--- a/tools/protein_analysis/seq_analysis_utils.py	Tue Sep 01 09:56:36 2015 -0400
+++ b/tools/protein_analysis/seq_analysis_utils.py	Wed Feb 01 09:46:42 2017 -0500
@@ -12,17 +12,12 @@
 import subprocess
 from time import sleep
 
-__version__ = "0.0.1"
-
-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)
+__version__ = "0.0.2"
 
 try:
     from multiprocessing import cpu_count
 except ImportError:
-    #Must be under Python 2.5, this is copied from multiprocessing:
+    # Must be under Python 2.5, this is copied from multiprocessing:
     def cpu_count():
         """Returns the number of CPUs in the system."""
         if sys.platform == 'win32':
@@ -54,18 +49,18 @@
 def thread_count(command_line_arg, default=1):
     try:
         num = int(command_line_arg)
-    except:
+    except ValueError:
         num = default
     if num < 1:
-        sys_exit("Threads argument %r is not a positive integer" % command_line_arg)
-    #Cap this with the pysical limit of the machine,
+        sys.exit("Threads argument %r is not a positive integer" % command_line_arg)
+    # Cap this with the pysical limit of the machine,
     try:
         num = min(num, cpu_count())
     except NotImplementedError:
         pass
-    #For debugging,
-    #hostname = os.environ.get("HOSTNAME", "this machine")
-    #sys.stderr.write("Using %i cores on %s\n" % (num, hostname))
+    # For debugging,
+    # hostname = os.environ.get("HOSTNAME", "this machine")
+    # sys.stderr.write("Using %i cores on %s\n" % (num, hostname))
     return num
 
 
@@ -79,7 +74,7 @@
                 if truncate:
                     seq = seq[:truncate]
                 if max_len and len(seq) > max_len:
-                    raise ValueError("Sequence %s is length %i, max length %i" \
+                    raise ValueError("Sequence %s is length %i, max length %i"
                                      % (title.split()[0], len(seq), max_len))
                 yield title, seq
             title = line[1:].rstrip()
@@ -87,8 +82,8 @@
         elif title:
             seq += line.strip()
         elif not line.strip() or line.startswith("#"):
-            #Ignore blank lines, and any comment lines
-            #between records (starting with hash).
+            # Ignore blank lines, and any comment lines
+            # between records (starting with hash).
             pass
         else:
             handle.close()
@@ -98,11 +93,12 @@
         if truncate:
             seq = seq[:truncate]
         if max_len and len(seq) > max_len:
-            raise ValueError("Sequence %s is length %i, max length %i" \
+            raise ValueError("Sequence %s is length %i, max length %i"
                              % (title.split()[0], len(seq), max_len))
         yield title, seq
     raise StopIteration
 
+
 def split_fasta(input_filename, output_filename_base, n=500, truncate=None, keep_descr=False, max_len=None):
     """Split FASTA file into sub-files each of at most n sequences.
 
@@ -132,20 +128,20 @@
                 for title, seq in records:
                     handle.write(">%s\n" % title)
                     for i in range(0, len(seq), 60):
-                        handle.write(seq[i:i+60] + "\n")
+                        handle.write(seq[i:i + 60] + "\n")
             else:
                 for title, seq in records:
                     handle.write(">%s\n" % title.split()[0])
                     for i in range(0, len(seq), 60):
-                        handle.write(seq[i:i+60] + "\n")
+                        handle.write(seq[i:i + 60] + "\n")
             handle.close()
             files.append(new_filename)
-            #print "%i records in %s" % (len(records), new_filename)
+            # print "%i records in %s" % (len(records), new_filename)
     except ValueError, err:
-        #Max length failure from parser - clean up
+        # Max length failure from parser - clean up
         try:
             handle.close()
-        except:
+        except Exception:
             pass
         for f in files:
             if os.path.isfile(f):
@@ -155,35 +151,36 @@
         assert os.path.isfile(f), "Missing split file %r (!??)" % f
     return files
 
+
 def run_jobs(jobs, threads, pause=10, verbose=False):
     """Takes list of cmd strings, returns dict with error levels."""
     pending = jobs[:]
     running = []
     results = {}
     if threads == 1:
-        #Special case this for speed, don't need the waits
+        # Special case this for speed, don't need the waits
         for cmd in jobs:
             results[cmd] = subprocess.call(cmd, shell=True)
         return results
     while pending or running:
-        #See if any have finished
+        # See if any have finished
         for (cmd, process) in running:
-            return_code = process.poll() #non-blocking
+            return_code = process.poll()  # non-blocking
             if return_code is not None:
                 results[cmd] = return_code
-        running = [(cmd, process) for (cmd, process) in running \
+        running = [(cmd, process) for (cmd, process) in running
                    if cmd not in results]
         if verbose:
             print "%i jobs pending, %i running, %i completed" \
                   % (len(pending), len(running), len(results))
-        #See if we can start any new threads
+        # See if we can start any new threads
         while pending and len(running) < threads:
             cmd = pending.pop(0)
             if verbose:
                 print cmd
             process = subprocess.Popen(cmd, shell=True)
             running.append((cmd, process))
-        #Loop...
+        # Loop...
         sleep(pause)
     if verbose:
         print "%i jobs completed" % len(results)