332 lines
8.9 KiB
Python
332 lines
8.9 KiB
Python
#!/usr/bin/env python3
|
|
|
|
import os
|
|
import sys
|
|
import math
|
|
|
|
|
|
def get_total_CN(cov_file):
|
|
|
|
all_reg =[]
|
|
for line in open(cov_file, "r"):
|
|
line = line.strip().split()
|
|
all_reg.append(line)
|
|
|
|
av_nat1_cov = float(all_reg[0][3])/(float(all_reg[0][2]) - float(all_reg[0][1]))
|
|
av_vdr_cov = float(all_reg[1][3])/(float(all_reg[1][2]) - float(all_reg[1][1]))
|
|
av_egfr_cov = float(all_reg[2][3])/(float(all_reg[2][2]) - float(all_reg[2][1]))
|
|
# av_e1_int4 = float(all_reg[3][3])/(float(all_reg[3][2]) - float(all_reg[3][1]))
|
|
# av_int4_e9 = float(all_reg[4][3])/(float(all_reg[4][2]) - float(all_reg[4][1]))
|
|
|
|
av_ctrl_cov = (av_vdr_cov + av_egfr_cov)/2
|
|
|
|
comp_av = av_nat1_cov/av_ctrl_cov
|
|
temp_cn = 2 * comp_av
|
|
total_cn = round(temp_cn)
|
|
|
|
|
|
return [str(int(total_cn)), round(av_nat1_cov), round(av_ctrl_cov)]; # , str(av_e1_int4), str(av_int4_e9)];
|
|
|
|
|
|
def del_test(sv_del):
|
|
|
|
if os.stat(sv_del).st_size == 0:
|
|
return "None"
|
|
|
|
else:
|
|
for line in open(sv_del, "r"):
|
|
if "COVERAGE" in line:
|
|
line = line.strip().split()
|
|
|
|
ABHom = line[-1]
|
|
ABHet = line[-2]
|
|
GT = line[2]
|
|
DP = int(line[3])
|
|
|
|
if float(ABHom) == 1.0:
|
|
return "*(full_gene_del)/*(full_gene_del)"
|
|
elif float(ABHom) == -1.0:
|
|
return "*(full_gene_del)"
|
|
else:
|
|
pass
|
|
|
|
|
|
hap_adv_list = []
|
|
hap_t1 = []
|
|
|
|
|
|
def del_adv_test(hap_dbs, cand_allele1, cand_allele2, test_allele1, test_allele2, core_vars):
|
|
g = open(hap_dbs, "r")
|
|
for line in g:
|
|
line = line.strip().split()
|
|
hap_adv_list.append(line)
|
|
|
|
a1 = core_vars.split(";")
|
|
|
|
for i in a1:
|
|
if i[-3:] == "0/1":
|
|
hap_t1.append(i[:-4])
|
|
|
|
for elem in hap_adv_list:
|
|
if elem[1] == cand_allele1:
|
|
list_t1 = (elem[2]).split(';')
|
|
|
|
if elem[1] == cand_allele2:
|
|
list_t2 = (elem[2]).split(';')
|
|
|
|
if hap_t1[0] in list_t1:
|
|
return test_allele1
|
|
|
|
elif hap_t1[0] in list_t2:
|
|
return test_allele2
|
|
|
|
|
|
het_hom_list = []
|
|
het_hom_list_new = []
|
|
|
|
def dup_test_init(sv_dup, av_cov):
|
|
for line in open(sv_dup, "r"):
|
|
if "COVERAGE" in line:
|
|
continue
|
|
elif "AGGREGATED" in line:
|
|
continue
|
|
|
|
else:
|
|
fields = line.strip().split()
|
|
het_hom_list.append(fields)
|
|
|
|
test_list1 = []
|
|
|
|
for i in het_hom_list:
|
|
test_list1.append(int(i[2]))
|
|
|
|
av_read_cov = sum(test_list1)/len(test_list1)
|
|
norm_cov = (av_cov + av_read_cov)/2
|
|
|
|
for i in het_hom_list:
|
|
supp_reads = round(float(i[-2])*int(i[2]))
|
|
i.append(round(supp_reads/norm_cov, 3))
|
|
i.append(supp_reads)
|
|
het_hom_list_new.append(i)
|
|
|
|
|
|
return (het_hom_list_new)
|
|
|
|
|
|
hap_def_list = []
|
|
allele_cn_list = []
|
|
|
|
