pgx-main from prod added
This commit is contained in:
77
pgx-main/scripts/cyp2d6/b37/bin/bkg_modules.py
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77
pgx-main/scripts/cyp2d6/b37/bin/bkg_modules.py
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@@ -0,0 +1,77 @@
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#!/usr/bin/env python3
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import os
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import sys
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def get_backgroud_alleles(database, core_vars):
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dbs = []
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dbs_temp = []
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core_vars_list = core_vars.split(";")
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core_temp1 = core_vars_list[-1][:-4]
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core_temp2 = core_vars_list[0][:-4]
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for line in open(database, "r"):
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line = line.strip().split("\t")
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dbs.append(line)
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for record in dbs:
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temp_rec = record[1]
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if core_temp1 and core_temp2 in temp_rec:
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dbs_temp.append(record)
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scores = []
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candidates = []
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cand_vars = []
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for elem in dbs_temp:
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candidates.append(elem[0])
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record_core_var = elem[1].split(";")
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cand_vars.append(record_core_var)
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counter = 0
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for i in record_core_var:
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if i in core_vars_list:
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counter += 3
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elif i[:-4] in core_vars:
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counter += 1
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else:
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counter += -2
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scores.append(counter)
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cand_diplos = []
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diplo_vars2 = []
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if len(scores) == 0:
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diplo1 = '2.v1_2.v1'
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allele_res = '*2/*2'
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else:
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max_score = max(scores)
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indices = [i for i, x in enumerate(scores) if x == max_score or x == max_score - 1]
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for i in indices:
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diplo = candidates[i]
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diplo_vars1 = len(cand_vars[i])
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cand_diplos.append(diplo)
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diplo_vars2.append(diplo_vars1)
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min_index = diplo_vars2.index(min(diplo_vars2))
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diplo1 = cand_diplos[min_index]
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res1 = [i for i in range(len(diplo1)) if diplo1.startswith("_", i)]
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res2 = [i for i in range(len(diplo1)) if diplo1.startswith(".", i)]
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hap1 = "*" + str (diplo1[:res2[0]])
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hap2 = "*" + str (diplo1[res1[0]+1:res2[1]])
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allele_res = hap1 + "/" + hap2
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return [allele_res, diplo1];
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1056
pgx-main/scripts/cyp2d6/b37/bin/snv_def_modules.py
Normal file
1056
pgx-main/scripts/cyp2d6/b37/bin/snv_def_modules.py
Normal file
File diff suppressed because it is too large
Load Diff
802
pgx-main/scripts/cyp2d6/b37/bin/stellarpgx.py
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802
pgx-main/scripts/cyp2d6/b37/bin/stellarpgx.py
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@@ -0,0 +1,802 @@
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import os
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import sys
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import subprocess
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from snv_def_modules import *
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from sv_modules import *
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from bkg_modules import *
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print("--------------------------------------------\n")
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print("CYP2D6 Star Allele Calling with StellarPGx\n")
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print("--------------------------------------------\n")
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database = sys.argv[1]
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infile = sys.argv[2]
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infile_full = sys.argv[3]
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infile_full_gt = sys.argv[4]
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infile_spec = sys.argv[5]
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sv_del = sys.argv[6]
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sv_dup = sys.argv[7]
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cov_file = sys.argv[8]
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hap_dbs = sys.argv[9]
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act_score = sys.argv[10]
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cn = get_total_CN(cov_file)[0]
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print("Initially computed CN = {}".format(cn))
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supp_core_vars = get_core_variants(infile, cn)
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print("\nSample core variants:")
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print(supp_core_vars)
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snv_def_calls = cand_snv_allele_calling(database, infile, infile_full, infile_full_gt, infile_spec, cn)
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if snv_def_calls == None:
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bac_alleles = get_backgroud_alleles(database, supp_core_vars)
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if int(cn) == 0:
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print("\nResult:")
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print("*5/*5")
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elif bac_alleles == None:
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print("\nResult:")
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print("Possible novel allele or suballele present: interpret with caution")
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elif bac_alleles != None and int(cn) < 2:
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bac_alleles = bac_alleles[0].split("/")
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bac_alleles1 = bac_alleles[0] + "/" + "*5"
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print("\nResult:")
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print("Possible novel allele or suballele present: interpret with caution; experimental validation and expert review through PharmVar is recommended")
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print("\nLikely background alleles:")
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print("[" + bac_alleles1 + "]")
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else:
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print("\nCandidate alleles:")
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print("[" + bac_alleles[-1] + "]")
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print("\nResult:")
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print("Possible novel allele or suballele present: interpret with caution; experimental validation and expert review through PharmVar is recommended")
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print("\nLikely background alleles:")
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print("[" + bac_alleles[0] + "]")
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print("\nActivity score:")
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print("Indeterminate")
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print("\nMetaboliser status:")
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print("Indeterminate")
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sys.exit()
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best_diplos = snv_def_calls[0]
