code: def _compute_bits(self):
          
          bits = []
          totbits = 0
          bgbits  = 0
          bg      = self.background
          UNCERT  = lambda x: x*math.log(x)/math.log(2.0)
          for letter in ACGT:
              bgbits = bgbits + UNCERT(bg[letter])
          for i in range(self.width):
              tot = 0
              for letter in ACGT:
                  Pij = pow(2.0, self.logP[i][letter])
                  tot = tot + UNCERT(Pij)
                  #bit = Pij * self.ll[i][letter]
                  #if bit > 0:
                  #    tot = tot + bit
              #print tot, bgbits, tot-bgbits
              bits.append(max(0,tot-bgbits))
              totbits = totbits + max(0,tot-bgbits)
          self.bits = bits
          self.totalbits = totbits
docs: m._compute_bits() -- [utility] Set m.totbits to the number of bits and m.bits to a list of bits at each position