A better resolution to a possible circular dependency.

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder_casava_1_7.py

diff --git a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
index 12fec6df50a3277daf6cabf702fe59799d583484..ae8899eeda02df677ca79360035d1b3c4a3c09df 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
+++ b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
@@ -5,7 +5,7 @@ import glob
 import os
 import tempfile
 import shutil
-import unittest
+from unittest2 import TestCase
 
 from htsworkflow.pipelines import bustard
 from htsworkflow.pipelines import eland
@@ -13,7 +13,7 @@ from htsworkflow.pipelines import gerald
 from htsworkflow.pipelines import ipar
 from htsworkflow.pipelines import runfolder
 from htsworkflow.pipelines import srf
-from htsworkflow.pipelines.runfolder import ElementTree
+from htsworkflow.pipelines import ElementTree
 
 from htsworkflow.pipelines.test.simulate_runfolder import *
 
@@ -56,7 +56,7 @@ def make_runfolder(obj=None):
         obj.gerald_dir = gerald_dir
 
 
-class RunfolderTests(unittest.TestCase):
+class RunfolderTests(TestCase):
     """
     Test components of the runfolder processing code
     which includes firecrest, bustard, and gerald
@@ -197,7 +197,6 @@ class RunfolderTests(unittest.TestCase):
 
 
     def test_eland(self):
-        ls_tree(self.runfolder_dir)
         hg_map = {'Lambda.fa': 'Lambda.fa'}
         for i in range(1,22):
           short_name = 'chr%d.fa' % (i,)
@@ -299,13 +298,14 @@ class RunfolderTests(unittest.TestCase):
             glob.fnmatch.fnmatch("s_1_0001_qseq.txt", pattern),
             False)
 
-        print pattern
-
 
 def suite():
-    return unittest.makeSuite(RunfolderTests,'test')
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
+    return suite
 
 
 if __name__ == "__main__":
-    unittest.main(defaultTest="suite")
-
+    from unittest2 import main
+    main(defaultTest="suite")