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print("\nCandidate alleles:")
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print(best_diplos)
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snv_def_alleles = snv_def_calls[-1]
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if "or" in snv_def_alleles:
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pass
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else:
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snv_cand_alleles = snv_def_calls[1]
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dip_variants = get_all_vars_gt(infile_full_gt)
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print("\nResult:")
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# cn = get_total_CN(cov_file)[0]
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av_cov = get_total_CN(cov_file)[3]
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cn_in1_3pr = get_total_CN(cov_file)[2]
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cn_ex9_3pr = get_total_CN(cov_file)[4]
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in1_3pr_float = get_total_CN(cov_file)[5]
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cov_in4_3pr = get_total_CN(cov_file)[6]
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cov_5pr_in4 = get_total_CN(cov_file)[7]
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cn_2d7_ex9 = get_total_CN(cov_file)[8]
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cn_2d7_in4_in8 = get_total_CN(cov_file)[9]
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cov_2d7_ex2_in8 = get_total_CN(cov_file)[10]
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cov_2d7_5pr_in1 = get_total_CN(cov_file)[11]
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# print(float(cn_ex9_3pr))
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gene_alleles = ""
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if snv_def_alleles != '*2/*2':
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in_list = dup_test_init(sv_dup, av_cov)
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if cn == '2' and snv_def_alleles == '*4/*4':
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test_68 = hyb_test_5_68_4(sv_del, in1_3pr_float, av_cov)
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if test_68 == 'norm_art':
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pass
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elif test_68 == 'del_hyb':
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snv_def_alleles = (snv_def_alleles.replace('*4', '*5', 1)).replace('*4', '*68+*4')
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gene_alleles = snv_def_alleles
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print(snv_def_alleles)
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elif cn == '2':
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if 'or' in snv_def_alleles:
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print (snv_def_alleles)
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else:
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snv_def_alleles = snv_def_alleles.split("/")
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if snv_def_alleles[0] == '*2' or snv_def_alleles[1] == '*2':
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ind_star2 = snv_def_alleles.index('*2')
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ind_other = 1 - ind_star2
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test_13_2_v1 = hybrid_13_2_v1(cov_in4_3pr, cov_5pr_in4)
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test_13_2_v2 = hybrid_13_2_v2(cov_2d7_ex2_in8, cov_2d7_5pr_in1)
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if test_13_2_v1 == 'norm_var':
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gene_alleles = "/".join(snv_def_alleles)
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print(gene_alleles)
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elif test_13_2_v1 == 'hyb_13_2':
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gene_alleles = snv_def_alleles[ind_other] + "/" + "*13+*2"
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print(gene_alleles)
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elif test_13_2_v2 == 'hyb_13_2_v2':
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gene_alleles = snv_def_alleles[ind_other] + "/" + "*13"
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print(gene_alleles)
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elif snv_def_alleles[0] == '*39' or snv_def_alleles[1] == '*39':
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ind_star2 = snv_def_alleles.index('*39')
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ind_other = 1 - ind_star2
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test_83_single = hybrid_test_83_single(sv_dup, cn, av_cov, cn_ex9_3pr)
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if test_83_single == 'norm_star39':
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gene_alleles = "/".join(snv_def_alleles)
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print(gene_alleles)
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elif test_83_single == 'hyb_83_single':
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gene_alleles = snv_def_alleles[ind_other] + "/" + "*83"
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print(gene_alleles)
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elif snv_def_alleles[0] == '*10' or snv_def_alleles[1] == '*10':
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ind_star2 = snv_def_alleles.index('*10')
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ind_other = 1 - ind_star2
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test_36_single = hybrid_test_36_single(sv_dup, cn, av_cov, cn_ex9_3pr)
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if test_36_single == 'norm_star10':
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gene_alleles = "/".join(snv_def_alleles)
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print(gene_alleles)
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elif test_36_single == 'hyb_36_single':
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gene_alleles = snv_def_alleles[ind_other] + "/" + "*36"
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print(gene_alleles)
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else:
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gene_alleles = "/".join(snv_def_alleles)
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print(gene_alleles)
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elif cn == '0':
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del_confirm = del_test(sv_del)
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if del_confirm == '*5/*5':
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gene_alleles = del_confirm
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print (gene_alleles)
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elif del_confirm == '*5':
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gene_alleles = del_confirm + "/" + "*other"
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print(gene_alleles)
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else:
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gene_alleles = "*5/*5"
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print(gene_alleles)
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elif cn == '1':
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del_confirm = del_test(sv_del)
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if "or" in snv_def_alleles and del_confirm == 'None':
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print (snv_def_alleles + "\t" + "Possible CYP2D6 gene deletion (*5) present")
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elif "or" not in snv_def_alleles and del_confirm == 'None':
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snv_def_alleles = snv_def_alleles.split("/")
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snv_cand_alleles = "".join(snv_cand_alleles)
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snv_cand_alleles = snv_cand_alleles.split("_")
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if snv_def_alleles[0] == snv_def_alleles[1]:
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gene_alleles = snv_def_alleles[0] + "/" + "*5"
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print(gene_alleles)
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elif snv_def_alleles[0] != snv_def_alleles[1]:
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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)
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gene_alleles = samp_allele1 + "/" + "*5"
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print(gene_alleles)
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else:
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snv_def_alleles = snv_def_alleles.split("/")
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snv_cand_alleles = "".join(snv_cand_alleles)
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snv_cand_alleles = snv_cand_alleles.split("_")
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if snv_def_alleles[0] == snv_def_alleles[1]:
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if del_confirm == "*5/*5":
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del_confirm = "*5"
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else:
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del_confirm = "*5"
