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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
import os
import tempfile
import shutil
-from unittest
2
import TestCase
+from unittest import TestCase
from htsworkflow.pipelines import eland
from htsworkflow.pipelines import ipar
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(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
# 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
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)
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)
# 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):
# 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))
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))
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])
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)
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 l
1.mapped_reads.keys(
):
+ for k in l
ist(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))
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 l
1.match_codes.keys(
):
+ for k in l
ist(l1.match_codes.keys()
):
self.failUnlessEqual(l1.match_codes[k],
l2.match_codes[k])
elif isinstance(l1, eland.SequenceLane):
self.failUnlessEqual(l1.match_codes[k],
l2.match_codes[k])
elif isinstance(l1, eland.SequenceLane):
@@
-299,12
+299,12
@@
class RunfolderTests(TestCase):
def suite():
def suite():
- from unittest
2
import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(RunfolderTests))
return suite
if __name__ == "__main__":
- from unittest
2
import main
+ from unittest import main
main(defaultTest="suite")
main(defaultTest="suite")