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PvalueAdjust.py
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PvalueAdjust.py
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import os
def main():
print('Just for p-values adjust using BH method !')
def BH_qvalues(p_values, sort_ornot):
if p_values == []:
return []
Max_rank = {}; total_0 = len(p_values); Q_val = {}; q_values = []
if sort_ornot == 'Not':
openTmp = open('p-tmp', 'w')
p_val_str0 = '\n'.join(p_values)
openTmp.write(p_val_str0 + '\n')
openTmp.close()
os.system('msort -k n1 p-tmp >p-tmp.msort')
os.remove('p-tmp')
openTmpN = open('p-tmp.msort', 'r')
ii_0 = 0
while True:
lineTmpN = openTmpN.readline()
if not lineTmpN:
break
ii_0 += 1
Max_rank[float(lineTmpN.strip())] = ii_0
openTmpN.close()
os.remove('p-tmp.msort')
elif sort_ornot == 'Yes':
for ii_1 in range(total_0):
Max_rank[float(p_values[ii_1])] = ii_1 + 1
else:
os._exit()
p_uniq_sort = sorted(Max_rank.keys())
for p_val_0 in p_uniq_sort:
rank = Max_rank[p_val_0]
Q_val[p_val_0] = total_0 * float(p_val_0) / rank
for i_0 in range(len(p_uniq_sort) - 2, -1, -1):
if Q_val[p_uniq_sort[i_0]] > Q_val[p_uniq_sort[i_0 + 1]]:
Q_val[p_uniq_sort[i_0]] = Q_val[p_uniq_sort[i_0 + 1]]
for mm_0 in range(total_0):
if float(p_values[mm_0]) in Q_val.keys():
q_values.append(float(Q_val[float(p_values[mm_0])]))
return q_values
if __name__ == '__main__':
main()