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gene_alleles = del_confirm + "/" + snv_def_alleles[0]
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print(gene_alleles)
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elif snv_def_alleles[0] != snv_def_alleles[1]:
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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)
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if del_confirm == "*5/*5":
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del_confirm = "*5"
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else:
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del_confirm = "*5"
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gene_alleles = del_confirm + "/" + samp_allele1
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print(gene_alleles)
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elif (int(cn) == 3 or int(cn) == 4) and snv_def_alleles != None:
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orig = snv_def_alleles
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if "or" in snv_def_alleles:
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print (snv_def_alleles + "\t" + "Duplication present")
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else:
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snv_def_alleles = snv_def_alleles.split("/")
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snv_cand_alleles = "".join(snv_cand_alleles)
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snv_cand_alleles = snv_cand_alleles.split("_")
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if snv_def_alleles[0] == '*90' or snv_def_alleles[1] == '*90':
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alt_allele_ind = 1 - snv_def_alleles.index('*90')
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alt_allele = snv_def_alleles[alt_allele_ind]
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sp_allele = tandem_90_1(in_list, alt_allele, cn)
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sp_allele1 = sp_allele.split("/")
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|
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if "*10x2" in sp_allele1:
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test_36 = hybrid_test_36(sv_dup, cn, av_cov, cn_ex9_3pr, cn_2d7_ex9, cn_2d7_in4_in8)
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if test_36 == 'norm_dup':
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pass
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|
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elif test_36 == 'hyb_36_10':
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sp_allele = sp_allele.replace('*10x2', '*36+*10')
|
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|
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elif test_36 == 'hyb_36_36':
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sp_allele = sp_allele.replace('*10x2', '*36x2')
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gene_alleles = sp_allele
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print(sp_allele)
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|
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|
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elif snv_def_alleles[0] == '*57' or snv_def_alleles[1] == '*57':
|
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|
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alt_allele_ind = 1 - snv_def_alleles.index('*57')
|
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alt_allele = snv_def_alleles[alt_allele_ind]
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sp_allele = tandem_57_10(in_list, alt_allele, cn)
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print(sp_allele)
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|
||||
|
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elif snv_def_alleles[0] != snv_def_alleles[1]:
|
||||
|
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|
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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)
|
||||
|
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if phased_dup == 'check':
|
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phased_dup == 'No_call'
|
||||
|
||||
else:
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pass
|
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|
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phased_dup1 = phased_dup.split("/")
|
||||
|
||||
|
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if '*4x2' in phased_dup1:
|
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count1 = phased_dup1.count('*4x2')
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a_ind1 = phased_dup1.index('*4x2')
|
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a_ind2 = 1 - a_ind1
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other_hap = phased_dup1[a_ind2]
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|
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if count1 == 1:
|
||||
|
||||
test_68 = hybrid_test_68(sv_dup, cn, av_cov, cn_in1_3pr, in_list)
|
||||
|
||||
|
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if test_68 == 'norm_dup':
|
||||
pass
|
||||
elif test_68 == 'hyb_68':
|
||||
if int(cn_in1_3pr) < int(cn):
|
||||
phased_dup = phased_dup.replace('*4x2', '*68+*4')
|
||||
|
||||
elif int(cn_in1_3pr) == int(cn) and ('x' not in other_hap) and int(cn) == 4:
|
||||
phased_dup = phased_dup.replace('*4x2', '*68+*4')
|
||||
phased_dup = phased_dup.replace(other_hap, (other_hap + 'x2'))
|
||||
|
||||
elif count1 == 2:
|
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pass
|
||||
|
||||
if '*4x3' in phased_dup1:
|
||||
count1 = phased_dup1.count('*4x3')
|
||||
a_ind1 = phased_dup1.index('*4x3')
|
||||
a_ind2 = 1 - a_ind1
|
||||
other_hap = phased_dup1[a_ind2]
|
||||
|
||||
if count1 == 1:
|
||||
|
||||
test_68 = hybrid_test_68(sv_dup, cn, av_cov, cn_in1_3pr, in_list)
|
||||
|
||||
if test_68 == 'norm_dup':
|
||||
pass
|
||||
elif test_68 == 'hyb_68':
|
||||
if int(cn_in1_3pr) < int(cn):
|
||||
phased_dup = phased_dup.replace('*4x3', '*68+*4')
|
||||
|
||||
elif int(cn_in1_3pr) == int(cn) and 'x' not in other_hap:
|
||||
phased_dup = phased_dup.replace('*4x3', '*68+*4')
|
||||
|
||||
elif count1 == 2:
|
||||
pass
|
||||
|
||||
|
||||
if '*10x2' in phased_dup1:
|
||||
count2 = phased_dup1.count('*10x2')
|
||||
b_ind1 = phased_dup1.index('*10x2')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
|
||||
if count2 == 1:
|
||||
test_36 = hybrid_test_36(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_36 == 'norm_dup':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x2', '*36+*10')
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = phased_dup.replace('*10x2', '*36x2')
|
||||
|
||||
|
||||
if '*10x3' in phased_dup1:
|
||||
count3 = phased_dup1.count('*10x3')
|
||||
c_ind1 = phased_dup1.index('*10x3')
|
||||
c_ind2 = 1 - c_ind1
|
||||
|
||||
if count3 == 1:
|
||||
test_36 = hybrid_test_36_mod(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x3', '*36+*10x2')
|
||||
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = phased_dup.replace('*10x3', '*36x2+*10')
|
||||
|
||||
|
||||
if '*1x3' in phased_dup1:
|
||||
count2 = phased_dup1.count('*1x3')
|
||||
b_ind1 = phased_dup1.index('*1x3')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
|
||||
if count2 == 1:
|
||||
test_83 = hybrid_test_83(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_83 == 'norm_star39':
|
||||
pass
|
||||
|
||||
elif test_83 == 'hyb_83':
|
||||
phased_dup = phased_dup.replace('*1x3', '*1x2+*83')
|
||||
|
||||
|
||||
|
||||
if '*2' in phased_dup1:
|
||||
count2 = phased_dup1.count('*2')
|
||||
b_ind1 = phased_dup1.index('*2')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
if count2 == 1:
|
||||
test_13_2_v1 = hybrid_13_2_v1(cov_in4_3pr, cov_5pr_in4)
|
||||
test_13_2_v2 = hybrid_13_2_v2(cov_2d7_ex2_in8, cov_2d7_5pr_in1)
|
||||
|
||||
if test_13_2_v1 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v2 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v1 == 'hyb_13_2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
|
||||
|
||||
elif test_13_2_v2 == 'hyb_13_2_v2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13'
|
||||
|
||||
|
||||
|
||||
if '*2x2' in phased_dup1:
|
||||
count2 = phased_dup1.count('*2x2')
|
||||
b_ind1 = phased_dup1.index('*2x2')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
if count2 == 1:
|
||||
test_13_2_v1 = hybrid_13_2_v1(cov_in4_3pr, cov_5pr_in4)
|
||||
test_13_2_v2 = hybrid_13_2_v2(cov_2d7_ex2_in8, cov_2d7_5pr_in1)
|
||||
|
||||
if test_13_2_v1 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v2 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v1 == 'hyb_13_2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
|
||||
|
||||
elif test_13_2_v2 == 'hyb_13_2_v2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
|
||||
|
||||
|
||||
|
||||
gene_alleles = phased_dup
|
||||
print(phased_dup)
|
||||
|
||||
|
||||
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))
|
||||
|
||||
phased_dup1 = phased_dup.split("/")
|
||||
|
||||
if '*4x2' in phased_dup1:
|
||||
count1 = phased_dup1.count('*4x2')
|
||||
a_ind1 = phased_dup1.index('*4x2')
|
||||
a_ind2 = 1 - a_ind1
|
||||
|
||||
|
||||
if count1 == 1:
|
||||
test_68 = hybrid_test_68(sv_dup, cn, av_cov, cn_in1_3pr, in_list)
|
||||
|
||||
if test_68 == 'norm_dup':
|
||||
pass
|
||||
|
||||
elif test_68 == 'hyb_68':
|
||||
phased_dup.replace('*4x2', '*68+*4')
|
||||
|
||||
|
||||
if '*10x2' in phased_dup1:
|
||||
count2 = phased_dup1.count('*10x2')
|
||||
