commands.py 文件源码

def get_genotype_probability(aln_profile, aln_specificity, sigma=0.12):
    # 'aln_specificity' should be a set of unit vectors (at least one of the entry is larger than 1.)
    num_haps = len(aln_profile)
    aln_vec = unit_vector(aln_profile)
    genoprob = []
    for i in xrange(num_haps):
        v1 = unit_vector(aln_specificity[i])
        for j in xrange(i, num_haps):
            if j == i:
                genoprob.append(sum(np.power(aln_vec - v1, 2))) # homozygotes
            else:
                v2 = unit_vector(aln_specificity[j])
                geno_vec = unit_vector(v1 + v2)
                # compute directional similarity
                genoprob.append(sum(np.power(aln_vec - geno_vec, 2))) # for heterozygotes
    genoprob = np.exp(np.array(genoprob) / (-2 * sigma * sigma))
    return np.array(genoprob / sum(genoprob))