text: if __name__ == '__main__':
  	
  	#####
  	##temporary dev hack
  	import os,time
  	os.chdir('..')
  	#####
  	
  	from pyviko import core, mutation, restriction
  	
  	#ovr = core.readFasta('test/dem/over/2000.fasta')
  	#toKO = core.readFasta('test/dem/ko/2000.fasta')
  	'''#True batch script
  	t1 = time.time()
  	for i in range(len(toKO)):
  		m = mutation.Mutant(toKO[i][1],numMutations=1,regEx=True)
  		m.setOverGene(overSeq = ovr[i][1])
  		#print toKO[i][1]
  		print m.findMutants(ignoreRxSites = False, rSiteLength='all')[:5]
  		print
  		print m.findMutants()[:5]
  		print "done "+str(i)		
  		print
  	print time.time()-t1
  	'''
  	#testing RC search
  	ovr=['ATGATTACCCGGGTTTCCCAAAGGGTTTCATCCTAA']
  	z='''     TTACCCGGGTTTCCCAAAGGGTTTCAT'''
  	toKO  = ['ATGAAACCCTTTGGGAAACCCGGGTAA']
  	t1 = time.time()
  	for i in range(len(toKO))[:1]:
  		m = mutation.Mutant(toKO[i][1],numMutations=1,regEx=True)
  		m.setOverGene(overSeq = ovr[i][1])
  		#print toKO[i][1]
  		print m.findMutants(ignoreRxSites = False, rSiteLength='all')[:5]
  		print
  		print m.findMutants()[:5]
  		print "done "+str(i)		
  		print
  	print time.time()-t1
  	#overlaps = [core.findOverlap(toKO[i][1],ovr[i][1]) for i in range(len(toKO))]
  	#print overlaps
  	