b_ind1 = phased_dup1.index('*10x2')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
if count2 == 1:
|
||||
test_36 = hybrid_test_36(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
if test_36 == 'norm_dup':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x2', '*36+*10')
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = phased_dup.replace('*10x2', '*36x2')
|
||||
|
||||
if '*10x3' in phased_dup1:
|
||||
count3 = phased_dup1.count('*10x3')
|
||||
c_ind1 = phased_dup1.index('*10x3')
|
||||
c_ind2 = 1 - c_ind1
|
||||
|
||||
if count3 == 1:
|
||||
test_36 = hybrid_test_36_mod(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x3', '*36+*10x2')
|
||||
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = '*36+*10/*36+*10'
|
||||
|
||||
|
||||
if '*1x3' in phased_dup1:
|
||||
count2 = phased_dup1.count('*1x3')
|
||||
b_ind1 = phased_dup1.index('*1x3')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
|
||||
if count2 == 1:
|
||||
test_83 = hybrid_test_83(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_83 == 'norm_star39':
|
||||
pass
|
||||
|
||||
elif test_83 == 'hyb_83':
|
||||
phased_dup = phased_dup.replace('*1x3', '*1x2+*83')
|
||||
|
||||
|
||||
if '*2x2' in phased_dup1:
|
||||
count2 = phased_dup1.count('*2x2')
|
||||
b_ind1 = phased_dup1.index('*2x2')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
if count2 == 1:
|
||||
test_13_2_v1 = hybrid_13_2_v1(cov_in4_3pr, cov_5pr_in4)
|
||||
test_13_2_v2 = hybrid_13_2_v2(cov_2d7_ex2_in8, cov_2d7_5pr_in1)
|
||||
|
||||
if test_13_2_v1 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v2 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v1 == 'hyb_13_2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
|
||||
|
||||
elif test_13_2_v2 == 'hyb_13_2_v2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
|
||||
|
||||
|
||||
gene_alleles = phased_dup
|
||||
print(phased_dup)
|
||||
|
||||
|
||||
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)
|
||||
|
||||
if phased_dup == 'check':
|
||||
phased_dup = 'No_call'
|
||||
|
||||
else:
|
||||
pass
|
||||
|
||||
phased_dup1 = phased_dup.split("/")
|
||||
|
||||
if '*10x4' in phased_dup1:
|
||||
count3 = phased_dup1.count('*10x4')
|
||||
c_ind1 = phased_dup1.index('*10x4')
|
||||
c_ind2 = 1 - c_ind1
|
||||
|
||||
if count3 == 1:
|
||||
test_36 = hybrid_test_36_multi(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x4', '*36+*10x3')
|
||||
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = phased_dup.replace('*10x4', '*36x2+*10x2')
|
||||
|
||||
elif test_36 == 'hyb_36_36_36':
|
||||
phased_dup = phased_dup.replace('*10x4','*36x3+*10')
|
||||
|
||||
else:
|
||||
phased_dup = "No_call"
|
||||
|
||||
|
||||
elif '*10x3' in phased_dup1:
|
||||
count3 = phased_dup1.count('*10x3')
|
||||
c_ind1 = phased_dup1.index('*10x3')
|
||||
c_ind2 = 1 - c_ind1
|
||||
|
||||
if count3 == 1:
|
||||
test_36 = hybrid_test_36_multi(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x3', '*36+*10x2')
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = phased_dup.replace('*10x3', '*36x2+*10')
|
||||
|
||||
elif test_36 == 'hyb_36_36_36':
|
||||
phased_dup = phased_dup.replace('*10x3','*36x3')
|
||||
|
||||
elif '*10x' in phased_dup1:
|
||||
phased_dup = 'No_call'
|
||||
|
||||
|
||||
|
||||
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))
|
||||
|
||||
if phased_dup == 'check':
|
||||
phased_dup = 'No_call'
|
||||
|
||||
else:
|
||||
pass
|
||||
|
||||
phased_dup1 = phased_dup.split("/")
|
||||
|
||||
if '*10x4' in phased_dup1:
|
||||
count3 = phased_dup1.count('*10x4')
|
||||
c_ind1 = phased_dup1.index('*10x4')
|
||||
c_ind2 = 1 - c_ind1
|
||||
|
||||
if count3 == 1:
|
||||
test_36 = hybrid_test_36_multi(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x4', '*36+*10x3')
|
||||
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = '*36+*10/*36+*10x2'
|
||||
|
||||
elif test_36 == 'hyb_36_36_36':
|
||||
phased_dup = '*36+*10/*36x2+*10'
|
||||
|
||||
else:
|
||||
phased_dup = "No_call"
|
||||
|
||||
elif phased_dup1[0].startswith('*10x') or phased_dup1[1].startswith('*10x'):
|
||||
|
||||
if phased_dup1[0].startswith('*10x'):
|
||||
dup_10_hyb = phased_dup1[0]
|
||||
|
||||
elif phased_dup1[1].startswith('*10x'):
|
||||
dup_10_hyb = phased_dup1[1]
|
||||
|
||||
cn_star10 = dup_10_hyb[(dup_10_hyb.find('x') + 1 ):]
|
||||
|
||||
test_36 = hybrid_test_36_multi_10(sv_dup, cn, av_cov, cn_ex9_3pr, cn_star10)
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'check':
|
||||
phased_dup = 'No_call'
|
||||
|
||||
else:
|
||||
c_ind1 = phased_dup1.index(dup_10_hyb)
|
||||
c_ind2 = 1 - c_ind1
|
||||
phased_dup = str(phased_dup1[c_ind2]) + "/" + test_36
|
||||
|
||||
|
||||
gene_alleles = phased_dup
|
||||
print(phased_dup)
|
||||
|
||||
|
||||
|
||||
elif int(cn) > 2 and snv_def_alleles == None:
|
||||
|
||||
print("Possible rare CYP2D6/2D7 hybrid present")
|
||||
|
||||
|
||||
|
||||
print("\nActivity score:")
|
||||
|
||||
score_list = []
|
||||
|
||||
score_list1 = []
|
||||
score_list2 = []
|
||||
score_list3 = []
|
||||
|
||||
allele_dict = {}
|
||||
|
||||
def get_ac_score(act_score, star_alleles):
|
||||
for line in open(act_score, "r"):
|
||||
line = line.strip().split()
|
||||
score_list.append(line)
|
||||
|
||||
for i in score_list:
|
||||
allele_dict[i[0]] = i[1]
|
||||
|
||||
star_alleles = star_alleles.replace("/", "+")
|
||||
star_alleles = star_alleles.split("+")
|
||||
|
||||
for elem in star_alleles:
|
||||
if "x" not in elem:
|
||||
m_allele = elem
|
||||
n_allele = "1"
|
||||
elif "x" in elem:
|
||||
index1 = elem.find("x")
|
||||
m_allele = elem[:index1]
|
||||
n_allele = elem[index1+1:]
|
||||
|
||||
p_allele = allele_dict[m_allele] + "_" + n_allele
|
||||
p_allele = p_allele.split("_")
|
||||
score_list1.append(p_allele)
|
||||
|
||||
for i in score_list1:
|
||||
score_list2.append(i[0])
|
||||
|
||||
if "n" in score_list2:
|
||||
return "Indeterminate"
|
||||
|
||||
else:
|
||||
for i in score_list1:
|
||||
score_list3.append(float(i[0])*float(i[1]))
|
||||
|
||||
total_a_score = sum(score_list3)
|
||||
return total_a_score
|
||||
|
||||
|
||||
if gene_alleles in ["",'No_call','check']:
|
||||
ac_score = "Indeterminate"
|
||||
print(ac_score)
|
||||
|
||||
|
||||
elif gene_alleles != "":
|
||||
ac_score = get_ac_score(act_score, gene_alleles)
|
||||
print(ac_score)
|
||||
|
||||
|
||||
print("\nMetaboliser status:")
|
||||
|
||||
if ac_score == "Indeterminate":
|
||||
print ("Indeterminate")
|
||||
|
||||
elif ac_score == 0:
|
||||
print("Poor metaboliser (PM)")
|
||||
|
||||
elif 0 < ac_score < 1.25:
|
||||
print("Intermediate metaboliser (IM)")
|
||||
|
||||
elif 1.25 <= ac_score <= 2.25:
|
||||
print("Normal metaboliser (NM)")
|
||||
|
||||
elif ac_score > 2.25:
|
||||
print("Ultrarapid metaboliser (UM)")
|
||||
|
||||
611
pgx-main/scripts/cyp2d6/b37/bin/sv_modules.py
Normal file
611
pgx-main/scripts/cyp2d6/b37/bin/sv_modules.py
Normal file
@@ -0,0 +1,611 @@
|
||||
#!/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_2d6_cov = float(all_reg[2][3])/(float(all_reg[2][2]) - float(all_reg[2][1]))
|
||||
av_vdr_cov = float(all_reg[3][3])/(float(all_reg[3][2]) - float(all_reg[3][1]))
|
||||
av_in1_3pr = float(all_reg[1][3])/(float(all_reg[1][2]) - float(all_reg[1][1]))
|
||||
av_ex9_3pr = float(all_reg[0][3])/(float(all_reg[0][2]) - float(all_reg[0][1]))
|
||||
av_5pr_in1 = float(all_reg[4][3])/(float(all_reg[4][2]) - float(all_reg[4][1]))
|
||||
av_in4_3pr = float(all_reg[5][3])/(float(all_reg[5][2]) - float(all_reg[5][1]))
|
||||
av_5pr_in4 = float(all_reg[6][3])/(float(all_reg[6][2]) - float(all_reg[6][1]))
|
||||
av_2d7_ex9 = float(all_reg[7][3])/(float(all_reg[7][2]) - float(all_reg[7][1]))
|
||||
av_2d7_in4_in8 = float(all_reg[8][3])/(float(all_reg[8][2]) - float(all_reg[8][1]))
|
||||
av_egfr_cov = float(all_reg[9][3])/(float(all_reg[9][2]) - float(all_reg[9][1]))
|
||||
av_2d7_ex2_in8 = float(all_reg[10][3])/(float(all_reg[10][2]) - float(all_reg[10][1]))
|
||||
av_2d7_5pr_in1 = float(all_reg[11][3])/(float(all_reg[11][2]) - float(all_reg[11][1]))
|
||||
|
||||
av_ctrl_cov = (av_vdr_cov + av_egfr_cov)/2
|
||||
# av_ctrl_cov = av_vdr_cov
|
||||
|
||||
comp_av = av_2d6_cov/av_ctrl_cov
|
||||
temp_cn = 2 * comp_av + 0.15
|
||||
total_cn = round(temp_cn)
|
||||
|
||||
in1_3pr = round(2 * av_in1_3pr/av_ctrl_cov)
|
||||
ex9_3pr = (2 * av_ex9_3pr/av_ctrl_cov)
|
||||
|
||||
|
||||
return [str(total_cn), round(av_2d6_cov), str(int(in1_3pr)), round(av_ctrl_cov), str(ex9_3pr), round(av_in1_3pr), str(av_in4_3pr), str(av_5pr_in4), str(av_2d7_ex9), str(av_2d7_in4_in8), str(av_2d7_ex2_in8), str(av_2d7_5pr_in1)];
|
||||
|
||||
|
||||
samp_gt = ""
|
||||
samp_gt_hap1 = ""
|
||||
|
||||
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 "*5/*5"
|
||||
elif float(ABHom) == -1.0:
|
||||
return "*5"
|
||||
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 = []
|
||||
test_list3 = []
|
||||
het_list = []
|
||||
|
||||
|
||||
for i in in_list:
|
||||
if i[1] == "0/1":
|
||||
het_list.append(i)
|
||||
|
||||
# return het_list
|
||||
|
||||
# if len(het_list) > 1 and het_list[0][0] == "42522613~G>C":
|
||||
# het_list.pop(0)
|
||||
# else:
|
||||
# pass
|
||||
|
||||
for i in het_list:
|
||||
test_list1.append(i[0])
|
||||
test_list2.append(i[-2])
|
||||
test_list3.append(float(i[-4]))
|
||||
|
||||
max_het = max(test_list2)
|
||||
|
||||
# if max_het > 1:
|
||||
# max_het = min(test_list2)
|
||||
# else:
|
||||
# pass
|
||||
|
||||
max_het_pos = test_list2.index(max_het)
|
||||
var = test_list1[max_het_pos]
|
||||
|
||||
if max_het > 1:
|
||||
max_het = test_list3[max_het_pos]
|
||||
elif max_het > test_list3[max_het_pos]:
|
||||
