--- a/tools/samtools_idxstats/samtools_idxstats.py	Wed May 13 10:35:50 2015 -0400
+++ b/tools/samtools_idxstats/samtools_idxstats.py	Tue May 16 09:24:18 2017 -0400
@@ -10,35 +10,30 @@
 runs "samtools idxstats" and captures the output to the desired
 tabular file.
 """
-import sys
+
 import os
-import subprocess
+import sys
 import tempfile
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    #Galaxy seems to invert the order of the two lines
+    # Galaxy seems to invert the order of the two lines
     print "(Galaxy wrapper v0.0.2)"
     cmd = "samtools 2>&1 | grep -i ^Version"
     sys.exit(os.system(cmd))
 
-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) != 4:
-   sys_exit("Require three arguments: BAM, BAI, tabular filenames")
+    sys.exit("Require three arguments: BAM, BAI, tabular filenames")
 
 bam_filename, bai_filename, tabular_filename = sys.argv[1:]
 
 if not os.path.isfile(bam_filename):
-    sys_exit("Input BAM file not found: %s" % bam_filename)
+    sys.exit("Input BAM file not found: %s" % bam_filename)
 if not os.path.isfile(bai_filename):
     if bai_filename == "None":
-        sys_exit("Error: Galaxy did not index your BAM file")
-    sys_exit("Input BAI file not found: %s" % bai_filename)
+        sys.exit("Error: Galaxy did not index your BAM file")
+    sys.exit("Input BAI file not found: %s" % bai_filename)
 
-#Assign sensible names with real extensions, and setup symlinks:
+# Assign sensible names with real extensions, and setup symlinks:
 tmp_dir = tempfile.mkdtemp()
 bam_file = os.path.join(tmp_dir, "temp.bam")
 bai_file = os.path.join(tmp_dir, "temp.bam.bai")
@@ -48,14 +43,14 @@
 assert os.path.isfile(bai_file), bai_file
 assert os.path.isfile(bam_file + ".bai"), bam_file
 
-#Run samtools idxstats:
+# Run samtools idxstats:
 cmd = 'samtools idxstats "%s" > "%s"' % (bam_file, tabular_filename)
 return_code = os.system(cmd)
 
-#Remove the temp symlinks:
+# Remove the temp symlinks:
 os.remove(bam_file)
 os.remove(bai_file)
 os.rmdir(tmp_dir)
 
 if return_code:
-    sys_exit("Return code %i from command:\n%s" % (return_code, cmd))
+    sys.exit("Return code %i from command:\n%s" % (return_code, cmd))