--- a/tools/mira4_0/mira4.py	Fri Oct 02 06:12:23 2015 -0400
+++ b/tools/mira4_0/mira4.py	Thu Aug 10 11:09:10 2017 -0400
@@ -1,41 +1,42 @@
 #!/usr/bin/env python
 """A simple wrapper script to call MIRA and collect its output.
 """
+
+from __future__ import print_function
+
 import os
-import sys
+import shutil
 import subprocess
-import shutil
+import sys
+import tempfile
 import time
-import tempfile
+
 from optparse import OptionParser
 
-#Do we need any PYTHONPATH magic?
+# Do we need any PYTHONPATH magic?
 from mira4_make_bam import make_bam
 
-WRAPPER_VER = "0.0.4" #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):
-    """Run MIRA to find its version number"""
+    """Run MIRA to find its version number."""
     # At the commend line I would use: mira -v | head -n 1
     # 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
     return ver.split("\n", 1)[0].strip()
 
-#Parse Command Line
+
+# Parse Command Line
 usage = """Galaxy MIRA4 wrapper script v%s - use as follows:
 
 $ python mira4.py ...
@@ -68,35 +69,38 @@
 out_fasta = options.fasta
 out_log = options.log
 
-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, "mira")
-if not os.path.isfile(mira_binary):
-    sys_exit("Missing mira under $MIRA4, %r\nFolder contained: %s"
-             % (mira_binary, ", ".join(os.listdir(mira_path))))
-mira_convert = os.path.join(mira_path, "miraconvert")
-if not os.path.isfile(mira_convert):
-    sys_exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
-             % (mira_convert, ", ".join(os.listdir(mira_path))))
+    mira_binary = os.path.join(mira_path, "mira")
+    if not os.path.isfile(mira_binary):
+        sys.exit("Missing mira under $MIRA4, %r\nFolder contained: %s"
+                 % (mira_binary, ", ".join(os.listdir(mira_path))))
+    mira_convert = os.path.join(mira_path, "miraconvert")
+    if not os.path.isfile(mira_convert):
+        sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
+                 % (mira_convert, ", ".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 = "mira"
+    mira_convert = "miraconvert"
 
 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\n%s" % (mira_ver, mira_binary))
+    sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_binary))
 mira_convert_ver = get_version(mira_convert)
 if not mira_convert_ver.strip().startswith("4.0"):
-    sys_exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert))
+    sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert))
 if options.version:
-    print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)
+    print("%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER))
     if mira_ver != mira_convert_ver:
-        print "WARNING: miraconvert %s" % mira_convert_ver
+        print("WARNING: miraconvert %s" % mira_convert_ver)
     sys.exit(0)
 
 if not manifest:
-    sys_exit("Manifest is required")
+    sys.exit("Manifest is required")
 elif not os.path.isfile(manifest):
-    sys_exit("Missing input MIRA manifest file: %r" % manifest)
+    sys.exit("Missing input MIRA manifest file: %r" % manifest)
 
 
 try:
@@ -125,12 +129,12 @@
     text = handle.read()
     handle.close()
 
-    #At time of writing, this is at the end of a file,
-    #but could be followed by a space in future...
+    # At time of writing, this is at the end of a file,
+    # but could be followed by a space in future...
     text = text.replace("-DI:trt=/tmp", "-DI:trt=" + tempfile.gettempdir())
 
-    #Want to try to ensure this gets written to disk before MIRA attempts
-    #to open it - any networked file system may impose a delay...
+    # Want to try to ensure this gets written to disk before MIRA attempts
+    # to open it - any networked file system may impose a delay...
     handle = open(manifest, "w")
     handle.write(text)
     handle.flush()
@@ -140,41 +144,39 @@
 
 def log_manifest(manifest):
     """Write the manifest file to stderr."""
-    sys.stderr.write("\n%s\nManifest file\n%s\n" % ("="*60, "="*60))
+    sys.stderr.write("\n%s\nManifest file\n%s\n" % ("=" * 60, "=" * 60))
     with open(manifest) as h:
         for line in h:
             sys.stderr.write(line)
-    sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("="*60, "="*60))
+    sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("=" * 60, "=" * 60))
 
 
 def collect_output(temp, name, handle):
     """Moves files to the output filenames (global variables)."""
-    n3 = (temp, name, name, name)
     f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
     if not os.path.isdir(f):
         log_manifest(manifest)
-        sys_exit("Missing output folder")
+        sys.exit("Missing output folder")
     if not os.listdir(f):
         log_manifest(manifest)
-        sys_exit("Empty output folder")
+        sys.exit("Empty output folder")
     missing = []
 
     old_maf = "%s/%s_out.maf" % (f, name)
     if not os.path.isfile(old_maf):
-        #Triggered extractLargeContigs.sh?
+        # Triggered extractLargeContigs.sh?
         old_maf = "%s/%s_LargeContigs_out.maf" % (f, name)
 
-    #De novo or single strain mapping,
+    # De novo or single strain mapping,
     old_fasta = "%s/%s_out.unpadded.fasta" % (f, name)
     ref_fasta = "%s/%s_out.padded.fasta" % (f, name)
     if not os.path.isfile(old_fasta):
-        #Mapping (StrainX versus reference) or de novo
+        # Mapping (StrainX versus reference) or de novo
         old_fasta = "%s/%s_out_StrainX.unpadded.fasta" % (f, name)
         ref_fasta = "%s/%s_out_StrainX.padded.fasta" % (f, name)
     if not os.path.isfile(old_fasta):
         old_fasta = "%s/%s_out_ReferenceStrain.unpadded.fasta" % (f, name)
         ref_fasta = "%s/%s_out_ReferenceStrain.padded.fasta" % (f, name)
-        
 
     missing = False
     for old, new in [(old_maf, out_maf),
@@ -192,25 +194,27 @@
         for filename in sorted(os.listdir(f)):
             sys.stderr.write("%s\n" % filename)
 