max_het = test_list3[max_het_pos]
|
||||
else:
|
||||
pass
|
||||
|
||||
|
||||
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
|
||||
|
||||
# return hdb_list
|
||||
|
||||
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)
|
||||
|
||||
|
||||
# return allele_cn_list
|
||||
|
||||
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[3] < -1:
|
||||
res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(3)
|
||||
|
||||
elif allele_cn_list[1] < -1:
|
||||
res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(3)
|
||||
|
||||
|
||||
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)
|
||||
|
||||
# if len(het_list) > 1 and het_list[0][0] == "42522613~G>C":
|
||||
# het_list.pop(0)
|
||||
# else:
|
||||
# pass
|
||||
|
||||
|
||||
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])
|
||||
|
||||
elif allele_cn_list[3] < 0:
|
||||
res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1] + allele_cn_list[3] - 1)
|
||||
|
||||
elif allele_cn_list[1] < 0:
|
||||
res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3] + allele_cn_list[1] - 1)
|
||||
|
||||
|
||||
else:
|
||||
res_dip = 'check'
|
||||
|
||||
return res_dip
|
||||
|
||||
|
||||
def hybrid_test_68(sv_dup, c_num, av_cov, cn_in1_3pr1, in_list):
|
||||
|
||||
test_list1 = []
|
||||
test_list2 = []
|
||||
test_list3 = []
|
||||
|
||||
|
||||
for i in in_list:
|
||||
test_list1.append(i[0])
|
||||
test_list2.append(abs(float(i[-2])))
|
||||
test_list3.append(i[-1])
|
||||
|
||||
index1 = test_list1.index('42526694~G>A')
|
||||
index2 = test_list1.index('42524947~C>T')
|
||||
|
||||
val_68 = test_list3[index1]
|
||||
val_4 = test_list3[index2]
|
||||
|
||||
rt = val_68/val_4
|
||||
|
||||
|
||||
if rt <= 1.4:
|
||||
return 'norm_dup'
|
||||
|
||||
elif rt > 1.4:
|
||||
return 'hyb_68'
|
||||
|
||||
|
||||
else:
|
||||
return 'norm_dup'
|
||||
|
||||
|
||||
def hyb_test_5_68_4(sv_del, in1_3pr1_float, av_cov):
|
||||
test_del = []
|
||||
for line in open(sv_del, "r"):
|
||||
if "COVERAGE" in line:
|
||||
test_del.append(line.strip())
|
||||
|
||||
t1 = 2 * in1_3pr1_float/av_cov
|
||||
|
||||
if len(test_del) == 0 and (1.6 < t1 < 2.8):
|
||||
return 'norm_art'
|
||||
|
||||
elif len(test_del) > 0 and t1 < 1.6:
|
||||
return 'del_hyb'
|
||||
|
||||
|
||||
def hybrid_test_36(sv_dup, cn, av_cov, cn_ex9_3pr):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_dup'
|
||||
|
||||
elif ((int(cn) - 1) - 0.35) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
return 'hyb_36_10'
|
||||
elif (int(cn) - 2) <= float(cn_ex9_3pr) < (int(cn) - 2 + 0.65):
|
||||
return 'hyb_36_36'
|
||||
|
||||
|
||||
def hybrid_test_36_single(sv_dup, cn, av_cov, cn_ex9_3pr):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_star10'
|
||||
|
||||
elif ((int(cn) - 1) - 0.35) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
return 'hyb_36_single'
|
||||
|
||||
else:
|
||||
return 'norm_star10'
|
||||
|
||||
|
||||
|
||||
|
||||
def hybrid_test_36_mod(sv_dup, cn, av_cov, cn_ex9_3pr):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_mt'
|
||||
|
||||
elif ((int(cn) - 1) - 0.3) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
return 'hyb_36_10'
|
||||
elif ((int(cn) - 2) - 0.3) <= float(cn_ex9_3pr) < (int(cn) - 2 + 0.7):
|
||||
return 'hyb_36_36'
|
||||
|
||||
|
||||
def hybrid_test_36_multi(sv_dup, cn, av_cov, cn_ex9_3pr):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_mt'
|
||||
|
||||
elif ((int(cn) - 1) - 0.05) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
return 'hyb_36_10'
|
||||
elif (int(cn) - 2) <= float(cn_ex9_3pr) < (int(cn) - 2 + 0.95):
|
||||
return 'hyb_36_36'
|
||||
elif (int(cn) - 3) <= float(cn_ex9_3pr) < (int(cn) - 3 + 0.95):
|
||||
return 'hyb_36_36_36'
|
||||
else:
|
||||
return 'check'
|
||||
|
||||
|
||||
def hybrid_test_36_multi_10(sv_dup, cn, av_cov, cn_ex9_3pr, cn_star10):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_mt'
|
||||
|
||||
elif float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
cn_star36 = int(cn) - int(round(float(cn_ex9_3pr)))
|
||||
adj_cn_star10 = int(cn_star10) - cn_star36
|
||||
|
||||
if cn_star36 == 1:
|
||||
return '*36+*10x' + str(adj_cn_star10)
|
||||
else:
|
||||
return '*36x' + str(cn_star36) + '+*10x' + str(adj_cn_star10)
|
||||
|
||||
else:
|
||||
return 'check'
|
||||
|
||||
|
||||
def hybrid_13_2_v1(cov_in4_3pr, cov_5pr_in4):
|
||||
|
||||
if 0.85 < float(cov_in4_3pr)/float(cov_5pr_in4) < 1.2:
|
||||
return 'norm_var'
|
||||
elif 0.45 < float(cov_in4_3pr)/float(cov_5pr_in4) < 0.75:
|
||||
return 'hyb_13_2'
|
||||
else:
|
||||
return 'norm_var'
|
||||
|
||||
|
||||
def hybrid_13_2_v2(cov_2d7_ex2_in8, cov_2d7_5pr_in1):
|
||||
|
||||
if 0.85 < float(cov_2d7_ex2_in8)/float(cov_2d7_5pr_in1) < 1.2:
|
||||
return 'norm_var'
|
||||
elif 0.45 < float(cov_2d7_ex2_in8)/float(cov_2d7_5pr_in1) < 0.75:
|
||||
return 'hyb_13_2_v2'
|
||||
else:
|
||||
return 'norm_var'
|
||||
|
||||
|
||||
|
||||
def tandem_90_1(in_list, alt_allele, cn):
|
||||
|
||||
test_list1 = []
|
||||
test_list2 = []
|
||||
test_list3 = []
|
||||
|
||||
for i in in_list:
|
||||
test_list1.append(i[0])
|
||||
test_list2.append(abs(float(i[-2])))
|
||||
test_list3.append(i[-1])
|
||||
|
||||
|
||||
if len(test_list1) > 1:
|
||||
index1 = test_list1.index('42525100~T>C')
|
||||
a = test_list3[index1]
|
||||
test_list3.pop(index1)
|
||||
b = max(test_list3)
|
||||
|
||||
c = round(b/a)
|
||||
|
||||
if int(cn) == 3 and c == 1:
|
||||
res = alt_allele + "/" + "*90+*1"
|
||||
|
||||
elif int(cn) == 3 and c > 1:
|
||||
res = alt_allele + "x2" + "/" + "*90"
|
||||
|
||||
elif int(cn) == 4 and c == 2:
|
||||
res = alt_allele + "x2" + "/" + "*90+*1"
|
||||
|
||||
elif int(cn) == 4 and c >= 3:
|
||||
res = alt_allele + "x3" + "/" + "*90"
|
||||
|
||||
else:
|
||||
val1 = test_list2[0]
|
||||
val2 = round(val1 * int(cn))
|
||||
|
||||
if int(cn) == 3 and val2 == 1:
|
||||
res = '*1/*90+*1'
|
||||
|
||||
return res
|
||||
|
||||
|
||||
def tandem_57_10(in_list, alt_allele, cn):
|
||||
|
||||
test_list1 = []
|
||||
test_list2 = []
|
||||
test_list3 = []
|
||||
|
||||
for i in in_list:
|
||||
test_list1.append(i[0])
|
||||
test_list2.append(abs(float(i[-2])))
|
||||
test_list3.append(i[-1])
|
||||
|
||||
if len(test_list1) > 1:
|
||||
index1 = test_list1.index('42525908~G>A')
|
||||
a = test_list3[index1]
|
||||
test_list3.pop(index1)
|
||||
index2 = test_list1.index('42526694~G>A')
|
||||
m = test_list3[index2]
|
||||
test_list3.pop(index2)
|
||||
b = max(test_list3)
|
||||
|
||||
c = round(b/a)
|
||||
p = round(m/a)
|
||||
|
||||
if int(cn) == 3 and c == 1 and p > 1:
|
||||
res = alt_allele + "/" + "*57+*10"
|
||||
|
||||
elif int(cn) == 3 and c > 1 and p == 1:
|
||||
res = alt_allele + "x2" + "/" + "*57"
|
||||
|
||||
elif int(cn) == 4 and c == 2 and p > 1:
|
||||
res = alt_allele + "x2" + "/" + "*57+*10"
|
||||
|
||||
elif int(cn) == 4 and c >= 3 and p == 1:
|
||||
res = alt_allele + "x3" + "/" + "*57"
|
||||
|
||||
elif int(cn) == 4 and p == 1 and alt_allele == '*10':
|
||||
res = "*57+*10" + "/" + "*57+*10"
|
||||
|
||||
elif int(cn) == 4 and p > 1 and alt_allele == '*10':
|
||||
res = "*10x2" + "/" + "*57+*10"
|
||||
|
||||
|
||||
else:
|
||||
res = alt_allele + "/" + "*57+*10"
|
||||
|
||||
return res
|
||||
|
||||
|
||||
def hybrid_test_83_single(sv_dup, cn, av_cov, cn_ex9_3pr):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_star39'
|
||||
|
||||
elif ((int(cn) - 1) - 0.35) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
return 'hyb_83_single'
|
||||
|
||||
else:
|
||||
return 'norm_star39'
|
||||
|
||||
|
||||
def hybrid_test_83(sv_dup, cn, av_cov, cn_ex9_3pr):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_star39'
|
||||
|
||||
elif ((int(cn) - 1) - 0.35) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
return 'hyb_83'
|
||||
|
||||
else:
|
||||
return 'norm_star39'
|
||||
|
||||
77
pgx-main/scripts/cyp2d6/hg38/bin/bkg_modules.py
Normal file
77
pgx-main/scripts/cyp2d6/hg38/bin/bkg_modules.py
Normal file
@@ -0,0 +1,77 @@
|
||||
#!/usr/bin/env python3
|
||||
|
||||
|
||||
import os
|
||||
import sys
|
||||
|
||||
|
||||
def get_backgroud_alleles(database, core_vars):
|
||||
|
||||
dbs = []
|
||||
dbs_temp = []
|
||||
|
||||
core_vars_list = core_vars.split(";")
|
||||
core_temp1 = core_vars_list[-1][:-4]
|
||||
core_temp2 = core_vars_list[0][:-4]
|
||||
|
||||
for line in open(database, "r"):
|
||||
line = line.strip().split("\t")
|
||||
dbs.append(line)
|
||||
|
||||
for record in dbs:
|
||||
temp_rec = record[1]
|
||||
|
||||
if core_temp1 and core_temp2 in temp_rec:
|
||||
dbs_temp.append(record)
|
||||
|
||||
|
||||
scores = []
|
||||
candidates = []
|
||||
cand_vars = []
|
||||
|
||||
for elem in dbs_temp:
|
||||
candidates.append(elem[0])
|
||||
record_core_var = elem[1].split(";")
|
||||
cand_vars.append(record_core_var)
|
||||
|
||||
counter = 0
|
||||
|
||||
for i in record_core_var:
|
||||
if i in core_vars_list:
|
||||
counter += 3
|
||||
elif i[:-4] in core_vars:
|
||||
counter += 1
|
||||
else:
|
||||
counter += -2
|
||||
|
||||
scores.append(counter)
|
||||
|
||||
cand_diplos = []
|
||||
diplo_vars2 = []
|
||||
|
||||
if len(scores) == 0:
|
||||
diplo1 = '1.v1_1.v1'
|
||||
allele_res = '*1/*1'
|
||||
|
||||
else:
|
||||
max_score = max(scores)
|
||||
|
||||
indices = [i for i, x in enumerate(scores) if x == max_score or x == max_score - 1]
|
||||
|
||||
for i in indices:
|
||||
diplo = candidates[i]
|
||||
diplo_vars1 = len(cand_vars[i])
|
||||
cand_diplos.append(diplo)
|
||||
diplo_vars2.append(diplo_vars1)
|
||||
|
||||
min_index = diplo_vars2.index(min(diplo_vars2))
|
||||
|
||||
diplo1 = cand_diplos[min_index]
|
||||
|
||||