def dup_test_cn_3_4(sv_dup, hap_dbs, cand_allele1, cand_allele2, test_allele1, test_allele2, c_num, av_cov, in_list):
|
|
|
|
g = open(hap_dbs, "r")
|
|
for line in g:
|
|
line = line.strip().split()
|
|
hap_def_list.append(line)
|
|
|
|
|
|
test_list1 = []
|
|
test_list2 = []
|
|
het_list = []
|
|
|
|
|
|
for i in in_list:
|
|
if i[1] == "0/1":
|
|
het_list.append(i)
|
|
|
|
for i in het_list:
|
|
test_list1.append(i[0])
|
|
test_list2.append(i[-2])
|
|
|
|
|
|
max_het = max(test_list2)
|
|
max_het_pos = test_list2.index(max_het)
|
|
var = test_list1[max_het_pos]
|
|
|
|
for elem in hap_def_list:
|
|
if elem[1] == cand_allele1:
|
|
list_3t = elem
|
|
list_3t_2 = list_3t[2].split(';')
|
|
l3 = len(list_3t_2)
|
|
|
|
if elem[1] == cand_allele2:
|
|
list_4t = elem
|
|
list_4t_2 = list_4t[2].split(';')
|
|
l4 = len(list_4t_2)
|
|
|
|
hdb_list = list_3t_2 + list_4t_2
|
|
|
|
|
|
index_var = hdb_list.index(var)
|
|
|
|
if index_var < l3:
|
|
allele_cn_list.append(test_allele1)
|
|
allele_cn_list.append(int(round(max_het*int(c_num))))
|
|
|
|
elif index_var >= l3:
|
|
allele_cn_list.append(test_allele2)
|
|
allele_cn_list.append(int(round(max_het*int(c_num))))
|
|
|
|
|
|
if allele_cn_list[0] == test_allele1:
|
|
rt_2 = int(c_num) - allele_cn_list[1]
|
|
allele_cn_list.append(test_allele2)
|
|
allele_cn_list.append(rt_2)
|
|
|
|
elif allele_cn_list[0] == test_allele2:
|
|
rt_2 = int(c_num) - allele_cn_list[1]
|
|
allele_cn_list.append(test_allele1)
|
|
allele_cn_list.append(rt_2)
|
|
|
|
if allele_cn_list[1] == 0:
|
|
res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3] - 1)
|
|
|
|
elif allele_cn_list[3] == 0:
|
|
res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1] - 1)
|
|
|
|
elif allele_cn_list[1] == 1:
|
|
res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
|
|
|
|
elif allele_cn_list[3] == 1:
|
|
res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
|
|
|
|
elif allele_cn_list[1] == 2:
|
|
res_dip = allele_cn_list[0] + "x2" + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
|
|
|
|
elif allele_cn_list[3] == 2:
|
|
res_dip = allele_cn_list[2] + "x2" + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
|
|
|
|
|
|
else:
|
|
res_dip = 'check'
|
|
|
|
return res_dip
|
|
|
|
|
|
|
|
def dup_test_cn_n(sv_dup, hap_dbs, cand_allele1, cand_allele2, test_allele1, test_allele2, c_num, av_cov, in_list):
|
|
|
|
g = open(hap_dbs, "r")
|
|
for line in g:
|
|
line = line.strip().split()
|
|
hap_def_list.append(line)
|
|
|
|
|
|
test_list1 = []
|
|
test_list2 = []
|
|
het_list = []
|
|
|
|
|
|
for i in in_list:
|
|
if i[1] == "0/1":
|
|
het_list.append(i)
|
|
|
|
for i in het_list:
|
|
test_list1.append(i[0])
|
|
test_list2.append(i[-2])
|
|
|
|
max_het = max(test_list2)
|
|
max_het_pos = test_list2.index(max_het)
|
|
var = test_list1[max_het_pos]
|
|
|
|
|
|
for elem in hap_def_list:
|
|
if elem[1] == cand_allele1:
