803 lines
24 KiB
Python
803 lines
24 KiB
Python
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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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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elif test_36 == 'hyb_36_10':
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sp_allele = sp_allele.replace('*10x2', '*36+*10')
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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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elif snv_def_alleles[0] == '*57' or snv_def_alleles[1] == '*57':
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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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elif snv_def_alleles[0] != snv_def_alleles[1]:
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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'
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else:
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pass
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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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if count1 == 1:
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test_68 = hybrid_test_68(sv_dup, cn, av_cov, cn_in1_3pr, in_list)
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if test_68 == 'norm_dup':
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pass
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elif test_68 == 'hyb_68':
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if int(cn_in1_3pr) < int(cn):
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phased_dup = phased_dup.replace('*4x2', '*68+*4')
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elif int(cn_in1_3pr) == int(cn) and ('x' not in other_hap) and int(cn) == 4:
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phased_dup = phased_dup.replace('*4x2', '*68+*4')
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phased_dup = phased_dup.replace(other_hap, (other_hap + 'x2'))
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elif count1 == 2:
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pass
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if '*4x3' in phased_dup1:
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count1 = phased_dup1.count('*4x3')
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a_ind1 = phased_dup1.index('*4x3')
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a_ind2 = 1 - a_ind1
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other_hap = phased_dup1[a_ind2]
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if count1 == 1:
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test_68 = hybrid_test_68(sv_dup, cn, av_cov, cn_in1_3pr, in_list)
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if test_68 == 'norm_dup':
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pass
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elif test_68 == 'hyb_68':
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if int(cn_in1_3pr) < int(cn):
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phased_dup = phased_dup.replace('*4x3', '*68+*4')
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elif int(cn_in1_3pr) == int(cn) and 'x' not in other_hap:
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phased_dup = phased_dup.replace('*4x3', '*68+*4')
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elif count1 == 2:
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pass
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if '*10x2' in phased_dup1:
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count2 = phased_dup1.count('*10x2')
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b_ind1 = phased_dup1.index('*10x2')
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b_ind2 = 1 - b_ind1
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if count2 == 1:
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test_36 = hybrid_test_36(sv_dup, cn, av_cov, cn_ex9_3pr)
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if test_36 == 'norm_dup':
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pass
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elif test_36 == 'hyb_36_10':
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phased_dup = phased_dup.replace('*10x2', '*36+*10')
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elif test_36 == 'hyb_36_36':
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phased_dup = phased_dup.replace('*10x2', '*36x2')
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if '*10x3' in phased_dup1:
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count3 = phased_dup1.count('*10x3')
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c_ind1 = phased_dup1.index('*10x3')
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c_ind2 = 1 - c_ind1
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if count3 == 1:
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test_36 = hybrid_test_36_mod(sv_dup, cn, av_cov, cn_ex9_3pr)
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if test_36 == 'norm_mt':
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pass
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elif test_36 == 'hyb_36_10':
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phased_dup = phased_dup.replace('*10x3', '*36+*10x2')
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elif test_36 == 'hyb_36_36':
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phased_dup = phased_dup.replace('*10x3', '*36x2+*10')
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if '*1x3' in phased_dup1:
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count2 = phased_dup1.count('*1x3')
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b_ind1 = phased_dup1.index('*1x3')
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b_ind2 = 1 - b_ind1
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if count2 == 1:
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test_83 = hybrid_test_83(sv_dup, cn, av_cov, cn_ex9_3pr)
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if test_83 == 'norm_star39':
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pass
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elif test_83 == 'hyb_83':
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phased_dup = phased_dup.replace('*1x3', '*1x2+*83')
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if '*2' in phased_dup1:
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count2 = phased_dup1.count('*2')
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b_ind1 = phased_dup1.index('*2')
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b_ind2 = 1 - b_ind1
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if count2 == 1:
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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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pass
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elif test_13_2_v2 == 'norm_var':
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pass
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elif test_13_2_v1 == 'hyb_13_2':
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phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
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elif test_13_2_v2 == 'hyb_13_2_v2':
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phased_dup = phased_dup1[b_ind2] + "/" + '*13'
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if '*2x2' in phased_dup1:
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count2 = phased_dup1.count('*2x2')
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b_ind1 = phased_dup1.index('*2x2')
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b_ind2 = 1 - b_ind1
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if count2 == 1:
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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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pass
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elif test_13_2_v2 == 'norm_var':
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pass
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elif test_13_2_v1 == 'hyb_13_2':
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phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
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elif test_13_2_v2 == 'hyb_13_2_v2':
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phased_dup = phased_dup1[b_ind2] + "/" + '*13+*2'
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gene_alleles = phased_dup
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print(phased_dup)
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elif snv_def_alleles[0] == snv_def_alleles[1]:
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|
|
|
|
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)")
|
|
|