res1 = [i for i in range(len(diplo1)) if diplo1.startswith("_", i)]
|
||||
res2 = [i for i in range(len(diplo1)) if diplo1.startswith(".", i)]
|
||||
hap1 = "*" + str (diplo1[:res2[0]])
|
||||
hap2 = "*" + str (diplo1[res1[0]+1:res2[1]])
|
||||
allele_res = hap1 + "/" + hap2
|
||||
|
||||
return [allele_res, diplo1];
|
||||
1204
pgx-main/scripts/cyp2d6/hg38/bin/snv_def_modules.py
Normal file
1204
pgx-main/scripts/cyp2d6/hg38/bin/snv_def_modules.py
Normal file
File diff suppressed because it is too large
Load Diff
810
pgx-main/scripts/cyp2d6/hg38/bin/stellarpgx.py
Normal file
810
pgx-main/scripts/cyp2d6/hg38/bin/stellarpgx.py
Normal file
@@ -0,0 +1,810 @@
|
||||
import os
|
||||
import sys
|
||||
import subprocess
|
||||
from snv_def_modules import *
|
||||
from sv_modules import *
|
||||
from bkg_modules import *
|
||||
|
||||
print("--------------------------------------------\n")
|
||||
|
||||
print("CYP2D6 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("*5/*5")
|
||||
|
||||
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] + "/" + "*5"
|
||||
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] + "]")
|
||||
|
||||
print("\nActivity score:")
|
||||
print("Indeterminate")
|
||||
|
||||
print("\nMetaboliser status:")
|
||||
print("Indeterminate")
|
||||
|
||||
|
||||
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)[3]
|
||||
cn_in1_3pr = get_total_CN(cov_file)[2]
|
||||
cn_ex9_3pr = get_total_CN(cov_file)[4]
|
||||
in1_3pr_float = get_total_CN(cov_file)[5]
|
||||
cov_in4_3pr = get_total_CN(cov_file)[6]
|
||||
cov_5pr_in4 = get_total_CN(cov_file)[7]
|
||||
cn_2d7_ex9 = get_total_CN(cov_file)[8]
|
||||
cn_2d7_in4_in8 = get_total_CN(cov_file)[9]
|
||||
cov_2d7_ex2_in8 = get_total_CN(cov_file)[10]
|
||||
cov_2d7_5pr_in1 = get_total_CN(cov_file)[11]
|
||||
|
||||
|
||||
gene_alleles = ""
|
||||
|
||||
|
||||
if snv_def_alleles != '*1/*1':
|
||||
in_list = dup_test_init(sv_dup, av_cov)
|
||||
|
||||
if cn == '2' and snv_def_alleles == '*4/*4':
|
||||
|
||||
test_68 = hyb_test_5_68_4(sv_del, in1_3pr_float, av_cov)
|
||||
|
||||
if test_68 == 'norm_art':
|
||||
pass
|
||||
elif test_68 == 'del_hyb':
|
||||
snv_def_alleles = (snv_def_alleles.replace('*4', '*5', 1)).replace('*4', '*68+*4')
|
||||
|
||||
gene_alleles = snv_def_alleles
|
||||
print(gene_alleles)
|
||||
|
||||
|
||||
elif cn == '2':
|
||||
# print(snv_def_alleles)
|
||||
if 'or' in snv_def_alleles:
|
||||
# print ("\n")
|
||||
print (snv_def_alleles)
|
||||
else:
|
||||
snv_def_alleles = snv_def_alleles.split("/")
|
||||
|
||||
|
||||
if snv_def_alleles[0] == '*2' or snv_def_alleles[1] == '*2':
|
||||
ind_star2 = snv_def_alleles.index('*2')
|
||||
ind_other = 1 - ind_star2
|
||||
|
||||
test_13_2_v1 = hybrid_13_2_v1(cov_in4_3pr, cov_5pr_in4)
|
||||
test_13_2_v2 = hybrid_13_2_v2(cov_2d7_ex2_in8, cov_2d7_5pr_in1)
|
||||
|
||||
if test_13_2_v1 == 'norm_var':
|
||||
gene_alleles = "/".join(snv_def_alleles)
|
||||
print(gene_alleles)
|
||||
|
||||
elif test_13_2_v1 == 'hyb_13_2':
|
||||
gene_alleles = snv_def_alleles[ind_other] + "/" + "*13+*2"
|
||||
print(gene_alleles)
|
||||
|
||||
elif test_13_2_v2 == 'hyb_13_2_v2':
|
||||
gene_alleles = snv_def_alleles[ind_other] + "/" + "*13"
|
||||
print(gene_alleles)
|
||||
|
||||
|
||||
elif snv_def_alleles[0] == '*39' or snv_def_alleles[1] == '*39':
|
||||
ind_star2 = snv_def_alleles.index('*39')
|
||||
ind_other = 1 - ind_star2
|
||||
|
||||
test_83_single = hybrid_test_83_single(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
if test_83_single == 'norm_star39':
|
||||
gene_alleles = "/".join(snv_def_alleles)
|
||||
print(gene_alleles)
|
||||
|
||||
elif test_83_single == 'hyb_83_single':
|
||||
gene_alleles = snv_def_alleles[ind_other] + "/" + "*83"
|
||||
print(gene_alleles)
|
||||
|
||||
|
||||
elif snv_def_alleles[0] == '*10' or snv_def_alleles[1] == '*10':
|
||||
ind_star2 = snv_def_alleles.index('*10')
|
||||
ind_other = 1 - ind_star2
|
||||
|
||||
test_36_single = hybrid_test_36_single(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
if test_36_single == 'norm_star10':
|
||||
gene_alleles = "/".join(snv_def_alleles)
|
||||
print(gene_alleles)
|
||||
|
||||
elif test_36_single == 'hyb_36_single':
|
||||
gene_alleles = snv_def_alleles[ind_other] + "/" + "*36"
|
||||
print(gene_alleles)
|
||||
|
||||
|
||||
else:
|
||||
# print("\n")
|
||||
gene_alleles = "/".join(snv_def_alleles)
|
||||
print(gene_alleles)
|
||||
|
||||
|
||||
elif cn == '0':
|
||||
del_confirm = del_test(sv_del)
|
||||
if del_confirm == '*5/*5':
|
||||
gene_alleles = del_confirm
|
||||
print(gene_alleles)
|
||||
|
||||
elif del_confirm == '*5':
|
||||
samp_dip = del_confirm + "/" + "*other"
|
||||
print(samp_dip)
|
||||
|
||||
else:
|
||||
gene_alleles = "*5/*5"
|
||||
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 CYP2D6 gene deletion (*5) 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] + "/" + "*5"
|
||||
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 + "/" + "*5"
|
||||
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 == "*5/*5":
|
||||
del_confirm = "*5"
|
||||
else:
|
||||
del_confirm = "*5"
|
||||
|
||||
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 == "*5/*5":
|
||||
del_confirm = "*5"
|
||||
else:
|
||||
del_confirm = "*5"
|
||||
|
||||
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] == '*90' or snv_def_alleles[1] == '*90':
|
||||
|
||||
alt_allele_ind = 1 - snv_def_alleles.index('*90')
|
||||
alt_allele = snv_def_alleles[alt_allele_ind]
|
||||
sp_allele = tandem_90_1(in_list, alt_allele, cn)
|
||||
|
||||
|
||||
sp_allele1 = sp_allele.split("/")
|
||||
|
||||
if "*10x2" in sp_allele1:
|
||||
|
||||
test_36 = hybrid_test_36(sv_dup, cn, av_cov, cn_ex9_3pr, cn_2d7_ex9, cn_2d7_in4_in8)
|
||||
|
||||
if test_36 == 'norm_dup':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
sp_allele = sp_allele.replace('*10x2', '*36+*10')
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
sp_allele = sp_allele.replace('*10x2', '*36x2')
|
||||
|
||||
gene_alleles = sp_allele
|
||||
print(gene_alleles)
|
||||
|
||||
|
||||
elif snv_def_alleles[0] == '*57' or snv_def_alleles[1] == '*57':
|
||||
|
||||
alt_allele_ind = 1 - snv_def_alleles.index('*57')
|
||||
alt_allele = snv_def_alleles[alt_allele_ind]
|
||||
sp_allele = tandem_57_10(in_list, alt_allele, cn)
|
||||
|
||||
|
||||
print(sp_allele)
|
||||
|
||||
|
||||
|
||||
elif 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)
|
||||
|
||||
if phased_dup == 'check':
|
||||
phased_dup == 'No_call'
|
||||
|
||||
else:
|
||||
pass
|
||||
|
||||
phased_dup1 = phased_dup.split("/")
|
||||
|
||||
|
||||
if '*4x2' in phased_dup1:
|
||||
count1 = phased_dup1.count('*4x2')
|
||||
a_ind1 = phased_dup1.index('*4x2')
|
||||
a_ind2 = 1 - a_ind1
|
||||
other_hap = phased_dup1[a_ind2]
|
||||
|
||||
if count1 == 1:
|
||||
|
||||
test_68 = hybrid_test_68(sv_dup, cn, av_cov, cn_in1_3pr, in_list)
|
||||
|
||||
if test_68 == 'norm_dup':
|
||||
pass
|
||||
elif test_68 == 'hyb_68':
|
||||
if int(cn_in1_3pr) < int(cn):
|
||||
phased_dup = phased_dup.replace('*4x2', '*68+*4')
|
||||
|
||||
elif int(cn_in1_3pr) == int(cn) and ('x' not in other_hap) and int(cn) == 4:
|
||||
phased_dup = phased_dup.replace('*4x2', '*68+*4')
|
||||
phased_dup = phased_dup.replace(other_hap, (other_hap + 'x2'))
|
||||
|
||||
else:
|
||||
phased_dup = phased_dup.replace('*4x2', '*68+*4')
|
||||
|
||||
elif count1 == 2:
|
||||
pass
|
||||
|
||||
if '*4x3' in phased_dup1:
|
||||
count1 = phased_dup1.count('*4x3')
|
||||
a_ind1 = phased_dup1.index('*4x3')
|
||||
a_ind2 = 1 - a_ind1
|
||||
other_hap = phased_dup1[a_ind2]
|
||||
|
||||
if count1 == 1:
|
||||
|
||||
test_68 = hybrid_test_68(sv_dup, cn, av_cov, cn_in1_3pr, in_list)
|
||||
|
||||
if test_68 == 'norm_dup':
|
||||
pass
|
||||
elif test_68 == 'hyb_68':
|
||||
if int(cn_in1_3pr) < int(cn):
|
||||
phased_dup = phased_dup.replace('*4x3', '*68+*4')
|
||||
|
||||
elif int(cn_in1_3pr) == int(cn) and 'x' not in other_hap:
|
||||
phased_dup = phased_dup.replace('*4x3', '*68+*4')
|
||||
# phased_dup = phased_dup.replace(other_hap, (other_hap + 'x2'))
|
||||
|
||||
elif count1 == 2:
|
||||
pass
|
||||
|
||||
|
||||
if '*10x2' in phased_dup1:
|
||||
count2 = phased_dup1.count('*10x2')
|
||||
b_ind1 = phased_dup1.index('*10x2')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
|
||||
if count2 == 1:
|
||||
test_36 = hybrid_test_36(sv_dup, cn, av_cov, cn_ex9_3pr, cn_2d7_ex9, cn_2d7_in4_in8)
|
||||
|
||||
|
||||
if test_36 == 'norm_dup':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x2', '*36+*10')
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = phased_dup.replace('*10x2', '*36x2')
|
||||
|
||||
|
||||
if '*10x3' in phased_dup1:
|
||||
count3 = phased_dup1.count('*10x3')
|
||||
c_ind1 = phased_dup1.index('*10x3')
|
||||
c_ind2 = 1 - c_ind1
|
||||
|
||||
if count3 == 1:
|
||||
test_36 = hybrid_test_36_mod(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x3', '*36+*10x2')
|
||||
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = phased_dup.replace('*10x3', '*36x2+*10')
|
||||
|
||||
|
||||
if '*1x3' in phased_dup1:
|
||||
count2 = phased_dup1.count('*1x3')
|
||||
b_ind1 = phased_dup1.index('*1x3')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
|
||||
if count2 == 1:
|
||||
test_83 = hybrid_test_83(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_83 == 'norm_star39':
|
||||
pass
|
||||
|
||||
elif test_83 == 'hyb_83':
|
||||
phased_dup = phased_dup.replace('*1x3', '*1x2+*83')
|
||||
|
||||
|
||||
|
||||
if '*2' in phased_dup1:
|
||||
count2 = phased_dup1.count('*2')
|
||||
b_ind1 = phased_dup1.index('*2')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
