j=1
know2={}
path={}
for line in fp_path:
lines= line.strip("\n").split("\t")
know2[j] = lines[0]
path[j] = lines[2]
j = j+1
path_test =[]
path_sort = path.values()
for x,k in know2.items():
if k in kg_uniq:
path_test.append(path[x])
path_test.sort()
path_sort.sort()
test_path_dict = kongdeju.list2dict(path_test)
kegg_path_dict = kongdeju.list2dict(path_sort)
kegg_path_list = kegg_path_dict.keys()
kegg_path_list.sort()
outcome={}
outcome_short = {}
##########fisher exact test start##########
fisher_n = len(kg_uniq)
fisher_N = len(set(know2.values()))
for item in kegg_path_list:
kegg_M = kegg_path_dict[item]
if item in test_path_dict.keys():
test_k = test_path_dict[item]
else:
test_k = 0
p = fisher.pvalue(test_k,kegg_M,fisher_n-test_k,fisher_N-kegg_M).right_tail
for item in type_list: if item in Ti: Ti_num = Ti_num +1 else: Tv_num = Tv_num +1 try: ratio = float(Ti_num)/float(Tv_num) except: ratio = 0 return ratio fp = open(sys.argv[1],'r') lines = fp.readlines() dict_out = table2dict(lines) #####This is for chrome picture##### chrome_list = dict_out['Chr'] chrome_dict = kongdeju.list2dict(chrome_list) ####This is for genomic Ti/Tv####### refs = dict_out['Ref'] vars = dict_out['Alt'] exotic_type = dict_out['Func.refGene'] genome_type_list = [] exotic_type_list = [] for ref,var,exo in zip(refs,vars,exotic_type): type = ref + var if not '-' in type: genome_type_list.append(type) if exo == 'exonic': exotic_type_list.append(type) genome_ti_tv = round(Ti_Tv(genome_type_list),2) exotic_ti_tv = round(Ti_Tv(exotic_type_list),2)
Ti_num = Ti_num + 1
else:
Tv_num = Tv_num + 1
try:
ratio = float(Ti_num) / float(Tv_num)
except:
ratio = 0
return ratio
fp = open(sys.argv[1], 'r')
lines = fp.readlines()
dict_out = table2dict(lines)
#####This is for chrome picture#####
chrome_list = dict_out['Chr']
chrome_dict = kongdeju.list2dict(chrome_list)
####This is for genomic Ti/Tv#######
refs = dict_out['Ref']
vars = dict_out['Alt']
exotic_type = dict_out['Func.refGene']
genome_type_list = []
exotic_type_list = []
for ref, var, exo in zip(refs, vars, exotic_type):
type = ref + var
if not '-' in type:
genome_type_list.append(type)
if exo == 'exonic':
exotic_type_list.append(type)
genome_ti_tv = round(Ti_Tv(genome_type_list), 2)
exotic_ti_tv = round(Ti_Tv(exotic_type_list), 2)
else:
if line:
new_genes.append(line)
return new_genes
fp = open(sys.argv[1], 'r')
sample_no = sys.argv[2]
lines = fp.readlines()
dict_out = table2dict(lines)
genes = dict_out['Gene.refGene']
genes = real_gene(genes)
exo_type = dict_out['Func.refGene']
###sample_vairant_num######
genome_variant_num = len(exo_type)
exo_dict = kongdeju.list2dict(exo_type)
try:
exo_variant_num = exo_dict['exonic']
except:
exo_variant_num = 0
genes_num = len((set(genes)))
genes = list(set(genes))
#############get from mysql###################
conn = MySQLdb.connect(host='rdsikqm8sr3rugdu1muh3.mysql.rds.aliyuncs.com',
user='******',
passwd='btlc123',
db='clinic')
cursor = conn.cursor()
try:
pathway_dict = gene2pathway.gene2pathway(genes)
paths = []
new_genes.append(gene) else: if line: new_genes.append(line) return new_genes fp = open(sys.argv[1],'r') sample_no = sys.argv[2] lines = fp.readlines() dict_out = table2dict(lines) genes = dict_out['Gene.refGene'] genes = real_gene(genes) exo_type = dict_out['Func.refGene'] ###sample_vairant_num###### genome_variant_num = len(exo_type) exo_dict = kongdeju.list2dict(exo_type) try: exo_variant_num = exo_dict['exonic'] except: exo_variant_num = 0 genes_num = len((set(genes))) genes=list(set(genes)) #############get from mysql################### conn = MySQLdb.connect(host='rdsikqm8sr3rugdu1muh3.mysql.rds.aliyuncs.com',user='******',passwd='btlc123',db='clinic') cursor = conn.cursor() try: pathway_dict = gene2pathway.gene2pathway(genes) paths=[] for a,aitems in pathway_dict.items(): for b ,bitems in aitems.items(): paths.extend(bitems.keys())