pgx-main from prod added

pgx-main/scripts/sult1a1/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("SULT1A1 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)
+
+