darren/reproduce_setup
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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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56
pgx-main/scripts/slc22a1/hg38/bin/stellarpgx.py
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#!/usr/bin/env python3
import os
import sys
import subprocess
import math
from sv_modules import *
print("--------------------------------------------\n")
print("SLC22A1 Variant Analysis with StellarPGx\n")
print("--------------------------------------------\n")
infile = sys.argv[1]
cov_file = sys.argv[2]
def get_core_variants(infile, cn):
core_vars = []
for line in open(infile, "r"):
line = line.strip()
core_vars.append(line)
core_vars = ";".join(sorted(core_vars))
if int(cn) == 1:
core_vars = core_vars.replace("~0/1", "~1/1")
if os.stat(infile).st_size == 0:
core_vars = "No core SNVs detected; haplotypes equivalent to GRCh38 content"
return core_vars
cn = get_total_CN(cov_file)[0]
av_ctrl_cov = get_total_CN(cov_file)[2]
exon_cov = get_total_CN(cov_file)[3]
print("Initially computed Copy Number = {}".format(cn))
for i in range(1, len(exon_cov)):
if exon_cov[i-1]/av_ctrl_cov < 0.45 :
print ('Check exon {} for potential deletion if using high coverage WGS'.format(str(i)))
else:
pass
supp_core_vars = get_core_variants(infile, cn)
print("\nSample core variants:")
print(supp_core_vars)

56
pgx-main/scripts/slc22a1/hg38/bin/stellarpgx.py~
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#!/usr/bin/env python3
import os
import sys
import subprocess
import math
from sv_modules import *
print("--------------------------------------------\n")
print("${i^^} Variant Analysis with StellarPGx\n")
print("--------------------------------------------\n")
infile = sys.argv[1]
cov_file = sys.argv[2]
def get_core_variants(infile, cn):
core_vars = []
for line in open(infile, "r"):
line = line.strip()
core_vars.append(line)
core_vars = ";".join(sorted(core_vars))
if int(cn) == 1:
core_vars = core_vars.replace("~0/1", "~1/1")
if os.stat(infile).st_size == 0:
core_vars = "No core SNVs detected; haplotypes equivalent to GRCh38 content"
return core_vars
cn = get_total_CN(cov_file)[0]
av_ctrl_cov = get_total_CN(cov_file)[2]
exon_cov = get_total_CN(cov_file)[3]
print("Initially computed Copy Number = {}".format(cn))
for i in range(1, len(exon_cov)):
if exon_cov[i-1]/av_ctrl_cov < 0.45 :
print ('Check exon {} for potential deletion if using high coverage WGS'.format(str(i)))
else:
pass
supp_core_vars = get_core_variants(infile, cn)
print("\nSample core variants:")
print(supp_core_vars)

37
pgx-main/scripts/slc22a1/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_slc22a1_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_slc22a1_cov/av_ctrl_cov
temp_cn = 2 * comp_av
total_cn = round(temp_cn)
return [str(int(total_cn)), round(av_slc22a1_cov), round(av_ctrl_cov), exon_cov_list];