612 lines
17 KiB
Python
612 lines
17 KiB
Python
#!/usr/bin/env python3
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import os
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import sys
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import math
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def get_total_CN(cov_file):
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all_reg = []
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for line in open(cov_file, "r"):
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line = line.strip().split()
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all_reg.append(line)
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av_2d6_cov = float(all_reg[2][3])/(float(all_reg[2][2]) - float(all_reg[2][1]))
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av_vdr_cov = float(all_reg[3][3])/(float(all_reg[3][2]) - float(all_reg[3][1]))
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av_in1_3pr = float(all_reg[1][3])/(float(all_reg[1][2]) - float(all_reg[1][1]))
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av_ex9_3pr = float(all_reg[0][3])/(float(all_reg[0][2]) - float(all_reg[0][1]))
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av_in4_3pr = float(all_reg[4][3])/(float(all_reg[4][2]) - float(all_reg[4][1]))
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av_5pr_in4 = float(all_reg[5][3])/(float(all_reg[5][2]) - float(all_reg[5][1]))
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av_2d7_ex9 = float(all_reg[6][3])/(float(all_reg[6][2]) - float(all_reg[6][1]))
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av_2d7_in4_in8 = float(all_reg[7][3])/(float(all_reg[7][2]) - float(all_reg[7][1]))
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av_egfr_cov = float(all_reg[8][3])/(float(all_reg[8][2]) - float(all_reg[8][1]))
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av_2d7_ex2_in8 = float(all_reg[9][3])/(float(all_reg[9][2]) - float(all_reg[9][1]))
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av_2d7_5pr_in1 = float(all_reg[10][3])/(float(all_reg[10][2]) - float(all_reg[10][1]))
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av_ctrl_cov = (av_vdr_cov + av_egfr_cov)/2
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comp_av = av_2d6_cov/av_ctrl_cov
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temp_cn = 2 * comp_av
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total_cn = round(temp_cn)
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in1_3pr = round(2 * av_in1_3pr/av_ctrl_cov)
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ex9_3pr = (2 * av_ex9_3pr/av_ctrl_cov)
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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)];
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samp_gt = ""
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samp_gt_hap1 = ""
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def del_test(sv_del):
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if os.stat(sv_del).st_size == 0:
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return "None"
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else:
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for line in open(sv_del, "r"):
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if "COVERAGE" in line:
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line = line.strip().split()
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ABHom = line[-1]
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ABHet = line[-2]
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GT = line[2]
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DP = int(line[3])
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if float(ABHom) == 1.0:
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return "*5/*5"
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elif float(ABHom) == -1.0:
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return "*5"
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else:
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pass
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hap_adv_list = []
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hap_t1 = []
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def del_adv_test(hap_dbs, cand_allele1, cand_allele2, test_allele1, test_allele2, core_vars):
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g = open(hap_dbs, "r")
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for line in g:
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line = line.strip().split()
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hap_adv_list.append(line)
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a1 = core_vars.split(";")
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for i in a1:
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if i[-3:] == "0/1":
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hap_t1.append(i[:-4])
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for elem in hap_adv_list:
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if elem[1] == cand_allele1:
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list_t1 = (elem[2]).split(';')
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if elem[1] == cand_allele2:
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list_t2 = (elem[2]).split(';')
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if hap_t1[0] in list_t1:
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return test_allele1
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elif hap_t1[0] in list_t2:
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return test_allele2
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het_hom_list = []
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het_hom_list_new = []
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def dup_test_init(sv_dup, av_cov):
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for line in open(sv_dup, "r"):
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if "COVERAGE" in line:
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continue
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elif "AGGREGATED" in line:
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continue
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else:
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fields = line.strip().split()
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het_hom_list.append(fields)
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test_list1 = []
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for i in het_hom_list:
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test_list1.append(int(i[2]))
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av_read_cov = sum(test_list1)/len(test_list1)
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norm_cov = (av_cov + av_read_cov)/2
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for i in het_hom_list:
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supp_reads = round(float(i[-2])*int(i[2]))
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i.append(round(supp_reads/av_read_cov, 4))
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i.append(supp_reads)
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het_hom_list_new.append(i)
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return (het_hom_list_new)
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hap_def_list = []
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allele_cn_list = []
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def dup_test_cn_3_4(sv_dup, hap_dbs, cand_allele1, cand_allele2, test_allele1, test_allele2, c_num, av_cov, in_list):
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g = open(hap_dbs, "r")
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for line in g:
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line = line.strip().split()
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hap_def_list.append(line)
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test_list1 = []
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test_list2 = []
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het_list = []
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for i in in_list:
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if i[1] == "0/1":
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het_list.append(i)
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for i in het_list:
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test_list1.append(i[0])
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test_list2.append(i[-2])
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max_het = max(test_list2)
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max_het_pos = test_list2.index(max_het)
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var = test_list1[max_het_pos]
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for elem in hap_def_list:
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if elem[1] == cand_allele1:
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list_3t = elem
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list_3t_2 = list_3t[2].split(';')
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l3 = len(list_3t_2)
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if elem[1] == cand_allele2:
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list_4t = elem
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list_4t_2 = list_4t[2].split(';')
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l4 = len(list_4t_2)
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hdb_list = list_3t_2 + list_4t_2
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index_var = hdb_list.index(var)
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if index_var < l3:
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allele_cn_list.append(test_allele1)
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allele_cn_list.append(int(round(max_het*int(c_num))))
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elif index_var >= l3:
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allele_cn_list.append(test_allele2)
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allele_cn_list.append(int(round(max_het*int(c_num))))
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if allele_cn_list[0] == test_allele1:
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rt_2 = int(c_num) - allele_cn_list[1]
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allele_cn_list.append(test_allele2)
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allele_cn_list.append(rt_2)
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elif allele_cn_list[0] == test_allele2:
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rt_2 = int(c_num) - allele_cn_list[1]
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allele_cn_list.append(test_allele1)
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allele_cn_list.append(rt_2)
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if allele_cn_list[1] == 0:
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res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3] - 1)
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elif allele_cn_list[3] == 0:
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res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1] - 1)
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elif allele_cn_list[1] == 1:
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res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
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elif allele_cn_list[3] == 1:
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res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
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elif allele_cn_list[1] == 2:
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res_dip = allele_cn_list[0] + "x2" + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
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elif allele_cn_list[3] == 2:
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res_dip = allele_cn_list[2] + "x2" + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
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elif allele_cn_list[1] == -1:
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res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3] - 2)
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elif allele_cn_list[3] == -1:
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res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1] - 2)
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elif allele_cn_list[3] < -1:
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res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(3)
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elif allele_cn_list[1] < -1:
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res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(3)
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else:
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res_dip = 'check'
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return res_dip
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def dup_test_cn_n(sv_dup, hap_dbs, cand_allele1, cand_allele2, test_allele1, test_allele2, c_num, av_cov, in_list):
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g = open(hap_dbs, "r")
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for line in g:
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line = line.strip().split()
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hap_def_list.append(line)
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test_list1 = []
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test_list2 = []
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het_list = []
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for i in in_list:
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if i[1] == "0/1":
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het_list.append(i)
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for i in het_list:
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test_list1.append(i[0])
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test_list2.append(i[-2])
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max_het = max(test_list2)
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max_het_pos = test_list2.index(max_het)
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var = test_list1[max_het_pos]
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for elem in hap_def_list:
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if elem[1] == cand_allele1:
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list_3t = elem
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list_3t_2 = list_3t[2].split(';')
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l3 = len(list_3t_2)
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if elem[1] == cand_allele2:
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list_4t = elem
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list_4t_2 = list_4t[2].split(';')
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l4 = len(list_4t_2)
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hdb_list = list_3t_2 + list_4t_2
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index_var = hdb_list.index(var)
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if index_var < l3:
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allele_cn_list.append(test_allele1)
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allele_cn_list.append(int(round(max_het*int(c_num)-0.15)))
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elif index_var >= l3:
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allele_cn_list.append(test_allele2)
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allele_cn_list.append(int(round(max_het*int(c_num)-0.15)))
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if allele_cn_list[0] == test_allele1:
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rt_2 = int(c_num) - allele_cn_list[1]
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allele_cn_list.append(test_allele2)
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allele_cn_list.append(rt_2)
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elif allele_cn_list[0] == test_allele2:
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rt_2 = int(c_num) - allele_cn_list[1]
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allele_cn_list.append(test_allele1)
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allele_cn_list.append(rt_2)
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if allele_cn_list[1] == 0:
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res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3] - 1)
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elif allele_cn_list[3] == 0:
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res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1] - 1)
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elif allele_cn_list[1] == 1:
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res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
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elif allele_cn_list[3] == 1:
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res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
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elif allele_cn_list[1] == 2:
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res_dip = allele_cn_list[0] + "x2" + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
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elif allele_cn_list[3] == 2:
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res_dip = allele_cn_list[2] + "x2" + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
