--- a/tools/effectiveT3/effectiveT3.py	Mon Sep 21 05:52:29 2015 -0400
+++ b/tools/effectiveT3/effectiveT3.py	Wed Feb 01 09:22:21 2017 -0500
@@ -16,30 +16,26 @@
 import subprocess
 
 # The Galaxy auto-install via tool_dependencies.xml will set this environment variable
-effectiveT3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
-effectiveT3_jar = os.path.join(effectiveT3_dir, "TTSS_GUI-1.0.1.jar")
+effective_t3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
+effective_t3_jar = os.path.join(effective_t3_dir, "TTSS_GUI-1.0.1.jar")
 
 if "-v" in sys.argv or "--version" in sys.argv:
     # TODO - Get version of the JAR file dynamically?
-    print("Wrapper v0.0.16, TTSS_GUI-1.0.1.jar")
+    print("Wrapper v0.0.17, TTSS_GUI-1.0.1.jar")
     sys.exit(0)
 
-def sys_exit(msg, error_level=1):
-   """Print error message to stdout and quit with given error level."""
-   sys.stderr.write("%s\n" % msg)
-   sys.exit(error_level)
-
 if len(sys.argv) != 5:
-   sys_exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file")
+    sys.exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file")
 
 model, threshold, fasta_file, tabular_file = sys.argv[1:]
 
 if not os.path.isfile(fasta_file):
-   sys_exit("Input FASTA file not found: %s" % fasta_file)
+    sys.exit("Input FASTA file not found: %s" % fasta_file)
 
 if threshold not in ["selective", "sensitive"] \
-and not threshold.startswith("cutoff="):
-   sys_exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)
+    and not threshold.startswith("cutoff="):
+    sys.exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)
+
 
 def clean_tabular(raw_handle, out_handle):
     """Clean up Effective T3 output to make it tabular."""
@@ -48,65 +44,66 @@
     errors = 0
     for line in raw_handle:
         if not line or line.startswith("#") \
-        or line.startswith("Id; Description; Score;"):
+            or line.startswith("Id; Description; Score;"):
             continue
         assert line.count(";") >= 3, repr(line)
         # Normally there will just be three semi-colons, however the
         # original FASTA file's ID or description might have had
         # semi-colons in it as well, hence the following hackery:
         try:
-            id_descr, score, effective = line.rstrip("\r\n").rsplit(";",2)
+            id_descr, score, effective = line.rstrip("\r\n").rsplit(";", 2)
             # Cope when there was no FASTA description
             if "; " not in id_descr and id_descr.endswith(";"):
                 id = id_descr[:-1]
                 descr = ""
             else:
-                id, descr = id_descr.split("; ",1)
+                id, descr = id_descr.split("; ", 1)
         except ValueError:
-            sys_exit("Problem parsing line:\n%s\n" % line)
+            sys.exit("Problem parsing line:\n%s\n" % line)
         parts = [s.strip() for s in [id, descr, score, effective]]
         out_handle.write("\t".join(parts) + "\n")
         count += 1
         if float(score) < 0:
-           errors += 1
+            errors += 1
         if effective.lower() == "true":
-           positive += 1
+            positive += 1
     return count, positive, errors
 
+
 def run(cmd):
     # Avoid using shell=True when we call subprocess to ensure if the Python
     # script is killed, so too is the child process.
     try:
         child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     except Exception, err:
-        sys_exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
+        sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
     # Use .communicate as can get deadlocks with .wait(),
     stdout, stderr = child.communicate()
     return_code = child.returncode
     if return_code or stderr.startswith("Exception in thread"):
-        cmd_str= " ".join(cmd)  # doesn't quote spaces etc
+        cmd_str = " ".join(cmd)  # doesn't quote spaces etc
         if stderr and stdout:
-            sys_exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
+            sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
         else:
-            sys_exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
+            sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
 
 
-if not os.path.isdir(effectiveT3_dir):
-    sys_exit("Effective T3 folder not found: %r" % effectiveT3_dir)
+if not os.path.isdir(effective_t3_dir):
+    sys.exit("Effective T3 folder not found: %r" % effective_t3_dir)
 
-if not os.path.isfile(effectiveT3_jar):
-    sys_exit("Effective T3 JAR file not found: %r" % effectiveT3_jar)
+if not os.path.isfile(effective_t3_jar):
+    sys.exit("Effective T3 JAR file not found: %r" % effective_t3_jar)
 
-if not os.path.isdir(os.path.join(effectiveT3_dir, "module")):
-    sys_exit("Effective T3 module folder not found: %r" % os.path.join(effectiveT3_dir, "module"))
+if not os.path.isdir(os.path.join(effective_t3_dir, "module")):
+    sys.exit("Effective T3 module folder not found: %r" % os.path.join(effective_t3_dir, "module"))
 
-effectiveT3_model = os.path.join(effectiveT3_dir, "module", model)
-if not os.path.isfile(effectiveT3_model):
+effective_t3_model = os.path.join(effective_t3_dir, "module", model)
+if not os.path.isfile(effective_t3_model):
     sys.stderr.write("Contents of %r is %s\n"
-                     % (os.path.join(effectiveT3_dir, "module"),
-                        ", ".join(repr(p) for p in os.listdir(os.path.join(effectiveT3_dir, "module")))))
-    sys.stderr.write("Main JAR was found: %r\n" % effectiveT3_jar)
-    sys_exit("Effective T3 model JAR file not found: %r" % effectiveT3_model)
+                     % (os.path.join(effective_t3_dir, "module"),
+                        ", ".join(repr(p) for p in os.listdir(os.path.join(effective_t3_dir, "module")))))
+    sys.stderr.write("Main JAR was found: %r\n" % effective_t3_jar)
+    sys.exit("Effective T3 model JAR file not found: %r" % effective_t3_model)
 
 # We will have write access whereever the output should be,
 temp_file = os.path.abspath(tabular_file + ".tmp")
@@ -115,7 +112,7 @@
 tabular_file = os.path.abspath(tabular_file)
 fasta_file = os.path.abspath(fasta_file)
 
-cmd = ["java", "-jar", effectiveT3_jar,
+cmd = ["java", "-jar", effective_t3_jar,
        "-f", fasta_file,
        "-m", model,
        "-t", threshold,
@@ -124,14 +121,14 @@
 
 try:
     # Must run from directory above the module subfolder:
-    os.chdir(effectiveT3_dir)
-except:
-    sys_exit("Could not change to Effective T3 folder: %s" % effectiveT3_dir)
+    os.chdir(effective_t3_dir)
+except Exception:
+    sys.exit("Could not change to Effective T3 folder: %s" % effective_t3_dir)
 
 run(cmd)
 
 if not os.path.isfile(temp_file):
-   sys_exit("ERROR - No output file from Effective T3")
+    sys.exit("ERROR - No output file from Effective T3")
 
 out_handle = open(tabular_file, "w")
 out_handle.write("#ID\tDescription\tScore\tEffective\n")
@@ -143,11 +140,11 @@
 os.remove(temp_file)
 
 if errors:
-   print("%i sequences, %i positive, %i errors"
-         % (count, positive, errors))
+    print("%i sequences, %i positive, %i errors"
+          % (count, positive, errors))
 else:
-   print("%i/%i sequences positive" % (positive, count))
+    print("%i/%i sequences positive" % (positive, count))
 
-if count and count==errors:
-   # Galaxy will still  allow them to see the output file
-   sys_exit("All your sequences gave an error code")
+if count and count == errors:
+    # Galaxy will still  allow them to see the output file
+    sys.exit("All your sequences gave an error code")