--- a
+++ b/BioAid/MMBSearchTK/makeMMBSearchRef.py
@@ -0,0 +1,46 @@
+# This code was developed and authored by Jerzy Twarowski in Malkova Lab at the University of Iowa 
+# Contact: jerzymateusz-twarowski@uiowa.edu, tvarovski1@gmail.com
+
+import regex as re
+
+def createMMBSearchReference(file_path_in, file_path_out):
+  #good for human genome
+  file_in = open(file_path_in, "r")
+  save=False
+  readlines=True
+  while readlines:
+    try:
+      line = file_in.readline()
+    except:
+      print("Failed to read line. EOF? Exiting...")
+      readlines=False
+      break
+
+    if line[0] == ">":
+      if re.search("chromosome.*Primary.Assembly$", line) != None:
+        print(line)
+        linewords = line.split()
+        chromosome=linewords[4].strip(",")
+        if (chromosome=="1") | (chromosome=="2"):
+          chromosome=f">chr0{chromosome}\n"
+        elif chromosome=="X":
+          chromosome=f">chrX\n"
+        elif chromosome=="Y":
+          chromosome=f">chrY\n"
+        else:
+          chromosome=f">chr{chromosome}\n"
+        line=chromosome
+        print(line)
+        save=True
+      #fix for mitochondrial chr
+      elif re.search("mitochondrion, complete genome$", line) != None:
+        print(line)
+        line=f">chrM\n"
+        print(line)
+        save=True
+      else:
+        save=False
+
+    if save:
+      with open(file_path_out, "a") as file_out:
+        file_out.write(line)
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