382 lines
10 KiB
Python
382 lines
10 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_2a6_cov = float(all_reg[0][3])/(float(all_reg[0][2]) - float(all_reg[0][1]))
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av_vdr_cov = float(all_reg[1][3])/(float(all_reg[1][2]) - float(all_reg[1][1]))
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av_egfr_cov = float(all_reg[2][3])/(float(all_reg[2][2]) - float(all_reg[2][1]))
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av_e1_e2 = float(all_reg[3][3])/(float(all_reg[3][2]) - float(all_reg[3][1]))
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av_e3_e9 = float(all_reg[4][3])/(float(all_reg[4][2]) - float(all_reg[4][1]))
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av_3p_utr = float(all_reg[5][3])/(float(all_reg[5][2]) - float(all_reg[5][1]))
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av_ex1_ex4 = float(all_reg[6][3])/(float(all_reg[6][2]) - float(all_reg[6][1]))
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av_ex5_ex9 = float(all_reg[7][3])/(float(all_reg[7][2]) - float(all_reg[7][1]))
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av_ex3_ex4 = float(all_reg[8][3])/(float(all_reg[8][2]) - float(all_reg[8][1]))
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av_ex9_3pr = float(all_reg[9][3])/(float(all_reg[9][2]) - float(all_reg[9][1]))
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av_ex7_ex8 = 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_2a6_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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return [str(int(total_cn)), round(av_2a6_cov), round(av_ctrl_cov), str(av_e1_e2), str(av_e3_e9), str(av_3p_utr), str(av_ex1_ex4), str(av_ex5_ex9), str(av_ex3_ex4), str(av_ex9_3pr), str(av_ex7_ex8)];
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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 "*4/*4"
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elif float(ABHom) == -1.0:
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return "*4"
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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/norm_cov, 3))
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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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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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else:
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res_dip = 'check'
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return res_dip
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def hybrid_12_test1(cov_e1_e2, cov_e3_e9):
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if 0.65 < float(cov_e1_e2)/float(cov_e3_e9) < 1.25:
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return 'norm_var'
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elif 0.15 < float(cov_e1_e2)/float(cov_e3_e9) < 0.65:
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return 'hyb_12'
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elif float(cov_e1_e2)/float(cov_e3_e9) < 0.15:
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return 'hyb_12_2'
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else:
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return 'norm_var'
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def hybrid_12_34(cov_e1_e2, cov_e3_e9, cov_e1_e4, cov_e5_e9, cov_e3_e4):
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if 0.65 < float(cov_e1_e4)/float(cov_e5_e9) < 1.25:
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return 'norm_var'
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elif 0.65 < float(cov_e1_e2)/float(cov_e3_e9) < 1.25:
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return 'norm_var'
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elif 0.15 < float(cov_e1_e4)/float(cov_e5_e9) < 0.65 and (0.65 < float(cov_e1_e2)/float(cov_e3_e4) < 1.25):
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return 'hyb_34'
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elif 0.15 < float(cov_e1_e4)/float(cov_e5_e9) < 0.65 and (0.15 < float(cov_e1_e2)/float(cov_e3_e4) < 0.65):
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return 'hyb_12'
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elif float(cov_e1_e4)/float(cov_e5_e9) < 0.15:
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return 'hyb_34_2'
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elif 0.15 < float(cov_e1_e2)/float(cov_e3_e9) < 0.65:
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return 'hyb_12'
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elif float(cov_e1_e2)/float(cov_e3_e9) < 0.15:
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return 'hyb_12_2'
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else:
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return 'norm_var'
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def hybrid_47_test1(cov_e9_3pr, cov_e7_e8):
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if 0.25 < float(cov_e7_e8)/float(cov_e9_3pr) < 0.65:
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return 'hyb_47'
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else:
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return 'no_hyb_47'
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def hybrid_47_test2(cov_e9_3pr, cov_e7_e8, cov_ctrl):
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if float(cov_e9_3pr)/float(cov_ctrl) > 0.75:
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return 'hom_47'
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elif 0.25 < float(cov_e9_3pr)/float(cov_ctrl) < 0.75:
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return 'het_47'
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else:
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return 'no_hyb_47'
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def star_1b_test(cov_3p_utr, cov_ctrl):
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if float(cov_3p_utr)/float(cov_ctrl) < 0.25:
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return 'hom_1B'
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elif float(cov_3p_utr)/float(cov_ctrl) > 0.65:
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return 'no_1B'
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else:
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return 'het_1B'
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