360 lines
11 KiB
Python
360 lines
11 KiB
Python
#!/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("CYP2A6 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 int(cn) == 0:
|
|
print("\nResult:")
|
|
print("*4/*4")
|
|
|
|
elif bac_alleles == None:
|
|
print("\nResult:")
|
|
print("Possible novel allele or suballele present: interpret with caution")
|
|
|
|
|
|
elif bac_alleles != None and int(cn) < 2:
|
|
bac_alleles = bac_alleles[0].split("/")
|
|
bac_alleles1 = bac_alleles[0] + "/" + "*4"
|
|
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_alleles1 + "]")
|
|
|
|
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]
|
|
cov_e1_e2 = get_total_CN(cov_file)[3]
|
|
cov_e3_e9 = get_total_CN(cov_file)[4]
|
|
cov_3p_utr = get_total_CN(cov_file)[5]
|
|
cov_ctrl = get_total_CN(cov_file)[2]
|
|
cov_e1_e4 = get_total_CN(cov_file)[6]
|
|
cov_e5_e9 = get_total_CN(cov_file)[7]
|
|
cov_e3_e4 = get_total_CN(cov_file)[8]
|
|
cov_e9_3pr = get_total_CN(cov_file)[9]
|
|
cov_e7_e8 = get_total_CN(cov_file)[10]
|
|
|
|
|
|
gene_alleles = ""
|
|
|
|
|
|
conv_3p_utr = ['*5','*7','*8','*10','*19','*24','*28','*35','*36','*37']
|
|
|
|
|
|
if snv_def_alleles != '*1/*1' 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:
|
|
snv_def_alleles = snv_def_alleles.split("/")
|
|
|
|
|
|
if snv_def_alleles[0] == '*46' or snv_def_alleles[1] == '*46':
|
|
ind_star2 = snv_def_alleles.index('*46')
|
|
ind_other = 1 - ind_star2
|
|
|
|
test_1b = star_1b_test(cov_3p_utr, cov_ctrl)
|
|
|
|
|
|
if test_1b == 'no_1B' and (snv_def_alleles.count('*46') == 2):
|
|
gene_alleles = "*1" + "/" + "*1"
|
|
print(gene_alleles)
|
|
|
|
elif test_1b == 'het_1B' and (snv_def_alleles[ind_other] not in conv_3p_utr):
|
|
gene_alleles = snv_def_alleles[ind_other] + "/" + "*46"
|
|
print(gene_alleles)
|
|
|
|
elif test_1b =='hom_1B' and (snv_def_alleles[ind_other] in conv_3p_utr):
|
|
gene_alleles = snv_def_alleles[ind_other] + "/" + "*46"
|
|
print(gene_alleles)
|
|
|
|
|
|
|
|
elif snv_def_alleles[0] == '*1' or snv_def_alleles[1] == '*1':
|
|
ind_star2 = snv_def_alleles.index('*1')
|
|
ind_other = 1 - ind_star2
|
|
|
|
# test_12 = hybrid_12_test1(cov_e1_e2, cov_e3_e9)
|
|
|
|
test_12_34 = hybrid_12_34(cov_e1_e2, cov_e3_e9, cov_e1_e4, cov_e5_e9, cov_e3_e4)
|
|
|
|
test_1b = star_1b_test(cov_3p_utr, cov_ctrl)
|
|
|
|
if test_12_34 == 'norm_var':
|
|
|
|
if test_1b == 'no_1B':
|
|
gene_alleles = "/".join(snv_def_alleles)
|
|
print(gene_alleles)
|
|
|
|
elif test_1b == 'het_1B' and (snv_def_alleles[ind_other] not in conv_3p_utr):
|
|
gene_alleles = snv_def_alleles[ind_other] + "/" + "*46"
|
|
print(gene_alleles)
|
|
|
|
elif test_1b == 'hom_1B' and (snv_def_alleles.count('*1') == 2):
|
|
gene_alleles = "*46/*46"
|
|
print(gene_alleles)
|
|
|
|
elif test_1b =='hom_1B' and (snv_def_alleles[ind_other] in conv_3p_utr):
|
|
gene_alleles = snv_def_alleles[ind_other] + "/" + "*46"
|
|
print(gene_alleles)
|
|
|
|
elif test_1b =='hom_1B':
|
|
gene_alleles = snv_def_alleles[ind_other] + "/" + "*46"
|
|
print(gene_alleles)
|
|
|
|
else:
|
|
gene_alleles = "/".join(snv_def_alleles)
|
|
print(gene_alleles)
|
|
|
|
|
