from Bio.SeqUtils import *
nt_search(chromosome, scaffold)

from Bio.Seq import Seq
from Bio.SeqUtils import *

def findCoordinates (self):
    ''' Performs scaffold string search within chromosomes. Returns scaffold coordinates within said chromosome. '''

    for chromosome in self.chromosomes.keys():
        for scaffold in self.scaffolds.keys():
            # search forward strand.
            nt_forward = nt_search(self.chromosomes[chromosome], self.scaffolds[scaffold])
            if len(nt_forward) > 1:
                startCoord = nt_forward[1] + 1
                endCoord = (startCoord + len(self.scaffolds[scaffold]))
                # save coordinates

            else: # search reverse strand
                scaffold_seq = Seq(self.scaffolds[scaffold])
                reverse_seq = scaffold_seq.reverse_complement()
                nt_reverse = nt_search(self.chromosomes[chromosome], str(reverse_seq))
                if  len(nt_reverse) > 1:
                    startCoord = nt_reverse[1] + 1
                    endCoord = (startCoord + len(self.scaffolds[scaffold]))
                    # save coordinates
                    self.scaffolds[scaffold] = str(scaffold_seq.reverse_complement())

Traceback (most recent call last):
  File "scaffoldPlacer.py", line 98, in <module>
z.findCoordinates()
  File "scaffoldPlacer.py", line 60, in findCoordinates
nt_reverse = nt_search(self.chromosomes[chromosome], str(reverse_seq))
  File "/usr/local/lib/python2.7/site-packages/Bio/SeqUtils/__init__.py", line 191, in nt_search
m = re.search(pattern, s)
  File "/usr/local/lib/python2.7/re.py", line 142, in search
return _compile(pattern, flags).search(string)
  File "/usr/local/lib/python2.7/re.py", line 243, in _compile
p = sre_compile.compile(pattern, flags)
  File "/usr/local/lib/python2.7/sre_compile.py", line 523, in compile
groupindex, indexgroup
OverflowError: regular expression code size limit exceeded