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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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37
pgx-main/scripts/ugt2b7/hg38/bin/sv_modules.py
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@@ -1,37 +0,0 @@
#!/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_ugt2b7_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]))
exon_cov_list = []
all_reg = all_reg[3:]
a = list(range(1, len(all_reg)))
for i in a:
exon_cov = 'av_e' + str(i)
exon_cov = float(all_reg[i-1][3])/(float(all_reg[i-1][2]) - float(all_reg[i-1][1]))
exon_cov_list.append(exon_cov)
av_ctrl_cov = (av_vdr_cov + av_egfr_cov)/2
comp_av = av_ugt2b7_cov/av_ctrl_cov
temp_cn = 2 * comp_av
total_cn = round(temp_cn)
return [str(int(total_cn)), round(av_ugt2b7_cov), round(av_ctrl_cov), exon_cov_list];