|
elif test_12_34 == 'hyb_12':
|
|
|
|
gene_alleles = snv_def_alleles[ind_other] + "/" + "*12"
|
|
print(gene_alleles)
|
|
|
|
elif test_12_34 == 'hyb_12_2' and snv_def_alleles == "*1/*1":
|
|
gene_alleles = "*12/*12"
|
|
print(gene_alleles)
|
|
|
|
elif test_12_34 == 'hyb_34':
|
|
gene_alleles = snv_def_alleles[ind_other] + "/" + "*34"
|
|
print(gene_alleles)
|
|
|
|
elif test_12_34 == 'hyb_34_2' and snv_def_alleles == "*1/*1":
|
|
gene_alleles = "*34/*34"
|
|
print(gene_alleles)
|
|
|
|
else:
|
|
gene_alleles = "/".join(snv_def_alleles)
|
|
print(gene_alleles)
|
|
|
|
|
|
|
|
elif cn == '0':
|
|
del_confirm = del_test(sv_del)
|
|
test_47_1 = hybrid_47_test1(cov_e9_3pr, cov_e7_e8)
|
|
test_47_2 = hybrid_47_test2(cov_e9_3pr, cov_e7_e8, cov_ctrl)
|
|
|
|
if del_confirm == '*4/*4' and test_47_2 == 'no_hyb_47':
|
|
gene_alleles = '*4/*4'
|
|
|
|
elif del_confirm == '*4/*4' and test_47_2 == 'het_47':
|
|
gene_alleles = '*4/*47'
|
|
|
|
elif del_confirm == '*4/*4' and test_47_2 == 'hom_47':
|
|
gene_alleles = '*47/*47'
|
|
|
|
elif del_confirm == '*4' and test_47_1 == 'no_hyb_47':
|
|
gene_alleles = '*4' + "/" + "*other"
|
|
|
|
elif del_confirm == '*4' and test_47_1 == 'hyb_47':
|
|
gene_alleles = '*47' + "/" + "*other"
|
|
|
|
else:
|
|
gene_alleles = "*4/*4"
|
|
|
|
print(gene_alleles)
|
|
|
|
|
|
elif cn == '1':
|
|
del_confirm = del_test(sv_del)
|
|
test_47_1 = hybrid_47_test1(cov_e9_3pr, cov_e7_e8)
|
|
|
|
if "or" in snv_def_alleles and del_confirm == 'None':
|
|
print (snv_def_alleles + "\t" + "Possible CYP2A6 gene deletion (*4) 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] and test_47_1 == 'no_hyb_47':
|
|
gene_alleles = snv_def_alleles[0] + "/" + "*4"
|
|
print(gene_alleles)
|
|
|
|
elif snv_def_alleles[0] == snv_def_alleles[1] and test_47_1 == 'hyb_47':
|
|
gene_alleles = snv_def_alleles[0] + "/" + "*47"
|
|
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 + "/" + "*4"
|
|
|
|
if test_47_1 == 'no_hyb_47':
|
|
pass
|
|
elif test_47_1 == 'hyb_47':
|
|
gene_alleles = samp_allele1 + "/" + "*47"
|
|
|
|
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("_")
|
|
|
|
test_1b = star_1b_test(cov_3p_utr, cov_ctrl)
|
|
test_47_1 = hybrid_47_test1(cov_e9_3pr, cov_e7_e8)
|
|
|
|
if snv_def_alleles[0] == snv_def_alleles[1]:
|
|
del_confirm = "*4"
|
|
|
|
if snv_def_alleles[0] == '*1' and test_1b == 'hom_1B':
|
|
snv_def_alleles[0] = '*46'
|
|
gene_alleles = del_confirm + "/" + snv_def_alleles[0]
|
|
print(gene_alleles)
|
|
|
|
elif snv_def_alleles[0] in conv_3p_utr and test_47_1 == 'no_hyb_47':
|
|
gene_alleles = del_confirm + "/" + snv_def_alleles[0]
|
|
print(gene_alleles)
|
|
|
|
elif snv_def_alleles[0] in conv_3p_utr and test_47_1 == 'hyb_47':
|
|
gene_alleles = snv_def_alleles[0] + "/" + '*47'
|
|
print(gene_alleles)
|
|
else:
|
|
gene_alleles = del_confirm + "/" + snv_def_alleles[0]
|
|
print(gene_alleles)
|
|
|
|
# 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)
|
|
|
|
del_confirm == "*4"
|
|
|
|
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)
|
|
|
|
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 CYP2A6/2A7 hybrid present")
|