38 lines
991 B
Python
38 lines
991 B
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_slc6a4_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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exon_cov_list = []
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all_reg = all_reg[3:]
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a = list(range(1, len(all_reg)))
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for i in a:
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exon_cov = 'av_e' + str(i)
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exon_cov = float(all_reg[i-1][3])/(float(all_reg[i-1][2]) - float(all_reg[i-1][1]))
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exon_cov_list.append(exon_cov)
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av_ctrl_cov = (av_vdr_cov + av_egfr_cov)/2
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comp_av = av_slc6a4_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_slc6a4_cov), round(av_ctrl_cov), exon_cov_list];
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