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elif allele_cn_list[1] == 3:
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res_dip = allele_cn_list[0] + "x3" + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
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elif allele_cn_list[3] == 3:
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res_dip = allele_cn_list[2] + "x3" + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
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elif allele_cn_list[1] == 4:
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res_dip = allele_cn_list[0] + "x4" + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3])
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elif allele_cn_list[3] == 4:
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res_dip = allele_cn_list[2] + "x4" + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1])
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elif allele_cn_list[1] == -1:
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res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3] - 2)
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elif allele_cn_list[3] == -1:
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res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1] - 2)
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elif allele_cn_list[3] < 0:
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res_dip = allele_cn_list[2] + "/" + allele_cn_list[0] + "x" + str(allele_cn_list[1] + allele_cn_list[3] - 1)
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elif allele_cn_list[1] < 0:
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res_dip = allele_cn_list[0] + "/" + allele_cn_list[2] + "x" + str(allele_cn_list[3] + allele_cn_list[1] - 1)
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else:
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res_dip = 'check'
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return res_dip
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def hybrid_test_68(sv_dup, c_num, av_cov, cn_in1_3pr1, in_list):
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test_list1 = []
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test_list2 = []
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test_list3 = []
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for i in in_list:
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test_list1.append(i[0])
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test_list2.append(abs(float(i[-2])))
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test_list3.append(i[-1])
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index1 = test_list1.index('42130692~G>A')
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index2 = test_list1.index('42128945~C>T')
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val_68 = test_list3[index1]
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val_4 = test_list3[index2]
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rt = val_68/val_4
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if rt <= 1.4:
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return 'norm_dup'
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elif rt > 1.4:
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return 'hyb_68'
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else:
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return 'norm_dup'
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def hyb_test_5_68_4(sv_del, in1_3pr1_float, av_cov):
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test_del = []
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for line in open(sv_del, "r"):
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if "COVERAGE" in line:
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test_del.append(line.strip())
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# if len(test_del) == 0:
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# return 'norm_art'
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# elif len(test_del) > 0:
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# return 'del_hyb'
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t1 = 2 * in1_3pr1_float/av_cov
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if len(test_del) == 0 and (1.6 < t1 < 2.8):
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return 'norm_art'
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elif len(test_del) > 0 and t1 < 1.6:
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return 'del_hyb'
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def hybrid_test_36(sv_dup, cn, av_cov, cn_ex9_3pr, cn_2d7_ex9, cn_2d7_in4_in8):
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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):
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return 'hyb_36_10'
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elif (int(cn) - 2) <= float(cn_ex9_3pr) < (int(cn) - 2 + 0.7):
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return 'hyb_36_36'
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else:
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return 'norm_dup'
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def hybrid_test_36_single(sv_dup, cn, av_cov, cn_ex9_3pr):
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if int(round(float(cn_ex9_3pr))) == int(cn):
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return 'norm_star10'
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elif ((int(cn) - 1) - 0.35) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
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return 'hyb_36_single'
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else:
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return 'norm_star10'
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def hybrid_test_36_mod(sv_dup, cn, av_cov, cn_ex9_3pr):
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if int(round(float(cn_ex9_3pr))) == int(cn):
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return 'norm_mt'
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elif ((int(cn) - 1) - 0.05) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
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return 'hyb_36_10'
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elif (int(cn) - 2) <= float(cn_ex9_3pr) < (int(cn) - 2 + 0.95):
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return 'hyb_36_36'
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def hybrid_test_36_multi(sv_dup, cn, av_cov, cn_ex9_3pr):
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if int(round(float(cn_ex9_3pr))) == int(cn):
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return 'norm_mt'
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elif ((int(cn) - 1) - 0.05) < float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
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return 'hyb_36_10'
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elif (int(cn) - 2) <= float(cn_ex9_3pr) < (int(cn) - 2 + 0.95):
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return 'hyb_36_36'
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elif (int(cn) - 3) <= float(cn_ex9_3pr) < (int(cn) - 3 + 0.95):
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return 'hyb_36_36_36'
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else:
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return 'check'
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def hybrid_test_36_multi_10(sv_dup, cn, av_cov, cn_ex9_3pr, cn_star10):
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|
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if int(round(float(cn_ex9_3pr))) == int(cn):
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return 'norm_mt'
|
|
|
|
elif float(cn_ex9_3pr) < ((int(cn) - 1) + 0.5):
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|
cn_star36 = int(cn) - int(round(float(cn_ex9_3pr)))
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adj_cn_star10 = int(cn_star10) - cn_star36
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|
|
|
if cn_star36 == 1:
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|
return '*36+*10x' + str(adj_cn_star10)
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|
else:
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|
return '*36x' + str(cn_star36) + '+*10x' + str(adj_cn_star10)
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|
|
|
else:
|
|
return 'check'
|
|
|
|
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def hybrid_13_2_v1(cov_in4_3pr, cov_5pr_in4):
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|
|
|
if 0.85 < float(cov_in4_3pr)/float(cov_5pr_in4) < 1.2:
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|
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):
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|
|
|
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'
|