if count2 == 1:
|
||||
test_13_2_v1 = hybrid_13_2_v1(cov_in4_3pr, cov_5pr_in4)
|
||||
test_13_2_v2 = hybrid_13_2_v2(cov_2d7_ex2_in8, cov_2d7_5pr_in1)
|
||||
|
||||
if test_13_2_v1 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v2 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v1 == 'hyb_13_2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
|
||||
|
||||
elif test_13_2_v2 == 'hyb_13_2_v2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13'
|
||||
|
||||
|
||||
if '*2x2' in phased_dup1:
|
||||
count2 = phased_dup1.count('*2x2')
|
||||
b_ind1 = phased_dup1.index('*2x2')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
if count2 == 1:
|
||||
test_13_2_v1 = hybrid_13_2_v1(cov_in4_3pr, cov_5pr_in4)
|
||||
test_13_2_v2 = hybrid_13_2_v2(cov_2d7_ex2_in8, cov_2d7_5pr_in1)
|
||||
|
||||
if test_13_2_v1 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v2 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v1 == 'hyb_13_2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
|
||||
|
||||
elif test_13_2_v2 == 'hyb_13_2_v2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
|
||||
|
||||
|
||||
|
||||
gene_alleles = phased_dup
|
||||
print(gene_alleles)
|
||||
|
||||
|
||||
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))
|
||||
|
||||
phased_dup1 = phased_dup.split("/")
|
||||
|
||||
if '*4x2' in phased_dup1:
|
||||
count1 = phased_dup1.count('*4x2')
|
||||
a_ind1 = phased_dup1.index('*4x2')
|
||||
a_ind2 = 1 - a_ind1
|
||||
|
||||
|
||||
if count1 == 1:
|
||||
test_68 = hybrid_test_68(sv_dup, cn, av_cov, cn_in1_3pr, in_list)
|
||||
|
||||
if test_68 == 'norm_dup':
|
||||
pass
|
||||
|
||||
elif test_68 == 'hyb_68':
|
||||
phased_dup.replace('*4x2', '*68+*4')
|
||||
|
||||
|
||||
if '*10x2' in phased_dup1:
|
||||
count2 = phased_dup1.count('*10x2')
|
||||
b_ind1 = phased_dup1.index('*10x2')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
if count2 == 1:
|
||||
test_36 = hybrid_test_36(sv_dup, cn, av_cov, cn_ex9_3pr, cn_2d7_ex9, cn_2d7_in4_in8)
|
||||
# print (test_36)
|
||||
|
||||
if test_36 == 'norm_dup':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x2', '*36+*10')
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = phased_dup.replace('*10x2', '*36x2')
|
||||
|
||||
if '*10x3' in phased_dup1:
|
||||
count3 = phased_dup1.count('*10x3')
|
||||
c_ind1 = phased_dup1.index('*10x3')
|
||||
c_ind2 = 1 - c_ind1
|
||||
|
||||
if count3 == 1:
|
||||
test_36 = hybrid_test_36_mod(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x3', '*36+*10x2')
|
||||
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = '*36+*10/*36+*10'
|
||||
|
||||
|
||||
if '*1x3' in phased_dup1:
|
||||
count2 = phased_dup1.count('*1x3')
|
||||
b_ind1 = phased_dup1.index('*1x3')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
|
||||
if count2 == 1:
|
||||
test_83 = hybrid_test_83(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_83 == 'norm_star39':
|
||||
pass
|
||||
|
||||
elif test_83 == 'hyb_83':
|
||||
phased_dup = phased_dup.replace('*1x3', '*1x2+*83')
|
||||
|
||||
|
||||
|
||||
if '*2x2' in phased_dup1:
|
||||
count2 = phased_dup1.count('*2x2')
|
||||
b_ind1 = phased_dup1.index('*2x2')
|
||||
b_ind2 = 1 - b_ind1
|
||||
|
||||
if count2 == 1:
|
||||
test_13_2_v1 = hybrid_13_2_v1(cov_in4_3pr, cov_5pr_in4)
|
||||
test_13_2_v2 = hybrid_13_2_v2(cov_2d7_ex2_in8, cov_2d7_5pr_in1)
|
||||
|
||||
if test_13_2_v1 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v2 == 'norm_var':
|
||||
pass
|
||||
|
||||
elif test_13_2_v1 == 'hyb_13_2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
|
||||
|
||||
elif test_13_2_v2 == 'hyb_13_2_v2':
|
||||
phased_dup = phased_dup1[b_ind2] + "/" + '*13+*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)
|
||||
|
||||
if phased_dup == 'check':
|
||||
phased_dup = 'No_call'
|
||||
|
||||
else:
|
||||
pass
|
||||
|
||||
phased_dup1 = phased_dup.split("/")
|
||||
|
||||
if '*10x4' in phased_dup1:
|
||||
count3 = phased_dup1.count('*10x4')
|
||||
c_ind1 = phased_dup1.index('*10x4')
|
||||
c_ind2 = 1 - c_ind1
|
||||
|
||||
if count3 == 1:
|
||||
test_36 = hybrid_test_36_multi(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x4', '*36+*10x3')
|
||||
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = phased_dup.replace('*10x4', '*36x2+*10x2')
|
||||
|
||||
elif test_36 == 'hyb_36_36_36':
|
||||
phased_dup = phased_dup.replace('*10x4','*36x3+*10')
|
||||
|
||||
else:
|
||||
phased_dup = "No_call"
|
||||
|
||||
|
||||
elif '*10x3' in phased_dup1:
|
||||
count3 = phased_dup1.count('*10x3')
|
||||
c_ind1 = phased_dup1.index('*10x3')
|
||||
c_ind2 = 1 - c_ind1
|
||||
|
||||
if count3 == 1:
|
||||
test_36 = hybrid_test_36_multi(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x3', '*36+*10x2')
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = phased_dup.replace('*10x3', '*36x2+*10')
|
||||
|
||||
elif test_36 == 'hyb_36_36_36':
|
||||
phased_dup = phased_dup.replace('*10x3','*36x3')
|
||||
|
||||
else:
|
||||
phased_dup = "No_call"
|
||||
|
||||
|
||||
elif phased_dup1[0].startswith('*10x') or phased_dup1[1].startswith('*10x'):
|
||||
|
||||
if phased_dup1[0].startswith('*10x'):
|
||||
dup_10_hyb = phased_dup1[0]
|
||||
|
||||
elif phased_dup1[1].startswith('*10x'):
|
||||
dup_10_hyb = phased_dup1[1]
|
||||
|
||||
cn_star10 = dup_10_hyb[(dup_10_hyb.find('x') + 1 ):]
|
||||
|
||||
test_36 = hybrid_test_36_multi_10(sv_dup, cn, av_cov, cn_ex9_3pr, cn_star10)
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'check':
|
||||
phased_dup = 'No_call'
|
||||
|
||||
else:
|
||||
c_ind1 = phased_dup1.index(dup_10_hyb)
|
||||
c_ind2 = 1 - c_ind1
|
||||
phased_dup = str(phased_dup1[c_ind2]) + "/" + test_36
|
||||
|
||||
|
||||
gene_alleles = phased_dup
|
||||
print(gene_alleles)
|
||||
|
||||
|
||||
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))
|
||||
|
||||
if phased_dup == 'check':
|
||||
phased_dup = 'No_call'
|
||||
|
||||
else:
|
||||
pass
|
||||
|
||||
phased_dup1 = phased_dup.split("/")
|
||||
|
||||
|
||||
if '*10x4' in phased_dup1:
|
||||
count3 = phased_dup1.count('*10x4')
|
||||
c_ind1 = phased_dup1.index('*10x4')
|
||||
c_ind2 = 1 - c_ind1
|
||||
|
||||
if count3 == 1:
|
||||
test_36 = hybrid_test_36_multi(sv_dup, cn, av_cov, cn_ex9_3pr)
|
||||
|
||||
|
||||
if test_36 == 'norm_mt':
|
||||
pass
|
||||
|
||||
elif test_36 == 'hyb_36_10':
|
||||
phased_dup = phased_dup.replace('*10x4', '*36+*10x3')
|
||||
|
||||
|
||||
elif test_36 == 'hyb_36_36':
|
||||
phased_dup = '*36+*10/*36+*10x2'
|
||||
|
||||
elif test_36 == 'hyb_36_36_36':
|
||||
phased_dup = '*36+*10/*36x2+*10'
|
||||
|
||||
else:
|
||||
phased_dup = "No_call"
|
||||
|
||||
|
||||
elif '*10x' in phased_dup1:
|
||||
phased_dup = "No_call"
|
||||
|
||||
|
||||
gene_alleles = phased_dup
|
||||
print(gene_alleles)
|
||||
|
||||
|
||||
elif int(cn) > 2 and snv_def_alleles == None:
|
||||
print("Possible rare CYP2D6/2D7 hybrid present")
|
||||
|
||||
|
||||
|
||||
print("\nActivity score:")
|
||||
|
||||
score_list = []
|
||||
|
||||
score_list1 = []
|
||||
score_list2 = []
|
||||
score_list3 = []
|
||||
|
||||
allele_dict = {}
|
||||
|
||||
def get_ac_score(act_score, star_alleles):
|
||||
for line in open(act_score, "r"):
|
||||
line = line.strip().split()
|
||||
score_list.append(line)
|
||||
|
||||
for i in score_list:
|
||||
allele_dict[i[0]] = i[1]
|
||||
|
||||
star_alleles = star_alleles.replace("/", "+")
|
||||
star_alleles = star_alleles.split("+")
|
||||
|
||||
for elem in star_alleles:
|
||||
if "x" not in elem:
|
||||
m_allele = elem
|
||||
n_allele = "1"
|
||||
elif "x" in elem:
|
||||
index1 = elem.find("x")
|
||||
m_allele = elem[:index1]
|
||||
n_allele = elem[index1+1:]
|
||||
|
||||
p_allele = allele_dict[m_allele] + "_" + n_allele
|
||||
p_allele = p_allele.split("_")
|
||||
score_list1.append(p_allele)
|
||||
|
||||
for i in score_list1:
|
||||
score_list2.append(i[0])
|
||||
|
||||
if "n" in score_list2:
|
||||
return "Indeterminate"
|
||||
|
||||
else:
|
||||
for i in score_list1:
|
||||
score_list3.append(float(i[0])*float(i[1]))
|
||||
|
||||
total_a_score = sum(score_list3)
|
||||
return total_a_score
|
||||
|
||||
|
||||
|
||||
if gene_alleles in ["",'No_call','check']:
|
||||
ac_score = "Indeterminate"
|
||||
print(ac_score)
|
||||
|
||||
|
||||
elif gene_alleles != "":
|
||||
ac_score = get_ac_score(act_score, gene_alleles)
|
||||
print(ac_score)
|
||||
|
||||
|
||||
print("\nMetaboliser status:")
|
||||
|
||||
if ac_score == "Indeterminate":
|
||||
print ("Indeterminate")
|
||||
|
||||
elif ac_score == 0:
|
||||
print("Poor metaboliser (PM)")
|
||||
|
||||
elif 0 < ac_score < 1.25:
|
||||
print("Intermediate metaboliser (IM)")
|
||||
|
||||
elif 1.25 <= ac_score <= 2.25:
|
||||
print("Normal metaboliser (NM)")
|
||||
|
||||
elif ac_score > 2.25:
|
||||
print("Ultrarapid metaboliser (UM)")
|
||||
611
pgx-main/scripts/cyp2d6/hg38/bin/sv_modules.py
Normal file
611
pgx-main/scripts/cyp2d6/hg38/bin/sv_modules.py
Normal file
@@ -0,0 +1,611 @@
|
||||
#!/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_2d6_cov = float(all_reg[2][3])/(float(all_reg[2][2]) - float(all_reg[2][1]))
|
||||
av_vdr_cov = float(all_reg[3][3])/(float(all_reg[3][2]) - float(all_reg[3][1]))
|
||||
av_in1_3pr = float(all_reg[1][3])/(float(all_reg[1][2]) - float(all_reg[1][1]))
|
||||
av_ex9_3pr = float(all_reg[0][3])/(float(all_reg[0][2]) - float(all_reg[0][1]))
|
||||
av_in4_3pr = float(all_reg[4][3])/(float(all_reg[4][2]) - float(all_reg[4][1]))
|
||||
av_5pr_in4 = float(all_reg[5][3])/(float(all_reg[5][2]) - float(all_reg[5][1]))
|
||||
av_2d7_ex9 = float(all_reg[6][3])/(float(all_reg[6][2]) - float(all_reg[6][1]))
|
||||
