Initial port to python3

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder026.py

diff --git a/htsworkflow/pipelines/test/test_runfolder026.py b/htsworkflow/pipelines/test/test_runfolder026.py
index de68a2505cbb2e1e6f83726e23780008d6e90b83..eb491d54a8ee3c6ce35f2963fe4c475a27acb0e3 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder026.py
+++ b/htsworkflow/pipelines/test/test_runfolder026.py
@@ -4,7 +4,7 @@ from datetime import datetime, date
 import os
 import tempfile
 import shutil
-from unittest2 import TestCase
+from unittest import TestCase
 
 from htsworkflow.pipelines import firecrest
 from htsworkflow.pipelines import bustard
@@ -311,7 +311,7 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(b.date,     b2.date )
         self.failUnlessEqual(b.user,     b2.user)
         self.failUnlessEqual(len(b.phasing), len(b2.phasing))
-        for key in b.phasing.keys():
+        for key in list(b.phasing.keys()):
             self.failUnlessEqual(b.phasing[key].lane,
                                  b2.phasing[key].lane)
             self.failUnlessEqual(b.phasing[key].phasing,
@@ -326,8 +326,8 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, 'GERALD')
         self.failUnlessEqual(g.version, '1.68.2.2')
         self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.keys())))
+        self.failUnlessEqual(len(g.lanes), len(list(g.lanes.items())))
 
 
         # list of genomes, matches what was defined up in
@@ -364,8 +364,8 @@ class RunfolderTests(TestCase):
         # do it all again after extracting from the xml file
         self.failUnlessEqual(g.version, g2.version)
         self.failUnlessEqual(g.date, g2.date)
-        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
-        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+        self.failUnlessEqual(len(list(g.lanes.keys())), len(list(g2.lanes.keys())))
+        self.failUnlessEqual(len(list(g.lanes.items())), len(list(g2.lanes.items())))
 
         # test lane specific parameters from gerald config file
         for i in range(1,9):
@@ -393,13 +393,13 @@ class RunfolderTests(TestCase):
                                      g2_results.reads)
                 self.failUnlessEqual(len(g_results.mapped_reads),
                                      len(g2_results.mapped_reads))
-                for k in g_results.mapped_reads.keys():
+                for k in list(g_results.mapped_reads.keys()):
                     self.failUnlessEqual(g_results.mapped_reads[k],
                                          g2_results.mapped_reads[k])
 
                 self.failUnlessEqual(len(g_results.match_codes),
                                      len(g2_results.match_codes))
-                for k in g_results.match_codes.keys():
+                for k in list(g_results.match_codes.keys()):
                     self.failUnlessEqual(g_results.match_codes[k],
                                          g2_results.match_codes[k])
 
@@ -436,13 +436,13 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(l1.lane_id, l2.lane_id)
             self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
             self.failUnlessEqual(len(l1.mapped_reads), 3)
-            for k in l1.mapped_reads.keys():
+            for k in list(l1.mapped_reads.keys()):
                 self.failUnlessEqual(l1.mapped_reads[k],
                                      l2.mapped_reads[k])
 
             self.failUnlessEqual(len(l1.match_codes), 9)
             self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
-            for k in l1.match_codes.keys():
+            for k in list(l1.match_codes.keys()):
                 self.failUnlessEqual(l1.match_codes[k],
                                      l2.match_codes[k])
 
@@ -471,12 +471,12 @@ class RunfolderTests(TestCase):
 
 
 def suite():
-    from unittest2 import TestSuite, defaultTestLoader
+    from unittest import TestSuite, defaultTestLoader
     suite = TestSuite()
     suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
     return suite
 
 
 if __name__ == "__main__":
-    from unittest2 import main
+    from unittest import main
     main(defaultTest="suite")