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incomplete download of pgx-main

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Darren Wight
2025-08-18 12:12:55 +02:00
parent fe48df8676
commit 75c821b975
984 changed files with 0 additions and 878657 deletions
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pgx-main/scripts/cyp2c19/hg38/bin/stellarpgx.py
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#!/usr/bin/env python3
import os
import sys
import subprocess
from snv_def_modules import *
from sv_modules import *
from bkg_modules import *
print("--------------------------------------------\n")
print("CYP2C19 Star Allele Calling with StellarPGx\n")
print("--------------------------------------------\n")
database = sys.argv[1]
infile = sys.argv[2]
infile_full = sys.argv[3]
infile_full_gt = sys.argv[4]
infile_spec = sys.argv[5]
sv_del = sys.argv[6]
sv_dup = sys.argv[7]
cov_file = sys.argv[8]
hap_dbs = sys.argv[9]
act_score = sys.argv[10]
cn = get_total_CN(cov_file)[0]
print("Initially computed CN = {}".format(cn))
supp_core_vars = get_core_variants(infile, cn)
print("\nSample core variants:")
print(supp_core_vars)
snv_def_calls = cand_snv_allele_calling(database, infile, infile_full, infile_full_gt, infile_spec, cn)
if snv_def_calls == None:
bac_alleles = get_backgroud_alleles(database, supp_core_vars)
if bac_alleles == None:
print("\nResult:")
print("Possible novel allele or suballele present: interpret with caution")
else:
print("\nCandidate alleles:")
print("[" + bac_alleles[-1] + "]")
print("\nResult:")
print("Possible novel allele or suballele present: interpret with caution; experimental validation and expert review through PharmVar is recommended")
print("\nLikely background alleles:")
print("[" + bac_alleles[0] + "]")
sys.exit()
best_diplos = snv_def_calls[0]
print("\nCandidate alleles:")
print(best_diplos)
snv_def_alleles = snv_def_calls[-1]
if "or" in snv_def_alleles:
pass
else:
snv_cand_alleles = snv_def_calls[1]
dip_variants = get_all_vars_gt(infile_full_gt)
print("\nResult:")
av_cov = get_total_CN(cov_file)[1]
gene_alleles = ""
if snv_def_alleles != '*38/*38' and cn != '0':
in_list = dup_test_init(sv_dup, av_cov)
if cn == '2':
if 'or' in snv_def_alleles:
print (snv_def_alleles)
else:
gene_alleles = snv_def_alleles
print(gene_alleles)
elif cn == '0':
del_confirm = del_test(sv_del)
if del_confirm == '*36/*36':
gene_alleles = del_confirm
print (gene_alleles)
elif del_confirm == '*36':
gene_alleles = del_confirm + "/" + "*other"
print(gene_alleles)
else:
gene_alleles = "*36/*36"
print(gene_alleles)
elif cn == '1':
del_confirm = del_test(sv_del)
if "or" in snv_def_alleles and del_confirm == 'None':
print (snv_def_alleles + "\t" + "Possible CYP2C19 gene deletion present")
elif "or" not in snv_def_alleles and del_confirm == 'None':
snv_def_alleles = snv_def_alleles.split("/")
snv_cand_alleles = "".join(snv_cand_alleles)
snv_cand_alleles = snv_cand_alleles.split("_")
if snv_def_alleles[0] == snv_def_alleles[1]:
gene_alleles = snv_def_alleles[0] + "/" + "*36"
print(gene_alleles)
elif snv_def_alleles[0] != snv_def_alleles[1]:
samp_allele1 = del_adv_test(hap_dbs, snv_cand_alleles[0], snv_cand_alleles[1], snv_def_alleles[0], snv_def_alleles[1], supp_core_vars)
gene_alleles = samp_allele1 + "/" + "*36"
print(gene_alleles)
else:
snv_def_alleles = snv_def_alleles.split("/")
snv_cand_alleles = "".join(snv_cand_alleles)
snv_cand_alleles = snv_cand_alleles.split("_")
if snv_def_alleles[0] == snv_def_alleles[1]:
if del_confirm == "*36/*36":
del_confirm = "*36"
else:
del_confirm = "*36"
gene_alleles = del_confirm + "/" + snv_def_alleles[0]
print(gene_alleles)
elif snv_def_alleles[0] != snv_def_alleles[1]:
samp_allele1 = del_adv_test(hap_dbs, snv_cand_alleles[0], snv_cand_alleles[1], snv_def_alleles[0], snv_def_alleles[1], supp_core_vars)
if del_confirm == "*36/*36":
del_confirm = "*36"
else:
del_confirm = "*36"
gene_alleles = del_confirm + "/" + samp_allele1
print(gene_alleles)
elif (int(cn) == 3 or int(cn) == 4) and snv_def_alleles != None:
orig = snv_def_alleles
if "or" in snv_def_alleles:
print (snv_def_alleles + "\t" + "Duplication present")
else:
snv_def_alleles = snv_def_alleles.split("/")
snv_cand_alleles = "".join(snv_cand_alleles)
snv_cand_alleles = snv_cand_alleles.split("_")
if snv_def_alleles[0] != snv_def_alleles[1]:
phased_dup = dup_test_cn_3_4(sv_dup, hap_dbs, snv_cand_alleles[0], snv_cand_alleles[1], snv_def_alleles[0], snv_def_alleles[1], cn, av_cov, in_list)
phased_dup1 = phased_dup.split("/")
elif snv_def_alleles[0] == snv_def_alleles[1]:
rt_2 = int(cn) - 1
phased_dup = (snv_def_alleles[0] + "/" + snv_def_alleles[1] + "x" + str(rt_2))
gene_alleles = phased_dup
print(gene_alleles)
elif int(cn) > 4 and snv_def_alleles != None:
if "or" in snv_def_alleles:
print (snv_def_alleles + "\t" + "Duplication present")
else:
snv_def_alleles = snv_def_alleles.split("/")
snv_cand_alleles = "".join(snv_cand_alleles)
snv_cand_alleles = snv_cand_alleles.split("_")
if snv_def_alleles[0] != snv_def_alleles[1]:
phased_dup = dup_test_cn_n(sv_dup, hap_dbs, snv_cand_alleles[0], snv_cand_alleles[1], snv_def_alleles[0], snv_def_alleles[1], cn, av_cov, in_list)
elif snv_def_alleles[0] == snv_def_alleles[1]:
rt_2 = int(cn) - 1
phased_dup = (snv_def_alleles[0] + "/" + snv_def_alleles[1] + "x" + str(rt_2))
gene_alleles = phased_dup
print(phased_dup)
elif int(cn) > 2 and snv_def_alleles == None:
print("Possible rare CYP2C19 structural variant present")