def compute_likelihood_spec2(strand,start,stop,hyp,lamb):
i_list = xrange(stop,stop+10*mfl,+1) if strand == '+' else xrange(start,start-10*mfl,-1)
likelihood = alo(hyp[start:stop])
p_no_occ_so_far = 1 - likelihood
endpoint = stop if strand == '+' else start
for i in i_list:
likelihood += p_no_occ_so_far*(1-lamb)**abs(i-endpoint)*hyp[i%G]
p_no_occ_so_far *= (1-hyp[i%G])
return likelihood
def p_occ_in_seq_region(strand,start,stop,hyp):
return alo(hyp[start:stop])