def get_pvalue(List1, List2): star = [] ps = PyStats() for i in range(len(List1)): p = ps.fisher_test([ List1[i], List2[i], (List1[i] + List2[i]) / 2.0, (List1[i] + List2[i]) / 2.0 ]) if p < 10e-6: star.append('***') elif p < 0.0001: star.append('**') elif p < 0.01: star.append('*') else: star.append('') return star
G[fields[0]] = 1 inFile.close() ''' for k in D : print(k) print(D[k]) for k in D2 : print(k) print(D2[k]) ''' from PyStats.PyStatsClass import PyStats ps = PyStats() ouFile = open('16s.12s.tumor.normal.sv.exome', 'w') D3 = dict() for k in G: #ouFile.write(k+'\t') #ouFile.write(str(D.get(k,[0,0])[0]+D2.get(k,[0,0])[0])+'\t') #ouFile.write(str(D.get(k,[0,0])[1]+D2.get(k,[0,0])[1])+'\n') D3.setdefault(k, [0, 0, -1]) D3[k][0] = D.get(k, [0, 0])[0] + D2.get(k, [0, 0])[0] D3[k][1] = D.get(k, [0, 0])[1] + D2.get(k, [0, 0])[1] D3[k][2] = ps.fisher_test([20, 8, D3[k][0], D3[k][1]]) #for k in D3: # print(D3[k]) d = D3.items()