-    #For mapping mode, probably most people would expect a BAM file
-    #using the reference FASTA file...
+    # For mapping mode, probably most people would expect a BAM file
+    # using the reference FASTA file...
     if out_bam and out_bam != "-":
         if out_maf and out_maf != "-":
             msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
         else:
-            #Not collecting the MAF file, use original location        
+            # Not collecting the MAF file, use original location
             msg = make_bam(mira_convert, old_maf, ref_fasta, out_bam, handle)
         if msg:
-            sys_exit(msg)
+            sys.exit(msg)
+
 
 def clean_up(temp, name):
     folder = "%s/%s_assembly" % (temp, name)
     if os.path.isdir(folder):
         shutil.rmtree(folder)
 
-#TODO - Run MIRA in /tmp or a configurable directory?
-#Currently Galaxy puts us somewhere safe like:
-#/opt/galaxy-dist/database/job_working_directory/846/
+
+# TODO - Run MIRA in /tmp or a configurable directory?
+# Currently Galaxy puts us somewhere safe like:
+# /opt/galaxy-dist/database/job_working_directory/846/
 temp = "."
 
 name = "MIRA"
@@ -223,19 +227,19 @@
 
 assert os.path.isdir(temp)
 d = "%s_assembly" % name
-#This can fail on my development machine if stale folders exist
-#under Galaxy's .../database/job_working_directory/ tree:
+# This can fail on my development machine if stale folders exist
+# under Galaxy's .../database/job_working_directory/ tree:
 assert not os.path.isdir(d), "Path %r already exists:\n%s" % (d, os.path.abspath(d))
 try:
-    #Check path access
+    # Check path access
     os.mkdir(d)
-except Exception, err:
+except Exception as err:
     log_manifest(manifest)
     sys.stderr.write("Error making directory %s\n%s" % (d, err))
     sys.exit(1)
 
-#print os.path.abspath(".")
-#print cmd
+# print(os.path.abspath("."))
+# print(cmd)
 
 if out_log and out_log != "-":
     handle = open(out_log, "w")
@@ -251,34 +255,35 @@
 handle.write("============================ Starting MIRA now ===============================\n")
 handle.flush()
 try:
-    #Run MIRA
+    # Run MIRA
     child = subprocess.Popen(cmd_list,
                              stdout=handle,
                              stderr=subprocess.STDOUT)
-except Exception, err:
+except Exception as err:
     log_manifest(manifest)
     sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
-    #TODO - call clean up?
+    # TODO - call clean up?
     handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
     handle.close()
     sys.exit(1)
-#Use .communicate as can get deadlocks with .wait(),
+# Use .communicate as can get deadlocks with .wait(),
 stdout, stderr = child.communicate()
-assert not stdout and not stderr #Should be empty as sent to handle
+assert not stdout and not stderr  # Should be empty as sent to handle
 run_time = time.time() - start_time
 return_code = child.returncode
 handle.write("\n")
 handle.write("============================ MIRA has finished ===============================\n")
 handle.write("MIRA took %0.2f hours\n" % (run_time / 3600.0))
 if return_code:
-    print "MIRA took %0.2f hours" % (run_time / 3600.0)
+    print("MIRA took %0.2f hours" % (run_time / 3600.0))
     handle.write("Return error code %i from command:\n" % return_code)
     handle.write(cmd + "\n")
     handle.close()
     clean_up(temp, name)
     log_manifest(manifest)
-    sys_exit("Return error code %i from command:\n%s" % (return_code, cmd),
-             return_code)
+    sys.stderr.write("Return error code %i from command:\n" % return_code)
+    sys.stderr.write(cmd + "\n")
+    sys.exit(return_code)
 handle.flush()
 
 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
@@ -291,21 +296,23 @@
     handle.write("============================ (end of ec.log) =================================\n")
     handle.flush()
 
-#print "Collecting output..."
+# print("Collecting output...")
 start_time = time.time()
 collect_output(temp, name, handle)
 collect_time = time.time() - start_time
-handle.write("MIRA took %0.2f hours; collecting output %0.2f minutes\n" % (run_time / 3600.0, collect_time / 60.0))
-print("MIRA took %0.2f hours; collecting output %0.2f minutes\n" % (run_time / 3600.0, collect_time / 60.0))
+handle.write("MIRA took %0.2f hours; collecting output %0.2f minutes\n"
+             % (run_time / 3600.0, collect_time / 60.0))
+print("MIRA took %0.2f hours; collecting output %0.2f minutes\n"
+      % (run_time / 3600.0, collect_time / 60.0))
 
 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
-    #Treat as an error, but doing this AFTER collect_output
+    # Treat as an error, but doing this AFTER collect_output
     sys.stderr.write("Extract Large Contigs failed\n")
     handle.write("Extract Large Contigs failed\n")
     handle.close()
     sys.exit(1)
 
-#print "Cleaning up..."
+# print "Cleaning up..."
 clean_up(temp, name)
 
 handle.write("\nDone\n")