motif.py 文件源码

def p_overlap(self, s_overlap, motif_st, l_overlap, is_rc=False):
        """ p_overlap caclute the probability of a given sequence segment
        overlapping with a motif, given the alignment.

        Args:
            s_overlap: string representing overlapping portion of the motif
            motif_st: the begin idx of the motif
            l_overlap: the length of the alignment.
            is_rc: if the reverse complementary motif should be used.

        Returns:
            a float representation of the likelihood of observing
            overlapping sequence given this alignment.
        """
        motif_end = motif_st + l_overlap
        pwm = self.lmbda_rc if is_rc else self.lmbda
        pwm_overlap = np.array(pwm)[motif_st+1:motif_end+1]
        assert len(pwm_overlap) == len(s_overlap)
        prod = 1.0
        for base, rho in zip(s_overlap, pwm_overlap):
            prod *= np.exp(special.digamma(rho[tools.IDX[base]])-
                           special.digamma(sum(rho)))
        return prod