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
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.
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)
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])
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)
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):
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")