Adding comments and fixing bugs on exonerate_parser

src/util/exonerate_parser.py

 #!/usr/bin/env python3
 
+##
+# This script aims to extract the mismatches found by exonerate and
+
 import sys
 
 DEFAULT_DISTANCE = 10
@@ -7,7 +10,11 @@ LINE_HEADER_SIZE = 9
 
 def get_region_file(regions, folder, value):
     target_region = ""
-    for elem in regions:
+    if not isinstance(regions, list):
+
+    elif not isinstance(regions[0], list):
+        region_list = regions[0].replace("[", "").replace("]","").split(" ")
+    for elem in region_list:
         val = elem.split("_")
         #print(val, value)
         if int(val[0]) <= value < int(val[1]):
@@ -94,7 +101,6 @@ def main():
                 output.write(str(value2 + start) + ": " + prefix_3 + query[1][start:end] + suffix_3 + "\n\n")
                 pb_cnt += 1
                 file = get_region_file(regions, folder, y)
-                print(file)
                 extract_read_pile(file, value2 % size, distance, output, len(str(value1+start)+": "))
 
 if __name__ == "__main__":