Initial port to python3

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

diff --git a/htsworkflow/pipelines/test/test_runfolder_rta.py b/htsworkflow/pipelines/test/test_runfolder_rta.py
index 497fe7b33181cd6896fb0cac05c0ce19d79c0b24..b8c516de373b8f2659aeba605cdcaf5af963100e 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_rta.py
+++ b/htsworkflow/pipelines/test/test_runfolder_rta.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 eland
 from htsworkflow.pipelines import ipar
@@ -109,8 +109,8 @@ class RunfolderTests(TestCase):
 
         self.failUnlessEqual(g.version, '1.171')
         self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
-        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
@@ -136,7 +136,7 @@ class RunfolderTests(TestCase):
             self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
 
         # I want to be able to use a simple iterator
-        for l in g.lanes.values():
+        for l in list(g.lanes.values()):
           self.failUnlessEqual(l.analysis, 'eland_extended')
           self.failUnlessEqual(l.read_length, '37')
           self.failUnlessEqual(l.use_bases, 'Y'*37)
@@ -162,8 +162,8 @@ 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):
@@ -192,13 +192,13 @@ 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])
 
@@ -260,13 +260,13 @@ class RunfolderTests(TestCase):
             if isinstance(l1, eland.ElandLane):
               self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
               self.failUnlessEqual(len(l1.mapped_reads), 17)
-              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):
@@ -299,12 +299,12 @@ 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")