m._compute_bits() -- [utility] Set m.totbits to the number of bits and m.bits to a list of bits at each position

def _compute_bits(self):
        """
        m._compute_bits() -- [utility] Set m.totbits to the number of bits and m.bits to a list of bits at each position
        """
        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