--- a/tools/protein_analysis/promoter2.py	Tue Sep 01 09:56:36 2015 -0400
+++ b/tools/protein_analysis/promoter2.py	Wed Feb 01 09:46:42 2017 -0500
@@ -30,7 +30,7 @@
 import os
 import commands
 import tempfile
-from seq_analysis_utils import sys_exit, split_fasta, run_jobs, thread_count
+from seq_analysis_utils import split_fasta, run_jobs, thread_count
 
 FASTA_CHUNK = 500
 
@@ -38,91 +38,94 @@
     sys.exit(os.system("promoter -V"))
 
 if len(sys.argv) != 4:
-    sys_exit("Require three arguments, number of threads (int), input DNA FASTA file & output tabular file. "
-             "Got %i arguments." % (len(sys.argv)-1))
+    sys.exit("Require three arguments, number of threads (int), input DNA FASTA file & output tabular file. "
+             "Got %i arguments." % (len(sys.argv) - 1))
 
-num_threads = thread_count(sys.argv[3],default=4)
+num_threads = thread_count(sys.argv[3], default=4)
 fasta_file = os.path.abspath(sys.argv[2])
 tabular_file = os.path.abspath(sys.argv[3])
 
 tmp_dir = tempfile.mkdtemp()
 
+
 def get_path_and_binary():
-    platform = commands.getoutput("uname") #e.g. Linux
+    platform = commands.getoutput("uname")  # e.g. Linux
     shell_script = commands.getoutput("which promoter")
     if not os.path.isfile(shell_script):
-        sys_exit("ERROR: Missing promoter executable shell script")
+        sys.exit("ERROR: Missing promoter executable shell script")
     path = None
     for line in open(shell_script):
-        if line.startswith("setenv"): #could then be tab or space!
+        if line.startswith("setenv"):  # could then be tab or space!
             parts = line.rstrip().split(None, 2)
             if parts[0] == "setenv" and parts[1] == "PROM":
                 path = parts[2]
     if not path:
-        sys_exit("ERROR: Could not find promoter path (PROM) in %r" % shell_script)
+        sys.exit("ERROR: Could not find promoter path (PROM) in %r" % shell_script)
     if not os.path.isdir(path):
-        sys_exit("ERROR: %r is not a directory" % path)
+        sys.exit("ERROR: %r is not a directory" % path)
     bin = "%s/bin/promoter_%s" % (path, platform)
     if not os.path.isfile(bin):
-        sys_exit("ERROR: Missing promoter binary %r" % bin)
+        sys.exit("ERROR: Missing promoter binary %r" % bin)
     return path, bin
 
+
 def make_tabular(raw_handle, out_handle):
     """Parse text output into tabular, return query count."""
     identifier = None
     queries = 0
     for line in raw_handle:
-        #print repr(line)
+        # print repr(line)
         if not line.strip() or line == "Promoter prediction:\n":
             pass
         elif line[0] != " ":
-            identifier = line.strip().replace("\t", " ").split(None,1)[0]
+            identifier = line.strip().replace("\t", " ").split(None, 1)[0]
             queries += 1
         elif line == "  No promoter predicted\n":
-            #End of a record
+            # End of a record
             identifier = None
         elif line == "  Position  Score  Likelihood\n":
             assert identifier
         else:
             try:
-                position, score, likelihood = line.strip().split(None,2)
+                position, score, likelihood = line.strip().split(None, 2)
             except ValueError:
                 print "WARNING: Problem with line: %r" % line
                 continue
-                #sys_exit("ERROR: Problem with line: %r" % line)
+                # sys.exit("ERROR: Problem with line: %r" % line)
             if likelihood not in ["ignored",
                                   "Marginal prediction",
                                   "Medium likely prediction",
                                   "Highly likely prediction"]:
-                sys_exit("ERROR: Problem with line: %r" % line)
+                sys.exit("ERROR: Problem with line: %r" % line)
             out_handle.write("%s\t%s\t%s\t%s\n" % (identifier, position, score, likelihood))
     return queries
-    
+
 working_dir, bin = get_path_and_binary()
 
 if not os.path.isfile(fasta_file):
-   sys_exit("ERROR: Missing input FASTA file %r" % fasta_file)
+    sys.exit("ERROR: Missing input FASTA file %r" % fasta_file)
 
-#Note that if the input FASTA file contains no sequences,
-#split_fasta returns an empty list (i.e. zero temp files).
-#We deliberately omit the FASTA descriptions to avoid a
-#bug in promoter2 with descriptions over 200 characters.
+# Note that if the input FASTA file contains no sequences,
+# split_fasta returns an empty list (i.e. zero temp files).
+# We deliberately omit the FASTA descriptions to avoid a
+# bug in promoter2 with descriptions over 200 characters.
 fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "promoter"), FASTA_CHUNK, keep_descr=False)
-temp_files = [f+".out" for f in fasta_files]
+temp_files = [f + ".out" for f in fasta_files]
 jobs = ["%s %s > %s" % (bin, fasta, temp)
         for fasta, temp in zip(fasta_files, temp_files)]
 
+
 def clean_up(file_list):
     for f in file_list:
         if os.path.isfile(f):
             os.remove(f)
     try:
         os.rmdir(tmp_dir)
-    except:
+    except Exception:
         pass
 
 if len(jobs) > 1 and num_threads > 1:
-    #A small "info" message for Galaxy to show the user.
+    # A small "info" message for Galaxy to show the user.
     print "Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs))
 cur_dir = os.path.abspath(os.curdir)
 os.chdir(working_dir)
@@ -136,7 +139,7 @@
         except IOError:
             output = ""
         clean_up(fasta_files + temp_files)
-        sys_exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
+        sys.exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
                  error_level)
 
 del results
@@ -151,7 +154,7 @@
     data_handle.close()
     if not count:
         clean_up(fasta_files + temp_files)
-        sys_exit("No output from promoter2")
+        sys.exit("No output from promoter2")
     queries += count
 out_handle.close()