more use six.moves to import StringIO

diff --git a/encode_submission/encode3.py b/encode_submission/encode3.py
index 4e9b46640aa22ae306dcd00baae150ff84b35ca0..525edfd45427dae22c857185c6afa54197298d47 100644 (file)
--- a/encode_submission/encode3.py
+++ b/encode_submission/encode3.py
@@ -12,7 +12,7 @@ from optparse import OptionParser, OptionGroup
 import os
 from pprint import pprint, pformat
 import shlex
-from StringIO import StringIO
+from six.moves import StringIO
 import stat
 import sys
 import time

diff --git a/encode_submission/geo_gather.py b/encode_submission/geo_gather.py
index 751264cc4276a658491c387852a180fff94929a0..1aadb8398f92fec7a661e33cc9f219b4d656857a 100644 (file)
--- a/encode_submission/geo_gather.py
+++ b/encode_submission/geo_gather.py
@@ -9,7 +9,7 @@ from optparse import OptionParser, OptionGroup
 import os
 from pprint import pprint, pformat
 import shlex
-from StringIO import StringIO
+from six.moves import StringIO
 import stat
 import sys
 import time

diff --git a/encode_submission/ucsc_gather.py b/encode_submission/ucsc_gather.py
index a9fa72a83ddc1c4263e509070f50053d238fa405..bc3515b5c6511f101107d6a0dc94a6ac72c882f3 100644 (file)
--- a/encode_submission/ucsc_gather.py
+++ b/encode_submission/ucsc_gather.py
@@ -9,7 +9,7 @@ from optparse import OptionParser, OptionGroup
 import os
 from pprint import pprint, pformat
 import shlex
-from StringIO import StringIO
+from six.moves import StringIO
 import stat
 import sys
 import time

diff --git a/htsworkflow/pipelines/test/test_eland.py b/htsworkflow/pipelines/test/test_eland.py
index f6851883952332ab4005e06b6713bb011dc928ef..3e5820e30bc9303a09f2a865959e11b155a8ac61 100644 (file)
--- a/htsworkflow/pipelines/test/test_eland.py
+++ b/htsworkflow/pipelines/test/test_eland.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """More direct synthetic test cases for the eland output file processing
 """
-from StringIO import StringIO
+from six.moves import StringIO
 from unittest import TestCase
 
 from htsworkflow.pipelines.eland import ELAND, ElandLane, ElandMatches, \

diff --git a/htsworkflow/pipelines/test/test_genome_mapper.py b/htsworkflow/pipelines/test/test_genome_mapper.py
index d71755c90c7e639f24b83ad0683614379b04a263..011a42d04cad546923920bcfde9e6e197f3462b0 100644 (file)
--- a/htsworkflow/pipelines/test/test_genome_mapper.py
+++ b/htsworkflow/pipelines/test/test_genome_mapper.py
@@ -1,6 +1,6 @@
 from unittest import TestCase
 
-from StringIO import StringIO
+from six.moves import StringIO
 from htsworkflow.pipelines import genome_mapper
 
 class testGenomeMapper(TestCase):

diff --git a/htsworkflow/pipelines/test/test_genomemap.py b/htsworkflow/pipelines/test/test_genomemap.py
index 7640910afd0ae6078a658237049ac89d75f62957..2734676106f917d11dc9efc8aee5ea98f09f920d 100644 (file)
--- a/htsworkflow/pipelines/test/test_genomemap.py
+++ b/htsworkflow/pipelines/test/test_genomemap.py
@@ -2,7 +2,7 @@
 """More direct synthetic test cases for the eland output file processing
 """
 import os
-from StringIO import StringIO
+from six.moves import StringIO
 import shutil
 import tempfile
 from unittest import TestCase

diff --git a/htsworkflow/pipelines/test/test_retrieve_config.py b/htsworkflow/pipelines/test/test_retrieve_config.py
index 7ca87905d623e0ff6ce0c5c880851a283490176f..1b412c7d98832760cce6a9c4482638fe8b531508 100644 (file)
--- a/htsworkflow/pipelines/test/test_retrieve_config.py
+++ b/htsworkflow/pipelines/test/test_retrieve_config.py
@@ -1,7 +1,7 @@
 import csv
 import os
 import re
-from StringIO import StringIO
+from six.moves import StringIO
 
 try:
     import json

diff --git a/htsworkflow/pipelines/test/test_run_xml.py b/htsworkflow/pipelines/test/test_run_xml.py
index 42dedf9be9ed160fc2c6308ce88e3036e98fd1f6..9ef8dd08882b1df30a118d9aeb6a06eb2e2a03b8 100644 (file)
--- a/htsworkflow/pipelines/test/test_run_xml.py
+++ b/htsworkflow/pipelines/test/test_run_xml.py
@@ -1,6 +1,6 @@
 import os
 from unittest import TestCase
-from StringIO import StringIO
+from six.moves import StringIO
 
 from simulate_runfolder import TESTDATA_DIR
 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml

diff --git a/htsworkflow/pipelines/test/test_samplekey.py b/htsworkflow/pipelines/test/test_samplekey.py
index 7861a58763f3d764df43bd3942496fcf218b2e7f..aa0b96c52392d117c3862af0e388e37b27225915 100644 (file)
--- a/htsworkflow/pipelines/test/test_samplekey.py
+++ b/htsworkflow/pipelines/test/test_samplekey.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """More direct synthetic test cases for the eland output file processing
 """
-from StringIO import StringIO
+from six.moves import StringIO
 from unittest import TestCase
 
