def grad_descent(self):
iteration = 0
mutations = None
motif_dustbin = []
while (mutations is None or
any(fit > 0 for (site,pos,base,fit) in mutations)):
mutations = self.explore_site_mutations()
site_idx, pos, base, fit = max(mutations,
key=lambda tup:tup[3])#max by fitness
self.motif[site_idx] = string_replace(self.motif[site_idx],pos,base)
print "iteration:",iteration,site_idx,pos,base,fit
motif_dustbin.append(self.motif[:])
iteration += 1
def mutate_site(self,site_number,position,base):
site = self.motif[site_number]
self.motif[site_number] = string_replace(site,position,base)
