--- a/tools/protein_analysis/tmhmm2.py	Tue Sep 01 09:56:36 2015 -0400
+++ b/tools/protein_analysis/tmhmm2.py	Wed Feb 01 09:46:42 2017 -0500
@@ -21,7 +21,7 @@
 this to remove the redundant tags, and instead adds a comment line at the
 top with the column names:
 
- #ID	len	ExpAA	First60	PredHel	Topology 
+ #ID	len	ExpAA	First60	PredHel	Topology
  gi|2781234|pdb|1JLY|B	304	0.01	60	0.00	0	o
  gi|4959044|gb|AAD34209.1|AF069992_1	600	0.00	0	0.00	0	o
  gi|671626|emb|CAA85685.1|	473	0.19	0.00	0	o
@@ -43,12 +43,12 @@
 import sys
 import os
 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
 
 if len(sys.argv) != 4:
-    sys_exit("Require three arguments, number of threads (int), input protein FASTA file & output tabular file")
+    sys.exit("Require three arguments, number of threads (int), input protein FASTA file & output tabular file")
 
 num_threads = thread_count(sys.argv[1], default=4)
 fasta_file = sys.argv[2]
@@ -56,52 +56,55 @@
 
 tmp_dir = tempfile.mkdtemp()
 
+
 def clean_tabular(raw_handle, out_handle):
     """Clean up tabular TMHMM output, returns output line count."""
     count = 0
     for line in raw_handle:
         if not line.strip() or line.startswith("#"):
-            #Ignore any blank lines or comment lines
+            # Ignore any blank lines or comment lines
             continue
         parts = line.rstrip("\r\n").split("\t")
         try:
-            identifier, length, expAA, first60, predhel, topology = parts
-        except:
-            assert len(parts)!=6
-            sys_exit("Bad line: %r" % line)
+            identifier, length, exp_aa, first60, predhel, topology = parts
+        except ValueError:
+            assert len(parts) != 6
+            sys.exit("Bad line: %r" % line)
         assert length.startswith("len="), line
         length = length[4:]
-        assert expAA.startswith("ExpAA="), line
-        expAA = expAA[6:]
+        assert exp_aa.startswith("ExpAA="), line
+        exp_aa = exp_aa[6:]
         assert first60.startswith("First60="), line
         first60 = first60[8:]
         assert predhel.startswith("PredHel="), line
         predhel = predhel[8:]
         assert topology.startswith("Topology="), line
         topology = topology[9:]
-        out_handle.write("%s\t%s\t%s\t%s\t%s\t%s\n" \
-                   % (identifier, length, expAA, first60, predhel, topology))
+        out_handle.write("%s\t%s\t%s\t%s\t%s\t%s\n"
+                   % (identifier, length, exp_aa, first60, predhel, topology))
         count += 1
     return count
 
-#Note that if the input FASTA file contains no sequences,
-#split_fasta returns an empty list (i.e. zero temp files).
+# Note that if the input FASTA file contains no sequences,
+# split_fasta returns an empty list (i.e. zero temp files).
 fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "tmhmm"), FASTA_CHUNK)
-temp_files = [f+".out" for f in fasta_files]
+temp_files = [f + ".out" for f in fasta_files]
 jobs = ["tmhmm -short %s > %s" % (fasta, temp)
         for fasta, temp in zip(fasta_files, temp_files)]
 
+
 def clean_up(file_list):
+    """Remove temp files, and if possible the temp directory."""
     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))
 results = run_jobs(jobs, num_threads)
 for fasta, temp, cmd in zip(fasta_files, temp_files, jobs):
@@ -112,7 +115,7 @@
         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
 del jobs
@@ -125,7 +128,7 @@
     data_handle.close()
     if not count:
         clean_up(fasta_files + temp_files)
-        sys_exit("No output from tmhmm2")
+        sys.exit("No output from tmhmm2")
 out_handle.close()
 
 clean_up(fasta_files + temp_files)