av_2d7_in4_in8 = float(all_reg[7][3])/(float(all_reg[7][2]) - float(all_reg[7][1]))
|
||||
av_egfr_cov = float(all_reg[8][3])/(float(all_reg[8][2]) - float(all_reg[8][1]))
|
||||
av_2d7_ex2_in8 = float(all_reg[9][3])/(float(all_reg[9][2]) - float(all_reg[9][1]))
|
||||
av_2d7_5pr_in1 = float(all_reg[10][3])/(float(all_reg[10][2]) - float(all_reg[10][1]))
|
||||
|
||||
|
||||
av_ctrl_cov = (av_vdr_cov + av_egfr_cov)/2
|
||||
|
||||
comp_av = av_2d6_cov/av_ctrl_cov
|
||||
temp_cn = 2 * comp_av
|
||||
total_cn = round(temp_cn)
|
||||
|
||||
in1_3pr = round(2 * av_in1_3pr/av_ctrl_cov)
|
||||
ex9_3pr = (2 * av_ex9_3pr/av_ctrl_cov)
|
||||
|
||||
return [str(int(total_cn)), round(av_2d6_cov), str(int(in1_3pr)), round(av_ctrl_cov), str(ex9_3pr), round(av_in1_3pr), str(av_in4_3pr), str(av_5pr_in4), str(av_2d7_ex9), str(av_2d7_in4_in8), str(av_2d7_ex2_in8), str(av_2d7_5pr_in1)];
|
||||
|
||||
|
||||
samp_gt = ""
|
||||
samp_gt_hap1 = ""
|
||||
|
||||
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 "*5/*5"
|
||||
elif float(ABHom) == -1.0:
|
||||
return "*5"
|
||||
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/av_read_cov, 4))
|
||||
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])
|
||||
|
||||
elif allele_cn_list[1] == -1:
|
||||
res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3] - 2)
|
||||
|
||||
elif allele_cn_list[3] == -1:
|
||||
res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1] - 2)
|
||||
|
||||
elif allele_cn_list[3] < -1:
|
||||
res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(3)
|
||||
|
||||
elif allele_cn_list[1] < -1:
|
||||
res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(3)
|
||||
|
||||
|
||||
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])
|
||||
|
||||
elif allele_cn_list[1] == -1:
|
||||
res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3] - 2)
|
||||
|
||||
elif allele_cn_list[3] == -1:
|
||||
res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1] - 2)
|
||||
|
||||
elif allele_cn_list[3] < 0:
|
||||
res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1] + allele_cn_list[3] - 1)
|
||||
|
||||
elif allele_cn_list[1] < 0:
|
||||
res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3] + allele_cn_list[1] - 1)
|
||||
|
||||
|
||||
else:
|
||||
res_dip = 'check'
|
||||
|
||||
return res_dip
|
||||
|
||||
|
||||
|
||||
def hybrid_test_68(sv_dup, c_num, av_cov, cn_in1_3pr1, in_list):
|
||||
|
||||
test_list1 = []
|
||||
test_list2 = []
|
||||
test_list3 = []
|
||||
|
||||
|
||||
for i in in_list:
|
||||
test_list1.append(i[0])
|
||||
test_list2.append(abs(float(i[-2])))
|
||||
test_list3.append(i[-1])
|
||||
|
||||
index1 = test_list1.index('42130692~G>A')
|
||||
index2 = test_list1.index('42128945~C>T')
|
||||
|
||||
val_68 = test_list3[index1]
|
||||
val_4 = test_list3[index2]
|
||||
|
||||
rt = val_68/val_4
|
||||
|
||||
|
||||
if rt <= 1.4:
|
||||
return 'norm_dup'
|
||||
|
||||
elif rt > 1.4:
|
||||
return 'hyb_68'
|
||||
|
||||
|
||||
else:
|
||||
return 'norm_dup'
|
||||
|
||||
|
||||
def hyb_test_5_68_4(sv_del, in1_3pr1_float, av_cov):
|
||||
test_del = []
|
||||
for line in open(sv_del, "r"):
|
||||
if "COVERAGE" in line:
|
||||
test_del.append(line.strip())
|
||||
|
||||
# if len(test_del) == 0:
|
||||
# return 'norm_art'
|
||||
|
||||
# elif len(test_del) > 0:
|
||||
# return 'del_hyb'
|
||||
|
||||
t1 = 2 * in1_3pr1_float/av_cov
|
||||
|
||||
if len(test_del) == 0 and (1.6 < t1 < 2.8):
|
||||
return 'norm_art'
|
||||
|
||||
elif len(test_del) > 0 and t1 < 1.6:
|
||||
return 'del_hyb'
|
||||
|
||||
|
||||
def hybrid_test_36(sv_dup, cn, av_cov, cn_ex9_3pr, cn_2d7_ex9, cn_2d7_in4_in8):
|
||||
|
||||
|
||||
if ((int(cn) - 1) - 0.3) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5) or (2.5 < (2 * float(cn_2d7_ex9)/float(cn_2d7_in4_in8)) < 3.5):
|
||||
return 'hyb_36_10'
|
||||
|
||||
elif (int(cn) - 2) <= float(cn_ex9_3pr) < (int(cn) - 2 + 0.7):
|
||||
return 'hyb_36_36'
|
||||
else:
|
||||
return 'norm_dup'
|
||||
|
||||
|
||||
def hybrid_test_36_single(sv_dup, cn, av_cov, cn_ex9_3pr):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_star10'
|
||||
|
||||
elif ((int(cn) - 1) - 0.35) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
return 'hyb_36_single'
|
||||
|
||||
else:
|
||||
return 'norm_star10'
|
||||
|
||||
|
||||
|
||||
def hybrid_test_36_mod(sv_dup, cn, av_cov, cn_ex9_3pr):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_mt'
|
||||
|
||||
elif ((int(cn) - 1) - 0.05) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
return 'hyb_36_10'
|
||||
elif (int(cn) - 2) <= float(cn_ex9_3pr) < (int(cn) - 2 + 0.95):
|
||||
return 'hyb_36_36'
|
||||
|
||||
|
||||
def hybrid_test_36_multi(sv_dup, cn, av_cov, cn_ex9_3pr):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_mt'
|
||||
|
||||
elif ((int(cn) - 1) - 0.05) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
return 'hyb_36_10'
|
||||
elif (int(cn) - 2) <= float(cn_ex9_3pr) < (int(cn) - 2 + 0.95):
|
||||
return 'hyb_36_36'
|
||||
elif (int(cn) - 3) <= float(cn_ex9_3pr) < (int(cn) - 3 + 0.95):
|
||||
return 'hyb_36_36_36'
|
||||
else:
|
||||
return 'check'
|
||||
|
||||
|
||||
def hybrid_test_36_multi_10(sv_dup, cn, av_cov, cn_ex9_3pr, cn_star10):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_mt'
|
||||
|
||||
elif float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
cn_star36 = int(cn) - int(round(float(cn_ex9_3pr)))
|
||||
adj_cn_star10 = int(cn_star10) - cn_star36
|
||||
|
||||
if cn_star36 == 1:
|
||||
return '*36+*10x' + str(adj_cn_star10)
|
||||
else:
|
||||
return '*36x' + str(cn_star36) + '+*10x' + str(adj_cn_star10)
|
||||
|
||||
else:
|
||||
return 'check'
|
||||
|
||||
|
||||
def hybrid_13_2_v1(cov_in4_3pr, cov_5pr_in4):
|
||||
|
||||
if 0.85 < float(cov_in4_3pr)/float(cov_5pr_in4) < 1.2:
|
||||
return 'norm_var'
|
||||
elif 0.45 < float(cov_in4_3pr)/float(cov_5pr_in4) < 0.75:
|
||||
return 'hyb_13_2'
|
||||
else:
|
||||
return 'norm_var'
|
||||
|
||||
|
||||
def hybrid_13_2_v2(cov_2d7_ex2_in8, cov_2d7_5pr_in1):
|
||||
|
||||
if 0.85 < float(cov_2d7_ex2_in8)/float(cov_2d7_5pr_in1) < 1.2:
|
||||
return 'norm_var'
|
||||
elif 0.45 < float(cov_2d7_ex2_in8)/float(cov_2d7_5pr_in1) < 0.75:
|
||||
return 'hyb_13_2_v2'
|
||||
else:
|
||||
return 'norm_var'
|
||||
|
||||
|
||||
|
||||
def tandem_90_1(in_list, alt_allele, cn):
|
||||
|
||||
test_list1 = []
|
||||
test_list2 = []
|
||||
test_list3 = []
|
||||
|
||||
for i in in_list:
|
||||
test_list1.append(i[0])
|
||||
test_list2.append(abs(float(i[-2])))
|
||||
test_list3.append(i[-1])
|
||||
|
||||
|
||||
if len(test_list1) > 1:
|
||||
index1 = test_list1.index('42129098~T>C')
|
||||
a = test_list3[index1]
|
||||
test_list3.pop(index1)
|
||||
b = max(test_list3)
|
||||
|
||||
c = round(b/a)
|
||||
|
||||
if int(cn) == 3 and c == 1:
|
||||
res = alt_allele + "/" + "*90+*1"
|
||||
|
||||
elif int(cn) == 3 and c > 1:
|
||||
res = alt_allele + "x2" + "/" + "*90"
|
||||
|
||||
elif int(cn) == 4 and c == 2:
|
||||
res = alt_allele + "x2" + "/" + "*90+*1"
|
||||
|
||||
elif int(cn) == 4 and c >= 3:
|
||||
res = alt_allele + "x3" + "/" + "*90"
|
||||
|
||||
else:
|
||||
val1 = test_list2[0]
|
||||
val2 = round(val1 * int(cn))
|
||||
|
||||
if int(cn) == 3 and val2 == 1:
|
||||
res = '*1/*90+*1'
|
||||
elif int(cn) == 3 and val2 == 2:
|
||||
res = '*90/*90+*1'
|
||||
elif int(cn) == 4 and val2 == 1:
|
||||
res = '*1x2/*90+*1'
|
||||
elif int(cn) == 4 and val2 == 2:
|
||||
res = '*90+*1/*90+*1'
|
||||
elif int(cn) == 4 and val2 == 3:
|
||||
res = '*90x2/*90+*1'
|
||||
elif int(cn) == 3 and val2 == 3:
|
||||
res = '*90/*90x2'
|
||||
elif int(cn) == 4 and val2 == 4:
|
||||
res = '*90/*90x3'
|
||||
|
||||
return res
|
||||
|
||||
|
||||
def tandem_57_10(in_list, alt_allele, cn):
|
||||
|
||||
test_list1 = []
|
||||
test_list2 = []
|
||||
test_list3 = []
|
||||
|
||||
for i in in_list:
|
||||
test_list1.append(i[0])
|
||||
test_list2.append(abs(float(i[-2])))
|
||||
test_list3.append(i[-1])
|
||||
|
||||
if len(test_list1) > 1:
|
||||
index1 = test_list1.index('42129906~G>A')
|
||||
a = test_list3[index1]
|
||||
test_list3.pop(index1)
|
||||
index2 = test_list1.index('42130692~G>A')
|
||||
m = test_list3[index2]
|
||||
test_list3.pop(index2)
|
||||
b = max(test_list3)
|
||||
|
||||
c = round(b/a)
|
||||
p = round(m/a)
|
||||
|
||||
if int(cn) == 3 and c == 1 and p > 1:
|
||||
res = alt_allele + "/" + "*57+*10"
|
||||
|
||||
elif int(cn) == 3 and c > 1 and p == 1:
|
||||
res = alt_allele + "x2" + "/" + "*57"
|
||||
|
||||
elif int(cn) == 4 and c == 2 and p > 1:
|
||||
res = alt_allele + "x2" + "/" + "*57+*10"
|
||||
|
||||
elif int(cn) == 4 and c >= 3 and p == 1:
|
||||
res = alt_allele + "x3" + "/" + "*57"
|
||||
|
||||
elif int(cn) == 4 and p == 1 and alt_allele == '*10':
|
||||
res = "*57+*10" + "/" + "*57+*10"
|
||||
|
||||
elif int(cn) == 4 and p > 1 and alt_allele == '*10':
|
||||
res = "*10x2" + "/" + "*57+*10"
|
||||
|
||||
else:
|
||||
res = alt_allele + "/" + "*57+*10"
|
||||
|
||||
return res
|
||||
|
||||
|
||||
|
||||
def hybrid_test_83_single(sv_dup, cn, av_cov, cn_ex9_3pr):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_star39'
|
||||
|
||||
elif ((int(cn) - 1) - 0.35) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
return 'hyb_83_single'
|
||||
|
||||
else:
|
||||
return 'norm_star39'
|
||||
|
||||
|
||||
def hybrid_test_83(sv_dup, cn, av_cov, cn_ex9_3pr):
|
||||
|
||||
if int(round(float(cn_ex9_3pr))) == int(cn):
|
||||
return 'norm_star39'
|
||||
|
||||
elif ((int(cn) - 1) - 0.35) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
|
||||
return 'hyb_83'
|
||||
|
||||
else:
|
||||
return 'norm_star39'
|
||||
Reference in New Issue
Block a user