def gene_significant_mutated(self, iFile, samplePositionList): total_length = 0 total_num = 0 dict1 = dict() inFile = open("hg19_max_coding_length") for line in inFile: line = line.rstrip() fields = line.split("\t") dict1[fields[0]] = int(fields[1]) inFile.close() inFile = open(iFile) for line in inFile: line = line.rstrip() fields = line.split("\t") gn = sum([int(fields[x]) for x in samplePositionList]) gl = dict1[fields[0]] if gn > 0: total_length += gl total_num += gn inFile.close() # print(total_length) # print(total_num) ps = PyStats() inFile = open(iFile) ouFile = open(iFile + ".fisher_test", "w") for line in inFile: line = line.rstrip() fields = line.split("\t") gs = sum([int(fields[x]) for x in samplePositionList]) gl = dict1[fields[0]] f = ps.fisher_test([gs, gl, total_num, total_length]) ouFile.write(str(f) + "\t" + line + "\n") inFile.close() ouFile.close() ps.fdr_adjust_file(iFile + ".fisher_test")
def gene_significant_mutated(self, iFile, samplePositionList): total_length = 0 total_num = 0 dict1 = dict() inFile = open('hg19_max_coding_length') for line in inFile: line = line.rstrip() fields = line.split('\t') dict1[fields[0]] = int(fields[1]) inFile.close() inFile = open(iFile) for line in inFile: line = line.rstrip() fields = line.split('\t') gn = sum([int(fields[x]) for x in samplePositionList]) gl = dict1[fields[0]] if gn > 0: total_length += gl total_num += gn inFile.close() #print(total_length) #print(total_num) ps = PyStats() inFile = open(iFile) ouFile = open(iFile + '.fisher_test', 'w') for line in inFile: line = line.rstrip() fields = line.split('\t') gs = sum([int(fields[x]) for x in samplePositionList]) gl = dict1[fields[0]] f = ps.fisher_test([gs, gl, total_num, total_length]) ouFile.write(str(f) + '\t' + line + '\n') inFile.close() ouFile.close() ps.fdr_adjust_file(iFile + '.fisher_test')
def gene_two_group_ranksum_test(self, iFile, aList, bList): ps = PyStats() ps.ranksum_test_file(iFile, aList, bList)