 from htsworkflow.pipelines.samplekey import SampleKey

diff --git a/htsworkflow/pipelines/test/test_summary.py b/htsworkflow/pipelines/test/test_summary.py
index fbc025bd2aa79c8759bff1fcaaa93631856bdbf4..835d2069d22d714c2185cef8ae821648782fb70d 100644 (file)
--- a/htsworkflow/pipelines/test/test_summary.py
+++ b/htsworkflow/pipelines/test/test_summary.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 import os
-from StringIO import StringIO
+from six.moves import StringIO
 from unittest import TestCase
 
 from htsworkflow.pipelines import summary

diff --git a/htsworkflow/submission/daf.py b/htsworkflow/submission/daf.py
index 30edcdc54ba3ca60fc231334c5de2b3a38909568..35b9a6c7d22a55cd52c833f4db8e599d2c34bea3 100644 (file)
--- a/htsworkflow/submission/daf.py
+++ b/htsworkflow/submission/daf.py
@@ -5,7 +5,7 @@ import os
 from pprint import pformat
 import re
 import string
-from StringIO import StringIO
+from six.moves import StringIO
 import types
 import urlparse
 

diff --git a/htsworkflow/submission/test/test_daf.py b/htsworkflow/submission/test/test_daf.py
index 5bc9014267cfbbb2c1536e8c21ac83d3d7f57d23..87a0cd1c6afe4a3d82156e8c343e2a9752457599 100644 (file)
--- a/htsworkflow/submission/test/test_daf.py
+++ b/htsworkflow/submission/test/test_daf.py
@@ -1,7 +1,7 @@
 from contextlib import contextmanager
 import logging
 import os
-from StringIO import StringIO
+from six.moves import StringIO
 import shutil
 import tempfile
 from unittest import TestCase, TestSuite, defaultTestLoader

diff --git a/htsworkflow/submission/test/test_submission.py b/htsworkflow/submission/test/test_submission.py
index 0c4e0870399eb30dbc1702d5fa1912de2a3ab837..a59fc9d9a8d0d066f37b01f2d1b69b4dcc57aeff 100644 (file)
--- a/htsworkflow/submission/test/test_submission.py
+++ b/htsworkflow/submission/test/test_submission.py
@@ -1,6 +1,6 @@
 
 import os
-from StringIO import StringIO
+from six.moves import StringIO
 import shutil
 import tempfile
 from unittest import TestCase, TestSuite, defaultTestLoader

diff --git a/htsworkflow/submission/test/test_ucsc.py b/htsworkflow/submission/test/test_ucsc.py
index b4cb2d8bef2a24be839c2d631392c2311e6cac98..ebc461074152be6ea144aaa7e23bac811c7572ec 100644 (file)
--- a/htsworkflow/submission/test/test_ucsc.py
+++ b/htsworkflow/submission/test/test_ucsc.py
@@ -1,5 +1,5 @@
 from unittest import TestCase, TestSuite, defaultTestLoader
-from StringIO import StringIO
+from six.moves import StringIO
 
 from htsworkflow.submission import ucsc
 

diff --git a/htsworkflow/util/test/test_makebed.py b/htsworkflow/util/test/test_makebed.py
index 50d2c64a638f5f8b84bff93f0418090c3fc7094d..daf618b2136132f8287bec33b57e6b62857d5285 100644 (file)
--- a/htsworkflow/util/test/test_makebed.py
+++ b/htsworkflow/util/test/test_makebed.py
@@ -1,5 +1,5 @@
 import os
-from StringIO import StringIO
+from six.moves import StringIO
 from unittest import TestCase
 
 from htsworkflow.util import makebed

diff --git a/htsworkflow/util/test/test_validate.py b/htsworkflow/util/test/test_validate.py
index c906cd5592fdc689509fe8e67d6339c20091b668..dc253b8d3edbfc7f375d9198b63cbf97c1a7b12a 100644 (file)
--- a/htsworkflow/util/test/test_validate.py
+++ b/htsworkflow/util/test/test_validate.py
@@ -1,5 +1,5 @@
 import os
-from StringIO import StringIO
+from six.moves import StringIO
 from unittest import TestCase
 
 from htsworkflow.util import validate

diff --git a/samples/views.py b/samples/views.py
index e506c7d68789783e118ca6132d44a7e5e044c549..0684ee7f5589cf8436a5a1e6c1fff1cb8e023150 100644 (file)
--- a/samples/views.py
+++ b/samples/views.py
@@ -1,7 +1,6 @@
 from __future__ import absolute_import, print_function
 
 # Create your views here.
-import StringIO
 import logging
 import os
 import sys

diff --git a/test/test_copier.py b/test/test_copier.py
index 52bd8e2879dfe47e4bf444ead9924873728942ee..b88b1a49248ba7d539003163f6f468ade4f551a7 100644 (file)
--- a/test/test_copier.py
+++ b/test/test_copier.py
@@ -1,6 +1,6 @@
 from unittest import TestCase, skipIf
 
-from StringIO import StringIO
+from six.moves import StringIO
 from htsworkflow.automation.solexa import is_runfolder
 
 try:

diff --git a/test/test_srf2fastq.py b/test/test_srf2fastq.py
index e06ec82ed31e197e464665d2a68e9c99bb53d3b5..bbd1e4132462ad1dd6cb18d1ba4d763152c0d5fb 100644 (file)
--- a/test/test_srf2fastq.py
+++ b/test/test_srf2fastq.py
@@ -1,5 +1,5 @@
 import os
-from StringIO import StringIO
+from six.moves import StringIO
 import sys
 from unittest import TestCase