|
|
list_3t = elem
|
|
list_3t_2 = list_3t[2].split(';')
|
|
l3 = len(list_3t_2)
|
|
|
|
if elem[1] == cand_allele2:
|
|
list_4t = elem
|
|
list_4t_2 = list_4t[2].split(';')
|
|
l4 = len(list_4t_2)
|
|
|
|
hdb_list = list_3t_2 + list_4t_2
|
|
|
|
index_var = hdb_list.index(var)
|
|
|
|
if index_var < l3:
|
|
allele_cn_list.append(test_allele1)
|
|
allele_cn_list.append(int(round(max_het*int(c_num)-0.15)))
|
|
|
|
elif index_var >= l3:
|
|
allele_cn_list.append(test_allele2)
|
|
allele_cn_list.append(int(round(max_het*int(c_num)-0.15)))
|
|
|
|
|
|
if allele_cn_list[0] == test_allele1:
|
|
rt_2 = int(c_num) - allele_cn_list[1]
|
|
allele_cn_list.append(test_allele2)
|
|
allele_cn_list.append(rt_2)
|
|
|
|
elif allele_cn_list[0] == test_allele2:
|
|
rt_2 = int(c_num) - allele_cn_list[1]
|
|
allele_cn_list.append(test_allele1)
|
|
allele_cn_list.append(rt_2)
|
|
|
|
if allele_cn_list[1] == 0:
|
|
res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3] - 1)
|
|
|
|
elif allele_cn_list[3] == 0:
|
|
res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1] - 1)
|
|
|
|
elif allele_cn_list[1] == 1:
|
|
res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
|
|
|
|
elif allele_cn_list[3] == 1:
|
|
res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
|
|
|
|
elif allele_cn_list[1] == 2:
|
|
res_dip = allele_cn_list[0] + "x2" + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
|
|
|
|
elif allele_cn_list[3] == 2:
|
|
res_dip = allele_cn_list[2] + "x2" + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
|
|
|
|
elif allele_cn_list[1] == 3:
|
|
res_dip = allele_cn_list[0] + "x3" + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
|
|
|
|
elif allele_cn_list[3] == 3:
|
|
res_dip = allele_cn_list[2] + "x3" + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
|
|
|
|
elif allele_cn_list[1] == 4:
|
|
res_dip = allele_cn_list[0] + "x4" + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
|
|
|
|
elif allele_cn_list[3] == 4:
|
|
res_dip = allele_cn_list[2] + "x4" + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
|
|
|
|
|
|
else:
|
|
res_dip = 'check'
|
|
|
|
return res_dip
|
|
|
|
|
|
# def hybrid_29_test1(cov_e1_int4, cov_int4_e9):
|
|
|
|
# if 0.85 < float(cov_e1_int4)/float(cov_int4_e9) < 1.2:
|
|
# return 'norm_var'
|
|
|
|
# elif 0.45 < float(cov_e1_int4)/float(cov_int4_e9) < 0.75:
|
|
# return 'hyb_29'
|
|
|
|
# elif float(cov_e1_int4)/float(cov_int4_e9) < 0.15:
|
|
# return 'hyb_29_2'
|
|
|
|
# else:
|
|
# return 'norm_var'
|
|
|
|
|
|
# def hybrid_30_test1(cov_e1_int4, cov_int4_e9):
|
|
|
|
# if 0.85 < float(cov_e1_int4)/float(cov_int4_e9) < 1.2:
|
|
# return 'norm_var'
|
|
|
|
# elif 0.45 < float(cov_int4_e9)/float(cov_e1_int4) < 0.75:
|
|
# return 'hyb_30'
|
|
|
|
# elif float(cov_int4_e9)/float(cov_e1_int4) < 0.15:
|
|
# return 'hyb_30_2'
|
|
|
|
# else:
|
|
# return 'norm_var'
|
|
|