# 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)