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removed pgx-main

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Darren Wight
2025-08-18 12:05:31 +02:00
parent f66cd01b21
commit fcb0e9aa4c
956 changed files with 0 additions and 934400 deletions
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pgx-main/scripts/nat2/hg38/bin/sv_modules.py
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#!/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_nat2_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_nat2_cov/av_ctrl_cov
temp_cn = 2 * comp_av
total_cn = round(temp_cn)
return [str(int(total_cn)), round(av_nat2_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