.strand5p()
if not temp:
return None
if temp.sequence():
return ''.join([Strand.sequence(strand) \
for strand in self.strand5p().generator3pStrand()])
else:
return None
def sequenceExport(self):
vhNum5p = self.strand5p().virtualHelix().number()
idx5p = self.strand5p().idx5Prime()
seq = ''
if self.isLoop():
print "A loop exists"
raise Exception
for strand in self.strand5p().generator3pStrand():
seq = seq + Strand.sequence(strand, forExport=True)
if strand.connection3p() == None: # last strand in the oligo
vhNum3p = strand.virtualHelix().number()
idx3p = strand.idx3Prime()
output = "%d[%d],%d[%d],%s,%s,%s\n" % \
(vhNum5p, idx5p, vhNum3p, idx3p, seq, len(seq), self._color)
return output
def sequenceExport(self):
vhNum5p = self.strand5p().virtualHelix().number()
idx5p = self.strand5p().idx5Prime()
seq = ''
if self.isLoop():
# print "A loop exists"
raise Exception
for strand in self.strand5p().generator3pStrand():
seq = seq + Strand.sequence(strand, forExport=True)
if strand.connection3p() == None: # last strand in the oligo
vhNum3p = strand.virtualHelix().number()
idx3p = strand.idx3Prime()
output = "%d[%d],%d[%d],%s,%s,%s\n" % \
(vhNum5p, idx5p, vhNum3p, idx3p, seq, len(seq), self._color)
return output
