Initial port to python3

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

diff --git a/htsworkflow/pipelines/test/test_sequences.py b/htsworkflow/pipelines/test/test_sequences.py
index accd43ecf8786b4d25a96683bf861940006cf44f..6502c64901471753735b777fa292fd33652a4346 100644 (file)
--- a/htsworkflow/pipelines/test/test_sequences.py
+++ b/htsworkflow/pipelines/test/test_sequences.py
@@ -2,7 +2,7 @@
 import os
 import shutil
 import tempfile
-import unittest
+from unittest import TestCase
 
 import RDF
 
@@ -10,7 +10,7 @@ from htsworkflow.pipelines import sequences
 from htsworkflow.util.rdfhelp import get_model, load_string_into_model, \
      rdfNS, libraryOntology, dump_model, fromTypedNode
 
-class SequenceFileTests(unittest.TestCase):
+class SequenceFileTests(TestCase):
     """
     Make sure the sequence archive class works
     """
@@ -71,7 +71,7 @@ class SequenceFileTests(unittest.TestCase):
 
         self.assertEqual(f0.filetype, 'srf')
         self.assertEqual(f0.path, pathname)
-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))
         self.assertEqual(repr(f0), "<srf 42BW9AAXX 4 %s>" % (pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')
@@ -96,7 +96,7 @@ class SequenceFileTests(unittest.TestCase):
 
         self.assertEqual(f0.filetype, 'qseq')
         self.assertEqual(f0.path, pathname)
-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))
         self.assertEqual(repr(f0), "<qseq 42BW9AAXX 4 %s>" %(pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')
@@ -119,7 +119,7 @@ class SequenceFileTests(unittest.TestCase):
 
         self.assertEqual(f0.filetype, 'qseq')
         self.assertEqual(f0.path, pathname)
-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))
         self.assertEqual(repr(f0), "<qseq ilmn200901 1 %s>" %(pathname,))
         self.assertEqual(f0.lane, '1')
         self.assertEqual(f0.read, 1)
@@ -142,7 +142,7 @@ class SequenceFileTests(unittest.TestCase):
 
         self.assertEqual(f0.filetype, 'fastq')
         self.assertEqual(f0.path, pathname)
-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))
         self.assertEqual(repr(f0), "<fastq 42BW9AAXX 4 %s>" % (pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')
@@ -164,7 +164,7 @@ class SequenceFileTests(unittest.TestCase):
 
         self.assertEqual(f0.filetype, 'fastq')
         self.assertEqual(f0.path, pathname)
-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))
         self.assertEqual(repr(f0), "<fastq 42BW9AAXX 4 %s>" %(pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '4')
@@ -188,7 +188,7 @@ class SequenceFileTests(unittest.TestCase):
 
         self.assertEqual(f0.filetype, 'split_fastq')
         self.assertEqual(f0.path, pathname)
-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))
         self.assertEqual(repr(f0), "<split_fastq 42BW9AAXX 1 %s>" %(pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '1')
@@ -212,7 +212,7 @@ class SequenceFileTests(unittest.TestCase):
 
         self.assertEqual(f0.filetype, 'split_fastq')
         self.assertEqual(f0.path, pathname)
-        self.assertEqual(unicode(f0), unicode(pathname))
+        self.assertEqual(str(f0), str(pathname))
         self.assertEqual(repr(f0), "<split_fastq 42BW9AAXX 1 %s>" % (pathname,))
         self.assertEqual(f0.flowcell, '42BW9AAXX')
         self.assertEqual(f0.lane, '1')
@@ -612,7 +612,12 @@ class SimulateSimpleTree(SimulateTree):
 
 
 def suite():
-    return unittest.makeSuite(SequenceFileTests,'test')
+    from unittest import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(SequenceFileTests))
+    return suite
+
 
 if __name__ == "__main__":
-    unittest.main(defaultTest="suite")
+    from unittest import main
+    main(defaultTest="suite")