From: Diane Trout <diane@caltech.edu>
Date: Thu, 5 Dec 2013 22:48:46 +0000 (-0800)
Subject: Provide reporting of what command failed when bigWigInfo isn't available.
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=0d8dbe0fe4d0fdb5bdd40e030ab34365de8ee66f

Provide reporting of what command failed when bigWigInfo isn't available.
---

diff --git a/htsworkflow/util/ucsc.py b/htsworkflow/util/ucsc.py
index e9ff77e..b96c46a 100644
--- a/htsworkflow/util/ucsc.py
+++ b/htsworkflow/util/ucsc.py
@@ -3,6 +3,7 @@
 
 import logging
 import os
+import sys
 from subprocess import Popen, PIPE
 
 LOGGER = logging.getLogger(__name__)
@@ -51,17 +52,22 @@ class bigWigInfo:
     def scan_file(self, filename):
         cmd = ['bigWigInfo', 
                filename]
-        p = Popen(cmd, stdout=PIPE)
-        stdout, _ = p.communicate()
-        for line in stdout.split(os.linesep):
-            if len(line) > 0:
-                term, value = line.split(': ')
-                if term in ('isCompressed', 'isSwapped'):
-                    value = parseBoolean(value)
-                else:
-                    value = parseNumber(value)
-                LOGGER.debug('%s: %s', term, str(value))
-                setattr(self, term, value)
+        try:
+            p = Popen(cmd, stdout=PIPE)
+            stdout, _ = p.communicate()
+            for line in stdout.split(os.linesep):
+                if len(line) > 0:
+                    term, value = line.split(': ')
+                    if term in ('isCompressed', 'isSwapped'):
+                        value = parseBoolean(value)
+                    else:
+                        value = parseNumber(value)
+                    LOGGER.debug('%s: %s', term, str(value))
+                    setattr(self, term, value)
+        except OSError as e:
+            LOGGER.error("Exception %s trying to run: %s", str(e), ' '.join(cmd))
+            sys.exit(-1)
+