pg-main from prod server added

pgx-main/scripts/slc6a4/hg38/bin/sv_modules.py~

@@ -0,0 +1,37 @@
+#!/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_vkorc1_cov = float(all_reg[0][3])/(float(all_reg[0][2]) - float(all_reg[0][1]))
+    av_vdr_cov = float(all_reg[1][3])/(float(all_reg[1][2]) - float(all_reg[1][1]))
+    av_egfr_cov = float(all_reg[2][3])/(float(all_reg[2][2]) - float(all_reg[2][1]))
+
+    exon_cov_list = []
+    all_reg = all_reg[3:]
+
+    a = list(range(1, len(all_reg)))
+
+    for i in a:
+        exon_cov = 'av_e' + str(i)  
+        exon_cov = float(all_reg[i-1][3])/(float(all_reg[i-1][2]) - float(all_reg[i-1][1]))
+        exon_cov_list.append(exon_cov)
+        
+    av_ctrl_cov = (av_vdr_cov + av_egfr_cov)/2
+
+    comp_av = av_vkorc1_cov/av_ctrl_cov
+    temp_cn = 2 * comp_av
+    total_cn = round(temp_cn)
+
+
+    return [str(int(total_cn)), round(av_vkorc1_cov), round(av_ctrl_cov), exon_cov_list]; 
+