--- a/tools/mira4_0/mira4_bait.py	Fri Oct 02 06:12:23 2015 -0400
+++ b/tools/mira4_0/mira4_bait.py	Thu Aug 10 11:09:10 2017 -0400
@@ -1,17 +1,16 @@
 #!/usr/bin/env python
 """A simple wrapper script to call MIRA4's mirabait and collect its output.
 """
+
+from __future__ import print_function
+
 import os
+import shutil
+import subprocess
 import sys
-import subprocess
-import shutil
 import time
 
-WRAPPER_VER = "0.0.5" #Keep in sync with the XML file
-
-def sys_exit(msg, err=1):
-    sys.stderr.write(msg+"\n")
-    sys.exit(err)
+WRAPPER_VER = "0.0.11"  # Keep in sync with the XML file
 
 
 def get_version(mira_binary):
@@ -20,36 +19,40 @@
     # however there is some pipe error when doing that here.
     cmd = [mira_binary, "-v"]
     try:
-        child = subprocess.Popen(cmd,
+        child = subprocess.Popen(cmd, universal_newlines=True,
                                  stdout=subprocess.PIPE,
                                  stderr=subprocess.STDOUT)
-    except Exception, err:
+    except Exception as err:
         sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
         sys.exit(1)
     ver, tmp = child.communicate()
     del child
-    #Workaround for -v not working in mirabait 4.0RC4
+    # Workaround for -v not working in mirabait 4.0RC4
     if "invalid option" in ver.split("\n", 1)[0]:
         for line in ver.split("\n", 1):
             if " version " in line:
                 line = line.split()
-                return line[line.index("version")+1].rstrip(")")
-        sys_exit("Could not determine MIRA version:\n%s" % ver)
+                return line[line.index("version") + 1].rstrip(")")
+        sys.exit("Could not determine MIRA version:\n%s" % ver)
     return ver.split("\n", 1)[0]
 
-try:
+
+if "MIRA4" in os.environ:
     mira_path = os.environ["MIRA4"]
-except KeyError:
-    sys_exit("Environment variable $MIRA4 not set")
-mira_binary = os.path.join(mira_path, "mirabait")
-if not os.path.isfile(mira_binary):
-    sys_exit("Missing mirabait under $MIRA4, %r\nFolder contained: %s"
-             % (mira_binary, ", ".join(os.listdir(mira_path))))
+    mira_binary = os.path.join(mira_path, "mirabait")
+    if not os.path.isfile(mira_binary):
+        sys.exit("Missing mirabait under $MIRA4, %r\nFolder contained: %s"
+                 % (mira_binary, ", ".join(os.listdir(mira_path))))
+else:
+    sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n")
+    mira_path = None
+    mira_binary = "mirabait"
+
 mira_ver = get_version(mira_binary)
 if not mira_ver.strip().startswith("4.0"):
-    sys_exit("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
+    sys.exit("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
 if "-v" in sys.argv or "--version" in sys.argv:
-    print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)
+    print("%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER))
     sys.exit(0)
 
 
@@ -60,7 +63,7 @@
 elif format == "mira":
     format = "maf"
 elif format != "fasta":
-    sys_exit("Was not expected format %r" % format)
+    sys.exit("Was not expected format %r" % format)
 
 assert out_file.endswith(".dat")
 out_file_stem = out_file[:-4]
@@ -71,44 +74,44 @@
 if output_choice == "pos":
     pass
 elif output_choice == "neg":
-    #Invert the selection...
+    # Invert the selection...
     cmd_list.insert(1, "-i")
 else:
-    sys_exit("Output choice should be 'pos' or 'neg', not %r" % output_choice)
+    sys.exit("Output choice should be 'pos' or 'neg', not %r" % output_choice)
 if strand_choice == "both":
     pass
 elif strand_choice == "fwd":
-    #Ingore reverse strand...
+    # Ingore reverse strand...
     cmd_list.insert(1, "-r")
 else:
-    sys_exit("Strand choice should be 'both' or 'fwd', not %r" % strand_choice)
+    sys.exit("Strand choice should be 'both' or 'fwd', not %r" % strand_choice)
 
 cmd = " ".join(cmd_list)
-#print cmd
+# print cmd
 start_time = time.time()
 try:
-    #Run MIRA
-    child = subprocess.Popen(cmd_list,
+    # Run MIRA
+    child = subprocess.Popen(cmd_list, universal_newlines=True,
                              stdout=subprocess.PIPE,
                              stderr=subprocess.STDOUT)
-except Exception, err:
+except Exception as err:
     sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
     sys.exit(1)
-#Use .communicate as can get deadlocks with .wait(),
+# Use .communicate as can get deadlocks with .wait(),
 stdout, stderr = child.communicate()
-assert stderr is None # Due to way we ran with subprocess
+assert stderr is None  # Due to way we ran with subprocess
 run_time = time.time() - start_time
 return_code = child.returncode
-print "mirabait took %0.2f minutes" % (run_time / 60.0)
+print("mirabait took %0.2f minutes" % (run_time / 60.0))
 
 if return_code:
     sys.stderr.write(stdout)
-    sys_exit("Return error code %i from command:\n%s" % (return_code, cmd),
+    sys.exit("Return error code %i from command:\n%s" % (return_code, cmd),
              return_code)
 
-#Capture output
+# Capture output
 out_tmp = out_file_stem + "." + format
 if not os.path.isfile(out_tmp):
     sys.stderr.write(stdout)
-    sys_exit("Missing output file from mirabait: %s" % out_tmp)
+    sys.exit("Missing output file from mirabait: %s" % out_tmp)
 shutil.move(out_tmp, out_file)