Initial port to python3

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder_rta1_12.py

diff --git a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
index 8396bd0351265fe940a4b75dff3c421345272f56..00a3de5734093278ff0ee0c839c0e24a151364ec 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
+++ b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
@@ -5,7 +5,7 @@ import logging
 import os
 import tempfile
 import shutil
-from unittest2 import TestCase
+from unittest import TestCase
 
 from htsworkflow.pipelines import eland
 from htsworkflow.pipelines.samplekey import SampleKey
@@ -98,8 +98,8 @@ class RunfolderTests(TestCase):
 
         self.failUnlessEqual(g.software, 'CASAVA')
         self.failUnlessEqual(g.version, '1.8.1')
-        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
         # make_gerald_config.
@@ -141,11 +141,11 @@ class RunfolderTests(TestCase):
         self.failUnlessEqual(g.software, g2.software)
         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 g.lanes.keys():
+        for i in list(g.lanes.keys()):
             g_lane = g.lanes[i]
             g2_lane = g2.lanes[i]
             self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
@@ -171,13 +171,13 @@ class RunfolderTests(TestCase):
                 if isinstance(g_results, eland.ElandLane):
                   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])
 
@@ -197,7 +197,7 @@ class RunfolderTests(TestCase):
 
         eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
 
-        for lane in eland_container.values():
+        for lane in list(eland_container.values()):
             # I added sequence lanes to the last 2 lanes of this test case
             if lane.sample_name == '11113':
                 self.assertEqual(lane.reads, 24)
@@ -237,13 +237,13 @@ class RunfolderTests(TestCase):
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 1)
-              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])
             elif isinstance(l1, eland.SequenceLane):
@@ -275,12 +275,12 @@ class RunfolderTests(TestCase):
         self.failIfEqual(r2.gerald, None)
 
 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")