pgx-main from prod added

pgx-main/scripts/slc15a2/hg38/bin/stellarpgx.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python3
+
+import os
+import sys
+import subprocess
+import math
+from sv_modules import *
+
+
+print("--------------------------------------------\n")
+
+print("${i^^} Variant Analysis with StellarPGx\n")
+
+print("--------------------------------------------\n")
+
+
+infile = sys.argv[1]
+cov_file = sys.argv[2]
+
+
+def get_core_variants(infile, cn):
+    core_vars = []
+    for line in open(infile, "r"):
+        line = line.strip()
+        core_vars.append(line)
+    core_vars = ";".join(sorted(core_vars))
+
+    if int(cn) == 1:
+        core_vars = core_vars.replace("~0/1", "~1/1")
+
+    if os.stat(infile).st_size == 0:
+        core_vars = "No core SNVs detected; haplotypes equivalent to GRCh38 content"
+
+    return core_vars
+
+
+
+cn = get_total_CN(cov_file)[0]
+av_ctrl_cov = get_total_CN(cov_file)[2]
+exon_cov = get_total_CN(cov_file)[3]
+
+print("Initially computed Copy Number = {}".format(cn))
+
+for i in range(1, len(exon_cov)):
+    
+    if exon_cov[i-1]/av_ctrl_cov < 0.45 :
+        print ('Check exon {} for potential deletion if using high coverage WGS'.format(str(i)))
+    else:
+        pass
+
+supp_core_vars = get_core_variants(infile, cn)
+
+print("\nSample core variants:")
+print(supp_core_vars)
+
+

pgx-main/scripts/slc15a2/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_slc15a2_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_slc15a2_cov/av_ctrl_cov
+    temp_cn = 2 * comp_av
+    total_cn = round(temp_cn)
+
+
+    return [str(int(total_cn)), round(av_slc15a2_cov), round(av_ctrl_cov), exon_cov_list]; 
+