Simple, fast implementation of Fisher’s exact test. . For example, for the following table:

Perhaps we are interested in whether there is any difference of property in selected vs. non-selected groups, then we can do the Fisher’s exact test.

def fish_test(sample_hit, pop_hit, sample_count, root_count):
### sample_hit: 该样本中基因属于该term下面的个数
### pop_hit: 该物种的所有基因属于该term下面的个数
### sample_count: 样本中基因的个数
### root_count: 该物种在bp/cc/mf root 下基因的个数
sample_hit = int(sample_hit)
pop_hit = int(pop_hit)
sample_count = int(sample_count)
root_count = int(root_count)
sample_nhit = sample_count - sample_hit
pop_nhit = root_count - pop_hit
n1,n2,n3,n4 = (sample_hit, pop_hit - sample_hit,
sample_nhit, pop_nhit - sample_nhit)
p = abs(pvalue(n1,n2,n3,n4).right_tail)
return p