pg-main from prod server added

pgx-main/scripts/nudt15/hg38/bin/bkg_modules.py

@@ -0,0 +1,78 @@
+#!/usr/bin/env python3
+
+
+import os
+import sys
+
+
+def get_backgroud_alleles(database, core_vars):
+
+    dbs = []
+    dbs_temp = []
+
+    core_vars_list = core_vars.split(";")
+    core_temp1 = core_vars_list[-1][:-4]
+    core_temp2 = core_vars_list[0][:-4]
+
+    for line in open(database, "r"):
+        line = line.strip().split("\t")
+        dbs.append(line)
+
+    for record in dbs:
+        temp_rec = record[1]
+        
+        if core_temp1 and core_temp2 in temp_rec:
+            dbs_temp.append(record)
+
+            
+    scores = []
+    candidates = []
+    cand_vars = []
+
+    for elem in dbs_temp:
+        candidates.append(elem[0])
+        record_core_var = elem[1].split(";")
+        cand_vars.append(record_core_var)
+
+        counter = 0
+
+        for i in record_core_var:
+            if i in core_vars_list:
+                counter += 3
+            elif i[:-4] in core_vars:
+                counter += 1
+            else:
+                counter += -2
+
+        scores.append(counter)
+
+    cand_diplos = []
+    diplo_vars2 = []
+
+    if len(scores) == 0:
+        diplo1 = '1.v1_1.v1'
+        allele_res = '*1/*1'
+
+    else:
+        max_score = max(scores)
+
+        indices = [i for i, x in enumerate(scores) if x == max_score or x == max_score - 1]
+
+        for i in indices:
+            diplo = candidates[i]
+            diplo_vars1 = len(cand_vars[i])
+            cand_diplos.append(diplo)
+            diplo_vars2.append(diplo_vars1)
+
+        min_index = diplo_vars2.index(min(diplo_vars2))
+
+        diplo1 =  cand_diplos[min_index]
+
+
+        res1 = [i for i in range(len(diplo1)) if diplo1.startswith("_", i)]
+        res2 = [i for i in range(len(diplo1)) if diplo1.startswith(".", i)]
+        hap1 = "*" + str (diplo1[:res2[0]])
+        hap2 = "*" + str (diplo1[res1[0]+1:res2[1]])
+        allele_res =  hap1 + "/" + hap2 
+
+    return [allele_res, diplo1];