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)
def gene_two_group_ranksum_test(self, iFile, aList, bList):
ps = PyStats()
ps.ranksum_test_file(iFile, aList, bList)
