remove ,'s from more except blocks, and now a raise too

diff --git a/experiments/test_experiments.py b/experiments/test_experiments.py
index 5a39d44832ace72af08ffa42f2426bcb71b17846..7c5d20127243c8aa79e8232a949aa7279cbfa7d7 100644 (file)
--- a/experiments/test_experiments.py
+++ b/experiments/test_experiments.py
@@ -4,7 +4,7 @@ import re
 from lxml.html import fromstring
 try:
     import json
-except ImportError, e:
+except ImportError as e:
     import simplejson as json
 import os
 import shutil

diff --git a/htsworkflow/pipelines/genome_mapper.py b/htsworkflow/pipelines/genome_mapper.py
index 35830a2dc0a615f917a0a4dac2c3f9b1ea962874..83bdecb2cda88de376c114108a29a3c385053303 100644 (file)
--- a/htsworkflow/pipelines/genome_mapper.py
+++ b/htsworkflow/pipelines/genome_mapper.py
@@ -30,7 +30,7 @@ def getAvailableGenomes(genome_base_dir):
   # Need valid directory
   if not os.path.exists(genome_base_dir):
     msg = "Directory does not exist: %s" % (genome_base_dir)
-    raise IOError, msg
+    raise IOError(msg)
 
   # Find all subdirectories
   filepath_list = glob.glob(os.path.join(genome_base_dir, '*'))

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index 1d442145ae07f0bd17ac694bd9fd472e45337c04..3fdd8bf5a84e3fab4b95c81b771aa4de57eedab6 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -12,7 +12,7 @@ import urllib2
 
 try:
     import json
-except ImportError, e:
+except ImportError as e:
     import simplejson as json
 
 from htsworkflow.auth import apidata